bluuebunny/crossref_metadata_2025 huggingface dataset:
Alternative slip system activation in lattice-mismatched InP/InGaAs interfaces
Authors: Quitoriano N. J. , Fitzgerald E. A.
Published: April 2007

Relaxation of compressed InP and InGaAs at different strains and temperatures is examined in this study. For example, different compressive strain states of InP can be attained by depositing InP on an InxGa1−xAs graded buffer with different compositions, x. In slightly strained elemental and compound semiconductor films, including InP and InGaAs, relaxation occurs via the primary-slip system, a∕2⟨110⟩{111}, where glide takes place on {111}-type planes. At high lattice mismatches, Lomer edge dislocations are the predominant form of relaxation. In this work at intermediate lattice-mismatch strains, relaxation occurred via the secondary, a∕2⟨110⟩{110}, slip system in InP and InGaAs. For these strains above a critical strain of about 0.0085, both the primary- and secondary-slip systems are active evident by cross slip between these two slip systems. The extent of relaxation via the primary- or secondary-slip system was found to be dependant on growth temperature. Relaxation via the secondary-slip system, when it was active, increased as the temperature decreased and we found a 1.5 eV difference between the activation energy for glide via the primary- and secondary-slip systems.
Two-dimensional dusty plasma crystal as an electrostatic wiggler for free-electron laser
Authors: Mirzanejhad Saeed , Bahadory Behnam
Published: April 2007

The ability of a dusty plasma crystal to induce transverse motion to a relativistic electron, as a microstructure wiggler field in a free-electron laser (FEL), is presented. A dusty crystal wiggler with micrometer size can decrease FEL wavelength several orders of magnitudes. A relativistic electron dynamic through a two-dimensional monolayer hexagonal dusty crystal is analyzed. In addition to the usual transverse wiggling motion, second-harmonic amplitude is induced to the axial velocity. These conditions are compared with a magnetostatic planar wiggler, and it is shown that E0x∕V‖0 in dusty crystal has a role of Bw in a magnetostatic wiggler. The strength of this proposed wiggler can be increased by decreasing d, decreasing d∕λD ratio, or increasing qd in different experimental setups.
Monodisperse star-shaped compound and its blend in uncapped polyfluorene matrices as the active materials for high-performance pure blue light-emitting devices
Authors: Zhu Rui , Lai Wen-Yong , Wang Hong-Yu , Yu Nan , Wei Wei , Peng Bo , Huang Wei , Hou Lin-Tao , Peng Jun-Biao , Cao Yong
Published: April 2007

The authors have demonstrated high-performance blue light-emitting device based on a monodisperse star-shaped compound. The single-layer device fabricated with solution procedure exhibited a turn-on voltage of 3.5V, maximum luminance of 5545cdm−2, luminance efficiency (LE) of 1.09cdA−1, and external quantum efficiency (QEext) of 1.51% with the CIE coordinate of (0.16, 0.12). The authors also blended this highly efficient monodisperse compound in uncapped polyfluorene matrices. Enhanced performances of the uncapped polyfluorenes were obtained with improved electroluminescent stability. A maximum LE of 2.33cdA−1 and QEext of 2.95% were achieved.
Molecular dynamics simulation of the dynamical behaviors of an aromatic carboxylic acid molecule with different conformations on a Au (111) surface
Authors: Ju Shin-Pon , Lee Wen-Jay , Chen Hui-Chuan , Chang Jee-Gong
Published: April 2007

In this study, the behavior of a single tricarboxylic acid derivative, 1,3,5-tris(carboxymethoxy) benzene [TCMB, C6H3(OCH2COOH)3] on a Au (111) substrate at 50K has been investigated by molecular dynamics simulation. Four possible conformations of the TCMB molecule adsorbed on the Au (111) substrate are found and which display different trajectories of movement and dynamical behaviors. The lock-and-key geometry between the TCMB molecule of different conformations and atomic arrangement of the Au (111) surface was also observed.
High current density InN∕AlN heterojunction field-effect transistor with a SiNx gate dielectric layer
Authors: Lin Yu-Syuan , Koa Shun-Hau , Chan Chih-Yuan , Hsu Shawn S. H. , Lee Hong-Mao , Gwo Shangjr
Published: April 2007

In N ∕ Al N metal-insulator-semiconductor heterojunction field-effect transistors with a gate-modulated drain current and a clear pinch-off characteristic have been demonstrated. The devices were fabricated using high-quality InN (26nm)∕AlN (100nm) epifilms grown by plasma-assisted molecular-beam epitaxy on Si (111) substrates. The devices exhibited a current density higher than ∼530mA∕mm with a 5μm gate length. The pinch-off voltage was at ∼−7V with an associated drain leakage current less than 10μA∕mm. The observed high current density may be attributed to the high sheet carrier density due to the large spontaneous polarization difference between InN and AlN.
Forouhi-Bloomer and Tauc-Lorentz optical dispersions applied using spectroscopic ellipsometry to plasma-deposited fluorocarbon films
Authors: Easwarakhanthan T. , Beyssen D. , Le Brizoual L. , Alnot P.
Published: April 2007

Optical properties of the fluorocarbon (FC) films plasma deposited on Si substrates are evaluated in this work using multiple sample analysis (MSA)-based spectroscopic ellipsometry (SE) with representing the film optical constants by the Forouhi-Bloomer (FB) and Tauc-Lorentz (TL) optical dispersions. This SE analysis supported also with other film investigations results in a two-layer optical model consisting of an interface assimilated to FC species-permeated Si layer beneath a surface smooth, homogeneous, and isotropic FC bulk film. Both dispersions yield a low-dielectric constant quality visible range refractive index of 1.39 and almost identical model layer thicknesses. Deposition-dominated linear film growth is thus asserted. Specifically, the FB dispersion better describes the region near absorption cutoff with taking up a lower optical band gap (OBG) than that of the TL dispersion, indicating thereby that particular FC film absorptions included in the FB dispersion are excluded in the other. Also, the FB index spectrum tends to peak towards a broad maximum in the ultraviolet (UV) wavelength range, whereas this trend is absent in the TL index spectrum probably removed by the TL parameter cross correlations although reduced by MSA. Sample to sample analysis further shows that the TL parameter correlation is accentuated by the instrument-limited UV range. The FB parameters are much less affected by cross correlation such that even the sample to sample analysis may be readily used in conjuncture with the FB dispersion for thicker FC films above 150nm to monitor their index and OBG in tailoring desired film physical properties through deposition conditions.
Lithography-free fabrication of graphene devices
Authors: Staley N. , Wang H. , Puls C. , Forster J. , Jackson T. N. , McCarthy K. , Clouser B. , Liu Y.
Published: April 2007

We have developed a lithography-free, all-dry process for fabricating graphene devices using an ultrathin quartz filament as a shadow mask. This technique, which is free of the possible contamination of graphene during lithographic process, is simple to implement, versatile, and capable of achieving high throughput. We prepared devices for electrical transport as well as planar tunnel junction studies of n-layer graphene (nLG), with n=1,2,3, and higher using this technique. We observed possible weak localization behavior and an apparent reduction of density of states near the Fermi energy in nLG.
Spectral characteristics in long-period fiber gratings with nonuniform symmetrically ring shaped coatings
Authors: Cusano Andrea , Paladino Domenico , Cutolo Antonello , Del Villar Ignacio , Matias Ignacio R. , Arregui Francisco J.
Published: April 2007

In this work, the spectral characteristics of nonuniform symmetrically ring shaped coatings deposited on long-period fiber gratings have been theoretically and experimentally investigated. Electrostatic self-assembling technique was used to deposit with fine control uniform azimuthally symmetric coatings at nanoscale level. UV laser micromachining operating at 193nm was applied to selectively remove the coating with high spatial resolution on ring shaped geometry. Phase shift effects and multiple interference fringes have been observed for all the attenuation bands, strongly depending on the length of the uncoated region and the coating features (thickness and optical properties). The ability of the proposed structure to exhibit wavelength selective operation, combined with the effects of high refractive index coatings on the cladding modes distribution, provides a valid technological platform for the development of advanced photonic devices for sensing and telecommunication applications.
Barium strontium oxide coated carbon nanotubes as field emitters
Authors: Jin Feng , Liu Yan , Day Christopher M.
Published: April 2007

The authors report a field emitter structure based on oxide coated carbon nanotubes (CNTs). This emitter consists of a thin tungsten ribbon with CNTs on the surface and a thin layer of low work function barium strontium oxide coating on the CNTs. This oxide coated CNT emitter was designed to combine the benefits of the high field enhancement factor from CNTs and the low work function from the emissive oxide coating. The field emission properties of the emitters were characterized. A field enhancement factor of 467 and a work function of 1.9eV were obtained for the oxide coated CNTs. Compared to the uncoated CNTs, the field emission from the oxide coated CNTs increased by a factor of 2–3. At 4.4V∕μm, the field emission current of 23.6μA was obtained from an emitting surface of 0.012cm2.
Reversal of forward voltage drift in 4H-SiC p-i-n diodes via low temperature annealing
Authors: Caldwell Joshua D. , Stahlbush Robert E. , Hobart Karl D. , Glembocki Orest J. , Liu Kendrick X.
Published: April 2007

Recent reports have shown that Shockley stacking fault (SSF) growth in 4H-SiC may be reversed via low temperature (210–600°C) annealing. It is not clear if the associated drift in the forward voltage drop (Vf) is also reversed. Here we show that annealing of SSFs causes the complete and repeatable recovery of Vf. Furthermore, by looking at the time-dependent recovery of Vf during both the current stressing and thermal annealing of a single diode, we ascertain that the mechanisms for these two processes are different.
Small optical volume terahertz emitting microdisk quantum cascade lasers
Authors: Dunbar L. Andrea , Houdré Romuald , Scalari Giacomo , Sirigu Lorenzo , Giovannini Marcella , Faist Jérôme
Published: April 2007

The authors fabricate and characterize a series of quantum cascade laser micropillars emitting at ≈3.5THz. The optical confinement by double plasmon guiding in the vertical direction creates a large impedance mismatch between the confined optical modes and free space. Thus, unlike standard dielectric structures, large quality (Q) factors are maintained for small radius to wavelength ratios. The narrow bandwidth of the optical mode results in low threshold current (8mA) single-mode lasers. Cavity pulling enables a fine dynamic tuning of the emission wavelength. Comparison of the frequency shift due to cavity pulling and the Stark effect provides an experimental measure of the gain (36cm−1).
Single mode stimulated emission from prismlike gallium nitride submicron cavities
Authors: Lai C.-M. , Wu H.-M. , Huang P.-C. , Wang S.-L. , Peng L.-H.
Published: April 2007

The authors report single mode stimulated emission from optical pumping of prismlike gallium nitride (GaN) with a side length of 0.75μm. The cavities were formed by reaction-rate-limited photoetching that preserved the nonpolar {101¯0} or {112¯0} facets. They were characterized by an average quality factor above 103 and an equivalent facet reflectivity exceeding 98%, which allowed field amplification by repeated internal reflections in the transverse plane and field polarization along the c axis. Slight spectral blueshift (0.35nm) and narrowing in linewidth (∼0.4nm) were observed with increase of pump intensity. These observations manifested resonant coupling of the band edge emission to a single mode of the prismlike GaN cavity.
Narrow stripe-width, low-ridge high power quantum cascade lasers
Authors: Lyakh A. , Zory P. , Wasserman D. , Shu G. , Gmachl C. , D’Souza M. , Botez D. , Bour D.
Published: April 2007

Narrow stripe-width, low-ridge quantum cascade lasers operating at 5.3μm were fabricated from InP-based, metal-organic chemical-vapor-deposition-grown material. Maximum peak-pulsed output power of 12W at 14A was measured from a low-ridge laser with a high reflectivity coated back facet. Modeling shows that the lateral variation of the transverse conductivity is essential for an accurate description of the current spreading in these devices.
Low-threshold terahertz Si:As laser
Authors: Pavlov S. G. , Böttger U. , Hübers H.-W. , Zhukavin R. Kh. , Kovalevsky K. A. , Tsyplenkov V. V. , Shastin V. N. , Abrosimov N. V. , Riemann H.
Published: April 2007

The optical threshold of terahertz intracenter arsenic-doped silicon lasers has been reduced by two orders of magnitude by applying a compressive force to the laser crystal. The Si:As lasers were optically excited with radiation from a CO2 laser operating at a wavelength of 10.59μm. The lowest threshold intensity of 8kW∕cm2 was realized at about 3×108Pa stress applied along the [001] crystal axis. The uniaxial stress breaks the resonant interaction of electrons bound to donors with intervalley f phonons. This changes the upper laser state from 2p± to 2p0, lowers the laser threshold, and increases the output power.
Relationship between flux pinning and microstructure in MgB2 thin films with columnar grains formed by molecular beam epitaxy
Authors: Yamamoto H. , Tsukamoto A. , Saitoh K. , Okada M. , Kitaguchi H.
Published: April 2007

The relationship between flux pinning and microstructure in MgB2 thin films with columnar grains was investigated. Two kinds of as-grown MgB2 thin films were prepared with or without inclination of columnar grain growth with respect to the substrate plane by using molecular beam epitaxy. In a magnetic field, maximum Jc was obtained when the field angle matched the direction of columnar grain growth. The fabricated MgB2 thin films showed a high critical current density of Jc=1.3×105A∕cm2 in 14T at 4.2K. The present results give a direct proof of flux pinning originating in columnar grain boundaries for MgB2 thin films.
Organic photodetectors with electrically bistable electron acceptors and nanotubes
Authors: Sahu Satyajit , Batabyal Sudip K. , Pal Amlan J.
Published: April 2007

The authors provide two routes to increase the photocurrent of organic photodetectors that are based on electron-donor and electron-acceptor materials. During device fabrication, they introduce carbon nanotubes, which act as channels for electron transport. The channels in effect provide an approach to address the problem of low carrier mobility in the conjugated organics. The authors also make use of the (electrically) bistable nature of the acceptor material, namely, rose bengal in a favorable way. During device characterization, they switch its conductivity to decrease device resistance and yield higher photocurrent. Both the routes enhance photocurrent in these donor-acceptor-type photodetectors.
Amplified spontaneous emission from cyano substituted oligo(p-phenylene vinylene) single crystal with very high photoluminescent efficiency
Authors: Xie Weijie , Li Yupeng , Li Feng , Shen Fangzhong , Ma Yuguang
Published: April 2007

Amplified spontaneous emission (ASE) from high-quality crystal of cyano substituted oligo(p-phenylene vinylene) with very high photoluminescent efficiency is observed. The full widths at half maximum of the narrowed spectra can reach 10nm when the pumping energy is 50μJ/pulse. The threshold for ASE is about 7.9μJ/pulse corresponding to 39.5kW∕cm2, which is among the lowest values for organic crystals ever reported. The gain coefficient at the peak wavelength of ASE and loss coefficient caused by scattering are ∼33 and ∼3.9cm−1, respectively.
Frequency and temperature dependence of tunable dielectric properties of Ba(Zr0.2Ti0.8)O3 thin films grown on (001) MgO
Authors: Zhu X. H. , Li J. , Zheng D. N.
Published: April 2007

High quality Ba(Zr0.2Ti0.8)O3 (BZT) thin films were epitaxially grown on MgO single-crystal substrates. No structural phase transition took place in the temperature range of 80–300K, and the films displayed a typical behavior of relaxor ferroelectrics, which was demonstrated by micro-Raman spectroscopy. Frequency and temperature dependence of dielectric properties was systematically investigated for the BZT thin films. It was found that enhanced dielectric properties could be obtained over a wide frequency and temperature range. This is of great importance for practical microelectronic device applications. At room temperature, a high dielectric tunability of nearly 50% was achieved over the whole measurement frequency range of 10kHz–1MHz by applying an electric field with intensity as low as 40kV∕cm; meanwhile, a relatively low dielectric loss was obtained and the value could be further reduced significantly with the applied dc electric field, indicating an excellent figure of merit and promising applications in tunable microwave devices for the BZT films.
Forces acting on a current-driven moving vortex in a long Josephson junction
Authors: Chen D.-X. , Pardo E. , Sanchez A.
Published: April 2007

The current-driven vortex motion in a resistively shunted long Josephson junction is calculated. It is shown that the force on the vortex exerted by an ac Josephson current or a bias current routinely assumed for studying Josephson transmission lines is a Lorentz force, whereas the driving force on the vortex acted by a transport dc Josephson current is a London force, which could have an expression apparently similar to that of a Lorentz force with an opposite sign.
Ultraviolet-sensitive field-effect transistor utilized amorphous thin films of organic donor/acceptor dyad
Authors: Saragi Tobat P. I. , Pudzich Robert , Fuhrmann-Lieker Thomas , Salbeck Josef
Published: April 2007

The authors report on highly responsive ultraviolet (UV)-sensitive field-effect transistor based on amorphous thin films of organic donor/acceptor dyad. An optimal responsivity of up to 6.5A∕W can be obtained for UV light at 370nm. High ratios of photocurrent to dark current of up to 4.3×103 can also be obtained. The underlying mechanism can be sufficiently explained by ultrafast photoinduced intramolecular charge transfer between the acceptor and the donor. This result offers a potential application of organic semiconductors as active materials for UV detectors.
Combined micro-/nanoscale surface roughness for enhanced hydrophobic stability in carbon nanotube arrays
Authors: Wang Z. , Koratkar N. , Ci L. , Ajayan P. M.
Published: April 2007

Extreme water repellency is greatly desired for anticontamination and self-cleaning applications. Aligned multiwalled carbon nanotube arrays exhibit superhydrophobic behavior but suffer from poor hydrophobic stability and contact angle hysteresis. In this work the authors selectively grow multiwalled nanotubes onto a patterned substrate and engineer a novel high aspect ratio architecture which combines a micro- and a nano-scale roughness structure. While there is no significant difference in the static contact angle of the patterned and uniform nanotube arrays, dynamic measurements indicate a dramatic increase in hydrophobic stability for the patterned array caused by entrapped air pockets which prevent Cassie to Wenzel state transition.
Lubricant transfer from disk to slider in hard disk drives
Authors: Ma Yansheng , Liu Bo
Published: April 2007

The physics behind lubricant transfer from disk to slider and lubricant accumulation on the slider in hard disk drives is explained. The effect of slider air bearing pressure on the lubricant transfer is discussed. It is found that the lubricant transfer is not affected by slider air bearing pressure. Lubricant molecular weight plays a dominant role in the lubricant transfer and lubricant accumulation. The amount of lubricant transfer and accumulation decreases dramatically with the increase in lubricant molecular weight. A thinner lubricant and higher bonding ratio of lubricant on disk surface reduce the lubricant transfer and accumulation obviously.
200 femtometer sensitivity for near-field analysis of surface acoustic waves in a scanning electron / scanning probe microscope hybrid system
Authors: Thomas Ch. , Heiderhoff R. , Balk L. J.
Published: April 2007

In the microscopic hybrid system, a combination of a scanning electron microscope with a scanning probe microscope, both microprobes are used for local generation and detection of acoustic waves in the near field. At the example of ferroelectric domain imaging, a sensitivity of 200fm in the local detection of vertical surface oscillation is demonstrated whereas the spatial resolution is within several nanometers.
Vacancy mediated desorption of hydrogen from a sodium alanate surface: An ab initio spin-polarized study
Authors: Du A. J. , Smith Sean C. , Lu G. Q.
Published: April 2007

Ab initio spin-polarized density functional theory calculations are performed to explore the effect of single Na vacancy on NaAlH4(001) surface on the initial dehydrogenation kinetics. The authors found that two Al–H bond lengths become elongated and weakened due to the presence of a Na vacancy on the NaAlH4(001) surface. Spontaneous recombination from the surface to form molecular hydrogen is observed in the spin-polarized ab initio molecular dynamics simulation. The authors’ results indicate that surface Na vacancies play a critical role in accelerating the dehydrogenation kinetics in sodium alanate. The understanding gained here will aid in the rational design and development of complex hydride materials for hydrogen storage.
Quantum-dot-sensitized solar cells: Assembly of CdS-quantum-dots coupling techniques of self-assembled monolayer and chemical bath deposition
Authors: Lin Sheng-Chih , Lee Yuh-Lang , Chang Chi-Hsiu , Shen Yu-Jen , Yang Yu-Min
Published: April 2007

Two methods, coupling self-assembled monolayer and chemical bath deposition (CBD), were utilized to assemble cadmium sulfide (CdS) quantum dots (QDs) onto mesoporous TiO2 films for dye-sensitized solar cell (DSSC) applications. Colloidal CdS QDs were first self-assembled on the TiO2 surface. CBD was then introduced to replenish the incorporated amount and increase the coverage ratio of CdS QDs on the TiO2 surface. The preassembled CdS QDs act as nucleation sites in the CBD process, forming a CdS nanofilm with an interfacial structure capable of inhibiting the recombination of injected electrons. An efficiency as high as 1.35% for the QD-sensitized DSSC was achieved using the present strategy.
Daam1 regulates the endocytosis of EphB during the convergent extension of the zebrafish notochord
Authors: Kida Yasuyuki S. , Sato Takayuki , Miyasaka Kota Y. , Suto Asami , Ogura Toshihiko
Published: April 2007

Convergent extension (CE) movement of cells is one of the fundamental processes that control the organized morphogenesis of tissues and organs. The molecular events connecting the noncanonical Wnt pathway and CE movement, however, are not well understood. We show that subcellular localization of Daam1, an essential component of noncanonical Wnt signaling, changes dynamically during notochord formation. In the early phases, Daam1 complexes with EphB receptors and Disheveled 2. This complex is incorporated into endocytic vesicles in a dynamin-dependent manner, thereby resulting in the removal of EphB from the cell surface with subsequent switching of cell adhesiveness. In the next step, Daam1 colocalizes with the actin cytoskeleton to induce morphological extension of cells. We elucidate the molecular mechanism underlying the CE movement of notochord cells with Daam1 as a dynamic coordinator of endocytosis and cytoskeletal remodeling.
Structural and dynamic properties of propane coordinated to TpRh(CNR) from a confrontation between theory and experiment
Authors: Clot Eric , Eisenstein Odile , Jones William D.
Published: April 2007

Density functional calculations with the B3PW91 functional have been carried out on the TpRh(CNMe) species [Tp = HB(pyrazolyl)
3
] as a model for Tp′Rh(CNCH
2
CMe
3
) [Tp′ = HB(3,5-dimethylpyrazolyl)
3
] in interaction with propane. Two σ complexes have been found as minima coordinated through either a methyl or a methylene C

H bond, the former being more stable. The approach of the alkane to TpRh(CNMe) has been studied. Although no transition state could be located, study of this path reveals the key importance of the partial decoordination of one pyrazole ring. The full coordination of the alkane can only be achieved when the metal is essentially in a square pyramid coordination with one of the three pyrazole groups only weakly interacting with Rh. The main reaction of the methyl σ complex is oxidative addition, leading to the
n
-propyl hydride complex. In contrast, two reactions are found for the methylene σ complex: (
i
) oxidative addition to give the isopropyl complex and (
ii
) exchange between the secondary and primary C

H bonds to convert the methylene complex of propane into a methyl complex of propane. This latter reaction has a much lower barrier than the oxidative addition at the methylene C

H bond. The results account well for most of the experimental results obtained from kinetic studies. Steric factors are found to control the energy barriers between these various processes, disfavoring any process that brings the central carbon into close proximity to Rh.
Oscillation patterns in negative feedback loops
Authors: Pigolotti Simone , Krishna Sandeep , Jensen Mogens H.
Published: April 2007

Organisms are equipped with regulatory systems that display a variety of dynamical behavior ranging from simple stable steady states, to switching and multistability, to oscillations. Earlier work has shown that oscillations in protein concentrations or gene expression levels are related to the presence of at least one negative feedback loop in the regulatory network. Here, we study the dynamics of a very general class of negative feedback loops. Our main result is that, when a single negative feedback loop dominates the dynamical behavior, the sequence of maxima and minima of the concentrations exhibit a pattern that uniquely identifies the interactions of the loop. This allows us to devise an algorithm to (
i
) test whether observed oscillating time series are consistent with a single underlying negative feedback loop, and if so, (
ii
) reconstruct the precise structure of the loop, i.e., the activating/repressing nature of each interaction. This method applies even when some variables are missing from the data set, or if the time series shows transients, like damped oscillations. We illustrate the relevance and the limits of validity of our method with three examples: p53-Mdm2 oscillations, circadian gene expression in cyanobacteria, and cyclic binding of cofactors at the estrogen-sensitive pS2 promoter.
Three functional variants of IFN regulatory factor 5 (
IRF5
) define risk and protective haplotypes for human lupus
Authors: Graham Robert R. , Kyogoku Chieko , Sigurdsson Snaevar , Vlasova Irina A. , Davies Leela R. L. , Baechler Emily C. , Plenge Robert M. , Koeuth Thearith , Ortmann Ward A. , Hom Geoffrey , Bauer Jason W. , Gillett Clarence , Burtt Noel , Cunninghame Graham Deborah S. , Onofrio Robert , Petri Michelle , Gunnarsson Iva , Svenungsson Elisabet , Rönnblom Lars , Nordmark Gunnel , Gregersen Peter K. , Moser Kathy , Gaffney Patrick M. , Criswell Lindsey A. , Vyse Timothy J. , Syvänen Ann-Christine , Bohjanen Paul R. , Daly Mark J. , Behrens Timothy W. , Altshuler David
Published: April 2007

Systematic genome-wide studies to map genomic regions associated with human diseases are becoming more practical. Increasingly, efforts will be focused on the identification of the specific functional variants responsible for the disease. The challenges of identifying causal variants include the need for complete ascertainment of genetic variants and the need to consider the possibility of multiple causal alleles. We recently reported that risk of systemic lupus erythematosus (SLE) is strongly associated with a common SNP in IFN regulatory factor 5 (
IRF5
), and that this variant altered spicing in a way that might provide a functional explanation for the reproducible association to SLE risk. Here, by resequencing and genotyping in patients with SLE, we find evidence for three functional alleles of
IRF5
: the previously described exon 1B splice site variant, a 30-bp in-frame insertion/deletion variant of exon 6 that alters a proline-, glutamic acid-, serine- and threonine-rich domain region, and a variant in a conserved polyA+ signal sequence that alters the length of the 3′ UTR and stability of
IRF5
mRNAs. Haplotypes of these three variants define at least three distinct levels of risk to SLE. Understanding how combinations of variants influence
IRF5
function may offer etiological and therapeutic insights in SLE; more generally,
IRF5
and SLE illustrates how multiple common variants of the same gene can together influence risk of common disease.
H/ACA small nucleolar RNA pseudouridylation pockets bind substrate RNA to form three-way junctions that position the target U for modification
Authors: Wu Haihong , Feigon Juli
Published: April 2007

During the biogenesis of eukaryotic ribosomal RNA (rRNA) and spliceosomal small nuclear RNA (snRNA), uridines at specific sites are converted to pseudouridines by H/ACA ribonucleoprotein particles (RNPs). Each H/ACA RNP contains a substrate-specific H/ACA RNA and four common proteins, the pseudouridine synthase Cbf5, Nop10, Gar1, and Nhp2. The H/ACA RNA contains at least one pseudouridylation (ψ) pocket, which is complementary to the sequences flanking the target uridine. In this article, we show structural evidence that the ψ pocket can form the predicted base pairs with substrate RNA in the absence of protein components. We report the solution structure of the complex between an RNA hairpin derived from the 3′ ψ pocket of human U65 H/ACA small nucleolar RNA (snoRNA) and the substrate rRNA. The snoRNA–rRNA substrate complex has a unique structure with two offset parallel pairs of stacked helices and two unusual intermolecular three-way junctions, which together organize the substrate for docking into the active site of Cbf5. The substrate RNA interacts on one face of the snoRNA in the complex, forming a structure that easily could be accommodated in the H/ACA RNP, and explains how successive substrate RNAs could be loaded onto and unloaded from the H/ACA RNA in the RNP.
Projected impacts of climate change on salmon habitat restoration
Authors: Battin James , Wiley Matthew W. , Ruckelshaus Mary H. , Palmer Richard N. , Korb Elizabeth , Bartz Krista K. , Imaki Hiroo
Published: April 2007

Throughout the world, efforts are under way to restore watersheds, but restoration planning rarely accounts for future climate change. Using a series of linked models of climate, land cover, hydrology, and salmon population dynamics, we investigated the impacts of climate change on the effectiveness of proposed habitat restoration efforts designed to recover depleted Chinook salmon populations in a Pacific Northwest river basin. Model results indicate a large negative impact of climate change on freshwater salmon habitat. Habitat restoration and protection can help to mitigate these effects and may allow populations to increase in the face of climate change. The habitat deterioration associated with climate change will, however, make salmon recovery targets much more difficult to attain. Because the negative impacts of climate change in this basin are projected to be most pronounced in relatively pristine, high-elevation streams where little restoration is possible, climate change and habitat restoration together are likely to cause a spatial shift in salmon abundance. River basins that span the current snow line appear especially vulnerable to climate change, and salmon recovery plans that enhance lower-elevation habitats are likely to be more successful over the next 50 years than those that target the higher-elevation basins likely to experience the greatest snow–rain transition.
Early Cambrian record of failed durophagy and shell repair in an epibenthic mollusc
Authors: Skovsted Christian B , Brock Glenn A , Lindström Anna , Peel John S , Paterson John R , Fuller Margaret K
Published: April 2007

Predation is arguably one of the main driving forces of early metazoan evolution, yet the fossil record of predation during the Ediacaran–Early Cambrian transition is relatively poor. Here, we present direct evidence of failed durophagous (shell-breaking) predation and subsequent shell repair in the Early Cambrian (Botoman) epibenthic mollusc
Marocella
from the Mernmerna Formation and Oraparinna Shale in the Flinders Ranges, South Australia. This record pushes back the first appearance of durophagy on molluscs by approximately 40 Myr.
Spiders fluoresce variably across many taxa
Authors: Andrews Kindra , Reed Scott M , Masta Susan E
Published: April 2007

The evolution of fluorescence is largely unexplored, despite the newfound occurrence of this phenomenon in a variety of organisms. We document that spiders fluoresce under ultraviolet illumination, and find that the expression of this trait varies greatly among taxa in this species-rich group. All spiders we examined possess fluorophores in their haemolymph, but bright fluorescence appears to result when a spider sequesters fluorophores in its setae or cuticle. By sampling widely across spider taxa, we determine that fluorescent expression is labile and has evolved multiple times. Moreover, examination of the excitation and emission properties of extracted fluorophores reveals that spiders possess multiple fluorophores and that these differ among some families, indicating that novel fluorophores have evolved during spider diversification. Because many spiders fluoresce in wavelengths visible to their predators and prey (birds and insects), we propose that natural selection imposed by predator–prey interactions may drive the evolution of fluorescence in spiders.
Southern Hemisphere humpback whales wintering off Central America: insights from water temperature into the longest mammalian migration
Authors: Rasmussen Kristin , Palacios Daniel M , Calambokidis John , Saborío Marco T , Dalla Rosa Luciano , Secchi Eduardo R , Steiger Gretchen H , Allen Judith M , Stone Gregory S
Published: April 2007

We report on a wintering area off the Pacific coast of Central America for humpback whales (Megaptera novaeangliae) migrating from feeding areas off Antarctica. We document seven individuals, including a mother/calf pair, that made this migration (approx. 8300 km), the longest movement undertaken by any mammal. Whales were observed as far north as 11° N off Costa Rica, in an area also used by a boreal population during the opposite winter season, resulting in unique spatial overlap between Northern and Southern Hemisphere populations. The occurrence of such a northerly wintering area is coincident with the development of an equatorial tongue of cold water in the eastern South Pacific, a pattern that is repeated in the eastern South Atlantic. A survey of location and water temperature at the wintering areas worldwide indicates that they are found in warm waters (21.1–28.3°C), irrespective of latitude. We contend that while availability of suitable reproductive habitat in the wintering areas is important at the fine scale, water temperature influences whale distribution at the basin scale. Calf development in warm water may lead to larger adult size and increased reproductive success, a strategy that supports the energy conservation hypothesis as a reason for migration.
Transmissibility of swine flu at Fort Dix, 1976
Authors: Lessler Justin , Cummings Derek A.T , Fishman Steven , Vora Amit , Burke Donald S
Published: April 2007

Abstarct

The 1976 outbreak of A/New Jersey/76 influenza in Fort Dix is a rare example of an influenza virus with documented human to human transmission that failed to spread widely. Despite extensive epidemiological investigation, no attempt has been made to quantify the transmissibility of this virus. The World Health Organization and the United States Government view containment of emerging influenza strains as central to combating pandemic influenza. Computational models predict that it may be possible to contain an emergent pandemic influenza if virus transmissibility is low. The A/New Jersey/76 outbreak at the United States Army Training Center at Fort Dix, New Jersey in January 1976 caused 13 hospitalizations, 1 death and an estimated 230 cases. To characterize viral transmission in this epidemic, we estimated the basic reproductive number and serial interval using deterministic epidemic models and stochastic simulations. We estimated the basic reproductive number for this outbreak to be 1.2 (supported interval 1.1–1.4), the serial interval to be 1.9 days (supported interval 1.6–3.8 days), and that the virus had at least six serial human to human transmissions. This places the transmissibility of A/New Jersey/76 virus at the lower end of circulating flu strains, well below the threshold for control.
Diffraction of flexural waves by cracks in orthotropic thin elastic plates. Part II. Far field analysis
Authors: Thompson Ian , Abrahams I.David
Published: April 2007

The scattered field arising from diffraction of a plane flexural wave by a semi-infinite crack in an orthotropic Kirchhoff thin plate is analysed. The crack is aligned with a principal direction of the material, so that two of the plate's three planes of symmetry are preserved. An asymptotic approximation is derived via the method of steepest descents, and explicit expressions are given for the most significant contributions. The effects of anisotropy upon the scattered field are made clear, and numerical results are presented for several typical engineering materials.
Benefits to shorebirds from invasion of a non-native shellfish
Authors: Caldow Richard W.G , Stillman Richard A , Durell Sarah E.A. le V. dit , West Andy D , McGrorty Selwyn , Goss-Custard John D , Wood Philippa J , Humphreys John
Published: April 2007

Introductions of non-native species are seen as major threats to ecosystem function and biodiversity. However, invasions of aquatic habitats by non-native species are known to benefit generalist consumers that exhibit dietary switches and prey upon the exotic species in addition to or in preference to native ones. There is, however, little knowledge concerning the population-level implications of such dietary changes. Here, we show that the introduction of the Manila clamTapes philippinaruminto European coastal waters has presented the Eurasian oystercatcherHaematopus ostralegus ostraleguswith a new food resource and resulted in a previously unknown predator–prey interaction between these species. We demonstrate, with an individuals-based simulation model, that the presence of this non-native shellfish, even at the current low density, has reduced the predicted over-winter mortality of oystercatchers at one recently invaded site. Further increases in clam population density are predicted to have even more pronounced effects on the density dependence of oystercatcher over-winter mortality. These results suggest that if the Manila clam were to spread around European coastal waters, a process which is likely to be facilitated by global warming, this could have considerable benefits for many shellfish-eating shorebird populations.
Quantifying the risk from ovine BSE and the impact of control strategies
Authors: Fryer Helen R , Baylis Matthew , Sivam Kumar , McLean Angela R
Published: April 2007

Although no naturally infected sheep with bovine spongiform encephalopathy (BSE) has ever been discovered, it remains possible that BSE once infected the UK sheep population, has been transmitted between sheep, and is still present today. We constructed a mathematical model to assess the current maximum theoretical exposure to consumers from BSE-infected ovine material and to estimate the risk reduction that could be achieved by abattoir-based control options if BSE-infected sheep were ever found in the national flock. We predict that, if present, the exposure to consumers from a single BSE-infected sheep would be high: one sheep, close to the end of its incubation period, is likely to contribute 10–1000 times more infectious material than a fully infectious cow. Furthermore, 30% of this exposure comes from infectivity residing in lymphatic and peripheral tissue that cannot be completely removed from a carcass.

We are 95% confident that throughout Great Britain, no more than four sheep flocks currently harbour an ongoing BSE epidemic. However, since the exposure from a single infected sheep is high, the annual human exposure from four ‘typical’ BSE-infected flocks could be considerable. Small reductions in exposure could be achieved by strategies based on tissue testing, a 12-month age restriction or expanded definitions of high-risk tissues. A six-month age restriction is likely to be more effective and genotype-based strategies the most effective.
Is there a dysexecutive syndrome?
Authors: Stuss Donald T , Alexander Michael P
Published: April 2007

The role of the frontal lobes has often been described as a ‘paradox’ or a ‘riddle’. Ascribed to this region has been the loftiest of functions (e.g. executive; seat of wisdom); others contested that the frontal lobes played no special role. There has also been controversy about the unity or diversity of functions related to the frontal lobes. Based on the analysis of the effects of lesions of the frontal lobes, we propose that there are discrete categories of functions within the frontal lobes, of which ‘executive’ functioning is one. Within the executive category, the data do not support the concept of an undifferentiated central executive/supervisory system. The results are better explained as impairments in a collection of anatomically and functionally independent but interrelated attentional control processes. Evidence for three separate frontal attentional processes is presented. For each process, we present an operational description, the data supporting the distinctiveness of each process and the evidence for impairments of each process after lesions in specific frontal regions. These processes and their coarse frontal localizations areenergization—superior medial,task setting—left lateralandmonitoring—right lateral. The strength of the findings lies in replication: across different tasks; across different cognitive modalities (e.g. reaction time paradigms, memory); and across different patient groups. This convergence minimizes the possibility that any of the findings are limited to a specific task or to a specific set of patients. Although distinct, these processes are flexibly assembled in response to context, complexity and intention over real time into different networks within the frontal regions and between frontal and posterior regions.
Shifting and stopping: fronto-striatal substrates, neurochemical modulation and clinical implications
Authors: Robbins T.W
Published: April 2007

The neuropsychological basis of attentional set-shifting, task-set switching and stop-signal inhibition is reviewed through comparative studies of humans and experimental animals. Using human functional neuroimaging, plus neuropsychological investigation of patients with frontal damage quantified by structural magnetic resonance imaging, and through parallels with effects of specific lesions of the prefrontal cortex (PFC) and striatum in rats and marmosets, it is possible to define both distinct and overlapping loci for tasks such as extra-dimensional shifting and reversal learning, stop-signal reaction time and task-set switching. Notably, most of the paradigms implicate a locus in the right PFC, specifically the right inferior frontal gyrus, possibly associated with processes of response inhibition. The neurochemical modulation of fronto-striatal circuitry in parallel with effects on task performance has been investigated using specific neuropharmacological agents in animals and by human psychopharmacological investigations, sometimes in conjunction with functional imaging. Evidence is provided for double dissociations of effects of manipulations of prefrontal cortical catecholamine and indoleamine (5-HT) systems that have considerable implications in the treatment of disorders such as Parkinson's disease, attention deficit/hyperactivity disorder and depression, as well as in theoretical notions of how ‘fronto-executive’ functions are subject to state-dependent influences, probably related to stress, arousal and motivation.
Serum albumin‐associated peptides of patients with uterine endometrial cancer
Authors: Kikuchi Satoru , Honda Kazufumi , Handa Yasushi , Kato Hidenori , Yamashita Kohki , Umaki Tomoko , Shitashige Miki , Ono Masaya , Tsuchida Akihiko , Aoki Tatsuya , Hirohashi Setsuo , Yamada Tesshi
Published: April 2007

The incidence of endometrial cancer is predicted to increase in developed countries. Because of the relatively high incidence of complications and low diagnostic sensitivity associated with endometrial tissue sampling, there is an urgent need for the development of a safe and non‐invasive diagnostic method. The proteomic spectrum of albumin‐associated peptides was obtained from a total of 125 serum samples (92 from endometrial cancer patients and 33 from controls) by matrix‐assisted laser desorption/ionization hybrid quadrupole time‐of‐flight mass spectrometry, and the candidate markers were selected by the Mann–Whitney U‐test and receiver operator characteristics analysis. We selected three mass peaks at 4769, 6254 and 11 792 m/z from a total of 507 peaks as distinguishing cancer patients from controls (P < 0.00001 and area under curve of over 0.8). When the cut‐off points were defined as the averages of the values in the controls + 2 SD, the combination of the three peptides detected endometrial cancer with a sensitivity of 65.2% (60/92). Even stage I early endometrial cancers were detected with a sensitivity of 60.3% (38/63). Unfortunately, the three peptides were also detected in 44.6% (33/74) of myoma uteri patients, indicating that they are not specific to endometrial cancer. Although a large‐scale study is necessary to confirm the clinical significance of the peptide biomarkers identified in this study, direct profiling of serum‐albumin‐bound peptides by high‐resolution mass spectrometry was proven to have potential as a means of identifying biomarkers for a variety of diseases. (Cancer Sci 2007; 98: 822–829)