bluuebunny/crossref_metadata_2025 huggingface dataset:
Will zigzag graphene nanoribbon turn to half metal under electric field?
Authors: Kan Er-Jun , Li Zhenyu , Yang Jinlong , Hou J. G.
Published: December 2007

At B3LYP level of theory, we predict that the half-metallicity in zigzag edge graphene nanoribbon (ZGNR) can be realized when an external electric field is applied across the ribbon. The critical electric field decreases with the increase of the ribbon width to induce the half-metallicity. Both the spin polarization and half-metallicity are removed when the edge state electrons fully transferred from one side to the other under very strong electric field. The electric field range under which ZGNR remains half-metallic increases with the ribbon width. Our study demonstrates a rich field-induced spin polarization behavior, which may lead to some important applications in spinstronics.
Turbulent spots and waves in a model for plane Poiseuille flow
Authors: Lagha Maher
Published: December 2007

The structure of a turbulent spot in plane Poiseuille flow is investigated using a model derived from the Navier–Stokes equations through a Galerkin method. The mean profile of the streamwise velocity inside the turbulent spot has the characteristic flat profile of a turbulent Poiseuille flow. The waves developing at the wing tips of the spot have an asymmetric streamwise velocity with respect to the channel centerline, whereas their associated wall-normal velocity component is symmetric. On the outskirts of the spot, a large-scale flow occupying the full gap between the plates is observed. It is characterized by a streamwise inflow toward the spot and a spanwise outflow from the spot. A detailed comparison with the numerical simulations and the experiments in the literature shows that these results are in fair agreement with the main features of the transitional plane Poiseuille flow.
Statistics of electrical breakdown field in HfO2 and SiO2 films from millimeter to nanometer length scales
Authors: Sire Cédric , Blonkowski Serge , Gordon Michael J. , Baron Thierry
Published: December 2007

The statistics of electrical breakdown field (Ebd) of HfO2 and SiO2 thin films has been evaluated over multiple length scales using macroscopic testing of standardized metal-oxide-semiconductor (TiN∕SiO2∕Si) and metal-insulator-metal (TiN∕HfO2∕TiN) capacitors (10−2mm2–10μm2 area) on a full 200mm wafer along with conductive-atomic-force microscopy. It is shown that Ebd follows the same Weibull distribution when the data are scaled using the testing area. This overall scaling suggests that the defect density is ∼1015cm−2 and Ebd is ∼40MV∕cm for nanometer-length scales; as such, breakdown in these materials is most likely initiated by bond breaking rather than punctual defects.
Nanoscale field effect transistor for biomolecular signal amplification
Authors: Chen Yu , Wang Xihua , Hong Mi K. , Erramilli Shyamsunder , Mohanty Pritiraj , Rosenberg Carol
Published: December 2007

We report amplification of biomolecular recognition signal in lithographically defined silicon nanochannel devices. The devices are configured as field effect transistors (FET) in the reversed source-drain bias region. The measurement of the differential conductance of the nanowire channels in the FET allows sensitive detection of changes in the surface potential due to biomolecular binding. Narrower silicon channels demonstrate higher sensitivity to binding due to increased surface-to-volume ratio. The operation of the device in the negative source-drain region demonstrates signal amplification. The equivalence between protein binding and change in the surface potential is described.
Electrical characterization of AlxTiyOz mixtures and Al2O3–TiO2–Al2O3 nanolaminates
Authors: Jõgi Indrek , Kukli Kaupo , Kemell Marianna , Ritala Mikko , Leskelä Markku
Published: December 2007

Mixtures and nanolaminates of Al2O3 and TiO2 with different alumina to titania ratios were prepared by atomic layer deposition. The studies were aimed at electrical characterization of metal-insulator-semiconductor capacitors formed by combining an insulating oxide with large band gap (Al2O3) with an oxide with high dielectric permittivity (TiO2). In mixtures, the ratio of Al2O3 and TiO2 growth cycles varied from 10:2 to 5:5 with target layer thickness in the range of 6.2–8.8nm. In Al2O3–TiO2–Al2O3 nanolaminates, the thicknesses of Al2O3 and TiO2 constituent layers were in the ranges of 3–6 and 2–15nm, respectively. Appreciable step coverage on deep trenched substrates with high aspect ratio (1:40) was achieved with short pulse and purge times otherwise suited for the deposition of planar capacitors. The measurements confirmed the model calculations of leakage currents for laminates, mixtures, and pure Al2O3 films predicting the lowest leakage for pure Al2O3 films at all possible equivalent oxide thickness (EOT) values. Inclusion of TiO2 as an oxide of higher permittivity but lower band offsets on Si considerably increased the leakage. Currents in the films became strongly affected by chemical and structural defects induced by the deposition process. The as-deposited films possessed higher EOT values and lower breakdown fields, compared to the model predictions. Flatband voltage shifts and hysteresis width of capacitance-voltage curves were also affected by built-in defects. Postdeposition annealing somewhat improved the dielectric performance of the films deposited.
Local dielectric permittivity of HfO2 based slabs and stacks: A first principles study
Authors: Shi N. , Ramprasad R.
Published: December 2007

A recently developed theory of atomic-scale local dielectric permittivity has been used to determine the position dependent optical and static dielectric permittivity profiles of a few nanoscale HfO2 and Si–HfO2 heterojunction slabs. The dielectric constants at the interior regions of each component recovered their respective bulk values. Enhancement of the dielectric constant at the free surfaces and its variations at the Si–HfO2 interface could be correlated to the corresponding surface and interfacial chemistry.
Voltage-dependent electroluminescence from colloidal CdSe∕ZnS quantum dots
Authors: Yan Liang , Zhang Jia-Yu , Cui Yiping , Qiao Yi
Published: December 2007

Electroluminescence (EL) was obtained in the hybrid film of colloidal CdSe∕ZnS quantum dots (QDs) and poly(9-vinylcarbazole) (PVK), and the voltage and temperature dependences of the EL were measured. The quantum-confined Stark effect of colloidal QDs is clearly observed, and the QDs’ EL intensity rises with temperature. Electrons and holes are proposed to be separately transported in QDs and PVK, respectively.
Monolithic integration of InP based heterostructures on silicon using crystalline Gd2O3 buffers
Authors: Saint-Girons G. , Regreny P. , Largeau L. , Patriarche G. , Hollinger G.
Published: December 2007

An original approach of monolithic integration of InP based heterostructures on silicon is proposed based on the peculiar properties of the heterointerface between InP and crystalline Gd2O3. When grown on a crystalline Gd2O3∕Si(111) buffer, InP takes its bulk lattice parameter as soon as the growth begins, and the lattice mismatch (7.9%) is fully accommodated by the formation of a misfit dislocation network at the InP∕Gd2O3 heterointerface. This plastic compliant effect allows the monolithic growth of good quality InAsP∕InP heterostructures on Si, as attested by room-temperature photoluminescence experiments.
Systematic study on p-type doping control of InN with different Mg concentrations in both In and N polarities
Authors: Wang Xinqiang , Che Song-Bek , Ishitani Yoshihiro , Yoshikawa Akihiko
Published: December 2007

p -type conductivity control of In- and N-polar InN layers grown on GaN templates with different Mg concentrations ([Mg]) was systematically investigated by using electrolyte-based capacitance-voltage (ECV) analyses. With increasing [Mg], p-type conduction was confirmed for [Mg]s from ∼1018to∼3×1019cm−3. The conduction was reversed to n type at [Mg]s above 1020cm−3, however, due to overdoping effects introducing shallow donors in InN. Further, it was found that charges at the interface states located within forbidden band of InN greatly affected the ECV measurements resulting in overestimation of net acceptor concentrations, and some calibration was necessary to estimate them.
Transport properties of field-effect transistor with Langmuir-Blodgett films of C60 dendrimer and estimation of impurity levels
Authors: Kawasaki Naoko , Nagano Takayuki , Kubozono Yoshihiro , Sako Yuuki , Morimoto Yu , Takaguchi Yutaka , Fujiwara Akihiko , Chu Chih-Chien , Imae Toyoko
Published: December 2007

Field-effect transistor (FET) device has been fabricated with Langmuir-Blodgett films of C60 dendrimer. The device showed n-channel normally off characteristics with the field-effect mobility of 2.7×10−3cm2V−1s−1 at 300K, whose value is twice as high as that (1.4×10−3cm2V−1s−1) for the FET with spin-coated films of C60 dendrimer. This originates from the formation of ordered π-conduction network of C60 moieties. From the temperature dependence of field-effect mobility, a structural phase transition has been observed at around 300K. Furthermore, the density of states for impurity levels was estimated in the Langmuir-Blodgett films.
Control of transient biaxial order in calamitic nematics
Authors: Ciuchi F. , Ayeb H. , Lombardo G. , Barberi R. , Durand Georges E.
Published: December 2007

The biaxial order reconstruction in nematics (BORN) is a dynamical effect which can change the topology of nematic textures. The BORN can be induced in a nematic material submitted to strong external constraints, as in the case of bulk textural distortions due to an electric field in a π cell. In this work, we show how suitable dopants for a thermotropic calamitic nematic can influence its transient biaxial order and, hence, the electric BORN threshold.
Undoped polythiophene field-effect transistors with mobility of 1cm2V−1s−1
Authors: Hamadani B. H. , Gundlach D. J. , McCulloch I. , Heeney M.
Published: December 2007

We report on charge transport in organic field-effect transistors based on poly(2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene) as the active polymer layer with saturation field-effect mobilities as large as 1cm2V−1s−1. This is achieved by employing Pt instead of the commonly used Au as the contacting electrode and allows for a significant reduction in the metal/polymer contact resistance. The mobility increases as a function of decreasing channel length, consistent with a Poole-Frenkel model of charge transport, and reaches record mobilities of 1cm2V−1s−1 or more at channel lengths on the order of few microns in an undoped solution-processed polymer cast on an oxide gate dielectric.
Resistive switching devices based on nanocrystalline solid electrolyte (AgI)0.5(AgPO3)0.5
Authors: Guo H. X. , Yang B. , Chen L. , Xia Y. D. , Yin K. B. , Liu Z. G. , Yin J.
Published: December 2007

Resistive switching devices with a sandwich structure Ag∕(AgI)0.5(AgPO3)0.5∕Pt were fabricated on silicon(001) wafer by using the pulsed laser deposition method and the focused ion beam nanofabrication technique. (AgI)0.5(AgPO3)0.5 films deposited at room temperature show a nanocrystal structure and the composition of the films was identified by using x-ray photoelectron spectroscopy. The current-voltage characteristics of the Ag∕(AgI)0.5(AgPO3)0.5∕Pt memory units show good switching behaviors. The ratio of the conductance between the “ON” state (high conductance) and the “off” state (low conductance) reaches 1×106. The ON and OFF states can be effectively written, read, and erased up to 4×105 scanning cycles by using a set of voltage pulses with an amplitude less than 3V. It also could be observed that the time for the writing and erasing operations could be less than 150ns. The switching mechanism of the Ag∕(AgI)0.5(AgPO3)0.5∕Pt memory devices was ascribed to the possible formation and dissolution of Ag filaments in (AgI)0.5(AgPO3)0.5 films induced by the applied electrical pulses with different polarities.
Tailoring magnetic and magnetocaloric properties of martensitic transitions in ferromagnetic Heusler alloys
Authors: Aksoy Seda , Krenke Thorsten , Acet Mehmet , Wassermann Eberhard F. , Moya Xavier , Mañosa Lluís , Planes Antoni
Published: December 2007

Ni 50 Mn 34 In 16 undergoes a martensitic transformation around 250K and exhibits a field induced reverse martensitic transformation and substantial magnetocaloric effects. We substitute small amounts Ga for In, which are isoelectronic, to carry these technically important properties to close to room temperature by shifting the martensitic transformation temperature.
Electric-field-driven dielectric breakdown of metal-insulator-metal hafnium silicate
Authors: Lee Byoung Hun , Kang Chang Yong , Kirsch Paul , Heh Dawei , Young Chadwin D. , Park Hongbae , Yang Jiwoon , Bersuker Gennadi , Krishnan Siddarth , Choi Rino , Lee Hi-Deok
Published: December 2007

The breakdown characteristics of the crystalline and amorphous hafnium (Hf) silicates have been studied using metal-insulator-metal capacitors. It is found that, although the distribution of time-dependent dielectric breakdown and charge to breakdown (QBD) are affected by crystallization, the breakdown is primarily controlled by the electric field rather than charge fluence.
Ultrafast carrier dynamics in band edge and broad deep defect emission ZnSe nanowires
Authors: Othonos Andreas , Lioudakis Emmanouil , Philipose U. , Ruda Harry E.
Published: December 2007

Ultrafast carrier dynamics of ZnSe nanowires grown under different growth conditions have been studied. Transient absorption measurements reveal the dependence of the competing effects of state filling and photoinduced absorption on the probed energy states. The relaxation of the photogenerated carriers occupying defect states in the stoichiometric and Se-rich samples are single exponentials with time constants of 3–4ps. State filling is the main contribution for probe energies below 1.85eV in the Zn-rich grown sample. This ultrafast carrier dynamics study provides an important insight into the role that intrinsic point defects play in the observed photoluminescence from ZnSe nanowires.
Sustained suppression of Bcr-Abl-driven lymphoid leukemia by microRNA mimics
Authors: McLaughlin Jami , Cheng Donghui , Singer Oded , Lukacs Rita U. , Radu Caius G. , Verma Inder M. , Witte Owen N.
Published: December 2007

Many cancers and leukemias are associated with strong dominant oncogenic mutations that activate tyrosine kinases and other classes of molecules, including transcription factors and antiapoptotic mechanisms. Some of these events can be targeted with small molecules or antibody-based therapeutics, but many remain intractable. In addition, cancer-related enzyme targets can often mutate, and drug-resistant variants are selected. Therapies directed at the mRNA encoding dominant oncogenes could provide a more global set of technologies for cancer treatment. To test this concept, we have used the model of transformation of hematopoietic cells by the chimeric
Bcr-Abl
oncogene, a highly activated tyrosine kinase. Our results show that tandem arrays of miRNA mimics, but not single miRNA mimics, directed against the Abl portion of the mRNA and introduced by lentiviral vectors can effectively alter the leukemogenic potency when the degree of suppression of expression of Bcr-Abl is reduced >200-fold from control levels. Only methods capable of such dramatic sustained reduction in the level of expression of highly activated kinase oncogenes are likely to be effective in controlling malignant cell populations.
Measurement of residual stress on a unidirectional solidified Al2O3/YAG eutectic composite using synchrotron and neutron diffraction
Authors: Suzuki Hiroshi , Waku Yoshiharu , Nakagawa Narihito , Akita Koichi , Moriai Atsushi , Morii Yukio
Published: December 2007

The residual stress in the pure YAG phase was measured on the surface of an Al2O3–Y3Al5O12 (YAG) eutectic composite (Al2O3/YAG–MGC) using low energy synchrotron X-rays. The residual stress in the plane stress condition was significantly different between top and side surfaces of the specimen. In addition, the internal residual stress of the melt growth composite (MGC) was also measured using a neutron diffraction. The residual stress in the YAG phase rose from compression in the solidification direction to tension in the perpendicular direction. The residual stress in the Al2O3 phase was anisotropic compression and there was no tension in any direction. This anisotropic residual stress could be explained by the crystallographic anisotropy of thermal expansion in the Al2O3 phase. However, both phase stresses were not balanced, so that it is expected that there would be a stress distribution in the MGC.
Evolution of lattice strains in three dimensions during in situ compression of textured Zircaloy-2
Authors: Xu F. , Holt R.A. , Oliver E.C. , Daymond M.R.
Published: December 2007

The evolution of lattice strains in Zircaloy-2 was investigated in situ by time-of-flight neutron diffraction during uni-axial compression in three principal directions, normal, transverse and rolling. The material is a warm-worked Zircaloy-2 slab with basal plane normals mostly concentrated in ND. Lattice strains relative to the undeformed sample were measured by neutron diffraction during cyclic compression and unloading for three test directions and three scattering vector directions. Intensity variations of the reflections were monitored to assess the grain rotations. Substantial tensile twinning was inferred from the evolution of {0002} lattice strains and the intensity of prismatic and basal poles. The spread of lattice strains in the test direction (amongst different crystal orientations) is much greater in compression than in tension. The sources leading to this asymmetry were ascribed, through preliminary simulations using an elasto-plastic self-consistent model, to the compressive load, the occurrence of tensile twinning and thermal residual strains.
Influence of chemical composition and residual stresses on mechanical properties of duplex stainless steel studied by X-ray and neutron diffraction
Authors: Dakhlaoui R. , Braham C. , Baczmański A.
Published: December 2007

The parameters characterizing the elastoplastic mechanical behaviour of each phase in textured austenoferritic duplex stainless steels were determined using X-ray and neutron diffraction during uniaxial tensile test. A self consistent model was used to predict the evolution of the internal stresses during loading, and to identify critical resolved shear stresses\and strain hardening parameters of the material. Calculations based on this model were compared with the results of mechanical tests and diffraction data. The effect of residual stresses and the chemical composition on the elastoplastic phase behaviour was determined.
In situ measurement of crystalline lattice strains in phase IV polytetrafluoroethylene
Authors: Brown E.N. , Clausen B. , Brown D.W.
Published: December 2007

Measurements of crystalline lattice strain development during deformation of polytetrafluoroethylene (PTFE) have been performed utilizing neutron diffraction measurements at the SMARTS diffractometer at Los Alamos National Laboratory. The chemical structure of PTFE, (C2F4)n, makes it ideally suited for investigation by neutron methods as it is free of the hydrogen that causes limited penetration depths and poor diffraction acquisition in most polymers. Six primary diffraction peaks have been identified corresponding with deformation planes in the hexagonal unit cell. Deformation perpendicular to the prismatic planes occurs by interpolymer chain compression with a moduli ∼10 × bulk, while deformation perpendicular to the pyramidal planes occurs by interpolymer chain shear with a moduli ∼100–1000 × bulk, and deformation perpendicular to the basal plane occurs by intrapolymer chain compression with a moduli ∼1000 × bulk, corresponding with theoretical values for a PTFE chain modulus.
Characterization of laser peening residual stresses in Al 7075 by synchrotron diffraction and the contour method
Authors: Evans A. , Johnson G. , King A. , Withers P.J.
Published: December 2007

Laser peening is a mechanical surface treatment, used to improve the fatigue performance of metallic materials. The gains in performance derive from a deep case of compressive residual stress generated in the near-surface region. This compressive residual stress field is balanced by residual tension. The residual stress state has been characterized in two Al 7075 plate samples, one laser peened only at its centre and the other overlap peened over most of the top surface. The residual stress depth profiles were measured using energy dispersive synchrotron X-ray radiation. The profiles revealed greater compression in the sample peened at a single position. The samples were subsequently characterized using the contour method. The technique allowed the residual stress to be determined in 2D to the very near surface. Depth profiles of the two techniques exhibited good agreement.
Evaluation of residual stress distribution and deformation characteristics of thermal barrier coatings using hard synchrotron X-rays
Authors: Suzuki Kenji , Tanaka Keisuke
Published: December 2007

Thermal barrier coatings (TBCs) were made on cylindrical substrates with radii of 5, 10 and 15 mm. In addition to the cylindrical substrates, the TBC were also made on a plate substrate. First, NiCoCrAlY was pressureless plasma sprayed as a bond coating, and then zirconia with 8 mol% yittria was air plasma sprayed as the top coating. The TBC specimens were exposed in an atmosphere of air at 1373 K for 0, 200 and 500 h. The radial strain was measured with the strain scanning method using hard synchrotron X-rays. The hoop and axial stresses of the cylindrical specimens were measured using laboratory X-rays with successive removal of the surface by polishing. Using these measured stresses and strains, the distributions of the 3-dimensional components of the residual stress in the top coating were determined. The spalling stress became a maximum at about 50 mm from the interface. This position corresponded to the location of initiation of the spalling cracks. The value of the measured maximum spalling stress increased with the decrease in the radius of curvature. The difference of the measured distribution of the residual stress from the calculated distribution of the thermal stress was explained on the basis of the characteristics of the top coatings, such as the stress relaxation due to sliding between lamellae, a binding effect by the interface roughness and the spalling stress induced by the interface roughness.
Non-destructive determination of the 3D residual stress in a AA7050 upper wing skin-stringer panel using neutron diffraction
Authors: Pratihar S. , Ganguly S. , James J.A. , Fitzpatrick M.E. , Edwards L.
Published: December 2007

Neutron diffraction has been used to determine the full three dimensional residual stress in a demonstrator variable polarity plasma arc (VPPA) welded Al-7150 skin-stringer fatigue sample. Uniquely, the design of this demonstrator panel took into account the residual stress distribution likely to present due to the presence of the weld by using residual stress data measured on smaller laboratory-sized butt welded plates. The stress-free lattice parameter was obtained by measuring a comb sample and point-to-point strain corrections for the three principal directions were performed to determine strains and hence calculate stresses. A significant amount of stress redistribution was observed in the demonstrator sample when compared to the laboratory size plate specimen.
KCNE Peptides Differently Affect Voltage Sensor Equilibrium and Equilibration Rates in KCNQ1 K+ Channels
Authors: Rocheleau Jessica M. , Kobertz William R.
Published: December 2007

KCNQ1 voltage-gated K+ channels assemble with the family of KCNE type I transmembrane peptides to afford membrane-embedded complexes with diverse channel gating properties. KCNQ1/KCNE1 complexes generate the very slowly activating cardiac IKs current, whereas assembly with KCNE3 produces a constitutively conducting complex involved in K+ recycling in epithelia. To determine whether these two KCNE peptides influence voltage sensing in KCNQ1 channels, we monitored the position of the S4 voltage sensor in KCNQ1/KCNE complexes using cysteine accessibility experiments. A panel of KCNQ1 S4 cysteine mutants was expressed in Xenopus oocytes, treated with the membrane-impermeant cysteine-specific reagent 2-(trimethylammonium) ethyl methanethiosulfonate (MTSET), and the voltage-dependent accessibility of each mutant was determined. Of these S4 cysteine mutants, three (R228C, G229C, I230C) were modified by MTSET only when KCNQ1 was depolarized. We then employed these state-dependent residues to determine how assembly with KCNE1 and KCNE3 affects KCNQ1 voltage sensor equilibrium and equilibration rates. In the presence of KCNE1, MTSET modification rates for the majority of the cysteine mutants were ∼10-fold slower, as was recently reported to indicate that the kinetics of the KCNQ1 voltage sensor are slowed by KCNE1 (Nakajo, K., and Y. Kubo. 2007 J. Gen. Physiol. 130:269–281). Since MTS modification rates reflect an amalgam of reagent accessibility, chemical reactivity, and protein conformational changes, we varied the depolarization pulse duration to determine whether KCNE1 slows the equilibration rate of the voltage sensors. Using the state-dependent cysteine mutants, we determined that MTSET modification rates were essentially independent of depolarization pulse duration. These results demonstrate that upon depolarization the voltage sensors reach equilibrium quickly in the presence of KCNE1 and the slow gating of the channel complex is not due to slowly moving voltage sensors. In contrast, all cysteine substitutions in the S4 of KCNQ1/KCNE3 complexes were freely accessible to MTSET independent of voltage, which is consistent with KCNE3 shifting the voltage sensor equilibrium to favor the active state at hyperpolarizing potentials. In total, these results suggest that KCNE peptides differently modulate the voltage sensor in KCNQ1 K+ channels.
Sulfonylurea Receptors Type 1 and 2A Randomly Assemble to Form Heteromeric KATP Channels of Mixed Subunit Composition
Authors: Chan Kim W. , Wheeler Adam , Csanády László
Published: December 2007

ATP-sensitive potassium (KATP) channels play important roles in regulating insulin secretion, controlling vascular tone, and protecting cells against metabolic stresses. KATP channels are heterooctamers of four pore-forming inwardly rectifying (Kir6.2) subunits and four sulfonylurea receptor (SUR) subunits. KATP channels containing SUR1 (e.g. pancreatic) and SUR2A (e.g. cardiac) display distinct metabolic sensitivities and pharmacological profiles. The reported expression of both SUR1 and SUR2 together with Kir6.2 in some cells raises the possibility that heteromeric channels containing both SUR subtypes might exist. To test whether SUR1 can coassemble with SUR2A to form functional KATP channels, we made tandem constructs by fusing SUR to either a wild-type (WT) or a mutant N160D Kir6.2 subunit. The latter mutation greatly increases the sensitivity of KATP channels to block by intracellular spermine. We expressed, individually and in combinations, tandem constructs SUR1-Kir6.2 (S1-WT), SUR1-Kir6.2[N160D] (S1-ND), and SUR2A-Kir6.2[N160D] (S2-ND) in Xenopus oocytes, and studied the voltage dependence of spermine block in inside-out macropatches over a range of spermine concentrations and RNA mixing ratios. Each tandem construct expressed alone supported macroscopic K+ currents with pharmacological properties indistinguishable from those of the respective native channel types. Spermine sensitivity was low for S1-WT but high for S1-ND and S2-ND. Coexpression of S1-WT and S1-ND generated current components with intermediate spermine sensitivities indicating the presence of channel populations containing both types of Kir subunits at all possible stoichiometries. The relative abundances of these populations, determined by global fitting over a range of conditions, followed binomial statistics, suggesting that WT and N160D Kir6.2 subunits coassemble indiscriminately. Coexpression of S1-WT with S2-ND also yielded current components with intermediate spermine sensitivities, suggesting that SUR1 and SUR2A randomly coassemble into functional KATP channels. Further pharmacological characterization confirmed coassembly of not only S1-WT and S2-ND, but also of coexpressed free SUR1, SUR2A, and Kir6.2 into functional heteromeric channels.
Sparse inverse covariance estimation with the graphical lasso
Authors: Friedman Jerome , Hastie Trevor , Tibshirani Robert
Published: December 2007

We consider the problem of estimating sparse graphs by a lasso penalty applied to the inverse covariance matrix. Using a coordinate descent procedure for the lasso, we develop a simple algorithm—the graphical lasso—that is remarkably fast: It solves a 1000-node problem (∼500000 parameters) in at most a minute and is 30–4000 times faster than competing methods. It also provides a conceptual link between the exact problem and the approximation suggested by Meinshausen and Bühlmann (2006). We illustrate the method on some cell-signaling data from proteomics.
Characteristics of Calanus finmarchicus dormancy patterns in the Northwest Atlantic
Authors: Johnson Catherine L. , Leising Andrew W. , Runge Jeffrey A. , Head Erica J. H. , Pepin Pierre , Plourde Stéphane , Durbin Edward G.
Published: December 2007

Johnson, C. L., Leising, A. W., Runge, J. A., Head, E. J. H., Pepin, P., Plourde, S., and Durbin, E. G. 2008. Characteristics of Calanus finmarchicus dormancy patterns in the Northwest Atlantic. – ICES Journal of Marine Science, 65: 339–350. Demographic time-series from four fixed stations in the Northwest Atlantic Ocean demonstrate variable timing of entry into and emergence from dormancy in subpopulations of the planktonic copepod Calanus finmarchicus. A proxy for timing of entry was established as the date each year when the proportion of the fifth copepodid stage (CV) in the subpopulation rose to half its overall climatological maximum CV proportion at that station. The proxy for timing of emergence at each station was set as the first date when adults were more than 10% of the total abundance of copepodid stages. An alternate emergence proxy date was determined by back-calculating the spawning dates of the first early copepodid stages appearing in spring, using a stage-structured, individual-based model. No single environmental cue (photoperiod, surface temperature, or average surface-layer chlorophyll a concentration) consistently explained entry or emergence dates across all stations. Among hypotheses put forward to explain dormancy in Calanus species, we cannot eliminate the lipid accumulation window hypothesis for onset of dormancy or a lipid-modulated endogenous timer controlling dormancy duration. The fundamental premise of these hypotheses is that individuals can only enter dormancy if their food and temperature history allows them to accumulate sufficient lipid to endure overwintering, moult, and undergo early stages of gonad maturation.
Seasonal relationships between the copepod community and hydrographic conditions in the southern East China Sea
Authors: Lan Yang-Chi , Lee Ming-An , Chen Wen-Yu , Hsieh Feng-Jen , Pan Jia-Yi , Liu Don-Chung , Su Wei-Cheng
Published: December 2007

Lan, Y-C., Lee, M-A., Chen, W-Y., Hsieh, F-J., Pan, J-Y., Liu, D-C., and Su, W-C. 2008. Seasonal relationships between the copepod community and hydrographic conditions in the southern East China Sea. – ICES Journal of Marine Science, 65: 462–468. We studied the relationship between seasonal variation of the copepod community and hydrographic conditions in the southern East China Sea (ECS). Hydrographic conditions in the southwestern ECS were influenced by the China Coastal Current (CCC) from late autumn to early spring and by the South China Sea Current (SCSC) during the rest of the year, and in the southeastern ECS by the Kuroshio Current (KC) year-round. We identified 141 species of copepods belonging to 54 genera and 27 families. Diversity and evenness of copepods were higher in waters influenced by the KC and the SCSC, and lower in waters with intrusion of the CCC. The CCC transported dominant copepods such as Paracalanus aculeatus, Paracalanus parvus, and Calanus sinicus into the southwestern ECS in late autumn and winter, whereas the SCSC carried Temora discaudata, Oncaea venusta, and P. aculeatus in spring, and Undinula vulgaris, T. discaudata, and P. aculeatus in summer. In the southeastern ECS, the KC brought in tropical copepods having clear seasonal variations throughout the year. We examined the relationships between indicator copepod species and currents and oceanographic conditions, using canonical correlation analysis.
Spatiotemporal Relationships Between Disease Development and Airborne Inoculum in Unmanaged and Managed Botrytis Leaf Blight Epidemics
Authors: Carisse O. , Savary S. , Willocquet L.
Published: December 2007

Comparatively little quantitative information is available on both the spatial and temporal relationships that develop between airborne inoculum and disease intensity during the course of aerially spread epidemics. Botrytis leaf blight and Botrytis squamosa airborne inoculum were analyzed over space and time during 2 years (2002 and 2004) in a nonprotected experimental field, using a 6 × 8 lattice of quadrats of 10 × 10 m each. A similar experiment was conducted in 2004 and 2006 in a commercial field managed for Botrytis leaf blight using a 5 × 5 lattice of quadrats of 25 × 25 m each. Each quadrat was monitored weekly for lesion density (LD) and aerial conidium concentration (ACC). The adjustment of the Taylor's power law showed that heterogeneity in both LD and ACC generally increased with increasing mean. Unmanaged epidemics were characterized in either year, with aggregation indices derived from SADIE (Spatial Analysis by Distance Indices). For LD, the aggregation indices suggested a random pattern of disease early in the season, followed by an aggregated pattern in the second part of the epidemic. The index of aggregation for ACC in 2002 was significantly greater than 1 at only one date, while it was significantly greater than 1 at most sampling dates in 2004. In both years and for both variables, positive trends in partial autocorrelation were observed mainly for a spatial lag of 1. In 2002, the overall pattern of partial autocorrelations over sampling dates was similar for LD and ACC with no significant partial autocorrelation during the first part of the epidemic, followed by a period with significant positive autocorrelation, and again no autocorrelation on the last three sampling dates. In 2004, there was no significant positive autocorrelation for LD at most sampling dates while for ACC, there was a fluctuation between significant and non-significant positive correlation over sampling dates. There was a significant spatial correlation between ACC at given date (ti) and LD 1 week later (ti + 1) on most sampling dates in both 2002 and 2004 for the unmanaged and managed sites. It was concluded that LD and ACC were not aggregated in the early stage of epidemics, when both disease intensity and airborne conidia concentration were low. This was supported by the analysis of LD and ACC from a commercial field, where managed levels of disease were low, and where no aggregation of both variables was detected. It was further concluded that a reliable monitoring of airborne inoculum for management of Botrytis leaf blight is achievable in managed fields using few spore samplers per field.
A Soluble Form of the Tomato spotted wilt virus (TSWV) Glycoprotein GN (GN-S) Inhibits Transmission of TSWV by Frankliniella occidentalis
Authors: Whitfield A. E. , Kumar N. K. K. , Rotenberg D. , Ullman D. E. , Wyman E. A. , Zietlow C. , Willis D. K. , German T. L.
Published: December 2007

Tomato spotted wilt virus (TSWV) is an economically important virus that is transmitted in a persistent propagative manner by its thrips vector, Frankliniella occidentalis. Previously, we found that a soluble form of the envelope glycoprotein GN (GN-S) specifically bound thrips midguts and reduced the amount of detectable virus inside midgut tissues. The aim of this research was to (i) determine if GN-S alters TSWV transmission by thrips and, if so, (ii) determine the duration of this effect. In one study, insects were given an acquisition access period (AAP) with GN-S mixed with purified virus and individual insects were assayed for transmission. We found that GN-S reduced the percent of transmitting adults by eightfold. In a second study, thrips were given an AAP on GN-S protein and then placed on TSWV-infected plant material. Individual insects were assayed for transmission over three time intervals of 2 to 3, 4 to 5, and 6 to 7 days post-adult eclosion. We observed a significant reduction in virus transmission that persisted to the same degree throughout the time course. Real-time reverse transcription polymerase chain reaction analysis of virus titer in individual insects revealed that the proportion of thrips infected with virus was reduced threefold when insects were preexposed to the GN-S protein as compared to no exposure to protein, and nontransmitters were not infected with virus. These results demonstrate that thrips transmission of a tospovirus can be reduced by exogenous viral glycoprotein.
Comparative Behavior of Ralstonia solanacearum Biovar 2 in Diverse Plant Species
Authors: Álvarez B. , Vasse J. , Le-Courtois V. , Trigalet-Démery D. , López M. M. , Trigalet A.
Published: December 2007

Ralstonia solanacearum causes bacterial wilt in numerous plant species worldwide. Although biovar 2 mostly affects solanaceous crops, identification of new hosts remains a matter of concern since there is still no clear-cut distinction between host and nonhost plants. In this work we provide data based on histological studies on the status of 20 plant species, most of them of potential interest in crop rotation. Plants were watered with a β-glucuronidase-expressing derivative of R. solanacearum biovar 2, and after a month of incubation, sections of roots and stems were analyzed to localize the pathogen on surface, in cortex and/or xylem. Depending on whether the xylem was colonized or not, plants were classified as hosts or nonhosts, respectively. Hosts generally affected in a few xylem vessels or occasionally in all xylem bundles were classified as tolerant. These included some cabbage, kidney bean, and rutabaga cultivars, and the weed bittersweet nightshade (Solanum dulcamara). Nonhosts were the cultivars tested of alfalfa, barley, black radish, carrot, celery, colocynth, fennel, fiber flax, field bean, field pea, horseradish, maize, and zucchini. However, barley and maize, though nonhosts, may act as reservoirs for the pathogen. The present work constitutes a basis for further studies on cropping systems in fields where R. solanacearum has been detected.
Relationship Between the Fungal Complex Causing Fusarium Head Blight of Wheat and Environmental Conditions
Authors: Xu X.-M. , Nicholson P. , Thomsett M. A. , Simpson D. , Cooke B. M. , Doohan F. M. , Brennan J. , Monaghan S. , Moretti A. , Mule G. , Hornok L. , Beki E. , Tatnell J. , Ritieni A. , Edwards S. G.
Published: December 2007

Over 4 years, the environmental conditions and the causal agents of Fusarium head blight (FHB) disease of wheat were determined in field sites in four European countries: Hungary, Ireland, Italy, and the United Kingdom. Polymerase chain reaction-based methods were used to detect each species causing FHB and quantify its DNA (as a measurement of fungal abundance) in the samples. Canonical correspondence analysis (CCA) was used to determine the relationship of the incidence and abundance of each species with weather variables. CCA indicated that little variability in the species prevalence data was explained by the weather variables. In contrast, a greater proportion of variability in abundance data was accounted for by the weather variables. Most samples contained two or more species and statistical analysis suggested that these species tended to coexist at field sites. CCA also indicated that there were differences in the relationships of the prevalence and abundance of the six FHB species with environmental variables. Fusarium poae was associated with relatively drier and warmer conditions, whereas F. graminearum was associated with warmer/humid conditions. F. avenaceum and F. culmorum were both associated with niches of cooler/wet/humid conditions. Two Microdochium species were associated with regions of relatively cool/moderate temperatures and frequent rainfalls of short duration. The results also suggested that environmental conditions differentially affect the infection and colonization processes, and the comparative abundance of the six species.
Quantitative Relationships Between Different Injury Factors and Development of Brown Rot Caused byMonilinia fructigenain Integrated and Organic Apple Orchards
Authors: Holb I. J. , Scherm H.
Published: December 2007

In a 4-year study, the incidence of various types of injuries (caused by insects, birds, growth cracks, mechanical wounding, and other, unidentified factors) was assessed in relation to brown rot development (caused by Monilinia fructigena) on fruit of three apple cultivars (Prima, Jonathan, and Mutsu) in integrated and organic blocks of two apple orchards in Hungary. In addition, populations of male codling moths (Cydia pomonella) were monitored with pheromone traps season-long in both management systems. On average, injury incidence on fruit at harvest was 6.1 and 19.2% in the integrated and organic treatments, respectively. Insect injury, which was caused primarily by C. pomonella, had the highest incidence among the five injury types, accounting for 79.4% of the total injury by harvest in the organic blocks and 36.6% in the integrated blocks. Levels of all other injury types remained close to zero during most of the season, but the incidence of bird injury and growth cracks increased markedly in the final 3 to 5 weeks before harvest in both production systems. Brown rot developed more slowly and reached a lower incidence in the integrated (6.4% final incidence on average) compared with the organic blocks (20.1% average incidence). In addition, the disease developed later but attained higher levels as the cultivar ripening season increased from early-maturing Prima to late-maturing Mutsu. Overall, 94.3 to 98.7% of all injured fruit were also infected by M. fructigena, whereas the incidence of brown-rotted fruit without visible injury was very low (0.8 to 1.6%). Correlation coefficients (on a per plot basis) and association indices (on a per-fruit basis) were calculated between brown rot and the various injury types for two selected assessment dates 4 weeks preharvest and at harvest. At both dates, the strongest significant (P < 0.05) relationships were observed between brown rot and insect injury and between brown rot and the cumulative number of trapped C. pomonella. At the harvest assessment, two additional significant correlations were between brown rot and bird injury and between brown rot and growth cracks. In every case, correlation coefficients were larger in organic than in integrated blocks. Although it is well established that brown rot in pome fruits is closely associated with fruit injuries, this is the first study to provide season-long progress data on different injury types and quantitative analyses of their relative importance at different times in the growing season and across two distinct management systems.
Quantitative Trait Loci for Fusarium Head Blight Resistance in a Recombinant Inbred Population of Wangshuibai/Wheaton
Authors: Yu J.-B. , Bai G.-H. , Zhou W.-C. , Dong Y.-H. , Kolb F. L.
Published: December 2007

Use of diverse sources of Fusarium head blight (FHB)-resistant germplasm in breeding may significantly improve wheat resistance to FHB. Wangshuibai is an FHB-resistant Chinese landrace unrelated to cv. Sumai 3, the most commonly used FHB-resistant source. In all, 139 F6 recombinant inbred lines were developed from a cross between Wangshuibai and an FHB-susceptible cultivar, Wheaton, to map quantitative trait loci (QTL) for wheat resistance to initial infection (type I resistance), spread of FHB symptoms within a spike (type II resistance), and deoxynivalenol (DON) accumulation (type III resistance) in infected grain. The experiments were conducted in a greenhouse at Manhattan, KS from 2003 to 2005. More than 1,300 simple-sequence repeat and amplified fragment length polymorphism markers were analyzed in this population. Five QTL for type I resistance were detected on chromosomes 3AS, 3BS, 4B, 5AS, and 5DL after spray inoculation; seven QTL for type II resistance were identified on chromosomes 1A, 3BS, 3DL, 5AS, 5DL, and 7AL after point inoculation; and seven QTL for type III resistance were detected on chromosomes 1A, 1BL, 3BS, 5AS, 5DL, and 7AL with the data from both inoculation methods. These QTL jointly explained up to 31.7, 64, and 52.8% of the phenotypic variation for the three types of FHB resistance, respectively. The narrow-sense heritabilities were low for type I resistance (0.37 to 0.41) but moderately high for type II resistance (0.45 to 0.61) and type III resistance (0.44 to 0.67). The QTL on the distal end of 3BS, 5AS, and 5DL contributed to all three types of resistance. Two QTL, on 7AL and 1A, as well as one QTL near the centromere of 3BS (3BSc), showed effects on both type II and type III resistance. Selection for type II resistance may simultaneously improve type I and type III resistance as well. The QTL for FHB resistance identified in Wangshuibai have potential to be used to pyramid FHB-resistance QTL from different sources.
A Rapid Method for Detecting and Quantifying Bacterial DNA in Rust Fungal DNA Samples
Authors: Barnes C. W. , Szabo L. J.
Published: December 2007

Bacterial DNA contamination of rust fungal DNA can be a significant problem for sequencing the rust fungus. Sequence assembly is much more difficult if the sequence contigs are mixed with bacterial sequence. A quantitative real-time polymerase chain reaction (qPCR) assay was developed to quantify bacterial DNA within rust fungal DNA samples and the results were compared with those obtained from traditional CFU counts. Real-time PCR showed higher values of DNA contamination than CFU. However, the ranking of samples from low to high for bacterial contamination was consistent between the methods. Reasons for the differences between the methods are discussed. The qPCR assay was tested by adding known quantities of Escherichia coli DNA to Puccinia graminis DNA samples. The assay reliably quantified bacterial contamination at ≥ 1.0% of the total sample DNA. When bacterial contamination was <1.0%, fungal DNA also occasionally was amplified, nullifying the quantification measurement. However, primer specificity was not simply the product of the ratio of bacterial DNA to fungal DNA. Bacterial contamination could be quantified below 1.0% if the bacterial DNA concentration was ≈70 pg/μl or greater. Therefore, spiking the fungal samples with a known concentration of E. coli bacterial DNA successfully eliminated the amplification of fungal DNA, making quantification of contaminating bacterial DNA possible for samples with low contamination levels.