bluuebunny/crossref_metadata_2025 huggingface dataset:
Dissociation between Vascular Endothelial Growth Factor Receptor-2 and Blood Vessel Density in the Caudate Nucleus after Chronic Hydrocephalus
Authors: Deshpande Abhishek , Dombrowski Stephen M , Leichliter Anna , Krajcir Natalie , Zingales Nicholas , Inoue Masahiro , Schenk Soren , Fukamachi Kiyotaka , Luciano Mark G
Published: July 2009

Chronic hydrocephalus (CH) is characterized by the presence of ventricular enlargement, decreased cerebral blood flow (CBF), and brain tissue oxygen delivery. Although the underlying pathophysiological role of vascular endothelial growth factor (VEGF) is not clear, ischemic–hypoxic events in CH are known to trigger its release. Previously, we have shown increased VEGF receptor-2 (VEGFR-2) and blood vessel density (BVd) in the hippocampus after CH. We investigated changes in neuronal and glial VEGFR-2 density and BVd in the caudate nucleus in an experimental model of CH. Animals with CH were divided into short term (ST, 2 to 4 weeks) and long term (LT, 12 to 16 weeks) and were compared with surgical controls (SCs, 12 to 16 weeks). The cellular and BVds were estimated using immunohistochemical and stereological counting methods. Overall, percentage (%)VEGFR-2 neurons were approximately two times greater in CH (ST, LT) than in SC. By comparison, glial cell %VEGFR-2 was greater by 10% to 17% in ST and 4% to 11% lower in LT compared with that in SC. Blood vessel density was significantly lower in CH than in SC in the superficial caudate. Changes in cerebrospinal fluid ventricular volume and pressure, as well as in CBF did not correlate with either VEGFR-2 or BVd. These observed findings suggest that destructive forces may outweigh angiogenic forces and possibly show a disassociation between VEGFR-2 and BV expressions.
Microbial quorum sensing: a tool or a target for antimicrobial therapy?
Authors: Raina Sheetal , Vizio Daniela De , Odell Mark , Clements Mark , Vanhulle Sophie , Keshavarz Tajalli
Published: July 2009

Inter‐cell communication aided by released chemical signals when cell density reaches a critical concentration has been investigated for over 30 years as quorum sensing. Originally discovered in Gram‐negative bacteria, quorum‐sensing systems have also been studied extensively in Gram‐positive bacteria and dimorphic fungi. Microbial communities communicating via quorum sensing employ various chemical signals to supervise their surrounding environment, alter genetic expression and gain advantage over their competitors. These signals vary from acylhomoserine lactones to small modified or unmodified peptides to complex γ‐butyrolactone molecules. The scope of this review is to give an insight into some of the quorum‐sensing systems now known and to explore their role in microbial physiology and development of pathogenesis. Particular attention will be dedicated to the signalling molecules involved in quorum‐sensing‐mediated processes and the potential shown by some of their natural and synthetic analogues in the treatment of infections triggered by quorum sensing.
Polyamine catabolism and disease
Authors: Casero Robert A. , Pegg Anthony E.
Published: July 2009

In addition to polyamine homoeostasis, it has become increasingly clear that polyamine catabolism can play a dominant role in drug response, apoptosis and the response to stressful stimuli, and contribute to the aetiology of several pathological states, including cancer. The highly inducible enzymes SSAT (spermidine/spermine N1-acetyltransferase) and SMO (spermine oxidase) and the generally constitutively expressed APAO (N1-acetylpolyamine oxidase) appear to play critical roles in many normal and disease processes. The dysregulation of polyamine catabolism frequently accompanies several disease states and suggests that such dysregulation may both provide useful insight into disease mechanism and provide unique druggable targets that can be exploited for therapeutic benefit. Each of these enzymes has the potential to alter polyamine homoeostasis in response to multiple cell signals and the two oxidases produce the reactive oxygen species H2O2 and aldehydes, each with the potential to produce pathological states. The activity of SSAT provides substrates for APAO or substrates for the polyamine exporter, thus reducing the intracellular polyamine concentration, the net effect of which depends on the magnitude and rate of any increase in SSAT. SSAT may also influence cellular metabolism via interaction with other proteins and by perturbing the content of acetyl-CoA and ATP. The goal of the present review is to cover those aspects of polyamine catabolism that have an impact on disease aetiology or treatment and to provide a solid background in this ever more exciting aspect of polyamine biology.
Structural basis of transport of lysophospholipids by human serum albumin
Authors: Guo Shihui , Shi Xiaoli , Yang Feng , Chen Liqing , Meehan Edward J. , Bian Chuanbing , Huang Mingdong
Published: July 2009

Lysophospholipids play important roles in cellular signal transduction and are implicated in many biological processes, including tumorigenesis, angiogenesis, immunity, atherosclerosis, arteriosclerosis, cancer and neuronal survival. The intracellular transport of lysophospholipids is through FA (fatty acid)-binding protein. Lysophospholipids are also found in the extracellular space. However, the transport mechanism of lysophospholipids in the extracellular space is unknown. HSA (human serum albumin) is the most abundant carrier protein in blood plasma and plays an important role in determining the absorption, distribution, metabolism and excretion of drugs. In the present study, LPE (lysophosphatidylethanolamine) was used as the ligand to analyse the interaction of lysophospholipids with HSA by fluorescence quenching and crystallography. Fluorescence measurement showed that LPE binds to HSA with a Kd (dissociation constant) of 5.6 μM. The presence of FA (myristate) decreases this binding affinity (Kd of 12.9 μM). Moreover, we determined the crystal structure of HSA in complex with both myristate and LPE and showed that LPE binds at Sudlow site I located in subdomain IIA. LPE occupies two of the three subsites in Sudlow site I, with the LPE acyl chain occupying the hydrophobic bottom of Sudlow site I and the polar head group located at Sudlow site I entrance region pointing to the solvent. This orientation of LPE in HSA suggests that HSA is capable of accommodating other lysophospholipids and phospholipids. The study provides structural information on HSA–lysophospholipid interaction and may facilitate our understanding of the transport and distribution of lysophospholipids.
Medicare Private Practice for SLPs
Authors: Kander Mark
Published: July 2009

In July 2008, the Medicare Improvements for Patients and Providers Act (MIPPA) of 2008 (2008) was passed. This Act included a provision that will allow speech-language pathologists (SLPs) in private practice to bill the Medicare program beginning July 1, 2009. Applications for enrollment will be accepted by the Centers for Medicare and Medicaid Services (CMS) starting June 2, 2009.
Flux pinning and vortex dynamics in MgB2 doped with TiO2 and SiC inclusions
Authors: Prokhorov V. G. , Kaminsky G. G. , Svetchnikov V. L. , Park J. S. , Eom T. W. , Lee Y. P. , Kang J.-H. , Khokhlov V. A. , Mikheenko P.
Published: July 2009

The mixed-state superconducting properties of bulk MgB2+2at.%TiO2 and +8at.%SiC, prepared by in situ solid state reaction, are investigated. Analysis of the mixed-state parameters, such as the upper critical field, the coherence length, and the Ginzburg-Landau parameter, proves that MgB2+2at.%TiO2 is a high-κ type-II superconductor in the dirty limit, while MgB2+8at.%SiC corresponds to that in the moderately clean limit. It is shown that the grain-boundary pinning realized in fine-grained doped MgB2 polycrystals is of the anisotropic rather than the electron-scattering type. The field-cooled temperature dependences of the magnetic moment reveal a transition of the samples to the paramagnetic state at certain applied magnetic fields, which is treated as manifestation of the paramagnetic Meissner effect. The experimental results are discussed on the base of modern theoretical approaches.
Low-temperature phase segregation in La2∕3Ba1∕3MnO3: Manifestation of nonequilibrium thermodynamics
Authors: Beznosov A. B. , Fertman E. L. , Desnenko V. A. , Feher A. , Kajňaková M. , Ritter C. , Khalyavin D.
Published: July 2009

Thermodynamic characteristics of the perovskite-like compound La2∕3Ba1∕3MnO3, exhibiting a structural phase transformation of the martensitic type with a characteristic temperature Ts≈200K, are studied in the temperature range 2–340K. Step-like hysteretic temperature behavior of the effective heat capacity is revealed at 150–250K and attributed to the discrete kinetics and a latent heat of the martensitic transformation. The magnetic subsystem is found to exhibit a magnetic glass state below 220K and temperature hysteresis of the magnetic susceptibility clearly pronounced in the 40–100K and 180–230K regions. The Debye and Einstein temperatures, θD=230K and θE=500K, respectively, derived from the experimental Debye–Waller factors for the La∕Ba, Mn, and O sublattices, are used to refine contributions from the structural and magnetic transformations to the heat capacity and to reveal thermodynamically nonequilibrium states.
Elementary excitations and thermodynamics of zig-zag spin ladders with alternating nearest-neighbor exchange interactions
Authors: Zvyagin A. A. , Cheranovskii V. O.
Published: July 2009

A one-dimensional spin-1∕2 model in which the alternation of the exchange interactions between neighboring spins is accompanied by the next-nearest-neighbor (NNN) spin exchange (zig-zag spin ladder with alternation) is studied. The thermodynamic characteristics of the model quantum spin chain are obtained in the mean-field-like approximation. Depending on the strength of the NNN interactions, the model manifests either the spin-gapped behavior of low-lying excitations at low magnetic fields, or ferrimagnetic ordering in the ground state with gapless low-lying excitations. The system undergoes second-order or first-order quantum phase transitions, governed by the external magnetic field, NNN coupling strength, and the degree of the alternation. Hence, NNN spin–spin interactions in a dimerized quantum spin chain can produce a spontaneous magnetization. On the other hand, for quantum spin chains with a spontaneous magnetization, caused by NNN spin–spin couplings, the alternation of nearest-neighbor (NN) exchange interactions can cause destruction of that magnetization and the onset of a spin gap for low-lying excitations. Alternating NN interactions produce a spin gap between two branches of low-energy excitations, and the NNN interactions yield asymmetry of the dispersion laws of those excitations, with possible minima corresponding to incommensurate structures in the spin chain.
Magnetic ordering and charge transport in electron–doped La1−yCeyMnO3 (0.1⩽y⩽0.3) films
Authors: Prokhorov V. G. , Kaminsky G. G. , Flis V. S. , Hyun Y. H. , Park S. Y. , Lee Y. P. , Svetchnikov V. L.
Published: July 2009

The microstructure and the magnetic and transport properties of as-deposited La1−yCeyMnO3 (0.1⩽y⩽0.3) films prepared by pulsed laser deposition are investigated in a wide region of temperature and magnetic field. The microstructure analysis reveals that all films have a high c-oriented texture, an orthorhombic crystal lattice, and a negligible quantity of CeO2 inclusions. The observed strip-domain phase with a periodic spacing of about 3c, the crystal lattice of which is the same as for the basic film phase, exhibits magnetic behavior typical for the Griffiths phase. Regions of the double-period modulated phase are found at room temperature in the y=0.1 film, which is interpreted as Mn3+∕Mn2+ ordering with a partial ferromagnetic→antiferromagnetic transition at TN⩽80K. At the same time, the investigation reveals that the magnetic and transport properties of the electron–doped La1−yCeyMnO3 films, driven by cation doping, are similar to those for the hole-doped La∕Ca manganites. Therefore, one can conclude that there is no fundamental difference between the mechanisms of spin ordering and charge transport in the hole-doped and electron–doped manganites.
Effects of B and Ge codoping on minority carrier lifetime in Ga-doped Czochralski-silicon
Authors: Arivanandhan Mukannan , Gotoh Raira , Fujiwara Kozo , Uda Satoshi
Published: July 2009

We investigated the effects of B/Ge codoping on the minority carrier lifetime in gallium (Ga)-doped Czochralski-silicon (CZ-Si) crystals. Minority carrier lifetime decreased from 28 to 0.1 μs when the B concentration was increased from 1×1015 to 1×1017 cm−3 in Ga/B codoped CZ-Si crystals. The minority carrier lifetime increased from 30 to 76 μs with increasing Ge concentration from 1×1017 to 2×1020 cm−3 in Ga/Ge codoped CZ-Si crystals. Light-induced degradation experiments showed that Ga/B codoped CZ-Si degraded rapidly, while Ga/Ge codoped CZ-Si showed no degradation. Moreover, the flow pattern defect density related to grown-in microdefects in as-grown Ga/Ge codoped CZ-Si decreased with increasing Ge concentration. The experimental results are explained using a defect reaction model based on the formation of Ge-vacancy-oxygen dimer complexes in the CZ-Si crystal during postgrowth cooling.
Pyroelectric and photogalvanic crystal accelerators
Authors: Kukhtarev N. V. , Kukhtareva T. V. , Stargell G. , Wang J. C.
Published: July 2009

In this study, we have derived equations for the pyroelectric and photogalvanic contribution to the electrical charging of the photosensitive ferroelectric crystal. Standard photorefractive equations are supplemented by the equation of state for the polarization density following the Devonshire–Ginsburg–Landau (DGL) approach. The photogalvanic voltage and current is considered for a wide intensity range, which includes the cw and the pulsed photoexcitation with high intensities when the impurity is fully ionized and when the traditional linear-recombination approach is not valid. The crystal electrostatic accelerators, based on charging of ferroelectric crystals by pyroelectric and photogalvanic effects, are discussed in relation to the generation of the self-focused electron beam, x rays, and neutrons.
Solar and wind energy resources and prediction
Authors: Liu Quanhua , Miao Qinxian , Liu Jue J. , Yang Wenli
Published: July 2009

Energy and environmental issues are among the most important problems of public concern. There are increasing debates about whether to resort to drilling more oil and mining more coal or to using renewable, sustainable, and clean resources such as solar and wind energies. Through our analyses and modeling on the basis of the National Center for Environment Prediction data, we confirm that the amount of usable solar and wind energies far exceeds the world’s total energy demand, with technology feasibility being considered. We also investigated the accuracy of forecasting solar and wind energies. Forecasting is important for scheduling applications and storage of solar and wind energies. A realistic approach to maintaining uninterrupted solar-generated electricity at night and during cloudy days would be to store solar energy as heat for use on demand. It is also interesting for people to know how much solar and wind energies are available from their own house roofs and backyards. Using the advanced Google map technique, we have developed a web-based tool with which anyone can find solar and wind energy amounts at any location in the world. The tool is available at www.renewableenergyst.org. The website also provides much additional renewable energy information which is useful to a wide range of audiences, including students, educators, and the general public.
The effect of Ni doping on the magnetic and transport properties in Pr0.5Ca0.5Mn1−xNixO3 manganites
Authors: Damari L. , Pelleg J. , Gorodetsky G. , Koren Ch. , Markovich V , Shames A. , Wu Xiaodong , Mogilyanski D. , Fita I. , Wisniewski A.
Published: July 2009

Structural, magnetic, and transport properties in Pr0.5Ca0.5Mn1−xNixO3 (x=0, 0.04, 0.07, 0.1) were investigated. It is remarkable that low Ni-doping levels at Mn sites induce drastic changes in the physical properties of Pr0.5Ca0.5MnO3 due to melting of the charge ordered state and the consequent capability of Ni ions to create ferromagnetic (FM) clusters. It was found that oxygen deficient samples (3−δ=2.84±0.03) exhibit resistivities higher by four to five orders than that of their stoichiometric counterparts and do not exhibit metal-insulator transition. Only a stoichiometric x=0.04 sample with higher content of the FM phase shows metal-insulator transition at T≈80 K. A change in slope in the zero field cooling magnetization curve observed for x=0.04 and 0.07 (may be slightly oxygen deficient samples) are indicative of spin-glass-like state. Applied hydrostatic pressure of about 10 kbars reduces the temperature of charge ordering in x=0 sample by about 10 K indicating on pressure induced suppression of the Jahn–Teller distortions. In distinct contrast to the behavior of Pr0.5Ca0.5Mn1−xCrxO3 samples, an applied pressure only slightly affects magnetization of x=0.04 and 0.07 samples possibly due to the difference in magnetic states obtained by substitution of Cr3+ and Ni2+. Electron magnetic resonance (EMR) unambiguously evidences on appearance of a FM phase on Ni doping. Temperature dependence of EMR spectra allow distinguishing between the magnetic states of two 4% Ni-doped samples and to speculate on the effect of magnetic inhomogeneities on the formation of the observed magnetic properties.
Simulation of electric displacement hysteresis and strain butterfly loops in perovskite ferroelectric films
Authors: Yang Feng , Zhou Y. C. , Tang M. H. , Liu Fen
Published: July 2009

A model for the electric displacement hysteresis and strain butterfly loops of ferroelectric films under electrical loading is proposed based on an improved Preisach model for nonlinear remanent polarization. Our model shows improved displacement and strain versus electric field loops that agree reasonably well with the experimental data. Compared to the previous model, the current model, including the history-dependent electric field effect, which is always neglected in the conventional model, provides electric displacement and strain loops with a full and symmetric shape. In addition, both the loops of electric displacement and strain under intrinsic defects and injected charges have also been investigated by our model.
Anisotropic lattice changes in femtosecond laser inscribed Nd3+:MgO:LiNbO3 optical waveguides
Authors: Ródenas A. , Maestro L. M. , Ramírez M. O. , Torchia G. A. , Roso L. , Chen F. , Jaque D.
Published: July 2009

We report on the fabrication and microspectroscopy imaging of femtosecond laser written double-filament based Nd3+:MgO:LiNbO3 optical waveguides. The waveguiding high refractive-index regions are identified by blueshifts of the Nd3+ ion fluorescence lines with no deterioration in the fluorescence efficiency, whereas filamentary low-index regions are identified by both a Nd3+ line redshift and a fluorescence efficiency reduction. The lattice structural micromodifications at the origin of both waveguide formation and Nd3+ fluorescence changes have been investigated by means of confocal micro-Raman experiments. We have found that the direct laser written filaments are mainly constituted by a large density of defects, together with a marked axial compression perpendicular to the filaments (along the optical c-axis). Conversely, the high-index waveguiding regions are characterized by a pronounced anisotropic dilatation of the LiNbO3 lattice xy-planes.
Multiple phonon processes contributing to inelastic scattering during thermal boundary conductance at solid interfaces
Authors: Hopkins Patrick E.
Published: July 2009

A new model is developed that accounts for multiple phonon processes on interface transmission between two solids. By considering conservation of energy and phonon population, the decay of a high energy phonon in one material into several lower energy phonons in another material is modeled assuming diffuse scattering. The individual contributions of each of the higher order inelastic phonon processes to thermal boundary conductance are calculated and compared to the elastic contribution. The overall thermal boundary conductance from elastic and inelastic (three or more phonon processes) scattering is calculated and compared to experimental data on five different interfaces. Improvement in value and trend is observed by taking into account multiple phonon inelastic scattering. Three phonon interfacial processes are predicted to dominate the inelastic contribution to thermal boundary conductance.
Influence of self-fields on coupled waves in free electron laser with ion-channel guiding
Authors: Masoudnia L. , Maraghechi B. , Mohsenpour T.
Published: July 2009

In this study, the equilibrium orbits and their stability, under the influence of self-electric and self-magnetic fields, are analyzed. A dispersion relation for the Raman regime free electron laser with a helical wiggler magnetic field and ion-channel guiding is derived and analyzed, taking into account self-field effects of the electron beam. This dispersion relation is solved numerically to study unstable couplings between all wave modes. New unstable orbits, in the first part of the group I orbits and in the resonance region of the group II orbits, are found. It was found that self-fields reduce the growth rate of the group I orbits and increase it in the group II orbits.
Nearly symmetrical proteins: Folding pathways and transition states
Authors: Zamparo Marco , Pelizzola Alessandro
Published: July 2009

The folding pathways of the B domain of protein A have been the subject of many experimental and computational studies. Based on a statistical mechanical model, it has been suggested that the native state symmetry leads to multiple pathways, highly dependent on temperature and denaturant concentration. Experiments, however, have not confirmed this scenario. By considering four nearly symmetrical proteins, one of them being the above molecule, here we show that, if contact energies are properly taken into account, a different picture emerges from kinetic simulations of the above-mentioned model. This is characterized by a dominant folding pathway, which is consistent with the most recent experimental results. Given the simplicity of the model, we also report on a direct sampling of the transition state.
Correlation of high temperature x-ray photoemission valence band spectra and conductivity in strained LaSrFeNi oxide on SrTiO3(110)
Authors: Braun A. , Zhang X. , Sun Y. , Müller U. , Liu Z. , Erat S. , Ari M. , Grimmer H. , Mao S. S. , Graule T.
Published: July 2009

Reversible and irreversible discontinuities at around 573 and 823 K in the electric conductivity of a strained 175 nm thin film of (La0.8Sr0.2)0.95Ni0.2Fe0.8O3−δ grown by pulsed laser deposition on SrTiO3 (110) are reflected by valence band changes as monitored in photoemission and oxygen K-edge x-ray absorption spectra (XAS). The irreversible jump at 823 K is attributed to depletion of doped electron holes concomitant with reduction of Fe3+ toward Fe2+, as evidenced by oxygen and iron core level soft XAS, and possibly of a chemical origin, whereas the reversible jump at 573 K possibly originates from structural changes.
Oxygen vacancies in high dielectric constant oxides La2O3, Lu2O3, and LaLuO3
Authors: Xiong Ka , Robertson John
Published: July 2009

We present first principles calculations of the energy levels of the oxygen vacancy in La2O3, Lu2O3, and LaLuO3. The levels are found to lie above the Si gap when aligned using the experimental band offsets. In hexagonal La2O3, Lu2O3, and LaLuO3, oxygen vacancies with four neighbors behave similarly to those in HfO2, which are identified as the main electron trap, while oxygen vacancies with six neighbors have no negative charged state so that they are less important for charge trapping. Oxygen vacancies in perovskite LaLuO3 only have positive charge state so they do not act as electron trap.
Realization and performance evaluation of high speed autofocusing for direct laser lithography
Authors: Rhee Hyug-Gyo , Kim Dong-Ik , Lee Yun-Woo
Published: July 2009

The autofocusing is one of the important parts in the automated vision inspection or measurement using optical microscopes. Moreover, laser micromachining or laser lithography requires a high speed and precision autofocusing. In this paper, we propose and realize an autofocusing system using two cylindrical lenses, which is the enhanced version of the previous astigmatism method. It shows very good performances, especially very high speed and the largest range in comparison with the previous astigmatic methods. The performance of our autofocusing system was evaluated by tracing the linear stage whose position was monitored by a commercial laser interferometer. Then we applied the autofocusing to the direct laser lithographic system, and successfully fabricated circular symmetry patterns on a 300 mm diameter surface with the resolution of less than 1 μm within the defocusing range of ±50 μm. The speed of the autofocusing was 150 Hz.
Injection of carriers from a ZnO nanostructured shell to a ZnS based microsphere core
Authors: Ahn Sung Il , Lee Seong Eui , Cho Yong-Hoon , Kim Gi Ryoung , Li Song-Mei , Choi Kyung Cheol , Lee Won Hee
Published: July 2009

ZnO nanostructures were synthesized on a microsphere ZnS:Cu,Cl (ZC) with various optical emission bands. Using an electroluminescence (EL) device with a semiliquid type of active layer, the carrier injection phenomenon through the nanostructure was observed. The EL from ZnO nanorods on the cubic ZC and the ZnO plate on the hexagonal ZC showed a nonlinear voltage-color characteristic and deep blue color, respectively, as explained by the carrier injection through the ZnO nanostructures. Both carrier injection cases appear to have been caused by the lowered band-gap energy at the boundary and by the structural factors that focused the applied electric field.
Enhancement of heterogeneous nucleation of β-Sn phases in Sn-rich solders by adding minor alloying elements with hexagonal closed packed structures
Authors: Cho Moon Gi , Kim Hyun You , Seo Sun-Kyoung , Lee Hyuck Mo
Published: July 2009

The measured undercooling of pure Sn was about 30 °C due to the difficulty of nucleating a solid β-Sn phase from a liquid phase. To promote the heterogeneous nucleation of β-Sn phases, the addition of impurity elements to the solders was suggested. Among the impurity elements, alloying elements with hexagonal closed packed (hcp) structures, such as Co, Zn, Ti, and Mg, were found effective to enhance heterogeneous nucleation of β-Sn phases in Sn-rich solders. Calculations of the density functional theory indicate that the interfacial energy between β-Sn and Zn was relatively low. Minor alloying elements with hcp crystals are expected to provide more favorable heterogeneous nucleation sites for β-Sn phases.
Heterogeneous boiling-up of superheated liquid at achievable superheat threshold
Authors: Ermakov G. V. , Lipnyagov E. V. , Perminov S. A. , Gurashkin A. L.
Published: July 2009

The classical theory of homogeneous nucleation describes well the superheat threshold observed in experiments. It may be assumed therefore that homogeneous boiling-up of a liquid takes place in experiments, and the theory has been verified experimentally well. The streak photography used in this study showed that boiling-up of a superheated liquid at the threshold of the achievable superheat occurs at a limited number of surface fluctuation centers in a vessel, rather than in the bulk as one would expect with homogeneous nucleation. Thus, the homogeneous theory, which rather accurately describes the heterogeneous threshold of the achievable superheat, obviously is not confirmed in experiments.
Protein elastic network models and the ranges of cooperativity
Authors: Yang Lei , Song Guang , Jernigan Robert L.
Published: July 2009

Elastic network models (ENMs) are entropic models that have demonstrated in many previous studies their abilities to capture overall the important internal motions, with comparisons having been made against crystallographic B-factors and NMR conformational variabilities. ENMs have become an increasingly important tool and have been widely used to comprehend protein dynamics, function, and even conformational changes. However, reliance upon an arbitrary cutoff distance to delimit the range of interactions has presented a drawback for these models, because the optimal cutoff values can differ somewhat from protein to protein and can lead to quirks such as some shuffling in the order of the normal modes when applied to structures that differ only slightly. Here, we have replaced the requirement for a cutoff distance and introduced the more physical concept of inverse power dependence for the interactions, with a set of elastic network models that are parameter-free, with the distance cutoff removed. For small fluctuations about the native forms, the power dependence is the inverse square, but for larger deformations, the power dependence may become inverse 6th or 7th power. These models maintain and enhance the simplicity and generality of the original ENMs, and at the same time yield better predictions of crystallographic B-factors (both isotropic and anisotropic) and of the directions of conformational transitions. Thus, these parameter-free ENMs can be models of choice whenever elastic network models are used.
Glucocorticoid stress hormones and the effect of predation risk on elk reproduction
Authors: Creel Scott , Winnie John A. , Christianson David
Published: July 2009

Predators affect prey demography through direct predation and through the costs of antipredator behavioral responses, or risk effects. Experiments have shown that risk effects can comprise a substantial proportion of a predator's total effect on prey dynamics, but we know little about their strength in wild populations, or the physiological mechanisms that mediate them. When wolves are present, elk alter their grouping patterns, vigilance, foraging behavior, habitat selection, and diet. These responses are associated with decreased progesterone levels, decreased calf production, and reduced population size [Creel S, Christianson D, Liley S, Winnie JA (2007)
Science
315:960]. Two general mechanisms for the effect of predation risk on reproduction have been proposed: the predation stress hypothesis and the predator-sensitive-food hypothesis. Here, we used enzyme immunoassay to measure fecal glucocorticoid metabolite concentrations for 1,205 samples collected from 4 elk populations over 4 winters to test the hypothesis that the effect of predation risk on elk reproduction is mediated by chronic stress. Across populations and years, fecal glucocorticoid concentrations were not related to predator-prey ratios, progesterone concentrations or calf-cow ratios. Overall, the effect of wolf presence on elk reproduction is better explained by changes in foraging patterns that carry nutritional costs than by changes in glucocorticoid concentrations.
The Rho-Guanine Nucleotide Exchange Factor Domain of Obscurin Activates RhoA Signaling in Skeletal Muscle
Authors: Ford-Speelman Diana L. , Roche Joseph A. , Bowman Amber L. , Bloch Robert J.
Published: July 2009

Obscurin is a large (∼800-kDa), modular protein of striated muscle that concentrates around the M-bands and Z-disks of each sarcomere, where it is well positioned to sense contractile activity. Obscurin contains several signaling domains, including a rho-guanine nucleotide exchange factor (rhoGEF) domain and tandem pleckstrin homology domain, consistent with a role in rho signaling in muscle. We investigated the ability of obscurin's rhoGEF domain to interact with and activate small GTPases. Using a combination of in vitro and in vivo approaches, we found that the rhoGEF domain of obscurin binds selectively to rhoA, and that rhoA colocalizes with obscurin at the M-band in skeletal muscle. Other small GTPases, including rac1 and cdc42, neither associate with the rhoGEF domain of obscurin nor concentrate at the level of the M-bands. Furthermore, overexpression of the rhoGEF domain of obscurin in adult skeletal muscle selectively increases rhoA expression and activity in this tissue. Overexpression of obscurin's rhoGEF domain and its effects on rhoA alter the expression of rho kinase and citron kinase, both of which can be activated by rhoA in other tissues. Injuries to rodent hindlimb muscles caused by large-strain lengthening contractions increases rhoA activity and displaces it from the M-bands to Z-disks, similar to the effects of overexpression of obscurin's rhoGEF domain. Our results suggest that obscurin's rhoGEF domain signals at least in part by inducing rhoA expression and activation, and altering the expression of downstream kinases in vitro and in vivo.
Expertomica metabolite profiling: getting more information from LC-MS using the stochastic systems approach
Authors: Urban Jan , Vaněk Jan , Soukup Jiří , Štys Dalibor
Published: July 2009

Mass spectrometers are sophisticated, fine instruments which are essential in a variety applications. However, the data they produce are usually interpreted in a rather primitive way, without considering the accuracy of this data and the potential errors in identifying peaks. Our new approach corrects this situation by dividing the LC-MS output into three components: (i) signature of the analyte, (ii) random noise and (iii) systemic noise. The systemic noise is related to the instrument and to the particular experiment; its characteristics change in time and depend on the analyzed substance. Working with these components allows us to quantify the probability of peak errors and, at the same time, to retrieve some peaks which get lost in the noise when using the existing methods. Our software tool, Expertomica metabolite profiling, automatically evaluates the given instrument, detects compounds and calculates the probability of individual peaks. It does not need any artificial user-defined parameters or thresholds.

Availability: MATLAB scripts with a simple graphical user interface are free to download from http://sourceforge.net/projects/expertomica-eda/. The software reads data exported by most Thermo and Agilent spectrometers, and it can also read the more general JCAMP-DX ASCII format. Other formats will be supported on request, assuming that the user can provide representative data samples.

Contact:  urban@greentech.cz
PIQA: pipeline for Illumina G1 genome analyzer data quality assessment
Authors: Martínez-Alcántara A. , Ballesteros E. , Feng C. , Rojas M. , Koshinsky H. , Fofanov V. Y. , Havlak P. , Fofanov Y.
Published: July 2009

Summary: PIQA is a quality analysis pipeline designed to examine genomic reads produced by Next Generation Sequencing technology (Illumina G1 Genome Analyzer). A short statistical summary, as well as tile-by-tile and cycle-by-cycle graphical representation of clusters density, quality scores and nucleotide frequencies allow easy identification of various technical problems including defective tiles, mistakes in sample/library preparations and abnormalities in the frequencies of appearance of sequenced genomic reads. PIQA is written in the R statistical programming language and is compatible with bustard, fastq and scarf Illumina G1 Genome Analyzer data formats.

Availability: The PIQA pipeline, installation instructions and examples are available at the supplementary web site (http://bioinfo.uh.edu/PIQA).

Contact:  yfofanov@bioinfo.uh.edu
Removal of maternal retinoic acid by embryonic CYP26 is required for correct Nodal expression during early embryonic patterning
Authors: Uehara Masayuki , Yashiro Kenta , Takaoka Katsuyoshi , Yamamoto Masamichi , Hamada Hiroshi
Published: July 2009

The abundance of retinoic acid (RA) is determined by the balance between its synthesis by retinaldehyde dehydrogenase (RALDH) and its degradation by CYP26. In particular, the dynamic expression of three CYP26 genes controls the regional level of RA within the body. Pregastrulation mouse embryos express CYP26 but not RALDH. We now show that mice lacking all three CYP26 genes manifest duplication of the body axis as a result of expansion of the Nodal expression domain throughout the epiblast. Mouse Nodal was found to contain an RA-responsive element in intron 1 that is highly conserved among mammals. In the absence of CYP26, maternally derived RA activates Nodal expression in the entire epiblast of pregastrulation embryos via this element. These observations suggest that maternal RA must be removed by embryonic CYP26 for correct Nodal expression during embryonic patterning.
Cell type specificity of PI3K signaling in Pdk1- and Pten-deficient brains
Authors: Chalhoub Nader , Zhu Guo , Zhu Xiaoyan , Baker Suzanne J.
Published: July 2009

Loss of PTEN causes unregulated activation of downstream components of phosphatidylinositol 3-kinase (PI3K) signaling, including PDK1, and disrupts normal nervous system development and homeostasis. We tested the contribution of Pdk1 to the abnormalities induced by Pten deletion in the brain. Conditional deletion of Pdk1 caused microcephaly. Combined deletion of Pdk1 and Pten rescued hypertrophy, but not migration defects of Pten-deficient neurons. Pdk1 inactivation induced strikingly different effects on the regulation of phosphorylated Akt in glia versus neurons. Our results show Pdk1-dependent and Pdk1-independent abnormalities in Pten-deficient brains, and demonstrate cell type specific differences in feedback regulation of the ubiquitous PI3K pathway.
Epigenetic control of skull morphogenesis by histone deacetylase 8
Authors: Haberland Michael , Mokalled Mayssa H. , Montgomery Rusty L. , Olson Eric N.
Published: July 2009

Histone deacetylases (Hdacs) are transcriptional repressors with crucial roles in mammalian development. Here we provide evidence that Hdac8 specifically controls patterning of the skull by repressing a subset of transcription factors in cranial neural crest cells. Global deletion of Hdac8 in mice leads to perinatal lethality due to skull instability, and this is phenocopied by conditional deletion of Hdac8 in cranial neural crest cells. Hdac8 specifically represses the aberrant expression of homeobox transcription factors such as Otx2 and Lhx1. These findings reveal how the identity and patterning of vertebrate-specific portions of the skull are epigenetically controlled by a histone deacetylase.
Quantitative epigenetics: DNA sequence variation need not apply: Figure 1.
Authors: Richards Eric J.
Published: July 2009

Two recent reports, including one by Reinders and colleagues (pp. 939–950) in the April 15, 2009, issue ofGenes & Development, describe the construction ofArabidopsisrecombinant inbred populations that maximize epigenetic rather than genetic variation. The distribution and behavior of phenotypic variation in these populations suggest that stable epialleles can control complex quantitative traits. However, stochastic epimutation and transposon movement in these populations present some unexpected technical hurdles to implementing quantitative epigenetic analysis.
Two Seven-Transmembrane Domain MILDEW RESISTANCE LOCUS O Proteins Cofunction inArabidopsisRoot Thigmomorphogenesis
Authors: Chen Zhongying , Noir Sandra , Kwaaitaal Mark , Hartmann H. Andreas , Wu Ming-Jing , Mudgil Yashwanti , Sukumar Poornima , Muday Gloria , Panstruga Ralph , Jones Alan M.
Published: July 2009

Directional root expansion is governed by nutrient gradients, positive gravitropism and hydrotropism, negative phototropism and thigmotropism, as well as endogenous oscillations in the growth trajectory (circumnutation). Null mutations in phylogenetically related Arabidopsis thaliana genes MILDEW RESISTANCE LOCUS O 4 (MLO4) and MLO11, encoding heptahelical, plasma membrane–localized proteins predominantly expressed in the root tip, result in aberrant root thigmomorphogenesis. mlo4 and mlo11 mutant plants show anisotropic, chiral root expansion manifesting as tightly curled root patterns upon contact with solid surfaces. The defect in mlo4 and mlo11 mutants is nonadditive and dependent on light and nutrients. Genetic epistasis experiments demonstrate that the mutant phenotype is independently modulated by the Gβ subunit of the heterotrimeric G-protein complex. Analysis of expressed chimeric MLO4/MLO2 proteins revealed that the C-terminal domain of MLO4 is necessary but not sufficient for MLO4 action in root thigmomorphogenesis. The expression of the auxin efflux carrier fusion, PIN1-green fluorescent protein, the pattern of auxin-induced gene expression, and acropetal as well as basipetal auxin transport are altered at the root tip of mlo4 mutant seedlings. Moreover, addition of auxin transport inhibitors or the loss of EIR1/AGR1/PIN2 function abolishes root curling of mlo4, mlo11, and wild-type seedlings. These results demonstrate that the exaggerated root curling phenotypes of the mlo4 and mlo11 mutants depend on auxin gradients and suggest that MLO4 and MLO11 cofunction as modulators of touch-induced root tropism.
Reactivation of an Inactive Centromere Reveals Epigenetic and Structural Components for Centromere Specification in Maize
Authors: Han Fangpu , Gao Zhi , Birchler James A.
Published: July 2009

Stable maize (Zea mays) chromosomes were recovered from an unstable dicentric containing large and small versions of the B chromosome centromere. In the stable chromosome, the smaller centromere had become inactivated. This inactive centromere can be inherited from one generation to the next attached to the active version and loses all known cytological and molecular properties of active centromeres. When separated from the active centromere by intrachromosomal recombination, the inactive centromere can be reactivated. The reactivated centromere regains the molecular attributes of activity in anaphase I of meiosis. When two copies of the dicentric chromosome with one active and one inactive centromere are present, homologous chromosome pairing reduces the frequency of intrachromosomal recombination and thus decreases, but does not eliminate, the reactivation of inactive centromeres. These findings indicate an epigenetic component to centromere specification in that centromere inactivation can be directed by joining two centromeres in opposition. These findings also indicate a structural aspect to centromere specification revealed by the gain of activity at the site of the previously inactive sequences.
Aberrant mRNA Transcripts and the Nonsense-Mediated Decay Proteins UPF2 and UPF3 Are Enriched in theArabidopsisNucleolus
Authors: Kim Sang Hyon , Koroleva Olga A. , Lewandowska Dominika , Pendle Ali F. , Clark Gillian P. , Simpson Craig G. , Shaw Peter J. , Brown John W.S.
Published: July 2009

The eukaryotic nucleolus is multifunctional and involved in the metabolism and assembly of many different RNAs and ribonucleoprotein particles as well as in cellular functions, such as cell division and transcriptional silencing in plants. We previously showed that Arabidopsis thaliana exon junction complex proteins associate with the nucleolus, suggesting a role for the nucleolus in mRNA production. Here, we report that the plant nucleolus contains mRNAs, including fully spliced, aberrantly spliced, and single exon gene transcripts. Aberrant mRNAs are much more abundant in nucleolar fractions, while fully spliced products are more abundant in nucleoplasmic fractions. The majority of the aberrant transcripts contain premature termination codons and have characteristics of nonsense-mediated decay (NMD) substrates. A direct link between NMD and the nucleolus is shown by increased levels of the same aberrant transcripts in both the nucleolus and in Up-frameshift (upf) mutants impaired in NMD. In addition, the NMD factors UPF3 and UPF2 localize to the nucleolus, suggesting that the Arabidopsis nucleolus is therefore involved in identifying aberrant mRNAs and NMD.
An application of dynamic homology to morphological characters: direct optimization of setae sequences and phylogeny of the family Odontellidae (Poduromorpha, Collembola)
Authors: Agolin Mikaël , D’Haese Cyrille A.
Published: July 2009

The concept of character and the definition of the attribute are two major theoretical issues of phylogenetics. Lately, great progress has been made in the conceptual development of attributes as historical individuals undergoing series of transformations. While operational application of this ideographic concept of character has been possible since the publication of the direct optimization algorithm and POY software, it has been restricted to molecular characters only. The present paper proposes the first application of direct optimization to morphological characters, in the case study of the phylogeny of Odontellidae. This new homology regime is compared to the traditional homology scheme. The theoretical and operational limitations of the application of direct optimization to morphological characters are discussed. Some thoughts on the basics of its generalization to all morphological characters analyzed in a dynamic homology phylogenetic framework are given.  © The Willi Hennig Society 2009;.
Being Confined within? Constructions of the Good Childhood and Outdoor Play in Early Childhood Education and Care Settings in Ireland
Authors: Kernan Margaret , Devine Dympna
Published: July 2009

This study is based on a study of the experience of the outdoors in early childhood education and care settings in Ireland. Central to the analyses are the inter‐linkages drawn between constructions of a ‘good’ childhood, and children’s ‘need’ for outdoor play, as well as the contradictions which arise around competing discourses of safety and protection versus play and autonomy in the structuring of children’s everyday lives. The findings indicate that the outdoors is increasingly marginalised in young children’s everyday experiences. Conclusions are drawn with reference to the implications for the development of real and meaningful outdoor play experiences for children in early childhood education and care settings.
An anatomic basis for the communication of hypothalamic, cortical and mesolimbic circuitry in the regulation of energy balance
Authors: Kampe J. , Tschöp M.H. , Hollis J.H. , Oldfield Brian J.
Published: July 2009

Central neural control of complex feeding behaviour is likely to be influenced by a number of factors including homeostatic responses to peripheral nutrient status, cortical integration of feeding‐related cues and the underlying reward value of food. We have used retrogradely transported neurotropic viruses, as tools to map chains of synaptically‐connected neurons, in conjunction with neurochemical markers of feeding‐related peptides to expand the blueprint of the circuitries that underlie these different components of feeding behaviour. We have identified projections to insular and anterior cingulate cortex, extending from the arcuate nucleus through synaptic relays in the lateral hypothalamic area and midline thalamic nuclei. Cortically projecting neurons from the hypothalamic arcuate nucleus were found predominantly in its lateral aspects and contained anorexigenic peptides with no representation amongst more medially‐positioned neurons containing orexigenic peptides. Largely overlapping pathways were shown to project multisynaptically to the shell of the nucleus accumbens but those with origins in the arcuate nucleus had either orexigenic or anorexigenic phenotypes. Similar to the cortical projections, those relaying to the nucleus accumbens in the lateral hypothalamus contained the orexigenic peptides orexin‐A and melanin‐concentrating hormone in ∼30% of cases. Common to the neural pathways directed to all three virally‐injected areas were nodes of synaptic relays in the lateral hypothalamus and midline thalamic nuclei. These regions are well positioned to integrate sensory information about energy homeostasis and the reward value of food in the passage of this information to the ‘ingestive cortex’.