bluuebunny/crossref_metadata_2025 huggingface dataset:
Simultaneous measurements of the specific heat and thermal conductivity of suspended thin samples by transient electrothermal method
Authors: Feng Bo , Ma Weigang , Li Zhixin , Zhang Xing
Published: June 2009

The electrothermal technique is developed to simultaneously measure the specific heat and thermal conductivity of individual thin samples suspended across two heat sinks, resorting to pulsed direct currents with or without a dc offset. The temperature evolution due to Joule self-heating is recorded and compared with the numerical solutions of transient heat conduction equations using the finite volume method. The thermal conductivity is determined by the steady temperature level and the specific heat by the transient temperature rise or relaxation. This technique is applied to a 10 μm thick platinum wire and the thermal conductivity and specific heat are in good agreement with the literature values. In addition, the influences of thermal radiation and thermal boundary resistance between the sample and heat sinks on the experimental results are discussed.
Microwave properties of single-walled carbon nanotubes films below percolation threshold
Authors: Darne Chinmay , Xie Leiming , Zagozdzon-Wosik Wanda , Schmidt Howard K. , Wosik Jarek
Published: June 2009

A film residue obtained by evaporating surfactant-stabilized single-walled carbon nanotube (SWNT) suspension was characterized at 12 GHz using a scanning-sample dielectric resonator technique. Resonant frequency and quality factor changes were measured and cavity perturbation method was used to calculate the SWNT complex permittivity. The effective permittivity of the SWNT was determined as (3516-j316.5), which provided an average dielectric constant and conductivity for a single SWNT to be 8.1×105 and 8.4×106 S/m, respectively. Microwave induced losses originated only from the electric field, not from the magnetic field, thus indicating an absence of direct electrical contact between nanotubes and a below percolation-limit configuration.
Improving emission enhancement in surface plasmon coupling with an InGaN/GaN quantum well by inserting a dielectric layer of low refractive index between metal and semiconductor
Authors: Lu Yen-Cheng , Chen Yung-Sheng , Tsai Fu-Ji , Wang Jyh-Yang , Lin Cheng-Hung , Chen Cheng-Yen , Kiang Yean-Woei , Yang C. C.
Published: June 2009

The improved emission enhancement in surface plasmon polariton (SPP) coupling with an InGaN/GaN quantum well (QW) by inserting a SiO2 layer of lower refractive index between the deposited Ag and GaN layers is experimentally and numerically demonstrated. The inserted SiO2 layer leads to reduced SPP dissipation rate, increased evanescent field intensity beyond a certain depth in GaN, and decreased SPP density of state. The combination of these factors can result in further emission enhancement of QW through SPP coupling. For light-emitting diode application, the elongated evanescent field coverage can release the constraint of thin p-type GaN for effective SPP coupling. More importantly, the reduced SPP dissipation can result in more effective emission in such an SPP-QW coupling mechanism.
Electrical stability of inkjet-patterned organic complementary inverters measured in ambient conditions
Authors: Ng Tse Nga , Sambandan Sanjiv , Lujan Rene , Arias Ana Claudia , Newman Christopher R. , Yan He , Facchetti Antonio
Published: June 2009

Complementary organic inverters were fabricated by inkjet patterning of both the metal contacts and the semiconductors. Bottom-gate, bottom-contact organic thin-film transistors with Ta2O5-polymer bilayer dielectrics, inkjet-printed silver electrodes, and inkjet-printed organic semiconductors exhibit hole and electron mobilities as high as ∼10−2 cm2/V s. Complementary inverters based on these transistors operate in ambient and exhibit a gain of −4.4 with supply voltage VDD=+20 V and −3 dB cutoff at 100 kHz with a load of 0.02 pF. The electrical stability of the inverters was evaluated for analog and digital operation, and a noise margin ≥1.1 V at VDD=+15 V was measured with bias-stress effects included.
Strain-coupled ferroelectric polarization in BaTiO3–CaTiO3 superlattices
Authors: Seo Sung Seok A. , Lee Ho Nyung
Published: June 2009

We report on growth and ferroelectric (FE) properties of superlattices (SLs) composed of the FE BaTiO3 and the paraelectric CaTiO3. Previous theories have predicted that the polarization in (BaTiO3)n/(CaTiO3)n SLs increases as the sublayer thickness (n) increases when the same strain state is maintained. However, our BaTiO3/CaTiO3 SLs show a varying lattice-strain state and systematic reduction in polarization with increasing n while coherently strained SLs with n=1 and 2 show a FE polarization of ca. 8.5 μC/cm2. We suggest that the strain coupling plays a more important role in FE properties than the electrostatic interlayer coupling based on constant dielectric permittivities.
Effect of initial stress/strain state on order-disorder transformation of FePt thin films
Authors: Hsiao S. N. , Yuan F. T. , Chang H. W. , Huang H. W. , Chen S. K. , Lee H. Y.
Published: June 2009

Initial stress (σi) of a room-temperature deposited FePt films was manipulated to study the order-disorder transformation. We observed that, while σi was increased from −1.01 (compressive) to 0.18 GPa (tensile), the phase transformation activation energy decreased from 0.387 to 0.23 eV/atom. This causes a reduction in ordering temperature of about 100 °C. We also found that densification induces an increase in tensile stress of about 1 GPa before ordering. In the films with small σi, strong tension facilitates the nucleation of L10 FePt; however, if highly compressive σi cancels the densification tension, ordering is retarded causing higher ordering temperature.
Effects of semiconducting and metallic single-walled carbon nanotubes on performance of bulk heterojunction organic solar cells
Authors: Liu Liming , Stanchina William E. , Li Guangyong
Published: June 2009

This letter reports that the performance of organic solar cells made from blended films of regioregular poly 3-hexylthiophene and methanofullerene can be boosted by introducing single-walled carbon nanotubes (SWCNTs) into the active layer at low concentration. However, the performance degrades at higher SWCNTs concentration. The intensity dependent photocurrent measurement shows that the decreased performance at higher concentration of SWCNTs is attributed to bimolecular recombination in the presence of metallic SWCNTs. Meanwhile, it has been found that the increased performance at low concentration of SWCNTs is due to the increased carrier mobility as semiconducting SWCNTs provide lower resistance pathways.
On the phase diagram of water with density functional theory potentials: The melting temperature of ice Ih with the Perdew–Burke–Ernzerhof and Becke–Lee–Yang–Parr functionals
Authors: Yoo Soohaeng , Zeng Xiao Cheng , Xantheas Sotiris S.
Published: June 2009

The melting temperature (Tm) of ice Ih was determined from constant enthalpy and pressure (NPH) Born–Oppenheimer molecular dynamics simulations to be 417±3 K for the Perdew–Burke–Ernzerhof and 411±4 K for the Becke–Lee–Yang–Parr density functionals using a coexisting ice (Ih)-liquid phase at constant pressures of P=2500 and 10 000 bar and a density ρ=1 g/cm3, respectively. This suggests that ambient condition simulations at ρ=1 g/cm3 will rather describe a supercooled state that is overstructured when compared to liquid water.
Theoretical evidence for a first-order liquid-liquid phase transition in gallium
Authors: Carvajal Jara Diego Alejandro , Fontana Michelon Mateus , Antonelli Alex , de Koning Maurice
Published: June 2009

We report on theoretical results that lend support to recent experimental observations suggesting the existence of a first-order liquid-liquid phase transformation (LLPT) in gallium. Using molecular dynamics simulation based on a modified embedded-atom model, we observe a transition from a high-density to a low-density liquid in the supercooled regime. The first-order character of the transition is established through the detection of the release of latent heat and our findings suggest that the LLPT terminates in a critical point that is located in the tensile-strained domain of the metastable phase diagram.
Metal-oxide interfaces at the nanoscale
Authors: Zhou Guangwen
Published: June 2009

In contrast to the 6×7 spacing registry that yields a minimum coincidence misfit, we find that the nanoscale Cu2O–Cu interface formed during initial oxidation of Cu(111) surfaces adopts a 5×6 coincidence site lattice that is accommodated by an increased lattice misfit strain. A simple analysis on the equilibrium elastic strain in epitaxial oxide nanoislands reveals a previously unnoticed correlation between the interface structure and surface stresses at the nanoscale.
Control and elimination of nucleation-related defects in GaP/Si(001) heteroepitaxy
Authors: Grassman T. J. , Brenner M. R. , Rajagopalan S. , Unocic R. , Dehoff R. , Mills M. , Fraser H. , Ringel S. A.
Published: June 2009

GaP films were grown on offcut Si(001) substrates using migration enhanced epitaxy nucleation followed by molecular beam epitaxy, with the intent of controlling and eliminating the formation of heterovalent (III-V/IV) nucleation-related defects—antiphase domains, stacking faults, and microtwins. Analysis of these films via reflection high-energy electron diffraction, atomic force microscopy, and both cross-sectional and plan-view transmission electron microscopies indicate high-quality GaP layers on Si that portend a virtual GaP substrate technology, in which the aforementioned extended defects are simultaneously eliminated. The only prevalent remaining defects are the expected misfit dislocations due to the GaP–Si lattice mismatch.
Elimination of antiviral defense by viral RNase III
Authors: Cuellar Wilmer J. , Kreuze Jan F. , Rajamäki Minna-Liisa , Cruzado Karin R. , Untiveros Milton , Valkonen Jari P. T.
Published: June 2009

Sweet potato (
Ipomoea batatas
) is an important subsistence and famine reserve crop grown in developing countries where
Sweet potato chlorotic stunt virus
(SPCSV;
Closteroviridae
), a single-stranded RNA (ssRNA) crinivirus, synergizes unrelated viruses in co-infected sweet potato plants. The most severe disease and yield losses are caused by co-infection with SPCSV and a potyvirus,
Sweet potato feathery mottle virus
(SPFMV;
Potyviridae
). Potyviruses synergize unrelated viruses by suppression of RNA silencing with the P1/HC-Pro polyprotein; however, the SPCSV-SPFMV synergism is unusual in that the potyvirus is the beneficiary. Our data show that transformation of an SPFMV-resistant sweet potato variety with the double-stranded RNA (dsRNA)-specific class 1 RNA endoribonuclease III (RNase3) of SPCSV broke down resistance to SPFMV, leading to high accumulation of SPFMV antigen and severe disease symptoms similar to the synergism in plants co-infected with SPCSV and SPFMV. RNase3-transgenic sweet potatoes also accumulated higher concentrations of 2 other unrelated viruses and developed more severe symptoms than non-transgenic plants. In leaves, RNase3 suppressed ssRNA-induced gene silencing (RNAi) in an endonuclease activity-dependent manner. It cleaved synthetic double-stranded small interfering RNAs (siRNAs) of 21, 22, and 24 bp in vitro to products of approximately 14 bp that are inactive in RNAi. It also affected total siRNA isolated from SPFMV-infected sweet potato plants, suggesting a viral mechanism for suppression of RNAi by cleavage of siRNA. Results implicate RNase3 in suppression of antiviral defense in sweet potato plants and reveal RNase3 as a protein that mediates viral synergism with several unrelated viruses, a function previously described only for P1/HC-Pro.
Cadmium-mediated rescue from ER-associated degradation induces expression of its exporter
Authors: Adle David J. , Wei Wenzhong , Smith Nathan , Bies Joshua J. , Lee Jaekwon
Published: June 2009

Cadmium is a highly toxic environmental contaminant that has been implicated in various disorders. A major mechanism for cadmium detoxification in the yeast
Saccharomyces cerevisiae
relies on extrusion via Pca1, a P-type ATPase. While an N-terminal degron targets Pca1 for degradation before its secretion to the plasma membrane, cadmium in the growth media rapidly up-regulates Pca1 by preventing its turnover. Here we show that the endoplasmic reticulum-associated degradation (ERAD) system, known for its role in quality control of secretory proteins, is unexpectedly responsible for the regulation of Pca1 expression by cadmium. Direct cadmium sensing at the ER by a degron in Pca1 leads to an escape of Pca1 from ERAD. This regulated conversion of an ERAD substrate to a secretory competent state in response to a cellular need illustrates a mechanism for expressional control of a plasma membrane protein. Yeast has likely evolved this mode of regulation for a rapid response against cadmium toxicity at the expense of constant synthesis and degradation of Pca1. ERAD of a portion of secretory proteins might occur via signal-dependent regulatory mechanisms as demonstrated for Pca1.
Structure of CFA/I fimbriae from enterotoxigenic
Escherichia coli
Authors: Li Yong-Fu , Poole Steven , Nishio Kazuya , Jang Ken , Rasulova Fatima , McVeigh Annette , Savarino Stephen J. , Xia Di , Bullitt Esther
Published: June 2009

Adhesion pili (fimbriae) play a critical role in initiating the events that lead to intestinal colonization and diarrheal disease by enterotoxigenic
Escherichia coli
(ETEC), an
E. coli
pathotype that inflicts an enormous global disease burden. We elucidate atomic structures of an ETEC major pilin subunit, CfaB, from colonization factor antigen I (CFA/I) fimbriae. These data are used to construct models for 2 morphological forms of CFA/I fimbriae that are both observed in vivo: the helical filament into which it is typically assembled, and an extended, unwound conformation. Modeling and corroborative mutational data indicate that proline isomerization is involved in the conversion between these helical and extended forms. Our findings affirm the strong structural similarities seen between class 5 fimbriae (from bacteria primarily causing gastrointestinal disease) and class 1 pili (from bacteria that cause urinary, respiratory, and other infections) in the absence of significant primary sequence similarity. They also suggest that morphological and biochemical differences between fimbrial types, regardless of class, provide structural specialization that facilitates survival of each bacterial pathotype in its preferred host microenvironment. Last, we present structural evidence for bacterial use of antigenic variation to evade host immune responses, in that residues occupying the predicted surface-exposed face of CfaB and related class 5 pilins show much higher genetic sequence variability than the remainder of the pilin protein.
Inter-sarcomere coordination in muscle revealed through individual sarcomere response to quick stretch
Authors: Shimamoto Yuta , Suzuki Madoka , Mikhailenko Sergey V. , Yasuda Kenji , Ishiwata Shin'ichi
Published: June 2009

The force generation and motion of muscle are produced by the collective work of thousands of sarcomeres, the basic structural units of striated muscle. Based on their series connection to form a myofibril, it is expected that sarcomeres are mechanically and/or structurally coupled to each other. However, the behavior of individual sarcomeres and the coupling dynamics between sarcomeres remain elusive, because muscle mechanics has so far been investigated mainly by analyzing the averaged behavior of thousands of sarcomeres in muscle fibers. In this study, we directly measured the length-responses of individual sarcomeres to quick stretch at partial activation, using micromanipulation of skeletal myofibrils under a phase-contrast microscope. The experiments were performed at ADP-activation (1 mM MgATP and 2 mM MgADP in the absence of Ca
2+
) and also at Ca
2+
-activation (1 mM MgATP at pCa 6.3) conditions. We show that under these activation conditions, sarcomeres exhibit 2 distinct types of responses, either “resisting” or “yielding,” which are clearly distinguished by the lengthening distance of single sarcomeres in response to stretch. These 2 types of sarcomeres tended to coexist within the myofibril, and the sarcomere “yielding” occurred in clusters composed of several adjacent sarcomeres. The labeling of Z-line with anti-α-actinin antibody significantly suppressed the clustered sarcomere “yielding.” These results strongly suggest that the contractile system of muscle possesses the mechanism of structure-based inter-sarcomere coordination.
Intracellular Ca
2+
signaling and store-operated Ca
2+
entry are required in
Drosophila
neurons for flight
Authors: Venkiteswaran Gayatri , Hasan Gaiti
Published: June 2009

Neuronal Ca
2+
signals can affect excitability and neural circuit formation. Ca
2+
signals are modified by Ca
2+
flux from intracellular stores as well as the extracellular milieu. However, the contribution of intracellular Ca
2+
stores and their release to neuronal processes is poorly understood. Here, we show by neuron-specific siRNA depletion that activity of the recently identified store-operated channel encoded by
dOrai
and the endoplasmic reticulum Ca
2+
store sensor encoded by
dSTIM
are necessary for normal flight and associated patterns of rhythmic firing of the flight motoneurons of
Drosophila melanogaster
. Also,
dOrai
overexpression in flightless mutants for the
Drosophila
inositol 1,4,5-trisphosphate receptor (InsP
3
R) can partially compensate for their loss of flight. Ca
2+
measurements show that Orai gain-of-function contributes to the quanta of Ca
2+
-release through mutant InsP
3
Rs and elevates store-operated Ca
2+
entry in
Drosophila
neurons. Our data show that replenishment of intracellular store Ca
2+
in neurons is required for
Drosophila
flight.
In situ observation of graphene sublimation and multi-layer edge reconstructions
Authors: Huang Jian Yu , Ding Feng , Yakobson Boris I. , Lu Ping , Qi Liang , Li Ju
Published: June 2009

We induced sublimation of suspended few-layer graphene by in situ Joule-heating inside a transmission electron microscope. The graphene sublimation fronts consisted of mostly {1100} zigzag edges. Under appropriate conditions, a fractal-like “coastline” morphology was observed. Extensive multiple-layer reconstructions at the graphene edges led to the formation of unique carbon nanostructures, such as
sp
2
-bonded bilayer edges (BLEs) and nanotubes connected to BLEs. Flat fullerenes/nanopods and nanotubes tunneling multiple layers of graphene sheets were also observed. Remarkably, >99% of the graphene edges observed during sublimation are BLEs rather than monolayer edges (MLEs), indicating that BLEs are the stable edges in graphene at high temperatures. We reproduced the “coastline” sublimation morphologies by kinetic Monte Carlo (kMC) simulations. The simulation revealed geometrical and topological features unique to quasi-2-dimensional (2D) graphene sublimation and reconstructions. These reconstructions were enabled by bending, which cannot occur in first-order phase transformations of 3D bulk materials. These results indicate that substrate of multiple-layer graphene can offer unique opportunities for tailoring carbon-based nanostructures and engineering novel nano-devices with complex topologies.
Concept of magnet systems for LHD-type reactor
Authors: Imagawa S. , Takahata K. , Tamura H. , Yanagi N. , Mito T. , Obana T. , Sagara A.
Published: June 2009

Heliotron reactors have attractive features for fusion power plants such as having no need for current drive and a wide space between the helical coils for the maintenance of in-vessel components. Their main disadvantage was considered to be the necessarily large size of their magnet systems. According to the recent reactor studies based on the experimental results in the Large Helical Device, a major radius of plasma of 14–17 m with a central toroidal field of 6–4 T is needed to attain the self-ignition condition with a blanket space thicker than 1.1 m. The stored magnetic energy is estimated at 120–140 GJ. Although both the major radius and the magnetic energy are about three times as large as ITER, the maximum magnetic field and mechanical stress are comparable. In the preliminary structural analysis, the maximum stress intensity including the peak stress is less than the 1000 MPa that is allowed for strengthened stainless steel. Although the length of the helical coil is more than 150 m, that is about five times as long as the ITER TF coil, cable-in-conduit conductors can be adopted with a parallel winding method of five-in-hand. The concept of the parallel winding is proposed. Consequently, the magnet systems for helical reactors can be realized with a small extension of the ITER technology.
Experiments and modelling of active quasi-single helicity regime generation in a reversed field pinch
Authors: Frassinetti L. , Brunsell P.R. , Drake J.R.
Published: June 2009

The interaction of a static resonant magnetic perturbation (RMP) with a tearing mode (TM) is becoming a relevant topic in fusion plasma physics. RMPs can be generated by active coils and then used to affect the properties of TMs and of the corresponding magnetic islands. This paper shows how the feedback system of the EXTRAP T2R reversed field pinch (RFP) can produce a RMP that affects a rotating TM and stimulate the transition to the so-called quasi-single helicity (QSH) regime, a RFP plasma state characterized by a magnetic island surrounded by low magnetic chaos. The application of the RMP can increase the QSH probability up to 10% and enlarge the size of the corresponding island. Part of the experimental results are supported by a theoretical study that models the effect of the active coils on the magnetic island.
Kinetic analysis of the resistive wall modes in the ITER advanced tokamak scenario
Authors: Zheng L.J. , Kotschenreuther M.T. , Van Dam J.W.
Published: June 2009

It is found that n = 1 resistive wall modes in the ITER advanced scenario can be fully stabilized by modestly low rotation with a rotation frequency (normalized to the Alfvén frequency at the magnetic axis) of about Ω = 0.0075. The existence of this stabilization scheme is proved with the AEGIS-K (Adaptive EiGenfunction Independent Solution-Kinetic) code, which provides a fully kinetic (non-hybrid) and self-consistent (non-perturbative) description of the system. Wave-particle resonances, shear Alfvén continuum damping, trapped particle effect and the parallel electric effects are all taken into account. The rotation frequency for full stabilization is much larger than the diamagnetic drift frequency; therefore, finite Larmor radius effects are negligible. We also find that the rotation stabilization window opens first near the ideal wall limit.
Multi-scale transport simulation of toroidal momentum source profile effect on internal transport barrier collapse
Authors: Tokunaga S. , Yagi M. , Itoh S.-I. , Itoh K.
Published: June 2009

The mechanism of internal transport barrier (ITB) collapse in the reversed magnetic shear configuration is investigated using a global ion temperature gradient (ITG) driven drift wave turbulence code. A heating source and a toroidal momentum source are introduced to follow the self-consistent evolution of the ion temperature and flow profiles. A scenario of transport barrier collapse driven by a meso-scale mode excited in the barrier region is suggested. The importance of the quasi-linear effect due to profile modification as well as three-wave coupling is clearly shown by means of energy transfer analysis. The effect of the toroidal flow shear (TFS) profile on the dynamics of ITB evolution is investigated. It is found that the decorrelation between meso-scale modes and ITG driven modes due to the TFS can prevent global relaxation.
Particle simulation of energetic particle driven Alfvén modes in NBI heated DIII-D experiments
Authors: Vlad G. , Briguglio S. , Fogaccia G. , Zonca F. , Troia C. Di , Heidbrink W.W. , Van Zeeland M.A. , Bierwage A. , Wang X.
Published: June 2009

The mutual nonlinear interactions of shear Alfvén modes and alpha particles can enhance their transport in burning plasmas. Theoretical and numerical works have shown that rapid transport of energetic ions can take place because of fast growing Alfvén modes (e.g. energetic particle driven modes, EPMs). This kind of transport has been observed in experiments as well as in numerical simulations. Hybrid MHD-gyrokinetic codes can investigate linear and nonlinear dynamics of energetic particle (EP) driven modes, retaining the mutual interaction between waves and EPs self-consistently. Self-consistent nonlinear wave–particle interactions (both in configuration and velocity space) are crucial for a correct description of the mode dynamics in the case of strongly driven modes; thus, a non-perturbative approach is mandatory. The knowledge of the threshold characterizing the transition from weakly to strongly driven regimes is of primary importance for burning plasma operations (e.g. for ITER), in order to avoid EPM enhanced EP transport regimes. The hybrid MHD-gyrokinetic code (HMGC) has been applied to the interpretation of phenomena observed in present experiments with neutral beam (NB) heating. In reversed-shear beam-heated DIII-D discharges, a large discrepancy between the expected and measured EP radial density profiles has been observed in the presence of large Alfvénic activity. HMGC simulations with EP radial profiles expected from classical NB deposition as input give rise to strong EPM activity, resulting in relaxed EP radial profiles at saturation level close to experimental measurements. The frequency spectra obtained from several simulations with different toroidal mode numbers, as calculated during the saturated phase when the strong EPMs transform in weak reversed-shear Alfvén modes, are quite close to experimental observations both in absolute frequency and in radial localization. In this work, we discuss in particular the effects of nonlinear coupling between different toroidal mode numbers.
E-cadherin Surface Levels in Epithelial Growth Factor-stimulated Cells Depend on Adherens Junction Protein Shrew-1
Authors: Gross Julia Christina , Schreiner Alexander , Engels Knut , Starzinski-Powitz Anna
Published: June 2009

Gain- and loss-of-function studies indicate that the adherens junction protein shrew-1 acts as a novel modulator of E-cadherin internalization induced by epithelial growth factor (EGF) or E-cadherin function-blocking antibody during epithelial cell dynamics. Knocking down shrew-1 in MCF-7 carcinoma cells preserves E-cadherin surface levels upon EGF stimulation. Overexpression of shrew-1 leads to preformation of an E-cadherin/EGF receptor (EGFR) HER2/src-kinase/shrew-1 signaling complex and accelerated E-cadherin internalization. Shrew-1 is not sufficient to stimulate E-cadherin internalization, but facilitates the actions of EGFR and thus may promote malignant progression in breast cancer cells with constitutive EGFR stimulation by reducing surface E-cadherin expression.
Stathmin Regulates Centrosomal Nucleation of Microtubules and Tubulin Dimer/Polymer Partitioning
Authors: Ringhoff Danielle N. , Cassimeris Lynne
Published: June 2009

Stathmin is a microtubule-destabilizing protein ubiquitously expressed in vertebrates and highly expressed in many cancers. In several cell types, stathmin regulates the partitioning of tubulin between unassembled and polymer forms, but the mechanism responsible for partitioning has not been determined. We examined stathmin function in two cell systems: mouse embryonic fibroblasts (MEFs) isolated from embryos +/+, +/−, and −/− for the stathmin gene and porcine kidney epithelial (LLCPK) cells expressing stathmin-cyan fluorescent protein (CFP) or injected with stathmin protein. In MEFs, the relative amount of stathmin corresponded to genotype, where cells heterozygous for stathmin expressed half as much stathmin mRNA and protein as wild-type cells. Reduction or loss of stathmin resulted in increased microtubule polymer but little change to microtubule dynamics at the cell periphery. Increased stathmin level in LLCPK cells, sufficient to reduce microtubule density, but allowing microtubules to remain at the cell periphery, also did not have a major impact on microtubule dynamics. In contrast, stathmin level had a significant effect on microtubule nucleation rate from centrosomes, where lower stathmin levels increased nucleation and higher stathmin levels reduced nucleation. The stathmin-dependent regulation of nucleation is only active in interphase; overexpression of stathmin-CFP did not impact metaphase microtubule nucleation rate in LLCPK cells and the number of astral microtubules was similar in stathmin +/+ and −/− MEFs. These data support a model in which stathmin functions in interphase to control the partitioning of tubulins between dimer and polymer pools by setting the number of microtubules per cell.
A pattern-based nearest neighbor search approach for promoter prediction using DNA structural profiles
Authors: Gan Yanglan , Guan Jihong , Zhou Shuigeng
Published: June 2009

Motivation: Identification of core promoters is a key clue in understanding gene regulations. However, due to the diverse nature of promoter sequences, the accuracy of existing prediction approaches for non-CpG island (simply CGI)-related promoters is not as high as that for CGI-related promoters. This consequently leads to a low genome-wide promoter prediction accuracy.

Results: In this article, we first systematically analyze the similarities and differences between the two types of promoters (CGI- and non-CGI-related) from a novel structural perspective, and then devise a unified framework, called PNNP (Pattern-based Nearest Neighbor search for Promoter), to predict both CGI- and non-CGI-related promoters based on their structural features. Our comparative analysis on the structural characteristics of promoters reveals two interesting facts: (i) the structural values of CGI- and non-CGI-related promoters are quite different, but they exhibit nearly similar structural patterns; (ii) the structural patterns of promoters are obviously different from that of non-promoter sequences though the sequences have almost similar structural values. Extensive experiments demonstrate that the proposed PNNP approach is effective in capturing the structural patterns of promoters, and can significantly improve genome-wide performance of promoters prediction, especially non-CGI-related promoters prediction.

Availability: The implementation of the program PNNP is available at http://admis.tongji.edu.cn/Projects/pnnp.aspx.

Contact:  jhguan@tongji.edu.cn; sgzhou@fudan.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Natriuretic peptides and echocardiography in acute dyspnoea: implication of elevated levels with normal systolic function
Authors: Shah Keyur B. , Kop Willem J. , Christenson Robert H. , Diercks Deborah B. , Kuo Dick , Henderson Sue , Hanson Karen , Li Shu‐Ying , deFilippi Christopher R.
Published: June 2009

Aims

Previous evaluations of natriuretic peptide (NP) levels in patients with acute dyspnoea presenting to the emergency department (ED) have selected only a minority of patients for echocardiography. We aimed to evaluate the association between NPs and more subtle echocardiographic findings and to assess the potential for NPs to provide additional prognostic information beyond that provided by echocardiography in ‘all‐comers’ with acute dyspnoea.

Methods and results

Prospective echocardiograms were performed on 338/412 patients presenting to the ED with acute dyspnoea. B‐type natriuretic peptide and NT‐proBNP were measured on presentation. Patients were followed‐up for 1 year. Decompensated heart failure was diagnosed in 37% of patients and 13% died. The diagnostic accuracy (c‐statistic) of BNP and NT‐proBNP for identifying LVEF ≤ 40% was 0.88 (P < 0.001) and 0.86 (P < 0.001), respectively. The c‐statistics for BNP and NT‐proBNP for identifying diastolic dysfunction were 0.67 (P < 0.001) and 0.67 (P < 0.001); but only 0.57 (P = 0.09) and 0.60 (P = 0.02) in patients with LVEF ≥ 50%. Natriuretic peptides, but not LV mass or diastolic parameters, independently predicted mortality at 1 year in all patients and in those with an LVEF ≥ 50%.

Conclusion

In an acute dyspnoea population with ‘all‐comers’ undergoing echocardiography, NPs correlate strongly with structural abnormalities and identify those with preserved LVEF at highest risk for death. Careful interpretation of elevated NP values is needed in the presence of preserved systolic function.
Recognizing Psychological Distress in the Consultation
Authors: Howe Amanda
Published: June 2009

The new MRCGP curriculum devotes a whole section to the care of people with mental health problems—and rightly so, for up to 30% of us will have some kind of significant episode of psychological disturbance in our lifetimes. Far more of us suffer transient but problematic psychological distress, especially when we or others for whom we care are unwell. So the GP registrar doing a routine clinic in UK general practice will find that as many as one in four of their patients are experiencing psychological symptoms, with higher rates in the elderly. Previous articles have covered the specific tasks of performing mental health assessments and diagnosing depression: this article aims to review the broader context of psychological distress in the consultation. It pays additional attention to factors associated with psychological distress to which GPs and other primary care staff should be alert and to ways of addressing these in a sophisticated and humane manner. Finally, I address the queston of self-management—that is minimizing the ‘human sponge’ effect often incurred by empathic GPs at the start of training.
Psychosis in Primary Care
Authors: Cohen Alan
Published: June 2009

This paper describes the role of primary care clinicians in the management of people with psychosis. The paper uses the term ‘psychosis’ in the same way that severe mental illness is used in the Quality and Outcome Framework to mean those people who suffer from schizophrenia or bipolar disorder. The paper will cover some epidemiological characteristics of psychosis, features of people with acute psychosis, features of chronic psychosis and finally describe briefly changes to the Mental Health Act 2007 and the potential for these changes to affect the practice of medicine in primary care.
Contact Dermatitis
Authors: Verma Vineeta , Shah SN
Published: June 2009

Approximately 15% of GP consultations in the UK are for a skin condition. In the general population, about 4.5% of people have a contact allergy to nickel and 1–3% to an ingredient in cosmetics. Studies suggest that skin disorders (29%) are the second most common cause of occupational disease after musculoskeletal conditions (57%).
Benign Skin Tumours
Authors: Mirza Salma
Published: June 2009

Skin disorders are a common presentation in primary care accounting for up to 10% of GP consultations. Benign skin tumours make up a significant proportion of these, thus the ability to accurately assess and diagnose them and manage lesions appropriately is an essential competence in primary care.
Goodbye to Gobbledegook: An Introduction to Basic Statistics in Primary Care
Authors: Irving Greg
Published: June 2009

‘Smoking cigarettes causes lung cancer’. This may now seem like a somewhat uninteresting fact because it is such common knowledge, yet 60 years ago relatively few people were aware of this. It has only been with the aid of research methods and statistical techniques that such a consequence of smoking was introduced to society and is now well accepted. Such trends towards evidence-based medicine can only flourish in a culture of statistical literacy. Moreover, how can we even start to effectively critically analyse a scientific paper if we do not understand the basic statistical techniques the researcher has adopted? Part of the perceived complexity with this process is a (natural) fear of statistics and consequent lack of understanding of statistical processes. To obtain a functional level of statistical literacy, one must understand the vocabulary of statistical terms, statistical methods and the effect of statistics on study design.
Coordinated shifts to non-planktotrophic development in spatangoid echinoids during the Late Cretaceous
Authors: Cunningham John A. , Jeffery Abt Charlotte H.
Published: June 2009

Despite widespread interest in the interplay between evolutionary and developmental processes, we still know relatively little about the evolutionary history of larval development. Many clades exhibit multiple shifts from planktotrophic (feeding) to non-planktotrophic (non-feeding) larval development. An important question is whether these switches are scattered randomly through geological history or are concentrated in particular intervals of time. This issue is addressed using the Cretaceous spatangoid sea urchins, which are unusual in that larval strategy can be determined unambiguously from abundantly fossilized adult tests. Using a genus-level phylogeny, we identify five clades of non-planktotrophic taxa, each of which first appears in the fossil record in the Campanian or Maastrichtian (the final two Cretaceous stages). No examples of non-planktotrophy have been identified in any of the earlier stages of the Cretaceous. This strongly suggests that shifts to non-planktotrophic development are clustered in certain episodes of geological history, and this, in turn, implies that extrinsic factors operating at these times are responsible for driving shifts in developmental strategy.
Bone growth marks reveal protracted growth in New Zealand kiwi (Aves, Apterygidae)
Authors: Bourdon Estelle , Castanet Jacques , de Ricqlès Armand , Scofield Paul , Tennyson Alan , Lamrous Hayat , Cubo Jorge
Published: June 2009

The presence of bone growth marks reflecting annual rhythms in the cortical bone of non-avian tetrapods is now established as a general phenomenon. In contrast, ornithurines (the theropod group including modern birds and their closest relatives) usually grow rapidly in less than a year, such that no annual rhythms are expressed in bone cortices, except scarce growth marks restricted to the outer cortical layer. So far, cyclical growth in modern birds has been restricted to the EoceneDiatryma, the extant parrotAmazona amazonicaand the extinct New Zealand (NZ) moa (Dinornithidae). Here we show the presence of lines of arrested growth in the long bones of the living NZ kiwi (Apteryxspp., Apterygidae). Kiwis take 5–6 years to reach full adult body size, which indicates a delayed maturity and a slow reproductive cycle. Protracted growth probably evolved convergently in moa and kiwi sometime since the Middle Miocene, owing to the severe climatic cooling in the southwest Pacific and the absence of mammalian predators.
Carry-over effect of captive breeding reduces reproductive fitness of wild-born descendants in the wild
Authors: Araki Hitoshi , Cooper Becky , Blouin Michael S.
Published: June 2009

Supplementation of wild populations with captive-bred organisms is a common practice for conservation of threatened wild populations. Yet it is largely unknown whether such programmes actually help population size recovery. While a negative genetic effect of captive breeding that decreases fitness of
captive-bred
organisms has been detected, there is no direct evidence for a carry-over effect of captive breeding in their
wild-born
descendants, which would drag down the fitness of the wild population in subsequent generations. In this study, we use genetic parentage assignments to reconstruct a pedigree and estimate reproductive fitness of the wild-born descendants of captive-bred parents in a supplemented population of steelhead trout (
Oncorhynchus mykiss
). The estimated fitness varied among years, but overall relative reproductive fitness was only 37 per cent in wild-born fish from two captive-bred parents and 87 per cent in those from one captive-bred and one wild parent (relative to those from two wild parents). Our results suggest a significant carry-over effect of captive breeding, which has negative influence on the size of the wild population in the generation after supplementation. In this population, the population fitness could have been 8 per cent higher if there was no carry-over effect during the study period.
Female mice respond to male ultrasonic ‘songs’ with approach behaviour
Authors: Hammerschmidt K. , Radyushkin K. , Ehrenreich H. , Fischer J.
Published: June 2009

The ultrasonic vocalizations of mice are attracting increasing attention, because they have been recognized as an informative readout in genetically modified strains. In addition, the observation that male mice produce elaborate sequences of ultrasonic vocalizations (‘song’) when exposed to female mice or their scents has sparked a debate as to whether these sounds are—in terms of their structure and function—analogous to bird song. We conducted playback experiments with cycling female mice to explore the function of male mouse songs. Using a place preference design, we show that these vocalizations elicited approach behaviour in females. In contrast, the playback of whistle-like artificial control sounds did not evoke approach responses. Surprisingly, the females also did not respond to pup isolation calls. In addition, female responses did not vary in relation to reproductive cycle, i.e. whether they were in oestrus or not. Furthermore, our data revealed a rapid habituation of subjects to the experimental situation, which stands in stark contrast to other species' responses to courtship vocalizations. Nevertheless, our results clearly demonstrate that male mouse songs elicit females' interest.
Body condition but not dietary restriction prolongs lifespan in a semelparous capital breeder
Authors: Kasumovic Michael M. , Brooks Robert C. , Andrade Maydianne C. B.
Published: June 2009

Effects of diet on longevity are complex because acquired resources are shared among growth, reproduction and somatic maintenance. We simplify these axes by examining how dietary restriction and competitive contexts affect longevity using semelparous males of the Australian redback spider (
Latrodectus hasselti
). Plastic development of
L. hasselti
males results in trade-offs of body condition against faster development if females are present, facilitating scramble competition. In the absence of females, males develop slowly as high body condition adults, and are better equipped for mate searching. Here we focus on effects of diet and competitive context on body condition and longevity. Although male survival depended on body condition and exercise, contrary to studies in a wide range of taxa, dietary restriction did not increase longevity. However, there was an interactive effect of diet and competitive context on lifespan, because high-diet males reared in the absence of females lived longer than males reared in the presence of females. Thus males near females pay a survival cost of developing rapidly. This shows that life-history trade-offs affected by competitive context can impose longevity costs independent of the direct energy expenditure of searching, courtship, competition or reproduction.
Science should not be abandoned in a bid to resolve whaling disputes
Authors: Cooke Justin , Leaper Russell , Papastavrou Vassili
Published: June 2009

The International Whaling Commission (IWC) is currently engaged in an intensive negotiating process in an attempt to resolve international disputes about whaling. The IWC has pioneered and agreed a management procedure approach for setting catch limits for commercial whaling that was unanimously recommended by its Scientific Committee. It is disturbing that current negotiations are moving towards discarding this agreed and carefully developed scientific procedure in favour of ad hoc catch allowances based on political expediency.
Equation of motion for point vortices in multiply connected circular domains
Authors: Sakajo Takashi
Published: June 2009

The paper gives the equation of motion for
N
point vortices in a bounded planar multiply connected domain inside the unit circle that contains many circular obstacles, called the circular domain. The velocity field induced by the point vortices is described in terms of the Schottky–Klein prime function associated with the circular domain. The explicit representation of the equation enables us not only to solve the Euler equations through the point-vortex approximation numerically, but also to investigate the interactions between localized vortex structures in the circular domain. As an application of the equation, we consider the motion of two point vortices with unit strength and of opposite signs. When the multiply connected domain is symmetric with respect to the real axis, the motion of the two point vortices is reduced to that of a single point vortex in a multiply connected semicircle, which we investigate in detail.
Axisymmetric contact with friction of a rigid sphere with an elastic half-space
Authors: Zhupanska O. I.
Published: June 2009

The problem of normal contact with friction of a rigid sphere with an elastic half-space is considered. An analytical treatment of the problem is presented, with the corresponding boundary-value problem formulated in the toroidal coordinates. A general solution in the form of Papkovich–Neuber functions and the Mehler–Fock integral transform is used to reduce the problem to a single integral equation with respect to the unknown contact pressure in the slip zone. An analysis of contact stresses is carried out, and exact analytical solutions are obtained in limiting cases, including a full stick contact problem and a contact problem for an incompressible half-space.
Stability of some solutions for elliptic equations on a cylindrical domain
Authors: Valls Claudia
Published: June 2009

We study analytically a class of solutions for the elliptic equation

where
α
>0 and
ε
is a small parameter. This equation is ill-posed and most initial conditions do not lead to solutions. Nevertheless, we show that, for almost every
α
>0, it contains solutions that are defined for large values of time and they are very close (of order
O
(
ε
)) to a linear torus for long times (of order
O
(
ε
−1
)). The proof uses the fact that the equation leaves invariant a smooth centre manifold and, for the restriction of the system to the centre manifold, uses arguments of classical perturbation theory by considering the Hamiltonian formulation of the problem, the Birkhoff normal form and Neckhoroshev-type estimates.
Relative equilibria of four identical satellites
Authors: Albouy Alain , Fu Yanning
Published: June 2009

We consider the Newtonian 5-body problem in the plane, where four bodies have the same mass
m
, which is small compared with the mass
M
of the remaining body. We consider the (normalized) relative equilibria in this system and follow them to the limit when
m
/
M
→0. In some cases, two small bodies will coalesce at the limit. We call the other equilibria the relative equilibria of four separate identical satellites. We prove rigorously that there are only three such equilibria, all already known after the numerical researches by H. Salo and C. F. Yoder. Our main contribution is to prove that any equilibrium configuration possesses a symmetry, a statement indicated by J. Llibre as the missing key to proving that there is no other equilibrium.