bluuebunny/crossref_metadata_2025 huggingface dataset:
The bone diagnostic instrument II: Indentation distance increase
Authors: Hansma Paul , Turner Patricia , Drake Barney , Yurtsev Eugene , Proctor Alexander , Mathews Phillip , Lelujian Jason , Randall Connor , Adams Jonathan , Jungmann Ralf , Garza-de-Leon Federico , Fantner Georg , Mkrtchyan Haykaz , Pontin Michael , Weaver Aaron , Brown Morton B. , Sahar Nadder , Rossello Ricardo , Kohn David
Published: June 2008

The bone diagnostic instrument (BDI) is being developed with the long-term goal of providing a way for researchers and clinicians to measure bone material properties of human bone in vivo. Such measurements could contribute to the overall assessment of bone fragility in the future. Here, we describe an improved BDI, the Osteoprobe II™. In the Osteoprobe II™, the probe assembly, which is designed to penetrate soft tissue, consists of a reference probe (a 22 gauge hypodermic needle) and a test probe (a small diameter, sharpened rod) which slides through the inside of the reference probe. The probe assembly is inserted through the skin to rest on the bone. The distance that the test probe is indented into the bone can be measured relative to the position of the reference probe. At this stage of development, the indentation distance increase (IDI) with repeated cycling to a fixed force appears to best distinguish bone that is more easily fractured from bone that is less easily fractured. Specifically, in three model systems, in which previous mechanical testing and/or tests reported here found degraded mechanical properties such as toughness and postyield strain, the BDI found increased IDI. However, it must be emphasized that, at this time, neither the IDI nor any other mechanical measurement by any technique has been shown clinically to correlate with fracture risk. Further, we do not yet understand the mechanism responsible for determining IDI beyond noting that it is a measure of the continuing damage that results from repeated loading. As such, it is more a measure of plasticity than elasticity in the bone.
Calculations of potential functions and thermophysical behaviors for La62Al14Ni12Cu12 and Cu46Zr44Al7Y3 bulk metallic glasses
Authors: Chen Xiaohua , Zhang Yong , Chen Guoliang , Zhang Xingchao , Liu Lei
Published: June 2008

Bulk metallic glasses La62Al14Ni12Cu12 and Cu46Zr44Al7Y3 were prepared by copper mold suction casting. The thermal-physical behaviors of bulk metallic glasses were investigated by means of x-ray diffraction, differential scanning calorimetry, ultrasonic techniques, and dilatometry. By calculating the Mie potential function from experimental data, the values of potential function powers (m and n) and related physical parameters such as the mean binding energy, etc., are obtained. Thus, unlike what some people have done by assuming values of m−n (7–14), the values of average nearest-neighbor separation r0 and effective depth of pair potential ϕ0 can be obtained from calculated values of m and n from Mie potential functions and they agree very well with the results in the literature. The calculations can be well consistent with the thermophysical behaviors by comparing the two amorphous alloys. In addition, it was enhanced that the effective depth of pair potential correlated with the glass-forming ability of bulk metallic glass.
The effect of nanoparticles on the thermal conductivity of crystalline thin films at low temperatures
Authors: Katika Kamal M. , Pilon Laurent
Published: June 2008

This study is concerned with the prediction of the effective thermal conductivity of nanocomposite thin films consisting of nanoparticles randomly distributed in a solid matrix. Crystalline sodium chloride with embedded monodisperse silver nanoparticles is investigated as a case study for thin films where phonons are the main heat carriers. To the best of our knowledge, the equation for phonon radiative transfer is solved for the first time, with an exact scattering transport cross section of the nanoparticles as a function of frequency which was obtained from the literature. The one-dimensional equation for phonon radiative transfer based on the isotropic scaling approximation is solved on a spectral basis using the discrete ordinates method to predict the temperature profile and the heat flux across the nanocomposite thin films. The thermal conductivity is retrieved at temperatures where the effects of Umklapp and normal processes can be neglected and scattering by the particles on phonon transport dominates. The method of solution and closure laws were validated with experimental data of thermal conductivity for bulk samples at 2.53, 5.94, and 10.56 K. The effects of the film thickness (1 μm to 2.5 cm), nanoparticle diameter (5 to 100 nm) and volume fraction (0.0001 to 0.2) on the thermal conductivity of the nanocomposite thin film are investigated. The results indicate that the thermal conductivity decreases with decreasing particle radius as well as with increasing particle concentration. Finally, a dimensional analysis revealed a power-law relationship between the dimensionless thermal conductivity and a dimensionless length of the order of the acoustic thickness of the medium. These results can be used to design nanocomposite thin films for various low-temperature thermal applications by choosing optimal nanoparticle radius and volume fraction, and film thickness.
The effect of a neighboring metal layer on the high-frequency characteristics of a thin magnetic stripe
Authors: Vroubel Marina , Rejaei Behzad
Published: June 2008

The spin-wave spectrum of a ferromagnetic stripe placed above a metallic layer with finite conductivity is studied by using the magnetostatic Green’s function formalism. It is shown that the frequency and linewidth of the resonances are uniquely determined by complex, mode-dependent demagnetization factors. The formalism developed is used to analyze the resonance characteristics of the magnetic stripe as a function of its width and separation from the metallic layer.
A multifrequency high-field pulsed electron paramagnetic resonance/electron-nuclear double resonance spectrometer
Authors: Morley Gavin W. , Brunel Louis-Claude , van Tol Johan
Published: June 2008

We describe a pulsed electron paramagnetic resonance spectrometer operating at several frequencies in the range of 110–336GHz. The microwave source at all frequencies consists of a multiplier chain starting from a solid state synthesizer in the 12–15GHz range. A fast p-i-n-switch at the base frequency creates the pulses. At all frequencies a Fabry–Pérot resonator is employed and the π∕2 pulse length ranges from ∼100ns at 110GHzto∼600ns at 334GHz. Measurements of a single crystal containing dilute Mn2+ impurities at 12T illustrate the effects of large electron spin polarizations. The capabilities also allow for pulsed electron-nuclear double resonance (ENDOR) experiments as demonstrated by Mims ENDOR of K39 nuclei in Cr:K3NbO8.
Construction and development of a time-resolved x-ray magnetic circular dichroism–photoelectron emission microscopy system using femtosecond laser pulses at BL25SU SPring-8
Authors: Fukumoto Keiki , Matsushita Tomohiro , Osawa Hitoshi , Nakamura Tetsuya , Muro Takayuki , Arai Kuniaki , Kimura Takashi , Otani Yoshichika , Kinoshita Toyohiko
Published: June 2008

A femtosecond pulsed laser system has been installed at the BL25SU soft x-ray beamline at SPring-8 for time-resolved pump-probe experiments with synchronization of the laser pulses to the circularly polarized x-ray pulses. There are four different apparatuses situated at the beamline; for photoemission spectroscopy, two-dimensional display photoelectron diffraction, x-ray magnetic circular dichroism (XMCD) with electromagnetic coils, and photoelectron emission microscopy (PEEM). All four can be used for time-resolved experiments, and preliminary investigations have been carried out using the PEEM apparatus to observe magnetization dynamics in combination with XMCD. In this article, we describe the details of the stroboscopic pump-probe XMCD-PEEM experiment, and present preliminary data. The repetition rate of the laser pulses is set using a pulse selector to match the single bunches of SPring-8’s hybrid filling pattern, which consists of several single bunches and a continuous bunch train. Electrons ejected during the bunch train, which do not provide time-resolved signal, are eliminated by periodically reducing the channel plate voltage using a custom-built power supply. The pulsed laser is used to create 300ps long magnetic field pulses, which cause magnetic excitations in micron-sized magnetic elements which contain magnetic vortex structures. The observed frequency of the motion is consistent with previously reported observations and simulations.
Nucleation kinetics of Ru on silicon oxide and silicon nitride surfaces deposited by atomic layer deposition
Authors: Yim Sung-Soo , Lee Do-Joong , Kim Ki-Su , Kim Soo-Hyun , Yoon Tae-Sik , Kim Ki-Bum
Published: June 2008

The nucleation behavior of Ru deposited by atomic layer deposition (ALD) using bis(ethylcyclopentadienyl)ruthenium precursor and O2 reactant is investigated as a function of the number of ALD cycles. The substrates are thermally grown SiO2, NH3 plasma-treated SiO2, and chemical vapor deposited SiNx. The nucleation of Ru strongly depends on the substrate and is much enhanced on the nitride substrates. Transmission electron microscopy analysis reveals that the maximum density of the nuclei is 5.7×1010cm−2 on the SiO2 surface at 500 ALD cycles, 1.2×1012cm−2 on SiNx at 160 ALD cycles, and 2.3×1012cm−2 on NH3 plasma-nitrided SiO2 at 110 ALD cycles. Although the kinetics of Ru nucleation is different on the various substrates, the overall nucleation process in each case consists of an initial slow nucleation stage and a subsequent fast nucleation stage before the coalescence of the nuclei occurs. Considering the adsorption of Ru precursor on the substrate and the surface diffusion of deposited Ru during an ALD cycle, we suggest a model for describing the nucleation of an ALD film at the initial stage with a low surface coverage based on the atomistic nucleation theory of a thin film. The proposed model shows that the density of the nuclei is proportional to the (i+2)th power of the number of ALD cycles and (i+1)th power of the density of atoms deposited per ALD cycle, where i is the critical nuclei size. By applying the proposed model to the experimental results, the critical nuclei size i is found to be 1. The amounts of Ru atoms deposited per ALD cycle on the NH3 plasma-nitrided SiO2 and SiNx are 70 and 24 times larger, respectively, than that on the SiO2 surface. This model quantitatively describes the nucleation kinetics in the ALD system and is verified by a comparison with the experimental results of Ru on various substrates.
Transmissive x-ray beam position monitors with submicron position- and submillisecond time resolution
Authors: Fuchs Martin R. , Holldack Karsten , Bullough Mark , Walsh Susanne , Wilburn Colin , Erko Alexei , Schäfers Franz , Mueller Uwe
Published: June 2008

We present the development of fast transmissive center-of-mass x-ray beam position monitors with a large active area, based on a thinned position sensitive detector in both a duo- and a tetra-lateral variant. The detectors were tested at BESSY beamlines BL14.1, KMC-1, and KMC-2 and yielded signal currents of up to 3μA∕100mA ring current at 10keV photon energy using the monochromatic focused beam of BL14.1. The active area sizes were 1×1 and 3×3mm2 for the duo-lateral and 5×5mm2 for the tetra-lateral devices, with the duo-lateral detectors currently being available in sizes from 1×1to10×10mm2 and thicknesses between 5 and 10μm. The presented detectors’ thicknesses were measured to be 5 and 8μm with a corresponding transmission of up to 93% at 10keV and 15% at 2.5keV. Up to a detection bandwidth of 10kHz, the monitors provide submicron position resolution. For lower detection bandwidths, the signal-to-noise reaches values of up to 6×104 at 10Hz, corresponding to a position resolution of better than 50nm for both detector sizes. As it stands, this monitor design approach promises to be a generic solution for automation of state-of-the-art crystal monochromator beamlines.
Spin injection from Co2MnGa into an InGaAs quantum well
Authors: Hickey M. C. , Damsgaard C. D. , Holmes S. N. , Farrer I. , Jones G. A. C. , Ritchie D. A. , Jacobsen C. S. , Hansen J. B. , Pepper M.
Published: June 2008

We have demonstrated spin injection from a full Heusler alloy Co2MnGa thin film into a (100) InGaAs quantum well in a semiconductor light-emitting diode structure at a temperature of 5K. The detection is performed in the oblique Hanle geometry, allowing quantification of the effective spin lifetime and spin detection efficiency (22±4%). This work builds on existing studies on off-stoichiometric Heusler injectors into similar light-emitting-diode structures. The role of injector stoichiometry can therefore be quantitatively assessed with the result that the spin injection efficiency increases by a factor of approximately 2 as compared with an off-stoichiometric Co2.4Mn1.6Ga injector.
Narrow-band, tunable infrared emission from arrays of microstrip patches
Authors: Puscasu Irina , Schaich William L.
Published: June 2008

We demonstrate through a combination of theory and experiment that an array of microstrip patches leads to a surface with sharp and tunable emission bands. The physical mechanisms and locations for various emission peaks are described via both analytical theory and numerical simulations. These predictions agree well with our experimental data, taken on systems designed to emit strongly in the infrared. The main peak, which arises from plasmons trapped under a patch, can be well separated from other spectral structures, narrow in wavelength, but broad in angular distribution.
Barocaloric and magnetocaloric effects in La(Fe0.89Si0.11)13
Authors: de Medeiros L. G. , de Oliveira N. A. , Troper A.
Published: June 2008

In this paper we calculate the barocaloric and the magnetocaloric effects under applied pressure in the compound La(Fe0.89Si0.11)13. We use a microscopical model in the framework of the band theory of magnetism, where the Coulomb interaction between itinerant electrons is treated in the mean field approach. Our theoretical calculations point out that both the barocaloric potentials [ΔS]B and [ΔTad]B at fixed magnetic field, and the magnetocaloric potentials ΔS and ΔTad under simultaneous variation of magnetic field and pressure, reach large values in a wide range of temperatures.
Micromagnetic study of domain wall dynamics in bit-patterned nanodots
Authors: E Chunsheng , Rantschler James O. , Khizroev Sakhrat , Litvinov Dmitri
Published: June 2008

Domain wall dynamics in magnetic nanodots is critical to the understanding of the magnetization reversal mechanisms in bit-patterned arrays, the issues of writeablility, data rate maximization, and bit stability. In this work, micromagnetic simulations were carried out to investigate the dynamics of domain walls in disk-shaped nanostructures with large built-in perpendicular anisotropy. Due to the strong demagnetizing effect, the domain wall motion falls into the supercritical regime. A 90° phase shift of the wall velocity is developed due to the finite thicknesses. The mean value of the wall velocity increases as the domain wall propagates away from the center. This induced asymmetry causes the frequency of the wall oscillations to be halved. At large diameters, the wall acceleration deceases and the periodicity is lost. The in-plane magnetization configuration shows that multiple spin wave modes are present. The absence of the coherency in the magnetization orientations causes phase canceling. The out-of-phase motion of neighboring segments reduces the wall acceleration.
In
Al
Ga
As
∕
In
P
light-emitting transistors operating near 1.55μm
Authors: Huang Yong , Zhang Xue-Bing , Ryou Jae-Hyun , Dupuis Russell D. , Dixon Forest , Holonyak Nick , Feng Milton
Published: June 2008

Light-emitting transistors (LETs) operating at around 1.55μm were investigated using InP∕InAlGaAs heterostructures grown by metal organic chemical vapor deposition. By incorporating InGaAs quantum wells (QWs) in the base region of the N-InP∕p-InAlGaAs∕N-InAlAs heterojunction bipolar transistors, LET structures were achieved with a current gain of 45 and light emission at a wavelength of 1.65μm. The light output was found to be dependent on the base current. The larger the number of QWs incorporated in the base of the LETs, the larger the light output, with correspondingly reduced current gain. Secondary ion mass spectroscopy shows that the p-type dopant, zinc (Zn), which is commonly used in the growth of InAlGaAs, diffuses into the emitter and the base active QW region, leading to compromised electrical performance and light output intensity. Increasing the Zn doping level in the barrier layers of the QW structure causes the photoluminescence efficiency to decrease rapidly. Consequently, an alternative low-diffusivity dopant, carbon (C), was studied and a LET with a C-doped base was grown and fabricated. The highest light output was demonstrated for the C-doped LETs owing to the improved quality of the active layer.
Effects of Mg incorporation on the optical properties of ZnO prepared by the sol-gel method
Authors: Lin Yow-Jon , Wu Ping-Hsun , Tsai Chia-Lung , Liu Chia-Jyi , Lin Zhi-Ru , Chang Hsing-Cheng , Lee Ching-Ting
Published: June 2008

ZnO films with and without Mg doping (Zn1−xMgxO) were deposited on substrates by the sol-gel technique. X-ray photoelectron spectroscopy, x-ray diffraction, photoluminescence, and conductivity measurements were used to characterize the Zn1−xMgxO semiconductors. It is worth noting that the intensity of the band-edge luminescence (BEL) of the Zn0.973Mg0.027O film at room temperature was nearly six times the ZnO film. The enhanced BEL intensity has been attributed to the suppression of capacitance variation related to trapping/detrapping of charges, a decrease in the number of nonradiative recombination defects, and an increase in the nonradiative recombination lifetime.
Field sensing characteristics of magnetic tunnel junctions with (001) MgO tunnel barrier
Authors: Mazumdar Dipanjan , Shen Weifeng , Liu Xiaoyong , Schrag B. D. , Carter Matthew , Xiao Gang
Published: June 2008

We map the magnetic field sensitivity and low-frequency 1∕f voltage noise of high magnetoresistance MgO-based magnetic tunnel junctions in an orthogonal magnetic field arrangement. Large sensitivity values of over 1%/Oe are obtained only when a sufficiently large hard-axis bias field is applied. The low-frequency voltage noise is observed to scale with the field sensitivity. The magnetic field noise map reveals that the signal-to-noise ratios of these devices get gradually better at higher hard-axis bias fields.
Piezoresponse force microscopy of ferroelectric thin films: Frequency dependence of phase imaging
Authors: Morelli A. , Palasantzas G. , De Hosson J. Th. M.
Published: June 2008

The objective of this work is an evaluation of quantitative measurements of piezoresponse force microscopy for nanoscale characterization of ferroelectric films. To this end, we investigate how the piezoresponse phase difference ΔΦ between c domains depends on the frequency ω of the applied ac field much lower than the cantilever first resonance frequency. The main specimen under study was a 102nm thick film of Pb(Zr0.2Ti0.8)O3. For the sake of comparison, a 100nm thick PbTiO3 film was also used. From our measurements, we conclude a frequency dependent behavior ΔΦ∼ω−1, which can only be partially explained by the presence of adsorbates on the surface.
Piezoelectricity enhancement in ferroelectric ceramics due to orientation
Authors: Jayachandran K. P. , Guedes J. M. , Rodrigues H. C.
Published: June 2008

A continuum model simulation, explicitly incorporating anisotropic grain-level features, based on homogenization of materials predicts an enhancement of piezoelectricity in ferroelectric ceramics better than oriented single crystals. Incorporation of randomness in the orientation of polarization associated with the grains is demonstrated to offer great prospect in the design of ceramic ferroelectric materials such as BaTiO3.
Growth and structural properties of m-plane ZnO on MgO (001) by molecular beam epitaxy
Authors: Cagin E. , Yang J. , Wang W. , Phillips J. D. , Hong S. K. , Lee J. W. , Lee J. Y.
Published: June 2008

The growth of wurtzite ZnO on cubic MgO (001) substrates by molecular beam epitaxy is reported. ZnO epilayers exhibit the nonpolar m-plane orientation based on x-ray diffraction and transmission electron microscopy analysis. Comparative studies of ZnO grown by pulsed laser deposition on MgO (001) result in preferred growth in the polar c-plane orientation. Investigation by high resolution transmission electron microscopy confirms an abrupt ZnO∕MgO interface and monolayer spacing consistent with m-plane growth of ZnO. X-ray diffraction pole figures indicate two preferred rotational domains in-plane with a twist angle of 30°.
Increase of temperature due to Joule heating during current-induced magnetization switching of an MgO-based magnetic tunnel junction
Authors: Lee D. H. , Lim S. H.
Published: June 2008

Three-dimensional numerical calculations based on the finite element method are performed to calculate the increase of temperature caused by Joule heating during the current-induced magnetization switching of an MgO-based magnetic tunnel junction. The increase of temperature is found to be significantly large (the maximum being 145K) at critical conditions for the current-induced magnetization switching. The temperature increase also differs greatly, depending on the critical condition, requiring a correction in calculating the thermal stability parameter using the Slonczewski equation. After the correction, the thermal stability parameter increases substantially from 67 to 76.
Size-induced metal insulator transition and glassy magnetic behavior in La0.5Sr0.5CoO3 nanoparticles
Authors: Roy B. , Das S.
Published: June 2008

Structural, electrical, and magnetic properties of La0.5Sr0.5CoO3 nanoparticles prepared by sol-gel technique are investigated and the results reveal a size-induced metal insulator transition in the electrotransport behavior. The field cooled and zero field cooled magnetizations display a broad paramagnetic to ferromagnetic transition at Tc with a large magnetic irreversibility. Attempts are made to get an idea about the spin states in the nanoparticles. The observed frequency dependent shoulder in the in-phase (χ′) component and the peak in the out of phase (χ″) component of the ac susceptibility in the low temperature region indicate the glassy nature of the samples.
Are temperature effects on weight and quality of barley grains modified by resource availability?
Authors: Passarella Valeria S. , Savin Roxana , Slafer Gustavo A.
Published: June 2008

Under field conditions the occurrence of brief periods of moderately high (30–32°C) and very high temperatures (>35°C) is quite common during grain filling in small-grain cereals. These events occur under a wide range of different management and environmental conditions, such as different nitrogen supplies and source–sink ratios after flowering. The objective of the present work was to study whether the effect of a brief heat stress is modified by resource availability for the growing grains. We subjected spikes of barley 10 days after flowering to a heat treatment in factorial combination with different nitrogen availabilities and source–sink ratios during post-flowering to determine effects on grain weight and major malting quality attributes. Grain weight and screening percentage (proportion of grains <2.5 mm) were reduced by the mild heat stress. However, the magnitude of the effect was dependent on the nitrogen fertilisation and the source–sink treatments in which the heat stress was imposed. Grain protein and β-glucan percentages were increased by both nitrogen fertilisation and heat stress. Again, the magnitude of the increase was dependent upon the availability of resources. There was a trend to reduce malt extract in all treatments with respect to the control, but the reduction was only statistically significant with heat stress.
Grain yield stability of spring safflower (Carthamus tinctorius L.)
Authors: Mohammadi Reza , Pourdad Sayyed Saeid , Amri Ahmed
Published: June 2008

The additive main effect and multiplicative interaction (AMMI) model and the phenotypic stability parameters, ecovalence (W2), regression coefficient (b), coefficient of determination (R2), coefficient of variation (CV), stability variance (S2), AMMI stability value (ASV), and TOP (proportion of environments in which a genotype ranked in the top third), were used to evaluate simultaneously the yield performance and stability of 17 spring safflower genotypes and to evaluate 26 rainfed environments during 2003–05 in Iran. These parameters were designated as Type-A and Type-B for genotypes and environments, respectively. Among Type-B parameters, Spearman’s rank correlation showed that the AMMI stability value (ASVj), ecovalence (Wj2), genotypic variance (Sj2), and coefficient of variation (CVj) were significantly and positively associated (P < 0.01), indicating that one of these parameters can be used as an alternative to the others, but were significantly and negatively correlated with the genotypic selectivity (bj) parameter. The results showed that none of the Type-A statistics per se was useful for selecting high-yielding and stable genotypes. Based on these parameters, the genotypes G9, G10, and G11 combined high and stable yields while the highest yielding genotypes G1 and G17 were the most instable. Type-A and Type-B stability parameters are useful to identify genotypes with specific and large adaptations and the contrasting environments with high contribution to genotype × environment interaction.
Measurement of summer dormancy in temperate perennial pasture grasses
Authors: Norton M. R. , Lelièvre F. , Fukai S. , Volaire F.
Published: June 2008

The search to improve drought survival in temperate perennial grasses has led to a renewed interest in summer dormancy and how to quantify it. This endogenously controlled trait, found in some temperate perennial grasses, is associated with drought that normally occurs in summer. While cessation of leaf growth and senescence of herbage occurs in all grasses in response to drought, it is under summer irrigation that these same responses are observed only in summer-dormant germplasm and hence the trait can be identified in germplasm. Across the spectrum from completely summer-dormant to non-dormant, there is a range of expression. Our objective here is to highlight differences in characteristics of indices which measure summer dormancy and to identify aspects for incorporation into a superior index for use in measuring this trait.
The experimental program comprised three field trials that compared 6 cultivars and a fourth that assessed a larger group of 12 cultivars of the same three species, cocksfoot (Dactylis glomerata L.), tall fescue (Festuca arundinacea Schreb.), and phalaris (Phalaris aquatica L.). Seasonal herbage yield and foliage senescence were measured under three summer watering regimes: complete drought, mid-summer storm, and full irrigation at Mauguio, France. Different indices were calculated to compare against the approach which evaluates senescence under drought.
The key outcomes are as follows.
(1) The assessment of summer dormancy needs to be viewed as the plant response to a period of non-limiting water supply over summer. It makes little difference whether this is produced by full summer irrigation or a mid-summer simulated storm after a drought. Assessment of this trait under conditions of unbroken drought is discouraged because it can result in false scores.
(2) The determination of summer dormancy intensity under full summer irrigation is most appropriate for the intensive study of the dynamics of dormancy expression over the entire summer. A simulated mid-summer storm within a drought gives an instantaneous view of dormancy intensity at a specific observation date and may be well adapted to the requirements of plant breeding. These methods are complementary.
(3) Summer dormancy intensity can be assessed either by measuring herbage production or by a visual assessment of the level of herbage senescence.
(4) An index of summer dormancy based on comparing irrigated summer herbage yield of any cultivar with that of a high, summer-yielding, non-dormant control cultivar was able to provide a reliable score of dormancy intensity. This index functions across a range of cultivars and species of perennial grasses. Further refinement of the index is needed to identify ‘standard’ high and low summer-dormant populations.
Spontaneous conformational change and toxin binding in α7 acetylcholine receptor: Insight into channel activation and inhibition
Authors: Yi Myunggi , Tjong Harianto , Zhou Huan-Xiang
Published: June 2008

Nicotinic AChRs (nAChRs) represent a paradigm for ligand-gated ion channels. Despite intensive studies over many years, our understanding of the mechanisms of activation and inhibition for nAChRs is still incomplete. Here, we present molecular dynamics (MD) simulations of the α7 nAChR ligand-binding domain, both in apo form and in α-Cobratoxin-bound form, starting from the respective homology models built on crystal structures of the acetylcholine-binding protein. The toxin-bound form was relatively stable, and its structure was validated by calculating mutational effects on the toxin-binding affinity. However, in the apo form, one subunit spontaneously moved away from the conformation of the other four subunits. This motion resembles what has been proposed for leading to channel opening. At the top, the C loop and the adjacent β7-β8 loop swing downward and inward, whereas at the bottom, the F loop and the C terminus of β10 swing in the opposite direction. These swings appear to tilt the whole subunit clockwise. The resulting changes in solvent accessibility show strong correlation with experimental results by the substituted cysteine accessibility method upon addition of acetylcholine. Our MD simulation results suggest a mechanistic model in which the apo form, although predominantly sampling the “closed” state, can make excursions into the “open” state. The open state has high affinity for agonists, leading to channel activation, whereas the closed state upon distortion has high affinity for antagonists, leading to inhibition.
Characterization of the structure–function relationship at the ligament-to-bone interface
Authors: Moffat Kristen L. , Sun Wan-Hsuan S. , Pena Paul E. , Chahine Nadeen O. , Doty Stephen B. , Ateshian Gerard A. , Hung Clark T. , Lu Helen H.
Published: June 2008

Soft tissues such as ligaments and tendons integrate with bone through a fibrocartilaginous interface divided into noncalcified and calcified regions. This junction between distinct tissue types is frequently injured and not reestablished after surgical repair. Its regeneration is also limited by a lack of understanding of the structure–function relationship inherent at this complex interface. Therefore, focusing on the insertion site between the anterior cruciate ligament (ACL) and bone, the objectives of this study are: (
i
) to determine interface compressive mechanical properties, (
ii
) to characterize interface mineral presence and distribution, and (
iii
) to evaluate insertion site-dependent changes in mechanical properties and matrix mineral content. Interface mechanical properties were determined by coupling microcompression with optimized digital image correlation analysis, whereas mineral presence and distribution were characterized by energy dispersive x-ray analysis and backscattered scanning electron microscopy. Both region- and insertion-dependent changes in mechanical properties were found, with the calcified interface region exhibiting significantly greater compressive mechanical properties than the noncalcified region. Mineral presence was only detectable within the calcified interface and bone regions, and its distribution corresponds to region-dependent mechanical inhomogeneity. Additionally, the compressive mechanical properties of the tibial insertion were greater than those of the femoral. The interface structure–function relationship elucidated in this study provides critical insight for interface regeneration and the formation of complex tissue systems.
Abscisic acid regulation of guard-cell K
+
and anion channels in Gβ- and RGS-deficient
Arabidopsis
lines
Authors: Fan Liu-Min , Zhang Wei , Chen Jin-Gui , Taylor J. Philip , Jones Alan M. , Assmann Sarah M.
Published: June 2008

In mammals, basal currents through G protein-coupled inwardly rectifying K
+
(GIRK) channels are repressed by Gα
i/o
GDP, and the channels are activated by direct binding of free Gβγ subunits released upon stimulation of Gα
i/o
-coupled receptors. However, essentially all information on G protein regulation of GIRK electrophysiology has been gained on the basis of coexpression studies in heterologous systems. A major advantage of the model organism,
Arabidopsis thaliana
, is the ease with which knockout mutants can be obtained. We evaluated plants harboring mutations in the sole
Arabidopsis
Gα (At
GPA1
), Gβ (
AGB1
), and
Regulator of G protein Signaling
(At
RGS1
) genes for impacts on ion channel regulation. In guard cells, where K
+
fluxes are integral to cellular regulation of stomatal apertures, inhibition of inward K
+
(K
in
) currents and stomatal opening by the phytohormone abscisic acid (ABA) was equally impaired in At
gpa1
and
agb1
single mutants and the At
gpa1 agb1
double mutant. AGB1 overexpressing lines maintained a wild-type phenotype. The At
rgs1
mutation did not affect K
in
current magnitude or ABA sensitivity, but K
in
voltage-activation kinetics were altered. Thus,
Arabidopsis
cells differ from mammalian cells in that they uniquely use the Gα subunit or regulation of the heterotrimer to mediate K
in
channel modulation after ligand perception. In contrast, outwardly rectifying (K
out
) currents were unaltered in the mutants, and ABA activation of slow anion currents was conditionally disrupted in conjunction with cytosolic pH clamp. Our studies highlight unique aspects of ion channel regulation by heterotrimeric G proteins and relate these aspects to stomatal aperture control, a key determinant of plant biomass acquisition and drought tolerance.
Plectin isoform 1b mediates mitochondrion–intermediate filament network linkage and controls organelle shape
Authors: Winter Lilli , Abrahamsberg Christina , Wiche Gerhard
Published: June 2008

Plectin is a versatile intermediate filament (IF)–bound cytolinker protein with a variety of differentially spliced isoforms accounting for its multiple functions. One particular isoform, plectin 1b (P1b), remains associated with mitochondria after biochemical fractionation of fibroblasts and cells expressing exogenous P1b. Here, we determined that P1b is inserted into the outer mitochondrial membrane with the exon 1b–encoded N-terminal sequence serving as a mitochondrial targeting and anchoring signal. To study P1b-related mitochondrial functions, we generated mice that selectively lack this isoform but express all others. In primary fibroblasts and myoblasts derived from these mice, we observe a substantial elongation of mitochondrial networks, whereas other mitochondrial properties remain largely unaffected. Normal morphology of mitochondria could be restored by isoform-specific overexpression of P1b in P1b-deficient as well as plectin-null cells. We propose a model where P1b both forms a mitochondrial signaling platform and affects organelle shape and network formation by tethering mitochondria to IFs.
Cell motility through plasma membrane blebbing
Authors: Fackler Oliver T. , Grosse Robert
Published: June 2008

Plasma membrane blebs are dynamic cytoskeleton-regulated cell protrusions that have been implicated in apoptosis, cytokinesis, and cell movement. Influencing Rho–guanosine triphosphatase activities and subsequent actomyosin dynamics appears to constitute a core component for bleb formation. In this paper, we discuss recent evidence in support of a central role of nonapoptotic membrane blebbing for cell migration and cancer cell invasion as well as advances in our understanding of the underlying molecular mechanisms. Based on these studies, we propose that in a physiological context, bleb-associated cell motility reflects a cell's response to reduced substratum adhesion. The importance of blebbing as a functional protrusion is underscored by the existence of multiple molecular mechanisms that govern actin-mediated bleb retraction.
Centromere mitotic recombination in mammalian cells
Authors: Jaco Isabel , Canela Andrés , Vera Elsa , Blasco Maria A.
Published: June 2008

Centromeres are special structures of eukaryotic chromosomes that hold sister chromatid together and ensure proper chromosome segregation during cell division. Centromeres consist of repeated sequences, which have hindered the study of centromere mitotic recombination and its consequences for centromeric function. We use a chromosome orientation fluorescence in situ hybridization technique to visualize and quantify recombination events at mouse centromeres. We show that centromere mitotic recombination occurs in normal cells to a higher frequency than telomere recombination and to a much higher frequency than chromosome-arm recombination. Furthermore, we show that centromere mitotic recombination is increased in cells lacking the Dnmt3a and Dnmt3b DNA methyltransferases, suggesting that the epigenetic state of centromeric heterochromatin controls recombination events at these regions. Increased centromere recombination in Dnmt3a,3b-deficient cells is accompanied by changes in the length of centromere repeats, suggesting that prevention of illicit centromere recombination is important to maintain centromere integrity in the mouse.
Pathological integrin signaling enhances proliferation of primary lung fibroblasts from patients with idiopathic pulmonary fibrosis
Authors: Xia Hong , Diebold Deanna , Nho Richard , Perlman David , Kleidon Jill , Kahm Judy , Avdulov Svetlana , Peterson Mark , Nerva John , Bitterman Peter , Henke Craig
Published: June 2008

Idiopathic pulmonary fibrosis (IPF) is a relentlessly progressive lung disease in which fibroblasts accumulate in the alveolar wall within a type I collagen–rich matrix. Although lung fibroblasts derived from patients with IPF display durable pathological alterations in proliferative function, the molecular mechanisms differentiating IPF fibroblasts from their normal counterparts remain unknown. Polymerized type I collagen normally inhibits fibroblast proliferation, providing a physiological mechanism to limit fibroproliferation after tissue injury. We demonstrate that β1 integrin interaction with polymerized collagen inhibits normal fibroblast proliferation by suppression of the phosphoinositide 3-kinase (PI3K)–Akt–S6K1 signal pathway due to maintenance of high phosphatase activity of the tumor suppressor phosphatase and tensin homologue (PTEN). In contrast, IPF fibroblasts eluded this restraint, displaying a pathological pattern of β1 integrin signaling in response to polymerized collagen that leads to aberrant activation of the PI3K–Akt–S6K1 signal pathway caused by inappropriately low PTEN activity. Mice deficient in PTEN showed a prolonged fibroproliferative response after tissue injury, and immunohistochemical analysis of IPF lung tissue demonstrates activation of Akt in cells within fibrotic foci. These results provide direct evidence for defective negative regulation of the proliferative pathway in IPF fibroblasts and support the theory that the pathogenesis of IPF involves an intrinsic fibroblast defect.
Patterns, Models, and Predictions: Robert MacArthur's Approach to Ecology
Authors: Ishida Yoichi
Published: June 2008

Robert MacArthur's mathematical ecology is often regarded as ahistorical and has been criticized by historically oriented ecologists and philosophers for ignoring the importance of history. I clarify and defend his approach, especially his use of simple mathematical models to explain patterns in data and to generate predictions that stimulate empirical research. First I argue that it is misleading to call his approach ahistorical because it is not against historical explanation. Next I distinguish three kinds of criticism of his approach and argue that his approach is compatible with the first two of them. Finally, I argue that the third kind of criticism, advanced by Kim Sterelny and Paul Griffiths, is largely irrelevant to MacArthur's approach.
How Do Natural Selection and Random Drift Interact?
Authors: Abrams Marshall
Published: June 2008

One controversy about the existence of so called evolutionary forces such as natural selection and random genetic drift concerns the sense in which such “forces” can be said to interact. In this paper I explain how natural selection and random drift can interact. In particular, I show how population-level probabilities can be derived from individual-level probabilities, and explain the sense in which natural selection and drift are embodied in these population-level probabilities. I argue that whatever causal character the individual-level probabilities have is then shared by the population-level probabilities, and that natural selection and random drift then have that same causal character. Moreover, natural selection and drift can then be viewed as two aspects of probability distributions over frequencies in populations of organisms. My characterization of population-level probabilities is largely neutral about what interpretation of probability is required, allowing my approach to support various positions on biological probabilities, including those which give biological probabilities one or another sort of causal character.
Massive Modularity and Brain Evolution
Authors: Machery Edouard
Published: June 2008

Quartz (2002) argues that some recent findings about the evolution of the brain (Finlay and Darlington 1995) are inconsistent with evolutionary psychologists’ massive modularity hypothesis. In substance, Quartz contends that since the volume of the neocortex evolved in a concerted manner, natural selection did not act on neocortical systems independently of one another, which is a necessary condition for cognition to be massively modular. In this article, I argue that Quartz's argument fails to undermine the massive modularity hypothesis.
Prospects for a Dual Inheritance Model of Emotional Evolution
Authors: Linquist Stefan
Published: June 2008

A common objection to adaptationist accounts of human emotions is that they ignore the influence of culture. If complex emotions like guilt, shame and romantic jealousy are largely culturally determined, how could they be biological adaptations? Dual inheritance models of gene/culture coevolution provide a potential answer to this question. If complex emotions are developmentally ‘scaffolded’ by norms that are transmitted from parent to offspring with reasonably high fidelity, then these emotions can evolve to promote individual reproductive interests. This paper draws on case studies of emotional development to illustrate how complex emotions satisfy these conditions. Many of the norms and parenting strategies influencing emotional development are absorbed during the early stages of life when a child is in primary contact with its parents and before the onset of complex cognition. These conditions make it likely that emotion-governing norms are transmitted vertically and with relatively little cognitive ‘contamination’.
Are Neuroimages Like Photographs of the Brain?
Authors: Roskies Adina L.
Published: June 2008

Images come in many varieties, but for evidential purposes, photographs are privileged. Recent advances in neuroimaging provide us with a new type of image that is used as scientific evidence. Brain images are epistemically compelling, in part because they are liable to be viewed as akin to photographs of brain activity. Here I consider features of photography that underlie the evidential status we accord it, and argue that neuroimaging diverges from photography in ways that seriously undermine the photographic analogy. While neuroimaging remains an important source of scientific evidence, proper interpretation of brain images is much more complex than it appears.
Bird Brains and Aggro Apes: Questioning the Use of Animals in the Affect Program Theory of Emotion
Authors: Stieg Chuck
Published: June 2008

It is a common assumption amongst theorists that the phenomenon of animal emotion supports the affect program theory of emotion. I argue that this assumption is mistaken by exploring two cases of animal emotion from studies in ethology: aggression in chimpanzees and fear in piping plovers. While the affect program theory fails to account for the cognitive complexity involved in each case, I do not argue for a cognitive theory of emotion. Instead, I suggest that paying attention to animal emotions helps the emotion theorist avoid the dichotomy between the extreme versions of the affect program theory and cognitive theories.
Reduction and Emergence in Chemistry—Two Recent Approaches
Authors: Scerri Eric
Published: June 2008

Two articles on the reduction of chemistry are examined. The first, by McLaughlin (1992), claims that chemistry is reduced to physics and that there is no evidence for emergence or for downward causation between the chemical and the physical level. In a more recent article, Le Poidevin (2005) maintains that his combinatorial approach provides grounding for the ontological reduction of chemistry, which also circumvents some limitations in the physicalist program.
Newton's Methodology and Mercury's Perihelion Before and After Einstein
Authors: Harper William
Published: June 2008

Newton's methodology is significantly richer than the hypothetico-deductive model. It is informed by a richer ideal of empirical success that requires not just accurate prediction but also accurate measurement of parameters by the predicted phenomena. It accepts theory-mediated measurements and theoretical propositions as guides to research. All of these enrichments are exemplified in the classical response to Mercury's perihelion problem. Contrary to Kuhn, Newton's method endorses the radical transition from his theory to Einstein's. The richer themes of Newton's method are strikingly realized in a challenge to general relativity from a new problem posed by Mercury's perihelion.
Perceiving Causation via Videomicroscopy
Authors: Delehanty Megan
Published: June 2008

Although scientific images have begun to receive significant attention from philosophers, one type of image has thus far been ignored: moving images. As techniques such as live cell imaging and videomicroscopy are becoming increasingly important in many areas of biology, however, this oversight needs to be corrected. Biologists often claim that there are relevant differences between video and static images. Most interesting is the idea that video images allow us to see causal relationships. By identifying the conditions that would be required for this to be true and showing that they are not satisfied at the micro level, I will show that videomicroscopy does not provide us with special access to causal information.
Möbius invariant metrics bilipschitz equivalent to the hyperbolic metric
Authors: Herron David , Ma William , Minda David
Published: June 2008

We study three Möbius invariant metrics, and three affine invariant analogs, all of which are bilipschitz equivalent to the Poincaré hyperbolic metric. We exhibit numerous illustrative examples.