bluuebunny/crossref_metadata_2025 huggingface dataset:
Trimethyltin chloride induced chloride secretion across rat distal colon
Authors: Yu Haijie , Chen Siliang , Yang Zihuan , Pan Ao , Zhang Geng , Shan Jiajie , Tang Xiaojiang , Zhou Wenliang
Published: September 2009

TMT (trimethyltin chloride), an organotin, is ubiquitous in the environment. The consumption of contaminated food may cause exposure of the human diet to this toxic compound. The present study was to investigate the effects of TMT on the regulation of ion transport across the rat distal colon. The rat colonic mucosa was mounted in Ussing chambers. The effects of TMT were assessed using the Isc (short‐circuit current). Both apical and basolateral TMT induced, dose‐dependently, an increase in Isc, which was due to a stimulation of Cl− secretion as measured using ion substitution experiments and pharmacological manoeuvres. The secretion was also inhibited by several K+ channel blockers administrated at the basolateral side. When the apical side was permeabilized by nystatin, the TMT‐induced K+ conductance was effectively blocked by tetrapentylammonium, a Ca2+‐sensitive K+ channel blocker. The response of TMT was sensitive to the basolateral Ca2+ and the intracellular Ca2+ store, which could be disclosed by applying the inhibitors of ryanodine receptors and inositol 1,4,5‐trisphosphate receptors. In conclusion, TMT led to Cl− secretion, which was essentially regulated by basolateral Ca2+‐sensitive K+ channels. These results suggest the importance of K+ channels in the toxicity hazard of TMT.
Adenosine induces G2/M cell‐cycle arrest by inhibiting cell mitosis progression
Authors: Jia Kun‐Zhi , Tang Bo , Yu Lu , Cheng Wei , Zhang Rong , Zhang Jian‐Fa , Hua Zi‐Chun
Published: September 2009

Cellular adenosine accumulates under stress conditions. Few papers on adenosine are concerned with its function in the cell cycle. The cell cycle is the essential mechanism by which all living things reproduce and the target machinery when cells encounter stresses, so it is necessary to examine the relationship between adenosine and the cell cycle. In the present study, adenosine was found to induce G2/M cell‐cycle arrest. Furthermore, adenosine was found to modulate the expression of some important proteins in the cell cycle, such as cyclin B and p21, and to inhibit the transition of metaphase to anaphase in mitosis.
Localization and socialization: Experimental insights into the functional architecture of IP3 receptors
Authors: Diambra Luis , Marchant Jonathan S.
Published: September 2009

Inositol 1,4,5-trisphosphate (IP3)-evoked Ca2+ signals display great spatiotemporal malleability. This malleability depends on diversity in both the cellular organization and in situ functionality of IP3 receptors (IP3Rs) that regulate Ca2+ release from the endoplasmic reticulum (ER). Recent experimental data imply that these considerations are not independent, such that—as with other ion channels—the local organization of IP3Rs impacts their functionality, and reciprocally IP3R activity impacts their organization within native ER membranes. Here, we (i) review experimental data that lead to our understanding of the “functional architecture” of IP3Rs within the ER, (ii) propose an updated terminology to span the organizational hierarchy of IP3Rs observed in intact cells, and (iii) speculate on the physiological significance of IP3R socialization in Ca2+ dynamics, and consequently the emerging need for modeling studies to move beyond gridded, planar, and static simulations of IP3R clustering even over short experimental timescales.
What can we learn from the irregularity of Ca2+ oscillations?
Authors: Dupont Geneviève , Combettes Laurent
Published: September 2009

In most cells, Ca2+ increases in response to external stimulation are organized in the form of oscillations and waves that sometimes propagate from one cell to another. Numerous experimental and theoretical studies reveal that this spatiotemporal organization contains a non-negligible level of stochasticity. In this study, we extend the previous work based on a statistical analysis of experimental Ca2+ traces in isolated, hormone-stimulated hepatocytes and on stochastic simulations of Ca2+ oscillations based on the Gillespie’s algorithm. Comparison of the coefficients of variation in the periods of experimental and simulated Ca2+ spikes provides information about the clustering and the specific subtypes of the Ca2+ channels. In hepatocytes coupled by gap junctions, the global perfusion with a hormone leads to successive Ca2+ responses, giving the appearance of an intercellular wave. Statistical analysis of experimental Ca2+ oscillations in coupled hepatocytes confirms that this coordinated Ca2+ spiking corresponds to a phase wave but suggests the existence of an additional coupling mechanism.
Inositol trisphosphate receptor and ion channel models based on single-channel data
Authors: Gin Elan , Wagner Larry E. , Yule David I. , Sneyd James
Published: September 2009

The inositol trisphosphate receptor (IPR) plays an important role in controlling the dynamics of intracellular Ca2+. Single-channel patch-clamp recordings are a typical way to study these receptors as well as other ion channels. Methods for analyzing and using this type of data have been developed to fit Markov models of the receptor. The usual method of parameter fitting is based on maximum-likelihood techniques. However, Bayesian inference and Markov chain Monte Carlo techniques are becoming more popular. We describe the application of the Bayesian methods to real experimental single-channel data in three ion channels: the ryanodine receptor, the K+ channel, and the IPR. One of the main aims of all three studies was that of model selection with different approaches taken. We also discuss the modeling implications for single-channel data that display different levels of channel activity within one recording.
A model-based method for estimating Ca2+ release fluxes from linescan images in Xenopus oocytes
Authors: Baran Irina , Popescu Anca
Published: September 2009

We propose a model-based method of interpreting linescan images observed in Xenopus oocytes with the use of Oregon Green-1 as a fluorescent dye. We use a detailed modeling formalism based on numerical simulations that incorporate physical barriers for local diffusion, and, by assuming a Gaussian distribution of release durations, we derive the distributions of release Ca2+ amounts and currents, fluorescence amplitudes, and puff widths. We analyze a wide set of available data collected from 857 and 281 events observed in the animal and the vegetal hemispheres of the oocyte, respectively. A relatively small fraction of events appear to involve coupling of two or three adjacent clusters of Ca2+ releasing channels. In the animal hemisphere, the distribution of release currents with a mean of 1.4 pA presents a maximum at 1.0 pA and a rather long tail extending up to 5 pA. The overall distribution of liberated Ca2+ amounts exhibits a dominant peak at 120 fC, a smaller peak at 375 fC, and an average of 166 fC. Ca2+ amounts and release fluxes in the vegetal hemisphere appear to be 3.6 and 1.6 times smaller than in the animal hemisphere, respectively. Predicted diameters of elemental release sites are ∼1.0 μm in the animal and ∼0.5 μm in the vegetal hemisphere, but the side-to-side separation between adjacent sites appears to be identical (∼0.4 μm). By fitting the model to individual puffs we can estimate the quantity of liberated calcium, the release current, the orientation of the scan line, and the dimension of the corresponding release site.
Experimental evidence of oxidant-diffusion-limited oxidation of SiGe alloys
Authors: Zhang Yong , Li Cheng , Cai Kunhuang , Chen Yanghua , Chen Songyan , Lai Hongkai , Kang Junyong
Published: September 2009

Rate-limiting step, as well as self-limited oxidation of SiGe alloys is so far under controversy. Contrasting to the monoparabolic growth mode for oxidation of Si, a parabolic growth mode and self-limited oxidation of SiGe alloys at different temperature are clearly observed depending on the oxidation time. With modified Deal–Grove model, we extract the parabolic rate constants related to the oxygen diffusion at different temperature and the activation energy of oxygen diffusivity finding that oxygen diffusion is still the rate-limiting step. We attribute this oxidation behavior to the strain effects associated with the volume change in converting Si/SiGe to SiO2/mixed oxide at different oxidation stages.
Correlation between the spectroscopic and structural properties with the occupation of Eu3+ sites in powdered Eu3+-doped LiTaO3 prepared by the Pechini method
Authors: Gasparotto G. , Cebim M. A. , Goes M. S. , Lima S. A. M. , Davolos M. R. , Varela J. A. , Paiva-Santos C. O. , Zaghete M. A.
Published: September 2009

In this work we studied the structural and optical properties of lithium tantalate (LiTaO3) powders doped with Eu3+ ions. We have examined the different sites occupied by the rare earth ion through the correlation of the DRX data analyzed with the Rietveld method and some spectroscopic parameters derived from the Eu3+ luminescence. A direct relation was established between the lattice parameters and the “occupation fraction” of Eu3+ in each LiTaO3 site. The occupation fraction was set as the relative population of Eu3+ ions for each site obtained by means of the intensity, baricenter, and the spontaneous emission coefficients of the D05→F07 transitions. We concluded that the unit cell parameter a presents the same behavior of the Eu3+ occupation fraction in Ta5+ sites as a function of the Eu3+ content in LiTaO3. The same was observed for the variation in Eu3+ occupation fraction in the Li+ site and the unit cell parameter c with the Eu3+ content.
Spatiotemporal characteristics of calcium dynamics in astrocytes
Authors: Kang Minchul , Othmer Hans G.
Published: September 2009

Although Cai2+ waves in networks of astrocytes in vivo are well documented, propagation in vivo is much more complex than in culture, and there is no consensus concerning the dominant roles of intercellular and extracellular messengers [inositol 1,4,5–trisphosphate (IP3) and adenosine-5′-triphosphate (ATP)] that mediate Cai2+ waves. Moreover, to date only simplified models that take very little account of the geometrical struture of the networks have been studied. Our aim in this paper is to develop a mathematical model based on realistic cellular morphology and network connectivity, and a computational framework for simulating the model, in order to address these issues. In the model, Cai2+ wave propagation through a network of astrocytes is driven by IP3 diffusion between cells and ATP transport in the extracellular space. Numerical simulations of the model show that different kinetic and geometric assumptions give rise to differences in Cai2+ wave propagation patterns, as characterized by the velocity, propagation distance, time delay in propagation from one cell to another, and the evolution of Ca2+ response patterns. The temporal Cai2+ response patterns in cells are different from one cell to another, and the Cai2+ response patterns evolve from one type to another as a Cai2+ wave propagates. In addition, the spatial patterns of Cai2+ wave propagation depend on whether IP3, ATP, or both are mediating messengers. Finally, two different geometries that reflect the in vivo and in vitro configuration of astrocytic networks also yield distinct intracellular and extracellular kinetic patterns. The simulation results as well as the linear stability analysis of the model lead to the conclusion that Cai2+ waves in astrocyte networks are probably mediated by both intercellular IP3 transport and nonregenerative (only the glutamate-stimulated cell releases ATP) or partially regenerative extracellular ATP signaling.
Spatiotemporal intracellular calcium dynamics during cardiac alternans
Authors: Restrepo Juan G. , Karma Alain
Published: September 2009

Cellular calcium transient alternans are beat-to-beat alternations in the peak cytosolic calcium concentration exhibited by cardiac cells during rapid electrical stimulation or under pathological conditions. Calcium transient alternans promote action potential duration alternans, which have been linked to the onset of life-threatening ventricular arrhythmias. Here we use a recently developed physiologically detailed mathematical model of ventricular myocytes to investigate both stochastic and deterministic aspects of intracellular calcium dynamics during alternans. The model combines a spatially distributed description of intracellular calcium cycling, where a large number of calcium release units are spatially distributed throughout the cell, with a full set of ionic membrane currents. The results demonstrate that ion channel stochasticity at the level of single calcium release units can influence the whole-cell alternans dynamics by causing phase reversals over many beats during fixed frequency pacing close to the alternans bifurcation. They also demonstrate the existence of a wide range of dynamical states. Depending on the sign and magnitude of calcium-voltage coupling, calcium alternans can be spatially synchronized or desynchronized, in or out of phase with action potential duration alternans, and the node separating out-of-phase regions of calcium alternans can be expelled from or trapped inside the cell. This range of states is found to be larger than previously anticipated by including a robust global attractor where calcium alternans can be spatially synchronized but out of phase with action potential duration alternans. The results are explained by a combined theoretical analysis of alternans stability and node motion using general iterative maps of the beat-to-beat dynamics and amplitude equations.
Size analysis of carboxydextran coated superparamagnetic iron oxide particles used as contrast agents of magnetic resonance imaging
Authors: Chen D.-X. , Sun N. , Gu H.-C.
Published: September 2009

Superparamagnetic iron oxide particles in commercial products Resovist and SH U555C, used as magnetic resonance imaging contrast agents, are polydispersed and covered with a thick organic coating so that the average particle sizes were reported between 3 and 62nm with different definitions. It is unclear which size determines the transverse relaxation rate 1∕T2 of water suspensions of such particles. Comparing the measured 1∕T2 and average sizes of different definitions determined from magnetization curve, transmission electron microscopy image, x-ray diffraction, and dynamic light scattering, it is found that the 1∕T2 behavior is basically determined by the diameter of bare single-crystal magnetic particles having the particle-volume-weighted average volume (about 14 or 9nm for Resovist or SH U555C) and is slightly influenced by their thick organic coating. This is explained by the low partial density of the coating substance and the overwhelming water occupation adjacent to magnetic particles.
Synthesis and microwave electromagnetic properties of CoFe alloy nanoflakes prepared with hydrogen-thermal reduction method
Authors: Gong Y. X. , Zhen L. , Jiang J. T. , Xu C. Y. , Shao W. Z.
Published: September 2009

CoFe alloy nanoflakes (NFs) with diameter and thickness on nanoscale were prepared by hydrogen-thermal reduction in CoFe2O4 flakes at 400 °C for 60 min. The effective complex permittivity and permeability of CoFe alloy NFs/paraffin composites were measured and compared with that of CoFe alloy nanoparticles (NPs)/paraffin composites. Due to the two-dimensional shape character, the real part of permittivity and permeability of CoFe alloy NFs was rather higher than that of CoFe alloy NPs. Electromagnetic wave absorbing (EMA) performance of both CoFe alloy NFs and NPs was evaluated by using transmission line theory. The effective EMA band position of the coating with CoFe alloy NFs as fillers was found to locate in the range of 2–4 GHz, while the effective EMA band position of the coating containing CoFe alloy NPs as fillers was located in the range 8–18 GHz. A maximum reflection loss (RLmax) of −57.8 dB was achieved in a coating containing CoFe alloy NFs as fillers, which is much higher than the −16.6 dB of coatings with CoFe alloy NPs.
BN/ZnO heterojunction diodes with apparently giant ideality factors
Authors: Brötzmann M. , Vetter U. , Hofsäss H.
Published: September 2009

Until now, a common feature of many wide band gap heterojunction diodes is an unexplained large ideality factor n>2. In this context we investigate the diode characteristics of heterojunction diodes consisting of a crystalline semiconductor material such as ZnO covered with a thin semiconducting film of amorphous or disordered material. As thin disordered film we use sp2-bonded turbostratic boron nitride. These heterojunctions exhibit a pronounced rectifying behavior, low saturation current, and low parasitic currents. Moreover, we observe an apparently giant ideality factor reaching values of n>100. As a consequence, the turn-on voltage is around 5–10 V and the I-V curves can be measured for bias voltages between ±80 V without reaching saturation or electrical breakdown. We present a quantitative model for the unusual diode characteristics of these metal-amorphous semiconductor-semiconductor diodes. We demonstrate that the I-V characteristics of the heterojunctions are well described by a serial arrangement of an ideal Schottky diode, a Frenkel–Poole type resistance, and an Ohmic contact resistance, emulating a p-n- or Schottky diode characteristic with giant ideality factor. We propose that heterojunctions exhibiting apparently large ideality factors n⪢2 may possess an interfacial disordered or amorphous layer with Frenkel–Poole conduction properties.
Modeling of the polyethylene and poly(L-lactide) triblock copolymer: A dissipative particle dynamics study
Authors: Wang Yao-Chun , Lee Wen-Jay , Ju Shin-Pon
Published: September 2009

Dissipative particle dynamics (DPD), a mesoscopic simulation approach, has been used to investigate the effect of the arrangement of the microstructure and the effect of the volume fraction on the structural properties of the immiscible polyethylene (PE)/poly(L-lactide) (PLLA) polymer in the triblock copolymer system. In this work, the interaction parameter in DPD simulation, related to the Flory–Huggins interaction parameter χ, is estimated by the calculation of mixing energy for each pair of components in molecular dynamics simulation. The immiscibility property of PE and PLLA polymers induces phase separation and exhibits different architectures at different volume fractions. In order to obtain the structural property, the radius of gyration and the end-to-end distance are used to observe the detailed arrangement of the triblock copolymer. The results show first that the relative volume fractions of PE and PLLA directly affect the bridge and loop fraction, and, second, that whether or not the arrangement is symmetrical or asymmetrical affects the equilibrium structure in the triblock copolymer system. Moreover, as the chain length of the component chains within the PE-PLLA-PE triblock copolymer increase, those component chains become softer; therefore, this directly affects the bridge and loop fraction.
Excited states of methylene from quantum Monte Carlo
Authors: Zimmerman Paul M. , Toulouse Julien , Zhang Zhiyong , Musgrave Charles B. , Umrigar C. J.
Published: September 2009

The ground and lowest three adiabatic excited states of methylene are computed using the variational Monte Carlo and diffusion Monte Carlo (DMC) methods using progressively larger Jastrow–Slater multideterminant complete active space (CAS) wave functions. The highest of these states has the same symmetry, A11, as the first excited state. The DMC excitation energies obtained using any of the CAS wave functions are in excellent agreement with experiment, but single-determinant wave functions do not yield accurate DMC energies of the states of A11 symmetry, indicating that it is important to include in the wave function Slater determinants that describe static (strong) correlation. Excitation energies obtained using recently proposed pseudopotentials [Burkatzki et al., J. Chem. Phys. 126, 234105 (2007)] differ from the all-electron excitation energies by at most 0.04 eV.
Morphology, magnetic and dynamic properties of artificial structures assembled by acoustic vibrations
Authors: Paul K. B. , Malkinski L.
Published: September 2009

Cobalt micromagnetic particles with an average size of ≈1.6 μm and varying total mass of the powder were assembled on patterned media with perpendicular magnetization by acoustic vibrations onto designed shapes reflecting the primary material. The replicas were studied with scanning electron microscopy, vibrating sample magnetometry, and ferromagnetic resonance spectroscopy. Their properties were significantly influenced by the shape anisotropy induced through the parent molds. A tendency in the development of the physical characteristics of the replicas was observed as their geometrical parameters changed.
Spectroscopic investigation of the Ã A1″-X̃ A1′ electronic transition of HSiNCO
Authors: Dover Matthew R. , Evans Corey J. , Western Colin M.
Published: September 2009

The first spectroscopic observation of the previously unknown species HSiNCO has been reported. HSiNCO was generated by the fragmentation of trimethylsilylisocyanate with a high-voltage discharge source. The 000 band of the Ã A1″-X̃ A1′ transition has been recorded with full rotational resolution using laser-induced fluorescence spectroscopy and ground and excited state rotational and centrifugal distortion constants determined. Ten additional vibrational bands belonging to HSiNCO have also been observed in the laser-induced fluorescence spectrum and have been assigned based on predicted anharmonic vibrational frequencies. Due to the large change in geometry upon excitation, a number of axis-rotation peaks have been observed in the 000 band and the axis-rotation angle (θT) has been estimated to be 0.6°±0.2°. Dispersed fluorescence spectroscopy has been carried out and ν8 (the N–C–O out-of-plane bending mode) and a number of overtones of ν4 (the Si–H wagging mode) have been observed in the ground electronic state.
Electric field enhancement of electron emission rates from Z1/2 centers in 4H-SiC
Authors: Evwaraye A. O. , Smith S. R. , Mitchel W. C. , Farlow G. C.
Published: September 2009

Z 1 / 2 defect centers were produced by irradiating 4H-SiC bulk samples with 1 MeV electrons at room temperature. The emission rate dependence on the electric field in the depletion region was measured using deep level transient spectroscopy and double-correlation deep level transient spectroscopy. It is found that the Z1/2 defect level shows a strong electric field dependence with activation energy decreasing from Ec−0.72 eV at zero field to Ec−0.47 eV at 6.91×105 V/cm. The phonon assisted tunneling model of Karpus and Perel [Sov. Phys. JETP 64, 1376 (1986)] completely describes the experimental data. This model describes the dependence of the emission rate on electric field F as en(F)=eno exp(F2/Fc2), where Fc is the characteristic field that depends on the phonon assisted tunneling time τ2. The values of Fc and τ2 were determined and the analysis of the data leads to the suggestion that Z1/2 may be a substitutional point defect.
Device modeling for split-off band detectors
Authors: Matsik S. G. , Jayaweera P. V. V. , Perera A. G. U. , Choi K. K. , Wijewarnasuriya P.
Published: September 2009

An approach to develop room temperature detectors is to use transitions between the light/heavy hole bands and the split-off hole band to produce enhanced response at high temperature. Results are presented on a theoretical model to predict the response in these split-off detectors. The model calculates the dark and illuminated currents from the photoabsorption, carrier escape, and transport, explaining the experimental response. The variation in dark current, responsivity, and D∗ with the detector parameters is presented.
Efficient black silicon solar cell with a density-graded nanoporous surface: Optical properties, performance limitations, and design rules
Authors: Yuan Hao-Chih , Yost Vernon E. , Page Matthew R. , Stradins Paul , Meier Daniel L. , Branz Howard M.
Published: September 2009

We study optical effects and factors limiting performance of our confirmed 16.8% efficiency “black silicon” solar cells. The cells incorporate density-graded nanoporous surface layers made by a one-step nanoparticle-catalyzed etch and reflect less than 3% of the solar spectrum, with no conventional antireflection coating. The cells are limited by recombination in the nanoporous layer which decreases short-wavelength spectral response. The optimum density-graded layer depth is then a compromise between reflectance reduction and recombination loss. Finally, we propose universal design rules for high-efficiency solar cells based on density-graded surfaces.
Metallic nanoparticles as intermediate reflectors in tandem solar cells
Authors: Fahr Stephan , Rockstuhl Carsten , Lederer Falk
Published: September 2009

Tandem thin film solar cells made of amorphous and microcrystalline silicon offer the potential for high conversion efficiencies at low costs. However, their finite thickness imposed by intrinsic materials properties hinders the complete absorption of light and requires smart photon management. We reveal a genuine strategy to use metallic nanoparticles, appropriately tailored to provide a spectrally selective reflection, as an intermediate reflector. It enhances foremost light absorption in the top cell. We show that the current density for an optimized cell can be 1.16 times larger when compared to a cell without a spectrally selective intermediate reflector.
Introduction to Focus Issue: Intracellular Ca2+ Dynamics—A Change of Modeling Paradigm?
Authors: Falcke Martin
Published: September 2009

Intracellular Ca2+ concentration dynamics have been perceived as a prototypical deterministic intracellular reaction-diffusion system in biophysics for many years. Recent experimental findings challenge that view and suggest them to be fluctuation driven. That renders this system interesting for nonlinear physics, in general, since we can study the emergence of macroscopic behavior from mesoscopic dynamics. In particular, we can observe the random elemental events, called puffs, and the macroscopic pattern with the same experimental means. Here, we give a short introduction to the current discussion on theoretical and modeling concepts, and this Focus Issue reflecting it.
Fabrication of the gating nanopore device
Authors: Taniguchi Masateru , Tsutsui Makusu , Yokota Kazumichi , Kawai Tomoji
Published: September 2009

We synthesized gating nanopores with embedded nanogap electrodes in a solid-state nanopore using an 11-step nanofabrication process. We were able to detect Au nanoparticles passing through a 30-nm-diameter gating nanopore via an electric current between nanoelectrodes. The electric current was proportional to the duration of translocation time. The gating nanopore is expected to be a next-generated nanosystem that can be applied to single-molecule sensors.
Reproductive biology of wahoo, Acanthocybium solandri, from the Atlantic coast of Florida and the Bahamas
Authors: Jenkins Kristin L. Maki , McBride Richard S.
Published: September 2009

Despite its economic importance to many coastal nations, assessments of wahoo, Acanthocybium solandri, are hampered by a lack of basic life history information. In this study, wahoo were collected from Florida’s Atlantic coast and the northern Bahamas during 1997–2006 to examine reproductive seasonality, maturation, spawning frequency and fecundity. These samples demonstrated only a single, summer-spawning season, which did not support earlier postulations of spring spawning by wahoo near the Bahamas. The size and age at 50% female maturity were 925 mm fork length and 0.64 years, respectively. Spawning frequency was, on average, every 5 days during June–August, but 13% of mature females were inactive during this period. Batch fecundity was positively correlated with fish size, and varied between 0.44 and 1.67 million eggs. Parasites, previously unreported to occur in wahoo gonads and identified only as philometrid nematodes, were evident in 11% of these females. Most parasitised fish had vitellogenic oocytes, several even with oocytes with migrating nuclei or post-ovulatory follicles, so these parasitised fish were capable of spawning. Although wahoo have been noted to have relatively small gonads, and parasites are often found in female gonads, annual fecundity estimates are of the order of 10–100 million eggs. The significant contribution of older, larger females to egg production should be considered in managing this fishery.
Does otolith chemistry indicate diadromous lifecycles for five Australian riverine fishes?
Authors: Miles N. G. , West R. J. , Norman M. D.
Published: September 2009

Diadromy is an important characteristic of the lifecycle of many Australian coastal fishes, but many of these species remain poorly studied. The migratory patterns of five riverine fish species from south-eastern Australia were examined using otolith chemistry. Analyses of individual otoliths from wild-caught fishes revealed distinctive lateral variation in otolith Sr : Ca values that provide good evidence for an amphidromous lifecycle for two species: Myxus petardi and Gobiomorphus australis. Gobiomorphus coxii, Potamalosa richmondia and Notesthes robusta displayed Sr : Ca patterns that indicated that these species may have more complex movements between marine and fresh water. Overall, these results provided quantitative data that supported the lifecycles previously hypothesised for most of the studied fish species. However, M. petardi, which was thought to be catadromous, displayed Sr : Ca variations that suggested an amphidromous lifecycle, at least for the specimens examined. These results also provided further evidence to demonstrate that otolith chemistry is a useful tool for studying the movement patterns of diadromous species and this technique will be especially valuable in identifying species that are most at risk from river regulation and barriers to migration.
An inverse method to estimate stem surface heat flux in wildland fires
Authors: Bova Anthony S. , Dickinson Matthew B.
Published: September 2009

Models of wildland fire-induced stem heating and tissue necrosis require accurate estimates of inward heat flux at the bark surface. Thermocouple probes or heat flux sensors placed at a stem surface do not mimic the thermal response of tree bark to flames. We show that data from thin thermocouple probes inserted just below the bark can be used, by means of a one-dimensional inverse heat conduction method, to estimate net heat flux (inward minus outward heat flow) and temperature at the bark surface. Further, we estimate outward heat flux from emitted water vapor and bark surface re-radiation. Estimates of surface heat flux and temperature made by the inverse method confirm that surface-mounted heat flux sensors and thermocouple probes overestimate surface heat flux and temperature. As a demonstration of the utility of the method, we characterized uneven stem heating, due to leeward, flame-driven vortices, in a prescribed surface fire. Advantages of using an inverse method include lower cost, ease of multipoint measurements and negligible effects on the target stem. Drawbacks of the simple inverse model described herein include inability to estimate heat flux in very moist bark and uncertainty in estimates when extensive charring occurs.
Influence of a native legume on soil N and plant response following prescribed fire in sagebrush steppe
Authors: Goergen Erin M. , Chambers Jeanne C.
Published: September 2009

Woodland expansion affects grasslands and shrublands on a global scale. Prescribed fire is a potential restoration tool, but recovery depends on nutrient availability and species responses after burning. Fire often leads to long-term losses in total nitrogen, but presence of native legumes can influence recovery through addition of fixed nitrogen. We examined the effects of prescribed fire in the central Great Basin, Nevada, USA, on density, biomass and nutrient content of a native legume, Lupinus argenteus (Pursh), and the effects of Lupinus presence and prescribed fire on soil inorganic nitrogen and on neighboring plant functional groups. We examined three treatments – 1 year post-burn, 3 years post-burn and unburned control in three replicate blocks. Extractable soil inorganic nitrogen was variable and, despite a tendency towards increased inorganic nitrogen 1 year post-burn, differences among treatments were not significant. Extractable soil inorganic nitrogen was higher in Lupinus presence regardless of time since fire. Lupinus density increased after fire mainly owing to increased seedling numbers 3 years post-burn. Fire did not affect Lupinus tissue N and P concentrations, but cover of perennial grasses and forbs was higher in Lupinus presence. The invasive annual grass Bromus tectorum had low abundance and was unaffected by treatments. Results indicate that Lupinus has the potential to influence succession through modification of the post-fire environment.
Novel fuelbed characteristics associated with mechanical mastication treatments in northern California and south-western Oregon, USA
Authors: Kane Jeffrey M. , Varner J. Morgan , Knapp Eric E.
Published: September 2009

Mechanically masticated fuelbeds are distinct from natural or logging slash fuelbeds, with different particle size distributions, bulk density, and particle shapes, leading to challenges in predicting fire behavior and effects. Our study quantified some physical properties of fuel particles (e.g. squared quadratic mean diameter, proportion of non-cylindrical particles) and surface fuel loading with planar intercept and plot-based methods in 10 mechanically masticated sites in northern California and south-western Oregon. Total woody fuel load differed among masticated sites, ranging from 15.3 to 63.4 Mg ha–1, with the majority of the load concentrated in the 10-h (53.7%) and 1-h (29.2%) time-lag classes. Masticated fuels were densely packed, with total depths ranging from 4.6 to 8.0 cm and fuelbed bulk densities ranging from 45.9 to 115.3 kg m–3. To accurately quantify loading in masticated fuelbeds, we recommend using a hybrid methodology, where 1-h and 10-h fuel loadings are estimated using a plot-based method and 100-h and 1000-h fuel loadings are estimated using the standard planar intercept method. Most masticated fuelbeds differed in loading by fuel class and fuelbed depth, when compared with existing natural and slash-based fuelbeds, suggesting new fire behavior fuel models specific to masticated fuelbeds may be warranted.
The meaning of Neandertal skeletal morphology
Authors: Weaver Timothy D.
Published: September 2009

A procedure is outlined for distinguishing among competing hypotheses for fossil morphology and then used to evaluate current views on the meaning of Neandertal skeletal morphology. Three explanations have dominated debates about the meaning of Neandertal cranial features: climatic adaptation, anterior dental loading, and genetic drift. Neither climatic adaptation nor anterior dental loading are well supported, but genetic drift is consistent with the available evidence. Climatic adaptation and activity patterns are the most discussed explanations for Neandertal postcranial features. Robust empirical relationships between climate and body form in extant humans and other endotherms currently make climatic adaptation the most plausible explanation for the wide bodies and relatively short limbs of Neandertals, and many additional postcranial features are likely secondary consequences of these overall skeletal proportions. Activity patterns may explain certain Neandertal postcranial features, but unlike the situation for climate, relationships in extant humans between morphology and activities are typically not well established. For both the cranium and the postcranium, changes in diet or activity patterns may underlie why Neandertals and Pleistocene modern humans tend to be more robust than Holocene humans.
The
Corynebacterium diphtheriae
shaft pilin SpaA is built of tandem Ig-like modules with stabilizing isopeptide and disulfide bonds
Authors: Kang Hae Joo , Paterson Neil G. , Gaspar Andrew H. , Ton-That Hung , Baker Edward N.
Published: September 2009

Cell-surface pili are important virulence factors that enable bacterial pathogens to adhere to specific host tissues and modulate host immune response. Relatively little is known about the structure of Gram-positive bacterial pili, which are built by the sortase-catalyzed covalent crosslinking of individual pilin proteins. Here we report the 1.6-Å resolution crystal structure of the shaft pilin component SpaA from
Corynebacterium diphtheriae
, revealing both common and unique features. The SpaA pilin comprises 3 tandem Ig-like domains, with characteristic folds related to those typically found in non-pilus adhesins. Whereas both the middle and the C-terminal domains contain an intramolecular Lys–Asn isopeptide bond, previously detected in the shaft pilins of
Streptococcus pyogenes
and
Bacillus cereus
, the middle Ig-like domain also harbors a calcium ion, and the C-terminal domain contains a disulfide bond. By mass spectrometry, we show that the SpaA monomers are cross-linked in the assembled pili by a Lys–Thr isopeptide bond, as predicted by previous genetic studies. Together, our results reveal that despite profound dissimilarities in primary sequences, the shaft pilins of Gram-positive pathogens have strikingly similar tertiary structures, suggesting a modular backbone construction, including stabilizing intermolecular and intramolecular isopeptide bonds.
Barrier-to-autointegration factor (BAF) condenses DNA by looping
Authors: Skoko Dunja , Li Min , Huang Ying , Mizuuchi Michiyo , Cai Mengli , Bradley Christina M. , Pease Paul J. , Xiao Botao , Marko John F. , Craigie Robert , Mizuuchi Kiyoshi
Published: September 2009

Barrier-to-autointegration factor (BAF) is a protein that has been proposed to compact retroviral DNA, making it inaccessible as a target for self-destructive integration into itself (autointegration). BAF also plays an important role in nuclear organization. We studied the mechanism of DNA condensation by BAF using total internal reflection fluorescence microscopy. We found that BAF compacts DNA by a looping mechanism. Dissociation of BAF from DNA occurs with multiphasic kinetics; an initial fast phase is followed by a much slower dissociation phase. The mechanistic basis of the broad timescale of dissociation is discussed. This behavior mimics the dissociation of BAF from retroviral DNA within preintegration complexes as monitored by functional assays. Thus the DNA binding properties of BAF may alone be sufficient to account for its association with the preintegration complex.
A mathematical model of ischemic cutaneous wounds
Authors: Xue Chuan , Friedman Avner , Sen Chandan K.
Published: September 2009

Chronic wounds represent a major public health problem affecting 6.5 million people in the United States. Ischemia, primarily caused by peripheral artery diseases, represents a major complicating factor in cutaneous wound healing. In this work, we sought to develop a mathematical model of ischemic dermal wounds. The model consists of a coupled system of partial differential equations in the partially healed region, with the wound boundary as a free boundary. The extracellular matrix (ECM) is assumed to be viscoelastic, and the free boundary moves with the velocity of the ECM at the boundary. The model equations involve the concentration of oxygen, PDGF and VEGF, the densities of macrophages, fibroblasts, capillary tips and sprouts, and the density and velocity of the ECM. Simulations of the model demonstrate how ischemic conditions may limit macrophage recruitment to the wound-site and impair wound closure. The results are in general agreement with experimental findings.
Nonaminoglycoside compounds induce readthrough of nonsense mutations
Authors: Du Liutao , Damoiseaux Robert , Nahas Shareef , Gao Kun , Hu Hailiang , Pollard Julianne M. , Goldstine Jimena , Jung Michael E. , Henning Susanne M. , Bertoni Carmen , Gatti Richard A.
Published: September 2009

Large numbers of genetic disorders are caused by nonsense mutations for which compound-induced readthrough of premature termination codons (PTCs) might be exploited as a potential treatment strategy. We have successfully developed a sensitive and quantitative high-throughput screening (HTS) assay, protein transcription/translation (PTT)–enzyme-linked immunosorbent assay (ELISA), for identifying novel PTC-readthrough compounds using ataxia-telangiectasia (A-T) as a genetic disease model. This HTS PTT-ELISA assay is based on a coupled PTT that uses plasmid templates containing prototypic A-T mutated (ATM) mutations for HTS. The assay is luciferase independent. We screened ∼34,000 compounds and identified 12 low-molecular-mass nonaminoglycosides with potential PTC-readthrough activity. From these, two leading compounds consistently induced functional ATM protein in ATM-deficient cells containing disease-causing nonsense mutations, as demonstrated by direct measurement of ATM protein, restored ATM kinase activity, and colony survival assays for cellular radiosensitivity. The two compounds also demonstrated readthrough activity in mdx mouse myotube cells carrying a nonsense mutation and induced significant amounts of dystrophin protein.
Pathogenicity of a disease-associated human IL-4 receptor allele in experimental asthma
Authors: Tachdjian Raffi , Mathias Clinton , Al Khatib Shadi , Bryce Paul J. , Kim Hong S. , Blaeser Frank , O'Connor Brian D. , Rzymkiewicz Danuta , Chen Andrew , Holtzman Michael J. , Hershey Gurjit K. , Garn Holger , Harb Hani , Renz Harald , Oettgen Hans C. , Chatila Talal A.
Published: September 2009

Polymorphisms in the interleukin-4 receptor α chain (IL-4Rα) have been linked to asthma incidence and severity, but a causal relationship has remained uncertain. In particular, a glutamine to arginine substitution at position 576 (Q576R) of IL-4Rα has been associated with severe asthma, especially in African Americans. We show that mice carrying the Q576R polymorphism exhibited intense allergen-induced airway inflammation and remodeling. The Q576R polymorphism did not affect proximal signal transducer and activator of transcription (STAT) 6 activation, but synergized with STAT6 in a gene target– and tissue-specific manner to mediate heightened expression of a subset of IL-4– and IL-13–responsive genes involved in allergic inflammation. Our findings indicate that the Q576R polymorphism directly promotes asthma in carrier populations by selectively augmenting IL-4Rα–dependent signaling.
Reproducing the manual annotation of multiple sequence alignments using a SVM classifier
Authors: Blouin Christian , Perry Scott , Lavell Allan , Susko Edward , Roger Andrew J.
Published: September 2009

Motivation: Aligning protein sequences with the best possible accuracy requires sophisticated algorithms. Since the optimal alignment is not guaranteed to be the correct one, it is expected that even the best alignment will contain sites that do not respect the assumption of positional homology. Because formulating rules to identify these sites is difficult, it is common practice to manually remove them. Although considered necessary in some cases, manual editing is time consuming and not reproducible. We present here an automated editing method based on the classification of ‘valid’ and ‘invalid’ sites.

Results: A support vector machine (SVM) classifier is trained to reproduce the decisions made during manual editing with an accuracy of 95.0%. This implies that manual editing can be made reproducible and applied to large-scale analyses. We further demonstrate that it is possible to retrain/extend the training of the classifier by providing examples of multiple sequence alignment (MSA) annotation. Near optimal training can be achieved with only 1000 annotated sites, or roughly three samples of protein sequence alignments.

Availability: This method is implemented in the software MANUEL, licensed under the GPL. A web-based application for single and batch job is available at http://fester.cs.dal.ca/manuel.

Contact:  cblouin@cs.dal.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
Getting a Better Grip on Research: The Fate of Those Who Ignore History
Authors: Maskrey Neal , Greenhalgh Trisha
Published: September 2009

Those who ignore history are doomed to repeat it George Santayana American philosopher and poet, 1863–1952

This is the first paper in a series of five describing the use of evidence to support decisions made in clinical practice. The series covers large elements of Statement 2: The general practice consultation, Statement 3.3: Ethics and values based medicine and Statement 3.5: Evidence-based practice of the GP Curriculum.
Hand and Wrist Problems in Primary Care
Authors: Warwick David
Published: September 2009

Musculoskeletal disorders account for 15–20% of GP consultations and cause a significant amount of morbidity and disability. This article covers a selection of hand and wrist problems that either commonly present to the GP or are rather more rare but important, and provides a management strategy for each.
Introduction
Authors: Curd Patricia , Graham Daniel W.
Published: September 2009

This article is concerned with the first philosophers and scientists in the Western tradition. It studies the Presocratic philosophers. One can approach early Greek philosophy through either particular figures of the period or thematic studies that cover broader time periods. If the term “Presocratic philosopher” is a conventional designation established by scholars, it marks out a set of figures who do seem to merit special attention. So as long as there is a tribe of philosophers in the West, they will look back to the first antecedents of their profession. And it seems that the Presocratics are the obvious candidates for founders of the movement.
Heraclitus: Flux, Order, and Knowledge
Authors: Graham Daniel W.
Published: September 2009

Renewed interest in the Presocratics of the last few decades has not ignored Heraclitus, and some new and fruitful lines of inquiry are now being pursued. This article on Heraclitus presents a unified Heraclitus who is a thoughtful critic of his predecessors, and keenly interested in the possibility of human understanding. This Heraclitus rejects the Milesian account of a single substance with systematic changes and transformations that guarantee the stability of the whole. He recognizes that his new views will be difficult to understand, but provides hints and lessons to allow his hearer or reader to grasp his philosophical account. Parmenides of Elea, too, has not been ignored by the scholarly community—a number of new interpretations of Parmenides have appeared in the last decade.
Signs and Arguments in Parmenides B8
Authors: McKirahan Richard
Published: September 2009

David Sedley recently complained that despite the enormous amount of work on Parmenides in the past generation, the details of Parmenides' arguments have received insufficient attention. It is universally recognized that Parmenides' introduction of argument into philosophy was a move of paramount importance. It is also recognized that the arguments of fragment B8 are closely related. At the beginning of B8, Parmenides asserts that what-is has several attributes; he offers a series of proofs that what-is indeed has those attributes. This article undertakes a close analysis of fragment B8, teasing out the structure of the arguments, and showing what parts of the traditional and new interpretations of Parmenides those arguments do (or do not) support. It presents some surprising conclusions and opens up spaces for new interpretations.