bluuebunny/crossref_metadata_2025 huggingface dataset:
Preparation and characterization of epitaxial ilmenite-hematite films
Authors: Dou J. , Navarrete L. , Kale P. , Padmini P. , Pandey R. K. , Guo H. , Gupta A. , Schad R.
Published: March 2007

The solid solution system ilmenite-hematite [(FeTiO3)1−x–(Fe2O3)x] is a potential candidate for applications in spintronics due to its intrinsic ferrimagnetic and semiconducting properties. Epitaxial ilmenite-hematite films with x=0.33, which have the highest room temperature magnetic moment, were grown on α-Al2O3 (0001) substrates using pulsed laser deposition technique with varying oxygen partial pressure in the ambient gas. Structural, magnetic, electrical, and optical properties are found to be largely dependent on the oxygen content of the films which is controlled by substrate temperature and ambient gas composition. The highest crystalline and magnetic ordering and the lowest resistivity values could be obtained for growth at high temperatures and under low oxygen pressure. A narrowing of the band gap (to around 2.4eV) was observed for films grown under high oxygen pressure in comparison with films grown in vacuum or argon (around 3.3eV).
Electrical properties of heterostructure Si∕poly(diphenylenephthalide)∕Cu
Authors: Salikhov R. B. , Lachinov A. N. , Rakhmeyev R. G.
Published: March 2007

Organic-inorganic multilayer structures of the silicon∕polymer∕metal type have been fabricated. The current-voltage characteristics of these structures versus temperature are measured. The obtained results are treated within different models of charge transport such as Richardson-Schottky thermionic emission, Fowler-Nordheim tunneling, and Pool-Frenkel and hopping mechanisms. The conclusions about the mechanisms of charge transport at different electric fields and temperatures have been made. The Richardson-Schottky model is in good quantitative agreement with the experimental data in the case of the metal-polymer interface with the energy barriers of 0.26–0.10eV. The charge transport in the polymer is explained by the hopping mechanism near the Fermi level with the activation energies being of 0.01–0.04eV.
Lattice dynamics of the filled skutterudite CeOs4Sb12
Authors: Yang C. P. , Wang H. , Iwasa K. , Kohgi M. , Sugawara H. , Sato H.
Published: March 2007

Inelastic neutron scattering was performed on both poly- and single-crystalline samples to study the lattice dynamics of the Ce-filled antimonide skutterudite. For powder samples, no well-defined extra phonon excitation peak, which was reported to indicate a local Einstein oscillating mode, was detected in the low-energy region of the vibrational density of states within the experimental accuracy. However, a coherent phonon was clearly observed in single crystals at different temperatures. The dispersion curves were measured along two symmetry axes[0 1 1] and [1 0 0] at room temperature and compared with theoretical calculation by Feldman et al. [Phys. Rev. B 73, 014306 (2006)] using the model of local density approximation.
Langevin stabilization of molecular-dynamics simulations of polymers by means of quasisymplectic algorithms
Authors: Larini L. , Mannella R. , Leporini D.
Published: March 2007

Algorithms for the numerical integration of Langevin equations are compared in detail from the point of view of their accuracy, numerical efficiency, and stability to assess them as potential candidates for molecular-dynamics simulations of polymeric systems. Some algorithms are symplectic in the deterministic frictionless limit and prove to stabilize long time-step integrators. They are tested against other popular algorithms. The optimal algorithm depends on the main goal: accuracy or efficiency. The former depends on the observable of interest. A recently developed quasisymplectic algorithm with great accuracy in the position evaluation exhibits better overall accuracy and stability than the other ones. On the other hand, the well-known BrünGer-Brooks-Karplus [Chem. Phys. Lett. 105, 495 (1982)] algorithm is found to be faster with limited accuracy loss but less stable. It is also found that using higher-order algorithms does not necessarily improve the accuracy. Moreover, they usually require more force evaluations per single step, thus leading to poorer performances.
Magnetic susceptibility of martensitic Ni–Mn–Ga film
Authors: Chernenko Volodymyr A. , Hagler Michael , Müllner Peter , Kniazkyi Volodymyr M. , L’vov Victor A. , Ohtsuka Makoto , Besseghini Stefano
Published: March 2007

The present work deals with the magnetic anisotropy of a textured Ni51.4Mn28.3Ga20.3 thin film sputter deposited on alumina ceramic substrate. This film is a ferromagnetic martensite with a strong uniaxial magnetocrystalline anisotropy. The magnetization versus magnetic field dependencies at different angles between the direction of magnetic field and the film plane are measured with a vibrating sample magnetometer. The initial magnetic susceptibility decreases with increasing inclination with respect to the film plane. A consistent procedure is introduced for the quantitative determination of (i) the angle of the easy-magnetic axis with respect to the film normal and (ii) the ratio between the magnetic anisotropy energy and the magnetostatic energy (quality factor). These values proved to be equal to 67°±4° and 2.9±0.3, respectively.
Density functionals that are one- and two- are not always many-electron self-interaction-free, as shown for H2+, He2+, LiH+, and Ne2+
Authors: Ruzsinszky Adrienn , Perdew John P. , Csonka Gábor I. , Vydrov Oleg A. , Scuseria Gustavo E.
Published: March 2007

The common density functionals for the exchange-correlation energy make serious self-interaction errors in the molecular dissociation limit when real or spurious noninteger electron numbers N are found on the dissociation products. An “M-electron self-interaction-free” functional for positive integer M is one that produces a realistic linear variation of total energy with N in the range of M−1<N⩽M, and so can avoid these errors. This desideratum is a natural generalization to all M of the more familiar one of one-electron self-interaction freedom. The intent of this paper is not to advocate for any functional, but to understand what is required for a functional to be M-electron self-interaction-free and thus correct even for highly stretched bonds. The original Perdew-Zunger self-interaction correction (SIC) and our scaled-down variant of it are exactly one- and nearly two-electron self-interaction-free, but only the former is nearly so for atoms with M>2. Thus all these SIC’s produce an exact binding energy curve for H2+, and an accurate one for He2+, but only the unscaled Perdew-Zunger SIC produces an accurate one for Ne2+, where there are more than two electrons on each fragment Ne+0.5. We also discuss LiH+, which is relatively free from self-interaction errors. We suggest that the ability of the original and unscaled Perdew-Zunger SIC to be nearly M-electron self-interaction-free for atoms of all M stems in part from its formal resemblance to the Hartree-Fock theory, with which it shares a sum rule on the exchange-correlation hole of an open system.
An experimental study of the size effect on adiabatic gas-liquid two-phase flow patterns and void fraction in microchannels
Authors: Xiong Renqiang , Chung J. N.
Published: March 2007

Adiabatic gas-liquid flow patterns and void fractions in microchannels were experimentally investigated. Using nitrogen and water, experiments were conducted in rectangular microchannels with hydraulic diameters of 0.209mm, 0.412mm and 0.622mm, respectively. Gas and liquid superficial velocities were varied from 0.06–72.3m∕s and 0.02–7.13m∕s, respectively. The main objective is focused on the effects of microscale channel sizes on the flow regime map and void fraction. The instability of flow patterns was observed. Four groups of flow patterns including bubbly slug flow, slug-ring flow, dispersed-churn flow, and annular flow were observed in microchannels of 0.412mm and, 0.622mm. In the microchannel of 0.209mm, the bubbly slug flow became the slug flow and the dispersed-churn flow disappeared. The current flow regime maps showed the transition lines shifted to higher gas superficial velocity due to a dominant surface tension effect as the channel size was reduced. The regime maps presented by other authors for minichannels were found to not be applicable for microchannels. Time-averaged void fractions were measured by analyzing 8000 high speed video images for each flow condition. The void fractions hold a nonlinear relationship with the homogeneous void fraction as opposed to the relatively linear trend for the minichannels. A new correlation was developed to predict the nonlinear relationship that fits most of the current experimental data and those of the 0.1mm diameter tube reported by Kawahara et al. [Int. J. Multiphase Flow 28, 1411 (2002)] within ±15%.
Envelope-kinetic analysis of the electron kinetic effects on Raman backscatter and Raman backward laser amplification
Authors: Hur Min Sup , Yoo Seung Hoon , Suk Hyyong
Published: March 2007

The electron kinetic effects on Raman backscattering and Raman backward laser amplification were analyzed. The analysis is based on the envelope-kinetic equations of a plasma wave, which are composed of the conventional envelope equation of a fluid plasma and the kinetic term. One major goal of this paper is to close the envelope-kinetic model by analyzing the kinetic term, which was not fully covered in the previous work [M. S. Hur et al., Phys. Rev. Lett. 95, 115003 (2005)]. It was found that the closed envelope-kinetic equation in the nontrapping regime takes the same form as the envelope equation of the fluid plasma used in the three-wave model. For the closure in the trapping-dominant regime, the test particle technique is employed to calculate the kinetic term. Results from the full kinetic and test particle simulations agree well with each other, while the latter has a great advantage in computation speed. The frequency shift and resonance breaking by the trapped particles are discussed with the help of a new diagnostic inserted in the full kinetic averaged particle-in-cell code.
Switchable AlxGa1−xAs all-optical delay line at 1.55μm
Authors: Bristow A. D. , Iyer R. , Aitchison J. S. , van Driel H. M. , Smirl Arthur L.
Published: March 2007

The authors demonstrate an on-chip optical delay in AlxGa1−xAs that operates at room temperature and 1.55μm. A nonlinear directional coupler for optical switching and a 188ps long racetrack structure provide bit delays of >100 for picosecond pulses. In the linear regime the transmission ratio of the slow channel is 74%, which reduces to 40% with increasing peak intensity. (Meanwhile, the fast channel output increases from 26% to 60%.) Switching occurs due to a nonlinear detuning of the directional coupler, limited by three-photon absorption and time-averaging effects. This proof-of-principle device can operate at up to 5GHz and is promising for optical buffering applications.
Angle-resolved x-ray absorption near edge structure study of vertically aligned single-walled carbon nanotubes
Authors: Li Zhongrui , Zhang Liang , Resasco Daniel E. , Mun Bongjin Simon , Requejo Félix G.
Published: March 2007

Vertically aligned single-walled carbon nanotube (SWNT) forest was studied by using angular-dependent C K-edge x-ray absorption near edge structure (XANES) with linearly polarized x-ray beam. The XANES analysis found a crust of entangled nanotubes on top of the forest formed at the first stage of the forest growth, which shapes the morphology of the entire forest and constricts the nanotubes to grow to the same length. It indicates that this type of SWNT forest has a different growth mechanism from the multiwalled carbon nanotube forest.
On the mathematical structure and hidden symmetries of the Born-Infeld field equations
Authors: Cirilo-Lombardo Diego Julio
Published: March 2007

The mathematical structure of the Born-Infeld field equations was analyzed from the point of view of the symmetries. To this end, the field equations were written in the most compact form by means of quaternionic operators constructed according to all the symmetries of the theory, including the extension to a noncommutative structure. The quaternionic structure of the phase space was explicitly derived and described from the Hamiltonian point of view, and the analogy between the Born-Infeld theory and the Maxwell (linear) electrodynamics in curved space-time was explicitly shown. Our results agree with the observation of Gibbons and Rasheed [Nucl. Phys. B 454, 185 (1995); Phys. Lett. B 365, 46 (1996)] that there exists a discrete symmetry in the structure of the field equations that is unique in the case of the Born-Infeld nonlinear electrodynamics.
Monte Carlo study of Widom-Rowlinson interface
Authors: Malijevský Al. , Sokołowski S.
Published: March 2007

We report the results of Monte Carlo investigations of the structure and the interfacial tension of the liquid-liquid interface of the Widom-Rowlinson mixture. The results are compared with a mean-field theory.
Current-voltage characteristics of p-GaAs∕n-GaN heterojunction fabricated by wafer bonding
Authors: Liang Ting , Guo Xia , Guan Baolu , Guo Jing , Gu Xiaoling , Lin Qiaoming , Wu Di , Gao Guo , Zhu Yanxu , Shen Guandi
Published: March 2007

p - Ga As ∕ n - Ga N heterojunction was fabricated by wafer bonding. Its current-voltage characteristic was systematically investigated at room temperature and at a variety of low temperature. The curves of different temperatures in the logarithmic scales indicate space-charge-limited currents (SCLCs) in the high voltage region (>0.4V). SCLC current-transport mechanism was confirmed by fitting data. Single-charge injection and the amorphous layer at the bonding interface are presumably the reasons to cause SCLCs.
Phase delay and group velocity determination at a planar defect state in three dimensional photonic crystals
Authors: Galisteo-López J. F. , Galli M. , Andreani L. C. , Mihi A. , Pozas R. , Ocaña M. , Míguez H.
Published: March 2007

Phase sensitive optical transmission measurements have been performed on three dimensional opal-based photonic crystals containing a planar defect. From numerical derivation of the measured phase, the group velocity has been retrieved. Strong modulations in the group velocity are seen to correlate with a recovery in the transmission inside the forbidden spectral interval, demonstrating the presence of a localized defect state. Accordingly, the phase change measured across the forbidden interval doubles in the lattice containing a planar defect with respect to the defect-free crystal, as expected when introducing a localized state inside the pseudogap. All results have been modeled with a scalar wave approximation in a two band model including extinction.
Carbon contacted nanotube field effect transistors
Authors: Austing D. G. , Lefebvre J. , Bond J. , Finnie P.
Published: March 2007

The authors demonstrate that multiwalled carbon nanotube forests make exceptionally good source and drain contacts for single walled carbon nanotube field effect transistors. Fabrication is straightforward, involving only a single step of photolithography, followed by chemical vapor deposition. Bridging nanotubes are identified either by conventional scanning electron microscopy or by global photoluminescence imaging using only white light illumination. Gate voltage sweeps show that these devices are similar to conventional nanotube transistors but with surprisingly high on currents from the viewpoint of simple models of the contact-channel interface.
Co clustering and ferromagnetism in chemical vapor deposited Ti1−xCoxO2−δ thin films
Authors: Kang Sueng-Hee , Quynh Hoa Nguyen Thi , Yoon Soon-Gil , Kim Eui-Tae , Lee Zonghoon , Radmilovic Velimir
Published: March 2007

Stoichiometric Ti1−xCoxO2 and oxygen-deficient Ti1−xCoxO2−δ thin films were grown on Si (001) by plasma-enhanced metal-organic chemical vapor deposition and their microstructures and ferromagnetic properties were investigated. The stoichiometric film grown at 430°C showed no discernable Co metal clustering or measurable coercive field. In contrast, oxygen-deficient films fabricated without supplying O2 contained significant Co clusters of ∼10–20nm, which appeared to be the major reason for the observed room-temperature ferromagnetism. With increasing oxygen vacancies of the films, the coercive field and saturation magnetization values increased to ∼460Oe and ∼27emu∕cm3 (1.55μB∕Co atom) approached that for bulk cobalt, respectively.
Tuning alloy disorder in diluted magnetic semiconductors in high fields to 89T
Authors: Crooker S. A. , Samarth N.
Published: March 2007

Alloy disorder in II-VI diluted magnetic semiconductors (DMS) is typically reduced when the local magnetic spins align in an applied magnetic field. An important and untested expectation of current models of alloy disorder, however, is that alloy fluctuations in many DMS compounds should increase again in very large magnetic fields of the order of 100T. Here the authors measure the disorder potential in a Zn0.70Cd0.22Mn0.08Se quantum well via the low temperature photoluminescence linewidth using a pulsed magnet system to ∼89T. Above 70T, the linewidth is observed to increase again, in accord with a simple model of alloy disorder.
180° ferroelectric domains as elastic domains
Authors: Chen Lang , Roytburd A. L.
Published: March 2007

Thermodynamic analysis shows that 180° ferroelectric domains under an external electric field behave as elastic domains due to the converse piezoelectric effect. The interdomain elastic interaction between 180° ferroelectric domains is an important factor in determining the effective dielectric and piezoelectric responses of thin film constrained by a substrate and therefore cannot be neglected.
Ferroelectric and dielectric properties of Nd3+∕Zr4+ cosubstituted Bi4Ti3O12 thin films
Authors: Zhong X. L. , Wang J. B. , Liao M. , Sun L. Z. , Shu H. B. , Tan C. B. , Zhou Y. C.
Published: March 2007

Thin films of Nd3+∕Zr4+ cosubstituted Bi4Ti3O12 (BIT), i.e., Bi3.15Nd0.85Ti2.8Zr0.2O12 (BNTZ), were fabricated on Pt∕Ti∕SiO2∕Si(100) substrates by chemical solution deposition and annealed at different temperatures of 600, 650, 700, and 800°C. The effects of annealing temperature on the microstructure, leakage current, ferroelectric, and dielectric properties of the BNTZ films were investigated in detail. Significantly, compared with the Bi3.15Nd0.85Ti3O12 film, the BNTZ thin film has a lower coercive field (2Ec) and leakage current density and a slightly larger remnant polarization (2Pr). It shows that Nd3+∕Zr4+ cosubstitution in BIT film might be an effective way to improve ferroelectric properties of BIT.
Magnetically assembled carbon nanotube tipped pipettes
Authors: Freedman J. R. , Mattia D. , Korneva G. , Gogotsi Y. , Friedman G. , Fontecchio A. K.
Published: March 2007

The authors have developed a biological probe at the nanoscale with a magnetic carbon nanotube (mCNT) tip that has the ability to transfer fluids. Fabrication is performed by injection of mCNTs into micropipettes, which are then positioned as probe tips via magnetophoresis, and affixed with polymeric adhesive. In this letter the authors discuss the magnetic fabrication process and demonstrate the versatility of this probe.
Correlation of hole mobility, exciton diffusion length, and solar cell characteristics in phthalocyanine/fullerene organic solar cells
Authors: Terao Yuhki , Sasabe Hiroyuki , Adachi Chihaya
Published: March 2007

The authors investigated heterojunction organic solar cells composed of different metal phthalocyanines (MPcs, M=Fe, Co, Ni, Cu, and H2)/fullerene (C60) and compared the solar cell characteristics with the field-effect hole mobilities (μh) and exciton diffusion length (Lex) of the different MPcs. They observed that the short circuit current (JSC) is linearly dependent on the μh of the MPcs, except for ZnPc. They also estimated the Lex of the MPcs by creating a line of best fit using the action spectra of the external quantum efficiency in the solar cells and found that JSC is closely correlated with the Lex of the MPcs.
Temperature dependence of the photoluminescence emission from thiol-capped PbS quantum dots
Authors: Turyanska L. , Patanè A. , Henini M. , Hennequin B. , Thomas N. R.
Published: March 2007

The authors report the temperature dependence of the near-infrared photoluminescence (PL) emission from thiol-capped PbS quantum dots. The high thermal stability of the PL allows the authors to study the thermal broadening of the dot emission over an extended temperature range (4–300K). The authors show that the linewidth of the dot PL emission is strongly enhanced at temperatures above 150K. This behavior is attributed to dephasing of the quantum electronic states by carrier interaction with longitudinal optical phonons. The authors’ data also indicate that the strength of the carrier-phonon coupling is larger in smaller dots.
Effects of Mn doping on dielectric and piezoelectric properties of 0.71Pb(Mg1∕3Nb2∕3)O3–0.29PbTiO3 single crystals
Authors: Luo Laihui , Zhou Dan , Tang Yanxue , Jia Yanmin , Xu Haiqing , Luo Haosu
Published: March 2007

The dielectric and piezoelectric properties of the Mn-doped 0.71Pb(Mg1∕3Nb2∕3)O3–0.29PbTiO3 (PMNT) crystals oriented along ⟨001⟩ and ⟨110⟩ directions, respectively, have been investigated. The investigations have shown that 3at.% Mn substitution results in (i) a large increment of coercive field at the cost of piezoelectric response, (ii) an increased Curie temperature and an enhanced stability of the ferroelectric rhombohedral phase, which enable a wider operation temperature range, and (iii) enhanced linearity in electric field induced strain with lower hysteresis. The hardened PMNT crystals favor their applications in high power transducers.
Dominant effect of near-interface native point defects on ZnO Schottky barriers
Authors: Brillson L. J. , Mosbacker H. L. , Hetzer M. J. , Strzhemechny Y. , Jessen G. H. , Look D. C. , Cantwell G. , Zhang J. , Song J. J.
Published: March 2007

The authors used depth-resolved cathodoluminescence spectroscopy and current-voltage measurements to probe metal-ZnO diodes as a function of native defect concentration, oxygen plasma processing, and metallization. The results show that resident native defects in ZnO single crystals and native defects created by the metallization process dominate metal-ZnO Schottky barrier heights and ideality factors. Results for ZnO(0001¯) faces processed with room temperature remote oxygen plasmas to remove surface adsorbates and reduce subsurface native defects demonstrate the pivotal importance of crystal growth quality and metal-ZnO reactivity in forming near-interface states that control Schottky barrier properties.
Organic solar cells from water-soluble poly(thiophene)/fullerene heterojunction
Authors: Yang Jihua , Garcia Andres , Nguyen Thuc-Quyen
Published: March 2007

We report the characteristics of solar cells with a heterojunction structure con-taining water-soluble polythiophene and a fullerene (C60) (indium tin oxide/sodium poly[2-(3-thienyl)-ethoxy-4-butylsulfonate] (PTEBS:Na+)∕C60∕2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline/Al). The devices show that the PTEBS:Na+ layer acts as an electron donor and the photovoltaic effect is dominated by the PTEBS:Na+∕C60 interface. By post-device-fabrication treatment through the application of a positive bias, the devices show a short-circuit current density exceeding 0.97±0.02mA∕cm2, an open-circuit voltage of 0.67±0.02V, a fill factor of 0.53±0.02, and a power conversion efficiency of 0.43±0.02% at AM 1.5 solar illumination (80mW∕cm2).
Synthesis and photoluminescence of Mn-doped zinc sulfide nanoparticles
Authors: Son Dongyeon , Jung Dae-Ryong , Kim Jongmin , Moon Taeho , Kim Chunjoong , Park Byungwoo
Published: March 2007

Mn-doped zinc sulfide nanoparticles were synthesized using a liquid-solid-solution method, as a simple synthetic route for preparing nearly monodispersed nanocrystals with a diameter of 7.3±0.7nm. The influence of doping concentration for optimum luminescence properties was studied with the nonuniform distribution of local strain and the capping effect. The improved photoluminescence properties of the 450°C-annealed samples with 1.0at.% Mn doping are attributed to both the removal of water/organics and the enhanced crystallinity (reduced local strain).
Dielectric relaxations in Ba(Fe1∕2Ta1∕2)O3 giant dielectric constant ceramics
Authors: Wang Z. , Chen X. M. , Ni L. , Liu Y. Y. , Liu X. Q.
Published: March 2007

Dielectric relaxations of Ba(Fe1∕2Ta1∕2)O3 ceramics were investigated and discussed over a broad temperature and frequency range. Two dielectric relaxations following Arrhenius law were observed at 153–382 and 440–623K, where there was a giant dielectric constant step between them. The frequency dependent rapid drop of dielectric constant at 153–382K was nearly a Debye relaxation with the intrinsic nature, while the high temperature dielectric relaxation with an extremely high dielectric constant peak and very strong frequency dispersion was attributed to the defect ordering but not a typical relaxor ferroelectric behavior. The O2 annealing almost completely suppressed the dielectric peak and subsequently extended the giant dielectric step, while the low temperature dielectric relaxation and the magnitude of such step were not obviously affected.
Template fabrication of SiO2 nanotubes
Authors: Fan Xia , Meng Xiang-Min , Zhang Xiao-Hong , Lee Chun-Sing , Lee Shuit-Tong
Published: March 2007

The authors report the preparation of silica nanotubes by a simple two-stage thermal evaporation of ZnSe and SiO powders. Firstly, nanocables with single crystalline ZnSe nanowire cores and amorphous SiO2 shells were formed by a combined vapor-liquid-solid and SiO-assisted growth process. The ZnSe cores were then evaporated at high temperatures leaving behind SiO2 nanotubes. As-fabricated SiO2 nanotubes were studied with scanning electron microscopy, transmission electron microscopy, energy-dispersive x-ray spectroscopic analysis, and photoluminescence measurement. The SiO2 nanotubes were found to be amorphous, diameter uniform, smooth, and rigid. This method can be used to prepare other materials and morphology-controlled nanotubes.
Phylogeny of the freshwater crab genus Somanniathelphusa Bott (Decapoda:Parathelphusidae) from Taiwan and the coastal regions of China, with notes on their biogeography
Authors: Shih Hsi-Te , Fang Shao-Hua , Ng Peter K. L.
Published: March 2007

It is generally accepted that the southern part of mainland China was connected to, and then separated from, the island of Taiwan many times as a result of successive glaciation events, the most recent being 15 000 years ago. On the basis of this, many biogeographical hypotheses have been proposed to explain the origins and relationships of the flora and fauna of Taiwan and mainland China. However, no clear genetic evidence from the flora and fauna of Taiwan has been forthcoming to support the geological history or biogeographical hypotheses. Land-locked freshwater crabs of the genus Somanniathelphusa Bott, 1968 (Crustacea : Brachyura : Parathelphusidae) inhabit the lowland coastal plains of East Asia and also Taiwan Island, which is their only known locality outside of the main continent. Of the eight species of Somanniathelphusa known from Taiwan and the coastal regions of China (Fujian, Guangdong and Hong Kong), five are studied here: S. amoyensis Naiyanetr & Dai, 1997; S. taiwanensis Bott, 1968; S. zanklon Ng & Dudgeon, 1992; S. zhangpuensis Naiyanetr & Dai, 1997; and S. zhapoensis Naiyanetr & Dai, 1997. Somanniathelphusa taiwanensis has a restricted range in west-central Taiwan, which has been explained by the invasion of species from the mainland via the landbridge of Taiwan Strait during glaciation. This is confirmed by a molecular phylogenetic analysis of the species and its congeners on the mainland. Based on the comparisons of DNA sequences encoding part of the mitochondrial large subunit (16S) rRNA gene and cytochrome oxidase I (COI), two major groups are discernible. Somanniathelphusa zhapoensis from western Guangdong belongs to its own distinct group. The remaining species belong to the second group, but two constituent clades can be recognised, here referred to as the ‘S. taiwanensis’ and ‘S. zanklon’ clades, respectively. These two clades are currently isolated by a major mountain range between Fujian and Guangdong. The molecular evidence also strongly supports the recent invasion of Taiwan by the genus Somanniathelphusa from Fujian during the last glacial event.
The Philodromus pulchellus-group in the Mediterranean: taxonomic revision, phylogenetic analysis and biogeography (Araneae:Philodromidae)
Authors: Muster Christoph , Bosmans Robert , Thaler Konrad
Published: March 2007

The Philodromus pulchellus species-group is defined and diagnosed. Eleven species are included, described or redescribed, keyed and illustrated: P. afroglaucinus, sp. nov. from Algeria; P. bistigma Simon, 1870, P. glaucinus Simon, 1870, P. lamellipalpis, sp. nov. from Algeria; P. medius O. P.-Cambridge, 1872; P. pardalis, sp. nov. from northern Africa and the Iberian peninsula; P. pulchellus Lucas, 1846, P. punctigerus O. P.-Cambridge, 1908, P. ruficapillus Simon, 1885, P. simoni de Mello-Leitão, 1929, and P. wunderlichi, sp. nov. from the western Canary Islands. The validity of P. bistigma and P. medius is re-established (formerly in synonymy with P. pulchellus); neotype and lectotype, respectively are newly designated. The following new synonymies are proposed: P. torquatus O. P.- Cambridge, 1908 = P. pulchellus; P. salinarum Denis, 1939 = P. glaucinus; P. glaucinoides Wunderlich, 1987 = P. punctigerus; P. marionschmidti (Schmidt, 1990) = P. pulchellus. Philodromus albopictus Simon, 1875 and P. rubidus Simon, 1870 are considered nomina dubia. Determination of phylogenetic relationships within the group is difficult owing to continuous character variation, resulting in partially incongruent reconstructions using morphological and molecular data (partial mitochondrial cytochrome c oxidase I gene). Dispersal vicariance analysis provides support for a western Mediterranean origin of the group.
A review of the biology and systematics of Chlamydopsinae (Coleoptera:Histeridae)
Authors: Caterino Michael S. , Dégallier Nicolas
Published: March 2007

The histerid subfamily Chlamydopsinae is a clade of obligate inquilines of social insects, mainly ants. They show a wide range of bizarre morphological characteristics, including highly varied trichomes, associated with this lifestyle. They occur throughout Australia and Indomalaysia, with a few species occurring as far from this centre of diversity as India and Japan. At present the subfamily contains 12 genera and 174 species, several of which are newly described herein (Teretriopsis theryi, gen. nov., sp. nov., Papuopsis andersoni, gen. nov., sp. nov. and Quasimodopsis riedeli, gen. nov. sp. nov.). This paper presents a phylogenetic analysis based on morphological characters of all of the main lineages of the family, provides a complete catalogue of the species, a key to all the genera, and proposes several new combinations. The phylogenetic analysis reveals two large clades, one (including the genera Chlamydopsis Westwood, Eucurtia Mjöberg, and Ectatommiphila Lea) is largely restricted to the Australian continent, whereas the other, containing all other genera, is much more widespread, including many Australian species, but extending also through Indomalaysia into south-east Asia. The beetles are known to utilise many hosts, including ants in four different subfamilies (Myrmicinae, Ponerinae, Dolichoderinae, and Formicinae), as well as termites in the genus Eutermes. However, host records are not yet sufficiently comprehensive to exhibit any clear phylogenetic signal.
β cell transdifferentiation does not contribute to preneoplastic/metaplastic ductal lesions of the pancreas by genetic lineage tracing
in vivo
Authors: Strobel Oliver , Dor Yuval , Stirman Amy , Trainor Amanda , Fernández-del Castillo Carlos , Warshaw Andrew L. , Thayer Sarah P.
Published: March 2007

Inflammatory injury to the pancreas results in regeneration of normal tissue and formation of metaplastic lesions of a ductal phenotype. These metaplastic ductal lesions (MDL) are called tubular complexes (TC), mucinous metaplasia, or pancreatic intraepithelial neoplasia. Because they are regularly found in chronic pancreatitis and pancreatic cancer, their formation is thought to represent a step in inflammation-mediated carcinogenesis. Despite these lesions' ductal character, their origin is controversial. All known pancreatic cell lineages have been suggested as the origin.
In vitro
studies suggest that differentiated cells in the pancreas remain highly plastic and can transdifferentiate as a mechanism of regeneration and metaplasia.
In vivo
studies suggest that islets, specifically β cells, may be the cell of origin. However,
in vitro
studies are subject to ductal cell contamination, and previous
in vivo
studies interpret static data rather than direct evidence. Using genetic lineage tracing
in vivo
, we investigate whether transdifferentiation of β cells contributes to regeneration or metaplasia in pancreatitis. RIP-CreER;Z/AP mice were used to heritably tag β cells in the adult pancreas. Injury by cerulein pancreatitis resulted in regeneration of normal tissue and metaplasia with formation of two distinct types of TC and mucinous lesions. Lineage tracing revealed that none of these MDL are of β cell origin; nor do β cells contribute to regeneration of normal acinar and ductal tissue, which indicates that the plasticity of differentiated pancreatic islet cells, suggested by earlier static and
in vitro
studies, plays no role in regeneration, metaplasia, and carcinogenesis
in vivo
.
RBP-J
(
Rbpsuh
) is essential to maintain muscle progenitor cells and to generate satellite cells
Authors: Vasyutina Elena , Lenhard Diana C. , Wende Hagen , Erdmann Bettina , Epstein Jonathan A. , Birchmeier Carmen
Published: March 2007

In the developing muscle, a pool of myogenic progenitor cells is formed and maintained. These resident progenitors provide a source of cells for muscle growth in development and generate satellite cells in the perinatal period. By the use of conditional mutagenesis in mice, we demonstrate here that the major mediator of Notch signaling, the transcription factor
RBP-J
, is essential to maintain this pool of progenitor cells in an undifferentiated state. In the absence of
RBP-J
, these cells undergo uncontrolled myogenic differentiation, leading to a depletion of the progenitor pool. This results in a lack of muscle growth in development and severe muscle hypotrophy. In addition, satellite cells are not formed late in fetal development in conditional
RBP-J
mutant mice. We conclude that
RBP-J
is required in the developing muscle to set aside proliferating progenitors and satellite cells.
General transcription factor specified global gene regulation in archaea
Authors: Facciotti Marc T. , Reiss David J. , Pan Min , Kaur Amardeep , Vuthoori Madhavi , Bonneau Richard , Shannon Paul , Srivastava Alok , Donohoe Samuel M. , Hood Leroy E. , Baliga Nitin S.
Published: March 2007

Cells responding to dramatic environmental changes or undergoing a developmental switch typically change the expression of numerous genes. In bacteria, σ factors regulate much of this process, whereas in eukaryotes, four RNA polymerases and a multiplicity of generalized transcription factors (GTFs) are required. Here, by using a systems approach, we provide experimental evidence (including protein-coimmunoprecipitation, ChIP-Chip, GTF perturbation and knockout, and measurement of transcriptional changes in these genetically perturbed strains) for how archaea likely accomplish similar large-scale transcriptional segregation and modulation of physiological functions. We are able to associate GTFs to nearly half of all putative promoters and show evidence for at least 7 of the possible 42 functional GTF pairs. This report represents a significant contribution toward closing the gap in our understanding of gene regulation by GTFs for all three domains of life and provides an example for how to use various experimental techniques to rapidly learn significant portions of a global gene regulatory network of organisms for which little has been previously known.
Orai proteins interact with TRPC channels and confer responsiveness to store depletion
Authors: Liao Yanhong , Erxleben Christian , Yildirim Eda , Abramowitz Joel , Armstrong David L. , Birnbaumer Lutz
Published: March 2007

The TRPC (C-type transient receptor potential) class of ion channels has been hypothesized to participate in store-operated Ca
2+
entry (SOCE). Recently, however, STIM1 and Orai1 proteins have been proposed to form SOCE channels. Whether TRPCs participate in SOCE that is dependent on or regulated by Orai has not been explored. Here we show that Orai1 physically interacts with the N and C termini of TRPC3 and TRPC6, and that in cells overexpressing either TRPC3 or TRPC6 in a store-depletion insensitive manner, these TRPCs become sensitive to store depletion upon expression of an exogenous Orai. Thus, Orai-1, -2, and -3 enhanced thapsigargin-induced calcium entry by 50–150% in cells stably overexpressing either TRPC3 or TRPC6. Orai1 expression had no significant effect on endogenous, thapsigargin-induced calcium entry in wild-type cells (HEK-293, COS1), in HEK cells expressing a thapsigargin-sensitive variant of TRPC3 (TRPC3a), or in HEK cells overexpressing another membrane protein, V1aR. Single-channel cation currents present in membrane patches of TRPC3-overexpressing cells were suppressed by expression of Orai1. We propose that Orai proteins by interacting with TRPCs act as regulatory subunits that confer STIM1-mediated store depletion sensitivity to these channels.
Active tissue-specific DNA demethylation conferred by somatic cell nuclei in stable heterokaryons
Authors: Zhang Fan , Pomerantz Jason H. , Sen George , Palermo Adam T. , Blau Helen M.
Published: March 2007

DNA methylation is among the most stable epigenetic marks, ensuring tissue-specific gene expression in a heritable manner throughout development. Here we report that differentiated mesodermal somatic cells can confer tissue-specific changes in DNA methylation on epidermal progenitor cells after fusion in stable multinucleate heterokaryons. Myogenic factors alter regulatory regions of genes in keratinocyte cell nuclei, demethylating and activating a muscle-specific gene and methylating and silencing a keratinocyte-specific gene. Because these changes occur in the absence of DNA replication or cell division, they are mediated by an active mechanism. Thus, the capacity to transfer epigenetic changes to other nuclei is not limited to embryonic stem cells and oocytes but is also a property of highly specialized mammalian somatic cells. These results suggest the possibility of directing the reprogramming of readily available postnatal human progenitor cells toward specific tissue cell types.
A statistical phylogeography of influenza A H5N1
Authors: Wallace Robert G. , HoDac HoangMinh , Lathrop Richard H. , Fitch Walter M.
Published: March 2007

The geographic diffusion of highly pathogenic influenza A H5N1 has largely been traced from the perspective of the virus's victims. Birds of a variety of avian orders have been sampled across localities, and their infection has been identified by a general genetic test. Another approach tracks the migration from the perspective of the virus alone, by way of a phylogeography of H5N1 genetic sequences. Although several phylogenies in the literature have labeled H5N1 clades by geographic region, none has analytically inferred the history of the virus's migration. With a statistical phylogeography of 192 hemagglutinin and neuraminidase isolates, we show that the Chinese province of Guangdong is the source of multiple H5N1 strains spreading at both regional and international scales. In contrast, Indochina appears to be a regional sink, at the same time demonstrating bidirectional dispersal among localities within the region. An evolutionary trace of HA1across the phylogeography suggests a mechanism by which H5N1 is able to infect repeated cycles of host species across localities, regardless of the host species first infected in each locale. The trace also hypothesizes amino acid replacements that preceded the first recorded outbreak of pathogenic H5N1 in Hong Kong, 1997.
Yeast Formins Bni1 and Bnr1 Utilize Different Modes of Cortical Interaction during the Assembly of Actin Cables
Authors: Buttery Shawnna M. , Yoshida Satoshi , Pellman David
Published: March 2007

The budding yeast formins Bni1 and Bnr1 control the assembly of actin cables. These formins exhibit distinct patterns of localization and polymerize two different populations of cables: Bni1 in the bud and Bnr1 in the mother cell. We generated a functional Bni1-3GFP that improved the visualization of Bni1 in vivo at endogenous levels. Bni1 exists as speckles in the cytoplasm, some of which colocalize on actin cables. These Bni1 speckles display linear, retrograde-directed movements. Loss of polymerized actin or specifically actin cables abolished retrograde movement, and resulted in depletion of Bni1 speckles from the cytoplasm, with enhanced targeting of Bni1 to the bud tip. Mutations that impair the actin assembly activity of Bni1 abolished the movement of Bni1 speckles, even when actin cables were present. In contrast, Bnr1-GFP or 3GFP-Bnr1 did not detectably associate with actin cables and was not observed as cytoplasmic speckles. Finally, fluorescence recovery after photobleaching demonstrated that Bni1 was very dynamic, exchanging between polarized sites and the cytoplasm, whereas Bnr1 was confined to the bud neck and did not exchange with a cytoplasmic pool. In summary, our results indicate that formins can have distinct modes of cortical interaction during actin cable assembly.
Slug Is Required for Cell Survival during Partial Epithelial-Mesenchymal Transition of HGF-induced Tubulogenesis
Authors: Leroy Pascale , Mostov Keith E.
Published: March 2007

Transcription factors of the Snail family are key regulators of epithelial-mesenchymal transition (EMT). In many processes during development or disease, cells do not acquire all the characteristics associated with EMT, leading to what we refer to as partial EMT (p-EMT). However, little is known of the implications of the Snail transcription factors in processes that only involve a p-EMT. To assess this, we used the hepatocyte growth factor (HGF)-induced Madin-Darby canine kidney tubulogenesis system, which provides a three-dimensional culture model of a morphogenetic process including a p-EMT. We found that although Slug (Snail2) is highly and transitory up-regulated during the p-EMT phase of tubulogenesis, it is not a repressor of E-cadherin during this process. Using inducible knockdown of Slug, we demonstrate that Slug is not an inducer of cell movement and instead is required for survival during p-EMT. We conclude that in epithelial cells, promoting cell survival can be a primary function of Slug, rather than being acquired concomitantly with EMT.
Interphase-specific Phosphorylation-mediated Regulation of Tubulin Dimer Partitioning in Human Cells
Authors: Holmfeldt Per , Stenmark Sonja , Gullberg Martin
Published: March 2007

The microtubule cytoskeleton is differentially regulated by a diverse array of proteins during interphase and mitosis. Op18/stathmin (Op18) and microtubule-associated protein (MAP)4 have been ascribed opposite general microtubule-directed activities, namely, microtubule destabilization and stabilization, respectively, both of which can be inhibited by phosphorylation. Here, using three human cell models, we depleted cells of Op18 and/or MAP4 by expression of interfering hairpin RNAs and we analyzed the resulting phenotypes. We found that the endogenous levels of Op18 and MAP4 have opposite and counteractive activities that largely govern the partitioning of tubulin dimers in the microtubule array at interphase. Op18 and MAP4 were also found to be the downstream targets of Ca2+- and calmodulin-dependent protein kinase IV and PAR-1/MARK2 kinase, respectively, that control the demonstrated counteractive phosphorylation-mediated regulation of tubulin dimer partitioning. Furthermore, to address mechanisms regulating microtubule polymerization in response to cell signals, we developed a system for inducible gene product replacement. This approach revealed that site-specific phosphorylation of Op18 is both necessary and sufficient for polymerization of microtubules in response to the multifaceted signaling event of stimulation of the T cell antigen receptor complex, which activates several signal transduction pathways.
pcaMethods—a bioconductor package providing PCA methods for incomplete data
Authors: Stacklies Wolfram , Redestig Henning , Scholz Matthias , Walther Dirk , Selbig Joachim
Published: March 2007

Summary:  pcaMethods is a Bioconductor compliant library for computing principal component analysis (PCA) on incomplete data sets. The results can be analyzed directly or used to estimate missing values to enable the use of missing value sensitive statistical methods. The package was mainly developed with microarray and metabolite data sets in mind, but can be applied to any other incomplete data set as well.

Availability:  http://www.bioconductor.org

Contact:  selbig@mpimp-golm.mpg.de

Supplementary information: Please visit our webpage at http://bioinformatics.mpimp-golm.mpg.de/
Metabolic systems cost-benefit analysis for interpreting network structure and regulation
Authors: Carlson Ross P.
Published: March 2007

Motivation: Interpretation of bioinformatics data in terms of cellular function is a major challenge facing systems biology. This question is complicated by robust metabolic networks filled with structural features like parallel pathways and isozymes. Under conditions of nutrient sufficiency, metabolic networks are well known to be regulated for thermodynamic efficiency however; efficient biochemical pathways are anabolically expensive to construct. While parameters like thermodynamic efficiency have been extensively studied, a systems-based analysis of anabolic proteome synthesis ‘costs’ and the cellular function implications of these costs has not been reported.

Results: A cost-benefit analysis of an in silico Escherichia coli network revealed the relationship between metabolic pathway proteome synthesis requirements, DNA-coding sequence length, thermodynamic efficiency and substrate affinity. The results highlight basic metabolic network design principles. Pathway proteome synthesis requirements appear to have shaped biochemical network structure and regulation. Under conditions of nutrient scarcity and other general stresses, E.coli expresses pathways with relatively inexpensive proteome synthesis requirements instead of more efficient but also anabolically more expensive pathways. This evolutionary strategy provides a cellular function-based explanation for common network motifs like isozymes and parallel pathways and possibly explains ‘overflow’ metabolisms observed during nutrient scarcity.

Contact:  alicia@iastate.edu

Supplementary information: Supplementary data are available at Bioinformatics online.