bluuebunny/crossref_metadata_2025 huggingface dataset:
Structure–function studies for the panacea, valproic acid
Authors: Terbach Nicole , Williams Robin S.B.
Published: September 2009

The anticonvulsant properties of VPA (valproic acid), a branched short-chain fatty acid, were serendipitously discovered in 1963. Since then, therapeutic roles of VPA have increased to include bipolar disorder and migraine prophylaxis, and have more recently been proposed in cancer, Alzheimer's disease and HIV treatment. These numerous therapeutic roles elevate VPA to near ‘panacea’ level. Surprisingly, the mechanisms of action of VPA in the treatment of many of these disorders remain unclear, although it has been shown to alter a wide variety of signalling pathways and a small number of direct targets. To analyse the mechanism of action of VPA, a number of studies have defined the structural characteristics of VPA-related compounds giving rise to distinct therapeutic and cellular effects, including adverse effects such as teratogenicity and hepatotoxicity. These studies raise the possibility of identifying target-specific novel compounds, providing better therapeutic action or reduced side effects. This short review will describe potential therapeutic pathways targeted by VPA, and highlight studies showing structural constraints necessary for these effects.
Investigation of the H+–myo-inositol transporter (HMIT) as a neuronal regulator of phosphoinositide signalling
Authors: Daniel Elena Di , Kew James N. , Maycox Peter R.
Published: September 2009

Phosphoinositide signalling regulates a series of important neuronal processes that are thought to be altered in mood disorders. Furthermore, mood-stabilizing drugs inhibit key enzymes that regulate phosphoinositide production and alter neuronal growth cone morphology in an inositol-reversible manner. Inositol is taken up by neurons from the extracellular fluid, presumably via membrane transporters; it can also be synthesized by the enzyme MIP-synthase (myo-inositol-1-phosphate synthase) and, in addition, it is generated by inositol phospholipid hydrolysis. The neuronal-specific HMIT (H+–myo-inositol transporter) represents a potential regulator of inositol signalling in neurons that warrants further investigation.
The collective motion of carbon atoms in a (10,10) single wall carbon nanotube under axial tensile strain
Authors: Weng Meng-Hsiung , Ju Shin-Pon , Wu Wen-Shian
Published: September 2009

Molecular dynamics is employed to investigate the collective motion of carbon atoms of a (10,10) single walled carbon nanotube under tensile loading. The “slip vector” parameter is used to study the collective motion of a group of atoms and deformation behavior in three different directions (axial, tangential, and radial directions). According to the variations in the slip vectors in different directions and the stress-strain profile, the axial tensile process can be divided into three stages. In tensile loading process, two local deformation types (symmetrical and nonsymmetrical deformations) are observed before reaching the maximum stress. The variations in the slip vector values of each atom indicate a symmetrical rupture which is oriented 45° to the axis of the nanotube after reaching the maximum stress. By tensile loading, chainlike structures can be formed before the breaking of the nanotube.
Toward a predictive model of Ca2+ puffs
Authors: Thul R. , Thurley K. , Falcke M.
Published: September 2009

We investigate the key characteristics of Ca2+ puffs in deterministic and stochastic frameworks that all incorporate the cellular morphology of IP3 receptor channel clusters. In the first step, we numerically study the Ca2+ liberation in a three-dimensional representation of a cluster environment with reaction-diffusion dynamics in both the cytosol and the lumen. These simulations reveal that Ca2+ concentrations at a releasing cluster range from 80 to 170 μM and equilibrate almost instantaneously on the time scale of the release duration. These highly elevated Ca2+ concentrations eliminate Ca2+ oscillations in a deterministic model of an IP3R channel cluster at physiological parameter values as revealed by a linear stability analysis. The reason lies in the saturation of all feedback processes in the IP3R gating dynamics, so that only fluctuations can restore experimentally observed Ca2+ oscillations. In this spirit, we derive master equations that allow us to analytically quantify the onset of Ca2+ puffs and hence the stochastic time scale of intracellular Ca2+ dynamics. Moving up the spatial scale, we suggest to formulate cellular dynamics in terms of waiting time distribution functions. This approach prevents the state space explosion that is typical for the description of cellular dynamics based on channel states and still contains information on molecular fluctuations. We illustrate this method by studying global Ca2+ oscillations.
From puffs to global Ca2+ signals: How molecular properties shape global signals
Authors: Skupin Alexander , Falcke Martin
Published: September 2009

The universality of Ca2+ as second messenger in living cells is achieved by a rich spectrum of spatiotemporal cellular concentration dynamics. Ca2+ release from internal storage compartments plays a key role in shaping cytosolic Ca2+ signals. Deciphering this signaling mechanism is essential for a deeper understanding of its physiological function and general concepts of cell signaling. Here, we review recent experimental findings demonstrating the stochasticity of Ca2+ oscillations and its relevance for modeling Ca2+ dynamics. The stochasticity arises by the hierarchical signal structure that carries molecular fluctuations of single channels onto the level of the cell leading to a stochastic medium as theoretically predicted. The result contradicts the current opinion of Ca2+ being a cellular oscillator. We demonstrate that cells use array enhanced coherence resonance to form rather regular spiking signals and that the “oscillations” carry information despite the involved stochasticity. The knowledge on the underlying mechanism also allows for determination of intrinsic properties from global observations. In the second part of the paper, we briefly survey different modeling approaches with regard to the experimental results. We focus on the dependence of the standard deviation on the mean period of the oscillations. It shows that limit cycle oscillations cannot describe the experimental data and that generic models have to include the spatial aspects of Ca2+ signaling.
A novel pulse width modulation for grid-connected multilevel inverter
Authors: Selvaraj J. , Rahim N. A.
Published: September 2009

This paper presents a single-phase five-level grid-connected photovoltaic inverter with a novel dual reference modulation technique. Two reference signals identical to each other with an offset equivalent to the amplitude of the triangular carrier signal were used to generate pulse width modulation (PWM) signals. The inverter consists of a full-bridge inverter and an auxiliary circuit comprising of four diodes and a switch. The inverter produces output voltage in five levels: 0, +1/2Vdc, Vdc, −1/2Vdc, and −Vdc. A digital proportional-integral (PI) current control algorithm is implemented in DSP TMS320F2812 to keep the current injected into the grid sinusoidal and to have high dynamic performance with low total harmonic distortion (THD). The validity of the proposed inverter is verified through simulation and is implemented in a prototype. The experimental results are compared to conventional single-phase three-level grid-connected pulse width modulation (PWM) inverter in terms of THD.
Joule heating in single-walled carbon nanotubes
Authors: Ragab Tarek , Basaran Cemal
Published: September 2009

Joule heating in single-walled carbon nanotubes (CNTs) using a quantum mechanical approach is presented in this paper. The modeling is based on the energy transfer between the electrons and both acoustic and optical phonons. In this formulation, only the knowledge of the full energy dispersion relation, phonon dispersion relation, and the electron-phonon coupling potential is required for the calculations. For verification of the proposed model, the current-voltage relation for extremely long nanotubes is calculated and the results are compared with the experimental data. The electric field dependence of the amount of energy generated by Joule heating is plotted. Moreover the effect of the thermal environment on the behavior of Joule heating is studied. The formulation proposed in this paper can also be used for structures other than CNTs. Computations indicate that, contrary to popular opinion, metallic CNT does not follow Joule’s law of P=IV. Joule heating in CNT is significantly less than what is predicted with Joule law (P=IV), which would make it a perfect candidate to replace copper as interconnect material in electronics.
The study on the effect of erbium on diamond-like carbon deposited by pulsed laser deposition technique
Authors: Foong Y. M. , Hsieh J. , Li X. , Chua D. H. C.
Published: September 2009

Diamond-like carbon (DLC) films doped with a small fraction of erbium (0.5–2.0 at. %, at 0.5 at. % interval) were prepared by using a 248 nm KrF pulsed laser deposition technique. The effects of erbium on the surface morphology, microstructure, chemical binding states, tribological property, and the adhesion strength of DLC films were investigated. Atomic force microscopy showed that the surface roughness of the films increased with the increasing of erbium fraction, but generally the nanocomposite films were smooth with rms below 1 nm. Raman analysis showed broad peaks centered at 1550 cm−1 on all the samples. The deconvoluted Raman spectra on DLC doped with different fractions of erbium showed that the ID/IG ratio increased with increasing erbium content, and the comparative percent of sp3 is between 50% and 58% for erbium fraction between 0.5 and 2.0 at. %. High resolution x-ray photoelectron spectroscopy confirmed that the C 1s peaks had slightly shifted away from 285.2 (diamond) to 284.5 eV (graphite). The deconvolution of the spectra further confirmed the influence of erbium to the sp3 contents and revealed the presence of SiC with the increasing of Er fraction. Microscratch tester results showed that the adhesion strength (critical load) of the films improved with the presence of SiC bonding at the interface. This hinted that the presence of the heavier erbium may force the impinging carbon ions to react more with the interface to form silicon carbide bonds, thus enhancing the adhesion strength. Although the presence of erbium increased the surface roughness of the films, the coefficients of friction of the erbium doped DLC films were still closely resembled to pure DLC, i.e., 0.11–0.12 compared to 0.10 for pure DLC.
Nonresonant third-order nonlinear properties of NaPO3–WO3–Bi2O3 glasses in the near infrared
Authors: dos Santos F. E. P. , de Araújo C. B. , Gomes A. S. L. , Fedus K. , Boudebs G. , Manzani D. , Messaddeq Y.
Published: September 2009

The nonlinear (NL) refractive index, n2, of NaPO3–WO3–Bi2O3 glass with different relative amounts of the constituents was measured at 1064 and 800 nm using the Z-scan and the thermally managed eclipse Z-scan techniques, respectively. The values of n2≥10−15 cm2/W and negligible NL absorption coefficient were determined. The large values of the NL refractive index and the very small NL absorption indicate that these materials have large potential for all-optical switching applications.
Structure and magnetic properties of nanophase-LiFe1.5P2O7
Authors: Ramana C. V. , Kopec M. , Mauger A. , Gendron F. , Julien C. M.
Published: September 2009

The structure and magnetic properties of lithium iron pyrophosphate, i.e., Li2Fe3(P2O7)2 or LiFe1.5P2O7, synthesized using a facile metal acetate approach for application in lithium-ion batteries, are investigated in detail. The high-resolution transmission electron microscopy, selected area electron diffraction, and x-ray diffraction measurements indicate that Li2Fe3(P2O7)2 is crystallized in the monoclinic structure, without any indication of crystallographic defects such as dislocations or misfits, and exhibit smooth surface morphology. The evaluated lattice parameters are a=0.698 76 nm, b=0.812 36 nm, c=0.964 22 nm, and β=111.83° (P21/c space group). Infrared spectroscopic measurements indicate the presence of P2O7 groups, which are formed by the two PO4 tetrahedral groups connected together. The magnetic measurements indicate that Li2Fe3(P2O7)2 is a weak antiferromagnetic material with TN=20 K exhibiting a Curie constant Cp=3.38 emu K/mol per Fe ion and a negative value of the Weiss temperature (Θp=−15 K). The absence of higher valence state Fe impurities and antiferromagnetic interactions due to the greater distance between two equivalent magnetic ions, which vanishes the Fe–O–Fe superexchange interactions, is confirmed.
Small-angle polarized neutron studies of perpendicular magnetic recording media
Authors: Lister S. J. , Wismayer M. P. , Venkataramana V. , de Vries M. A. , Ray S. J. , Lee S. L. , Thomson T. , Kohlbrecher J. , Do H. , Ikeda Y. , Takano K. , Dewhurst C.
Published: September 2009

Polarized small-angle neutron scattering has been used to measure the local magnetic structure of writable thin-film perpendicular media with a granular CoCrPt-SiOx recording layer. By exploiting the cross terms between the nuclear and magnetic scattering, we are able to probe simultaneously both the grain structure and the subgranular magnetic structure of the recording layer, which has a thickness of only 15 nm and which is embedded within a full perpendicular media structure including soft underlayer. Two models are used to analyze the data, one analytical and the other a numerical approach based on transmission electron microscopy measurements of the grains. Both models show that the recording layer consists of ferromagnetically ordered core regions that are smaller in extent than the corresponding grains and allow a direct, quantitative comparison of these two length scales.
Progress and challenges in the automated construction of Markov state models for full protein systems
Authors: Bowman Gregory R. , Beauchamp Kyle A. , Boxer George , Pande Vijay S.
Published: September 2009

Markov state models (MSMs) are a powerful tool for modeling both the thermodynamics and kinetics of molecular systems. In addition, they provide a rigorous means to combine information from multiple sources into a single model and to direct future simulations/experiments to minimize uncertainties in the model. However, constructing MSMs is challenging because doing so requires decomposing the extremely high dimensional and rugged free energy landscape of a molecular system into long-lived states, also called metastable states. Thus, their application has generally required significant chemical intuition and hand-tuning. To address this limitation we have developed a toolkit for automating the construction of MSMs called MSMBUILDER (available at https://simtk.org/home/msmbuilder). In this work we demonstrate the application of MSMBUILDER to the villin headpiece (HP-35 NleNle), one of the smallest and fastest folding proteins. We show that the resulting MSM captures both the thermodynamics and kinetics of the original molecular dynamics of the system. As a first step toward experimental validation of our methodology we show that our model provides accurate structure prediction and that the longest timescale events correspond to folding.
Reduction of calcium release site models via fast/slow analysis and iterative aggregation/disaggregation
Authors: Hao Yan , Kemper Peter , Smith Gregory D.
Published: September 2009

Mathematical models of calcium release sites derived from Markov chain models of intracellular calcium channels exhibit collective gating reminiscent of the experimentally observed phenomenon of calcium puffs and sparks. Such models often take the form of stochastic automata networks in which the transition probabilities of each channel depend on the local calcium concentration and thus the state of the other channels. In order to overcome the state-space explosion that occurs in such compositionally defined calcium release site models, we have implemented several automated procedures for model reduction using fast/slow analysis. After categorizing rate constants in the single channel model as either fast or slow, groups of states in the expanded release site model that are connected by fast transitions are lumped, and transition rates between reduced states are chosen consistent with the conditional probability distribution among states within each group. For small problems these conditional probability distributions can be numerically calculated from the full model without approximation. For large problems the conditional probability distributions can be approximated without the construction of the full model by assuming rapid mixing of states connected by fast transitions. Alternatively, iterative aggregation/disaggregation may be employed to obtain reduced calcium release site models in a memory-efficient fashion. Benchmarking of several different iterative aggregation/disaggregation-based fast/slow reduction schemes establishes the effectiveness of automated calcium release site reduction utilizing the Koury–McAllister–Stewart method.
Determination of local refractive index variations in thin films by heterodyne interferometric scanning near-field optical microscopy
Authors: Diziain Séverine , Merolla Jean-Marc , Spajer Michel , Benvenuti Giacomo , Dabirian Ali , Kuzminykh Yury , Hoffmann Patrik , Bernal Maria-Pilar
Published: September 2009

We report on a heterodyne interferometric scanning near-field optical microscope developed for characterizing, at the nanometric scale, refractive index variations in thin films. An optical lateral resolution of 80 nm (λ/19) and a precision smaller than 10−4 on the refractive index difference have been achieved. This setup is suitable for a wide set of thin films, ranging from periodic to heterogeneous samples, and turns out to be a very promising tool for determining the optical homogeneity of thin films developed for nanophotonics applications.
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n-type metal-oxide-semiconductor field-effect transistor-embedded microcantilever sensor for observing the kinetics of chemical molecules interaction
Authors: Wang Jian , Wu Wengang , Huang Ying , Hao Yilong
Published: September 2009

This letter reports a silicon microcantilever sensor with an embedded n-type metal-oxide-semiconductor field-effect transistor (nMOSFET) for observing the kinetics of chemical molecules interaction based on surface stress sensing principle. In the sensors, the silicon cantilevers with gold coating and the channels of the embedded-nMOSFETs are configured along ⟨100⟩ crystal orientation. The kinetics of and the surface stress from chemical interactions between acetone, ethanol, nitroethane, and thiols molecules are observed, respectively, which follow the Langmuir model. The output signals of the nMOSFET-embedded cantilever sensors induced by various targets are different, which implies that the devices may allow for gaining insights into the kinetics of intermolecular interactions.
Multiple-timescale asymptotic analysis of transient coating flows
Authors: Groh C. M. , Kelmanson M. A.
Published: September 2009

New stability results for the widely studied paradigm “rotating cylinder coating flow” problem are found using a novel multiple-timescale asymptotic approach that is not only fully automated within an algebraic-manipulator platform, but also more widely applicable to diverse evolution equations, particularly those arising in thin-film flow on spatially periodic topographies. Hitherto undiscovered contributions to the capillary decay and gravitational drift in the Fourier modes comprising the coating-film thickness on the cylinder are found, the main discovery being the formal derivation of the functional form of a time-dependent decay rate that has previously been speculated only partially and heuristically. The new asymptotic approach admits analysis of the solution on a geometric progression of increasingly slow timescales, the slowest timescale being a priori dictated in the automated procedure. Theoretical results are in excellent agreement with those obtained from spectrally accurate numerical integrations of the evolution equation for the film thickness. The extent to which the predictions of prior related asymptotic studies are improved upon is quantified.
The influence of the gate dielectrics on threshold voltage instability in amorphous indium-gallium-zinc oxide thin film transistors
Authors: Lee Jaeseob , Park Jin-Seong , Pyo Young Shin , Lee Dong Bum , Kim Eun Hyun , Stryakhilev Denis , Kim Tae Woong , Jin Dong Un , Mo Yeon-Gon
Published: September 2009

We investigated the threshold voltage (Vth) instability for various gate dielectrics (SiNx and SiOx) in amorphous indium-gallium-zinc oxide (a-IGZO) thin film transistors (TFTs). The a-IGZO TFTs with SiNx 150 °C exhibited reasonable electrical performance (field-effect mobility of 8.1 cm2/V s and Ion/off ratio of >108) but showed huge Vth shift under positive gate bias. The TFTs with SiOx dielectrics exhibit smaller Vth instability than those of SiNx dielectrics. This behavior can be explained by using simple charge trapping into the gate insulators and the difference of Vth instability on various dielectrics may be originated from the hydrogen contents, providing high density of charge traps in gate dielectrics.
On the long time holographic grating recording process in azo-polymer
Authors: Sobolewska Anna , Bartkiewicz Stanislaw
Published: September 2009

The authors report on a complex diffraction efficiency dynamics of the holographic grating recording process in azobenzene-functionalized polymer for a long recording time. The nonexponential dynamics was explain by the mechanism which assumes (i) simultaneous formation of three coupling phase gratings with constant, equal 0 or π, phase shifts between them and (ii) occurrence of gratings erasure processes when the recording time is long. Based on these assumptions and applying the Bessel function, the diffraction efficiency dynamics was calculated.
High average power second harmonic generation in air
Authors: Beresna Martynas , Kazansky Peter G. , Svirko Yuri , Barkauskas Martynas , Danielius Romas
Published: September 2009

We demonstrate second harmonic vortex generation in atmospheric pressure air using tightly focused femtosecond laser beam. The circularly polarized ring-shaped beam of the second harmonic is generated in the air by fundamental beam of the same circular polarization, while the linear polarized beam produces two-lobe beam at the second harmonic frequency. The achieved normalized conversion efficiency and average second harmonic power are two orders of magnitude higher compared to those previously reported and can be increased up to 20 times by external gas flow. We demonstrate that the frequency doubling originates from the gradient of photoexcited free electrons created by pondermotive force.
Varying polymer crystallinity in nanofiber poly(3-alkylthiophene): PCBM solar cells: Influence on charge-transfer state energy and open-circuit voltage
Authors: Vandewal Koen , Oosterbaan Wibren D. , Bertho Sabine , Vrindts Veerle , Gadisa Abay , Lutsen Laurence , Vanderzande Dirk , Manca Jean V.
Published: September 2009

The effect of poly(3-alkylthiophene) (P3AT) crystallinity in (nanofiber P3AT):PCBM photovoltaic devices on the energy of the charge-transfer state (ECT) and on the open-circuit voltage (Voc) is investigated for poly(3-butythiophene), poly(3-pentylthiophene) and poly(3-hexylhiophene). P3AT crystallinity, expressed as the crystalline nanofiber mass fraction f to the total P3AT mass in the spin-coating dispersion, is varied between ∼0.1 and ∼0.9 by temperature control. ECT, as obtained by Fourier-transform photocurrent spectroscopy decreased with f as ECT=ECT0−0.2f eV. Alkyl side-chain length only influences ECT0. Voc relates to ECT as Voc=ECT/q−0.6 V.
Upper bound for the conductivity of nanotube networks
Authors: Pereira L. F. C. , Rocha C. G. , Latgé A. , Coleman J. N. , Ferreira M. S.
Published: September 2009

Films composed of nanotube networks have their conductivities regulated by the junction resistances formed between tubes. Conductivity values are enhanced by lower junction resistances but should reach a maximum that is limited by the network morphology. By considering ideal ballistic-like contacts between nanotubes, we use the Kubo formalism to calculate the upper bound for the conductivity of such films and show how it depends on the nanotube concentration as well as on their aspect ratio. Highest measured conductivities reported so far are approaching this limiting value, suggesting that further progress lies with metallic nanowires rather than carbon nanotubes.
Importance of saltmarsh to fish species of a large south-eastern Australian estuary during a spring tide cycle
Authors: Platell Margaret E. , Freewater Peter
Published: September 2009

The dietary compositions of fish species over saltmarsh in a large south-eastern Australian estuary (Brisbane Water) were explored to ascertain the importance of this habitat type to the fish community of that estuary. Following tidal inundation, 12 fish species (<120 mm total length) were obtained using fyke nets, with Ambassis jacksoniensis being particularly abundant. The stomachs of all fish contained undigested prey, implying that they fed while on the saltmarsh. Three species (A. jacksoniensis, Atherinosoma microstoma and Redigobius macrostoma) fed nearly exclusively on the crab zoeae that were released in high numbers by saltmarsh crabs. The diets of these three species significantly differed from those of the other species, which comprised mainly foraminiferans, copepods, crabs, polychaetes, terrestrial insects and/or detritus. Substantial partitioning of food resources also occurred between the other nine species. With increasing body size, A. jacksoniensis fed more on benthic prey (polychaetes and copepods) and less on crab zoeae. This study highlights the importance of saltmarsh as providing both protection and food resources for fish species during even short periods of tidal inundation by its provision of a superabundant food source (crab zoeae) and other prey, and underscores the need for recognition of saltmarsh in management plans for fish.
Do elasmobranch reactions to magnetic fields in water show promise for bycatch mitigation?
Authors: Rigg Damian P. , Peverell Stirling C. , Hearndon Mark , Seymour Jamie E.
Published: September 2009

Elasmobranchs are under increasing pressure from targeted fisheries worldwide, but unregulated bycatch is perhaps their greatest threat. This study tested five elasmobranch bycatch species (Sphyrna lewini, Carcharhinus tilstoni, Carcharhinus amblyrhynchos, Rhizoprionodon acutus, Glyphis glyphis) and one targeted teleost species (Lates calcarifer) to determine whether magnetic fields caused a reaction response and/or change in spatial use of experimental arena. All elasmobranch species reacted to magnets at distances between 0.26 and 0.58 m at magnetic strengths between 25 and 234 gauss and avoided the area around the magnets. Contrastingly, the teleosts showed no reaction response and congregated around the magnets. The different reactions of the teleosts and elasmobranchs are presumably driven by the presence of ampullae of Lorenzini in the elasmobranchs; different reaction distances between elasmobranch species appeared to correlate with their feeding ecology. Elasmobranchs with a higher reliance on the electroreceptive sense to locate prey reacted to the magnets at the greatest distance, except G. glyphis. Notably, this is the only elasmobranch species tested with a fresh- and salt-water phase in their ecology, which may account for the decreased magnetic sensitivity. The application of magnets worldwide to mitigate the bycatch of elasmobranchs appears promising based on these results.
Is settlement at small spatial scales by diadromous fishes from the Family Galaxiidae passive or active in a small coastal river?
Authors: Hale Robin , Swearer Stephen E. , Downes Barbara J.
Published: September 2009

Most marine fish and benthic invertebrate species have complex life cycles with sedentary adults and highly dispersive larvae. Mortality is often considerable at the end of the larval phase when species are undergoing settlement, so information about the biophysical mechanisms influencing larvae during this transition between habitats is crucial. For species dispersed passively, settlement is governed by oceanic processes controlling larval transport. However, many fishes have the ability to modify their dispersal behaviourally and patterns of settlement for these species are likely to be quite different. Predicting settlement patterns therefore requires knowledge of the relative importance of larval behaviour v. passive transport. In the present study, diadromous fishes from the Family Galaxiidae were surveyed to examine whether settlement is likely to result from fish settling passively (i.e. driven by environmental conditions) or whether larval behaviour may be important. Although catch rates were weakly negatively correlated with discharge, there was no evidence that fish were settling passively at the scales examined in the study. In comparison, fish appear to be using behaviours similar to selective tidal stream transport to facilitate movement into rivers from the ocean. If galaxiids have the ability to use these behaviours, larval behaviour may affect the distribution of settlers and be an important influence on the population dynamics of these species.
Empirical modelling of surface fire behaviour in maritime pine stands
Authors: Fernandes Paulo M. , Botelho Hermínio S. , Rego Francisco C. , Loureiro Carlos
Published: September 2009

An experimental burning program took place in maritime pine (Pinus pinaster Ait.) stands in Portugal to increase the understanding of surface fire behaviour under mild weather. The spread rate and flame geometry of the forward and backward sections of a line-ignited fire front were measured in 94 plots 10–15 m wide. Measured head fire rate of spread, flame length and Byram’s fire intensity varied respectively in the intervals of 0.3–13.9 m min–1, 0.1–4.2 m and 30–3527 kW m–1. Fire behaviour was modelled through an empirical approach. Rate of forward fire spread was described as a function of surface wind speed, terrain slope, moisture content of fine dead surface fuel, and fuel height, while back fire spread rate was correlated with fuel moisture content and cover of understorey vegetation. Flame dimensions were related to Byram’s fire intensity but relationships with rate of spread and fine dead surface fuel load and moisture are preferred, particularly for the head fire. The equations are expected to be more reliable when wind speed and slope are less than 8 km h–1 and 15°, and when fuel moisture content is higher than 12%. The results offer a quantitative basis for prescribed fire management.
The Tor and PKA signaling pathways independently target the Atg1/Atg13 protein kinase complex to control autophagy
Authors: Stephan Joseph S. , Yeh Yuh-Ying , Ramachandran Vidhya , Deminoff Stephen J. , Herman Paul K.
Published: September 2009

Macroautophagy (or autophagy) is a conserved degradative pathway that has been implicated in a number of biological processes, including organismal aging, innate immunity, and the progression of human cancers. This pathway was initially identified as a cellular response to nutrient deprivation and is essential for cell survival during these periods of starvation. Autophagy is highly regulated and is under the control of a number of signaling pathways, including the Tor pathway, that coordinate cell growth with nutrient availability. These pathways appear to target a complex of proteins that contains the Atg1 protein kinase. The data here show that autophagy in
Saccharomyces cerevisiae
is also controlled by the cAMP-dependent protein kinase (PKA) pathway. Elevated levels of PKA activity inhibited autophagy and inactivation of the PKA pathway was sufficient to induce a robust autophagy response. We show that in addition to Atg1, PKA directly phosphorylates Atg13, a conserved regulator of Atg1 kinase activity. This phosphorylation regulates Atg13 localization to the preautophagosomal structure, the nucleation site from which autophagy pathway transport intermediates are formed. Atg13 is also phosphorylated in a Tor-dependent manner, but these modifications appear to occur at positions distinct from the PKA phosphorylation sites identified here. In all, our data indicate that the PKA and Tor pathways function independently to control autophagy in
S. cerevisiae
, and that the Atg1/Atg13 kinase complex is a key site of signal integration within this degradative pathway.
Upregulation of threeDrosophilahomologs of human chromosome 21 genes alters synaptic function: Implications for Down syndrome
Authors: Chang Karen T. , Min Kyung-Tai
Published: September 2009

At the neuronal level of Down syndrome (DS) brains, there are evidences of altered shape, number, and density of synapses, as well as aberrant endocytosis associated with accumulation of enlarged endosomes, suggesting that proteins involved in synaptic vesicle recycling may play key roles in DS neurons. However, the exact mechanism underlying those anomalies is not well understood. We hypothesize that overexpression of three genes,dap160/itsn1,synj/synj1, andnla/dscr1, located on human chromosome 21 play important roles in DS neurons. Here, we systematically investigate the effects of multiple gene overexpression on synaptic morphology and endocytosis to identify possible dominant gene or genes. We found that overexpression of individual genes lead to abnormal synaptic morphology, but all three genes are necessary to cause impaired vesicle recycling and affect locomotor vigor. Furthermore, we report thatdap160overexpression alters the subcellular distribution of synaptojanin, and overexpression ofnlaregulates the phosphoinositol 5′ phosphatase activity of synaptojanin. These findings imply that restoring the level of any one of these genes may reduce endocytic defects seen in DS.
The evolution of antiherbivore defenses and their contribution to species coexistence in the tropical tree genusInga
Authors: Kursar Thomas A. , Dexter Kyle G. , Lokvam John , Pennington R. Toby , Richardson James E. , Weber Marjorie G. , Murakami Eric T. , Drake Camilla , McGregor Ruth , Coley Phyllis D.
Published: September 2009

Plants and their herbivores constitute more than half of the organisms in tropical forests. Therefore, a better understanding of the evolution of plant defenses against their herbivores may be central for our understanding of tropical biodiversity. Here, we address the evolution of antiherbivore defenses and their possible contribution to coexistence in the Neotropical tree genusInga(Fabaceae).Ingahas >300 species, has radiated recently, and is frequently one of the most diverse and abundant genera at a given site. For 37 species from Panama and Peru we characterized developmental, ant, and chemical defenses against herbivores. We found extensive variation in defenses, but little evidence of phylogenetic signal. Furthermore, in a multivariate analysis, developmental, ant, and chemical defenses varied independently (were orthogonal) and appear to have evolved independently of each other. Our results are consistent with strong selection for divergent defensive traits, presumably mediated by herbivores. In an analysis of community assembly, we found thatIngaspecies co-occurring as neighbors are more different in antiherbivore defenses than random, suggesting that possessing a rare defense phenotype increases fitness. These results imply that interactions with herbivores may be an important axis of niche differentiation that permits the coexistence of many species ofIngawithin a single site. Interactions between plants and their herbivores likely play a key role in the generation and maintenance of the conspicuously high plant diversity in the tropics.
Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins
Authors: Schrank Travis P. , Bolen D. Wayne , Hilser Vincent J.
Published: September 2009

Elucidating the complex interplay between protein structure and dynamics is a prerequisite to an understanding of both function and adaptation in proteins. Unfortunately, it has been difficult to experimentally decouple these effects because it is challenging to rationally design mutations that will either affect the structure but not the dynamics, or that will affect the dynamics but not the structure. Here we adopt a mutation approach that is based on a thermal adaptation strategy observed in nature, and we use it to study the binding interaction of
Escherichia coli
adenylate kinase (AK). We rationally design several single-site, surface-exposed glycine mutations to selectively perturb the excited state conformational repertoire, leaving the ground-state X-ray crystallographic structure unaffected. The results not only demonstrate that the conformational ensemble of AK is significantly populated by a locally unfolded state that is depopulated upon binding, but also that the excited-state conformational ensemble can be manipulated through mutation, independent of perturbations of the ground-state structures. The implications of these results are twofold. First, they indicate that it is possible to rationally design dynamic allosteric mutations, which do not propagate through a pathway of structural distortions connecting the mutated and the functional sites. Secondly and equally as important, the results reveal a general strategy for thermal adaptation that allows enzymes to modulate binding affinity by controlling the amount of local unfolding in the native-state ensemble. These findings open new avenues for rational protein design and fundamentally illuminate the role of local unfolding in function and adaptation.
Long-term risk preference and suboptimal decision making following adolescent alcohol use
Authors: Nasrallah Nicholas A. , Yang Tom W. H. , Bernstein Ilene L.
Published: September 2009

Individuals who abused alcohol at an early age show decision-making impairments. However, the question of whether maladaptive choice constitutes a predisposing factor to, or a consequence resulting from, alcohol exposure remains open. To examine whether a causal link exists between voluntary alcohol consumption during adolescence and adult decision making the present studies used a rodent model. High levels of voluntary alcohol intake were promoted by providing adolescent rats with access to alcohol in a palatable gel matrix under nondeprivation conditions. A probability-discounting instrumental response task offered a choice between large but uncertain rewards and small but certain rewards to assess risk-based choice in adulthood either 3 weeks or 3 months following alcohol exposure. While control animals' performance on this task closely conformed to a predictive model of risk-neutral value matching, rats that consumed high levels of alcohol during adolescence violated this model, demonstrating greater risk preference. Evidence of significant risk bias was still present when choice was assessed 3 months following discontinuation of alcohol access. These findings provide evidence that adolescent alcohol exposure may lead to altered decision making during adulthood and this model offers a promising approach to the investigation of the neurobiological underpinnings of this link.
Melanin-concentrating hormone directly inhibits GnRH neurons and blocks kisspeptin activation, linking energy balance to reproduction
Authors: Wu Min , Dumalska Iryna , Morozova Elena , van den Pol Anthony , Alreja Meenakshi
Published: September 2009

A link between energy balance and reproduction is critical for the survival of all species. Energy-consuming reproductive processes need to be aborted in the face of a negative energy balance, yet knowledge of the pathways mediating this link remains limited. Fasting and food restriction that inhibit fertility also upregulate the hypothalamic melanin-concentrating hormone (MCH) system that promotes feeding and decreases energy expenditure; MCH knockout mice are lean and have a higher metabolism but remain fertile. MCH also modulates sleep, drug abuse behavior, and mood, and MCH receptor antagonists are currently being developed as antiobesity and antidepressant drugs. Despite the clinical implications of MCH, the direct postsynaptic effects of MCH have never been reported in CNS neurons. Using patch-clamp recordings in brain slices from multiple lines of transgenic GFP mice, we demonstrate a strong inhibitory effect of MCH on an exclusive population of septal vGluT2-GnRH neurons that is activated by the puberty-triggering and preovulatory luteinizing hormone surge-mediating peptide, kisspeptin. MCH has no effect on kisspeptin-insensitive GnRH, vGluT2, cholinergic, or GABAergic neurons located within the same nucleus. The inhibitory effects of MCH are reproducible and nondesensitizing and are mediated via a direct postsynaptic Ba
2+
-sensitive K
+
channel mechanism involving the MCHR1 receptor. MCH immunoreactive fibers are in close proximity to vGluT2-GFP and GnRH-GFP neurons. Importantly, MCH blocks the excitatory effect of kisspeptin on vGluT2-GnRH neurons. Considering the role of MCH in regulating energy balance and of GnRH and kisspeptin in triggering puberty and maintaining fertility, MCH may provide a critical link between energy balance and reproduction directly at the level of the kisspeptin-activated vGluT2-GnRH neuron.
Loss of the plant DEAD-box protein ISE1 leads to defective mitochondria and increased cell-to-cell transport via plasmodesmata
Authors: Stonebloom Solomon , Burch-Smith Tessa , Kim Insoon , Meinke David , Mindrinos Michael , Zambryski Patricia
Published: September 2009

Plants have intercellular channels, plasmodesmata (PD), that span the cell wall to enable cell-to-cell transport of micro- and macromolecules. We identified anArabidopsis thalianaembryo lethal mutantincreased size exclusion limit 1(ise1) that results in increased PD-mediated transport of fluorescent tracers. Theise1mutants have a higher frequency of branched and twinned PD than wild-type embryos. Silencing ofISE1in matureNicotiana benthamianaleaves also leads to increased PD transport, as monitored by intercellular movement of a GFP fusion to the tobacco mosaic virus movement protein.ISE1encodes a putative plant-specific DEAD-box RNA helicase that localizes specifically to mitochondria. The N-terminal 100 aa of ISE1 specify mitochondrial targeting. Mitochondrial metabolism is compromised severely inise1mutant embryos, because their mitochondrial proton gradient is disrupted and reactive oxygen species production is increased. Although mitochondria are essential for numerous cell-autonomous functions, the present studies demonstrate that mitochondrial function also regulates the critical cell non-cell-autonomous function of PD.
TSLP and IL-7 use two different mechanisms to regulate human CD4+ T cell homeostasis
Authors: Lu Ning , Wang Yi-Hong , Wang Yui-Hsi , Arima Kazuhiko , Hanabuchi Shino , Liu Yong-Jun
Published: September 2009

Whether thymic stromal lymphopoietin (TSLP) directly induces potent human CD4+ T cell proliferation and Th2 differentiation is unknown. We report that resting and activated CD4+ T cells expressed high levels of IL-7 receptor a chain but very low levels of TSLP receptor (TSLPR) when compared with levels expressed in myeloid dendritic cells (mDCs). This was confirmed by immunohistology and flow cytometry analyses showing that only a subset of mDCs, with more activated phenotypes, expressed TSLPR in human tonsils in vivo. IL-7 induced strong STAT1, -3, and -5 activation and promoted the proliferation of naive CD4+ T cells in the presence of anti-CD3 and anti-CD28 monoclonal antibodies, whereas TSLP induced weak STAT5 activation, associated with marginally improved cell survival and proliferation, but failed to induce cell expansion and Th2 differentiation. The effect of TSLP on enhancing strong human T cell proliferation was observed only when sorted naive CD4+ T cells were cultured with mDCs at levels as low as 0.5%. TSLP could only induce naive CD4+ T cells to differentiate into Th2 cells in the presence of allogeneic mDCs. These results demonstrate that IL-7 and TSLP use different mechanisms to regulate human CD4+ T cell homeostasis.
The Croatian national open access journal platform
Authors: STOJANOVSKI Jadranka , PETRAK Jelka , MACAN Bojan
Published: September 2009

Until recently, Croatian scientific journals were accessible only in print form and only to a relatively small audience. A national online journals platform was therefore planned to offer publishers a simple tool for building online versions of their journals and to make them open access. The platform, named Hrčak, was launched in 2006, supported by governmental funds. It currently includes 170 open access (OA) journals. Most journals include backfiles from 2006 onwards; the average archived period is 6.3 years. 56.5% of the journals come from the fields of social sciences and humanities. Metadata from the Hrčak platform are regularly harvested by OA repositories. To increase the number of Croatian journals covered by relevant bibliographic and full‐text databases, Hrčak has forged links with Elsevier, Thomson Reuters and EBSCO. So far, the main achievements include assisting publishers in the process of electronic publishing, and improving accessibility to Croatian scientific output.
The Web's rich tapestry
Authors: DODDS Leigh
Published: September 2009

The Web has evolved as a hypertext environment whose value is derived from a simple ability to link resources together. The advanced linking features of some early hypertext systems might be implemented in the Web in various ways. The Semantic Web is one aspect of the continuing evolution of the Web which may be of value to the evolution of scholarly publishing and research, and may enable publishers to justify investment in the future. The key advantages are the ability to unlock value from the existing scholarly literature by enabling innovation in research tools; further encouraging the creation of a marketplace of services of value to the publishing industry; and ensuring that websites and content are well integrated into the Web as it exists now and in the future.
TRANSFER Code of Practice: the publisher's point of view
Authors: CAMPFENS Yvonne , PENTZ Ed
Published: September 2009

The movement of scholarly journals between publishers has been an established feature of the scholarly publishing landscape for many years. Transfers of journals owned by third parties (mostly societies) have proven to be particularly problematic for librarians and end‐users: the most common problems are loss of online access, cancelled subscriptions, and most notably disappearing archives. The UK Serials Group therefore brought representatives from all stakeholders to the table in an attempt to address these problems. The TRANSFER Working Group developed a Code of Practice through an open, consensus‐driven process with participation by all interested stakeholders; a legal review was also a crucial step in the development process. The development and release of the TRANSFER Code of Practice is an example of the positive effects of industry collaboration. To date, more than 25 publishers have endorsed the Code and are ‘TRANSFER Compliant’.