bluuebunny/crossref_metadata_2025 huggingface dataset:
Computer simulation of adhesion between hydrophilic and hydrophobic self-assembled monolayers in water
Authors: Pertsin Alexander , Grunze Michael
Published: August 2012

The grand canonical Monte Carlo technique and atomistic force fields are used to calculate the force-distance relations and free energies of adhesion between carboxyl and methyl terminated alkanethiolate self-assembled monolayers (SAMs) in water. Both symmetric and asymmetric confinements are considered, as formed by like and unlike SAMs, respectively. As the confinement is increased, water confined by the hydrophobic methyl terminated SAMs experiences capillary evaporation. As a consequence, the adhesion energy is determined by the direct interaction between bare SAMs. In the asymmetric system, an incomplete capillary evaporation is observed, with the number of water molecules dropped by more than an order of magnitude. The remaining water molecules are all adsorbed on the hydrophilic SAM, while the hydrophobic SAM is separated from the rest of the system by a thin vapor layer. The calculated free energies of adhesion are in acceptable agreement with experiment.
Rotating 2N-vortex solutions to the Gross-Pitaevskii equation on S2
Authors: Gelantalis Michael , Sternberg Peter
Published: August 2012

We establish the existence of rotating solutions to the Gross-Pitaevskii equation \documentclass[12pt]{minimal}\begin{document}$iU_t=\Delta U + \frac{1}{\varepsilon ^2}(1-|U|^2)U$\end{document}iUt=ΔU+1ɛ2(1−|U|2)Uposed on S2, that is for \documentclass[12pt]{minimal}\begin{document}$U:S^2\times \mathbb {R}\rightarrow \mathbb {C}.$\end{document}U:S2×R→C. These solutions possess vortices that for all time follow the vortex paths of known “relative equilibria” to the point-vortex problem on the two-sphere in the asymptotic regime ɛ ≪ 1. The approach is variational, based on minimization of the Ginzburg-Landau energy subject to a momentum constraint. We also establish orbital stability within a class of symmetric initial data.
Dielectric relaxation and alternating current conductivity of lanthanum, gadolinium, and erbium-polyvinyl alcohol doped films
Authors: Hanafy Taha A.
Published: August 2012

Fourier transform infrared (FTIR) spectrum dielectric constant, ε′, loss tangent, tan(δ), electric modulus, M*, and ac conductivity, σac, of pure polyvinyl alcohol (PVA) as well as La-, Gd-, and Er-PVA doped samples have been carried out. The dielectric properties have been studied in the temperature and frequency ranges; 300–450 K and 1 kHz–4 MHz, respectively. FTIR measurements reveal that La3+, Gd3+, and Er3+ ions form complex configuration within PVA structure. Two relaxation processes, namely, ρ and α were observed in pure PVA sample. The first process is due to the interfacial or Maxwell-Wagner-Sillers polarization. The second one is related to the micro-Brownian motion of the main chains. For doped PVA samples, α-relaxation process splits into αa and αc. This splitting is due to the segmental motion in the amorphous (αa) and crystalline (αc) phases of PVA matrix. Electric modulus analysis was discussed to understand the mechanism of the electrical transport process. The behavior of ac conductivity for all PVA samples indicates that the conduction mechanism is correlated barrier hopping.
Note: Spatial resolution of Fuji BAS-TR and BAS-SR imaging plates
Authors: Fiksel G. , Marshall F. J. , Mileham C. , Stoeckl C.
Published: August 2012

The spatial resolution of two types of imaging plates, Fuji BAS-TR and Fuji BAS-SR, has been measured using a knife-edge x-ray source of 8-keV Cu Kα radiation. The values for the spatial resolution, defined as the distance between 10% and 90% levels of the edge spread function, are 94 μm and 109 μm, respectively. The resolution values are important for quantitative analysis of x-ray and particle imaging and spectroscopic diagnostics.
The dynamics of liquid drops and their interaction with solids of varying wettabilities
Authors: Sprittles J. E. , Shikhmurzaev Y. D.
Published: August 2012

Microdrop impact and spreading phenomena are explored as an interface formation process using a recently developed computational framework. The accuracy of the results obtained from this framework for the simulation of high deformation free-surface flows is confirmed by a comparison with previous numerical studies for the large amplitude oscillations of free liquid drops. Our code's ability to produce high resolution benchmark calculations for dynamic wetting flows is then demonstrated by simulating microdrop impact and spreading on surfaces of greatly differing wettability. The simulations allow one to see features of the process which go beyond the resolution available to experimental analysis. Strong interfacial effects which are observed at the microfluidic scale are then harnessed by designing surfaces of varying wettability that allow new methods of flow control to be developed.
Plasmon excitations in sodium atomic planes: A time-dependent density functional theory study
Authors: Wang Bao-Ji , Xu Yuehua , Ke San-Huang
Published: August 2012

The collective electronic excitation in planar sodium clusters is studied by time-dependent density functional theory calculations. The formation and development of the resonances in photoabsorption spectra are investigated in terms of the shape and size of the two-dimensional (2D) systems. The nature of these resonances is revealed by the frequency-resolved induced charge densities present on a real-space grid. For long double chains, the excitation is similar to that in long single atomic chains, showing longitudinal modes, end and central transverse modes. However, for 2D planes consisting of (n × n) atoms with n being up to 16, new 2D characteristic modes emerge regardless of the symmetries considered. For in-plane excitations, besides the equivalent end mode, mixed modes with contrary polarity occur. The relation between the frequency of the primary modes and the system size is similar to the case of a 2D electron gas but with a correction due to the realistic atomic structure. For excitations perpendicular to the plane there are corner, side center, bulk center, and circuit modes. Our calculation reveals the importance of dimensionality for plasmon excitation and how it evolves from 1D to 2D.
Beam-driven three-dimensional electromagnetic strong turbulence
Authors: Graham D. B. , Robinson P. A. , Cairns Iver H.
Published: August 2012

Large scale beam-driven electromagnetic strong turbulence is investigated by numerically solving the three-dimensional electromagnetic Zakharov equations, where turbulence is driven at nonzero wavenumbers k. For electron thermal speeds ve/c ≳ 0.1, a significant fraction of driven Langmuir waves undergo electromagnetic decay into electromagnetic waves and ion-acoustic waves so that transverse waves contribute significantly to the total energy density. It is shown that as ve/c increases, the wavenumber and energy density of transverse waves produced increase. For ve/c≲0.1, beam-driven turbulence is approximately electrostatic. An approximately periodic cycle is observed, similar to previous two-dimensional electrostatic simulations, in which Langmuir waves are driven to larger mean energy densities until a series of backscatters occurs, shifting the Langmuir waves out of resonance with the driver and decreasing the wavenumber of the Langmuir waves. A low-k condensate results from which wave packets form and collapse, decreasing the mean energy density. Averaging over many of these periods, the statistical properties are calculated and the scaling behavior of the mean energy density is shown to agree well with the electrostatic two-component model prediction. When driven at nonzero k the scaling behavior is shown to depend weakly on ve/c, in contrast to when strong turbulence is driven at k = 0, where the scalings depend more strongly on ve/c.
Electron cyclotron resonance near the axis of the gas-dynamic trap
Authors: Bagulov D. S. , Kotelnikov I. A.
Published: August 2012

Propagation of an extraordinary electromagnetic wave in the vicinity of electron cyclotron resonance surface in an open linear trap is studied analytically, taking into account inhomogeneity of the magnetic field in paraxial approximation. Ray trajectories are derived from a reduced dispersion equation that makes it possible to avoid the difficulty associated with a transition from large propagation angles to the case of strictly longitudinal propagation. Our approach is based on the theory, originally developed by Zvonkov and Timofeev [Sov. J. Plasma Phys. 14, 743 (1988)], who used the paraxial approximation for the magnetic field strength, but did not consider the slope of the magnetic field lines, which led to considerable error, as has been recently noted by Gospodchikov and Smolyakova [Plasma Phys. Rep. 37, 768–774 (2011)]. We have found ray trajectories in analytic form and demonstrated that the inhomogeneity of both the magnetic field strength and the field direction can qualitatively change the picture of wave propagation and significantly affect the efficiency of electron cyclotron heating of a plasma in a linear magnetic trap. Analysis of the ray trajectories has revealed a criterion for the resonance point on the axis of the trap to be an attractor for the ray trajectories. It is also shown that a family of ray trajectories can still reach the resonance point on the axis if the latter generally repels the ray trajectories. As an example, results of general theory are applied to the electron cyclotron resonance heating experiment which is under preparation on the gas dynamic trap in the Budker Institute of Nuclear Physics [Shalashov et al., Phys. Plasmas 19, 052503 (2012)].
Efficient laser-induced 6-8 keV x-ray production from iron oxide aerogel and foil-lined cavity targets
Authors: Pérez F. , Kay J. J. , Patterson J. R. , Kane J. , Villette B. , Girard F. , Reverdin C. , May M. , Emig J. , Sorce C. , Colvin J. , Gammon S. , Jaquez J. , Satcher J. H. , Fournier K. B.
Published: August 2012

The performance of new iron-based laser-driven x-ray sources has been tested at the OMEGA laser facility for production of x rays in the 6.5–8.5 keV range. Two types of targets were experimentally investigated: low-density iron oxide aerogels (density 6−16  mg/cm3) and stainless steel foil-lined cavity targets (steel thickness 1−5  μm). The targets were irradiated by 40 beams of the OMEGA laser (500 J/beam, 1 ns pulse, wavelength 351 nm). All targets showed good coupling with the laser, with <5% of the incident laser light backscattered by the resulting plasma in all cases (typically <2.5%). The aerogel targets produced Te=2 to 3 keV, ne=0.12−0.2 critical density plasmas yielding a 40%–60% laser-to-x-ray total conversion efficiency (CE) (1.2%–3% in the Fe K-shell range). The foil cavity targets produced Te∼ 2 keV, ne∼ 0.15 critical density plasmas yielding a 60%–75% conversion efficiency (1.6%–2.2% in the Fe K-shell range). Time-resolved images illustrate that the volumetric heating of low-density aerogels allow them to emit a higher K-shell x-ray yield even though they contain fewer Fe atoms. However, their challenging fabrication process leads to a larger shot-to-shot variation than cavity targets.
δf Monte Carlo calculation of neoclassical transport in perturbed tokamaks
Authors: Kim Kimin , Park Jong-Kyu , Kramer Gerrit J. , Boozer Allen H.
Published: August 2012

Non-axisymmetric magnetic perturbations can fundamentally change neoclassical transport in tokamaks by distorting particle orbits on deformed or broken flux surfaces. This so-called non-ambipolar transport is highly complex, and eventually a numerical simulation is required to achieve its precise description and understanding. A new δf particle orbit code (POCA) has been developed for this purpose using a modified pitch-angle collision operator preserving momentum conservation. POCA was successfully benchmarked for neoclassical transport and momentum conservation in the axisymmetric configuration. Non-ambipolar particle flux is calculated in the non-axisymmetric case, and the results show a clear resonant nature of non-ambipolar transport and magnetic braking. Neoclassical toroidal viscosity (NTV) torque is calculated using anisotropic pressures and magnetic field spectrum, and compared with the combined and 1/ν NTV theory. Calculations indicate a clear δB2 scaling of NTV, and good agreement with the theory on NTV torque profiles and amplitudes depending on collisionality.
Laser induced fluorescence measurements of ion velocity and temperature of drift turbulence driven sheared plasma flow in a linear helicon plasma device
Authors: Chakraborty Thakur S. , McCarren D. , Lee T. , Fedorczak N. , Manz P. , Scime E. E. , Tynan G. R. , Xu M.
Published: August 2012

Using laser induced fluorescence (LIF), radial profiles of azimuthal ion fluid velocity and ion temperature are measured in the controlled shear de-correlation experiment (CSDX) linear helicon plasma device. Ion velocities and temperatures are derived from the measured Doppler broadened velocity distribution functions of argon ions. The LIF system employs a portable, high power (>300 mW), narrowband (∼1 MHz) tunable diode laser-based system operating at 668.614 nm. Previous studies in CSDX have shown the existence of a radially sheared azimuthal flow as measured with time delay estimation methods and Mach probes. Here, we report the first LIF measurements of sheared plasma fluid flow in CSDX. Above a critical magnetic field, the ion fluid flow profile evolves from radially uniform to peaked on axis with a distinct reversed flow region at the boundary, indicating the development of a sheared azimuthal flow. Simultaneously, the ion temperature also evolves from a radially uniform profile to a profile with a gradient. Measurements in turbulent and coherent drift wave mode dominated plasmas are compared.
An experimental exploration of the biomass gasification in a fluidized bed
Authors: Baskara Sethupathy S. , Chokkalingam V. , Natarajan E.
Published: August 2012

The present study investigates the gasification of saw dust in a bubbling fluidized bed with air and steam as a fluidizing and gasifying agent. The gasifier used for this study was 108 mm i.d. and 1400 mm high, and it was fed with saw dust at a flow rates of 5–10 kg/h. Experiments were carried out in a temperature range of 650–900 °C (50 °C intervals) with steam to biomass ratio (S/B) of 0 to 1. The behaviors of saw dust under the various parameters were studied and the optimum values were obtained. The work included the parametric study of the effects of reactor temperature, S/B ratio on gas composition, gas yield, low heating value (LHV), and carbon conversion effciency. It has been observed that the gas yields and the content of H2 in the gas increase with reactor temperature, while the yields of CO and CH4 in the product gas decrease. The experimental results showed that the fluidized bed gasification of saw dust produces gas with the maximum LHV obtained was 8100 kJ/Nm3 at 800 °C and the maximum carbon conversion efficiency was 85% at 850 °C.
Electronic tuning of integrated blue-violet GaN tunable coupled-cavity laser
Authors: Guziy O. , Grzanka S. , Leszczyński M. , Perlin P. , Schemmann M. , Salemink H. W. M.
Published: August 2012

We demonstrate an integrated tunable coupled-cavity InGaN/GaN laser with the emission wavelength centered on 409 nm. The electronic tuning range was 1.6 nm and threshold currents were 650 mA per cavity for 8.7-μm-wide laser ridges. Multimode laser emission with an average full width at half maximum of 0.3 nm was observed. We estimate the refractive index change due to free-carrier injection and optical gain to explain the experimental tuning range.
Germany differentiates its universities
Authors: Feder Toni
Published: August 2012

Winners and losers in a bid for money and prestige say the process has helped universities plan for the future. Many also see the heightened competition as good for research.
Theoretical challenges in understanding galaxy evolution
Authors: Ostriker Jeremiah P. , Naab Thorsten
Published: August 2012

The concordance cosmological model provides initial conditions and a reliable framework for simulating the evolution of primordial fluctuations into galaxies. But many unsolved problems remain.
Intrinsically disordered proteins
Authors: Tompa Peter , Han Kyou-Hoon
Published: August 2012

Researchers are discovering an ever-increasing number of proteins that perform key cellular tasks without having the fixed, three-dimensional structure once thought mandatory for a protein to do its job.
Ash from the thermal gasification of pig manure—effects on ryegrass yield, element uptake, and soil properties
Authors: Kuligowski Ksawery , Gilkes Robert John , Poulsen Tjalfe Gorm , Yusiharni Baiq Emielda
Published: August 2012

Effects of thermally gasified pig manure ash (GA) and lime-free gasified ash (LF-GA) on properties of an acidic soil (pH 4.5) and the growth and elemental uptake of ryegrass (Lolium rigidum Gaudin) were investigated. The GA was an effective liming agent (2% addition raised soil pH from 4.5 to 7.9); both GA and LF-GA increased soil electrical conductivity and bicarbonate-extractable phosphorus (P). Soil fertilised with LF-GA supported slightly higher plant dry matter (DM) yield than GA (1.5–1.7 v. 1.2–1.5 g DM/kg soil) for the first harvest, due to greater initial P availability at pH <5 than at pH >6. However, plant yields for the subsequent two harvests were similar, as soil acidity dissolved lime in untreated ash (GA) over time. Maximum yields for ash-treated soil and soil treated with mono-calcium phosphate (MCP) were similar. Relative agronomic effectiveness of P sources for three harvests, based on plant P content compared with values for MCP, were 6, 11, and 12% for GA and 19, 10, and 33% for LF-GA. Internal efficiency of P utilisation was similar for all three P sources for each harvest, indicating that differences in yield were mostly a consequence of differences in P supply. Heavy metal concentrations in plants fertilised with ash were minor and within regulatory limits. In general, application of ash did not systematically affect the concentrations of elements (Al, B, Cd, Mg, Mn, Fe, Pb, S, Se) in plants.
Peptidylarginine deiminase 2-catalyzed histone H3 arginine 26 citrullination facilitates estrogen receptor α target gene activation
Authors: Zhang Xuesen , Bolt Michael , Guertin Michael J. , Chen Wei , Zhang Sheng , Cherrington Brian D. , Slade Daniel J. , Dreyton Christina J. , Subramanian Venkataraman , Bicker Kevin L. , Thompson Paul R. , Mancini Michael A. , Lis John T. , Coonrod Scott A.
Published: August 2012

Cofactors for estrogen receptor α (ERα) can modulate gene activity by posttranslationally modifying histone tails at target promoters. Here, we found that stimulation of ERα-positive cells with 17β-estradiol (E2) promotes global citrullination of histone H3 arginine 26 (H3R26) on chromatin. Additionally, we found that the H3 citrulline 26 (H3Cit26) modification colocalizes with ERα at decondensed chromatin loci surrounding the estrogen-response elements of target promoters. Surprisingly, we also found that citrullination of H3R26 is catalyzed by peptidylarginine deiminase (PAD) 2 and not by PAD4 (which citrullinates H4R3). Further, we showed that PAD2 interacts with ERα after E2 stimulation and that inhibition of either PAD2 or ERα strongly suppresses E2-induced H3R26 citrullination and ERα recruitment at target gene promoters. Collectively, our data suggest that E2 stimulation induces the recruitment of PAD2 to target promoters by ERα, whereby PAD2 then citrullinates H3R26, which leads to local chromatin decondensation and transcriptional activation.
Coxsackievirus B3 mutator strains are attenuated in vivo
Authors: Gnädig Nina F. , Beaucourt Stéphanie , Campagnola Grace , Bordería Antonio V. , Sanz-Ramos Marta , Gong Peng , Blanc Hervé , Peersen Olve B. , Vignuzzi Marco
Published: August 2012

Based on structural data of the RNA-dependent RNA polymerase, rational targeting of key residues, and screens for Coxsackievirus B3 fidelity variants, we isolated nine polymerase variants with mutator phenotypes, which allowed us to probe the effects of lowering fidelity on virus replication, mutability, and in vivo fitness. These mutator strains generate higher mutation frequencies than WT virus and are more sensitive to mutagenic treatments, and their purified polymerases present lower-fidelity profiles in an in vitro incorporation assay. Whereas these strains replicate with WT-like kinetics in tissue culture, in vivo infections reveal a strong correlation between mutation frequency and fitness. Variants with the highest mutation frequencies are less fit in vivo and fail to productively infect important target organs, such as the heart or pancreas. Furthermore, whereas WT virus is readily detectable in target organs 30 d after infection, some variants fail to successfully establish persistent infections. Our results show that, although mutator strains are sufficiently fit when grown in large population size, their fitness is greatly impacted when subjected to severe bottlenecking, which would occur during in vivo infection. The data indicate that, although RNA viruses have extreme mutation frequencies to maximize adaptability, nature has fine-tuned replication fidelity. Our work forges ground in showing that the mutability of RNA viruses does have an upper limit, where larger than natural genetic diversity is deleterious to virus survival.
Detection of ultra-rare mutations by next-generation sequencing
Authors: Schmitt Michael W. , Kennedy Scott R. , Salk Jesse J. , Fox Edward J. , Hiatt Joseph B. , Loeb Lawrence A.
Published: August 2012

Next-generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of ∼1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, we have developed a method termed Duplex Sequencing. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors result in mutations in only one strand and can thus be discounted as technical error. We determine that Duplex Sequencing has a theoretical background error rate of less than one artifactual mutation per billion nucleotides sequenced. In addition, we establish that detection of mutations present in only one of the two strands of duplex DNA can be used to identify sites of DNA damage. We apply the method to directly assess the frequency and pattern of random mutations in mitochondrial DNA from human cells.
Self-surface assembly of cellulosomes with two miniscaffoldins on
Saccharomyces cerevisiae
for cellulosic ethanol production
Authors: Fan Li-Hai , Zhang Zi-Jian , Yu Xiao-Yu , Xue Ya-Xu , Tan Tian-Wei
Published: August 2012

Yeast to directly convert cellulose and, especially, the microcrystalline cellulose into bioethanol, was engineered through display of minicellulosomes on the cell surface of
Saccharomyces cerevisiae
. The construction and cell surface attachment of cellulosomes were accomplished with two individual miniscaffoldins to increase the display level. All of the cellulases including a celCCA (endoglucanase), a celCCE (cellobiohydrolase), and a Ccel_2454 (β-glucosidase) were cloned from
Clostridium cellulolyticum
, ensuring the thermal compatibility between cellulose hydrolysis and yeast fermentation. Cellulases and one of miniscaffoldins were secreted by α-factor; thus, the assembly and attachment to anchoring miniscaffoldin were accomplished extracellularly. Immunofluorescence microscopy, flow cytometric analysis (FACS), and cellulosic ethanol fermentation confirmed the successful display of such complex on the yeast surface. Enzyme–enzyme synergy, enzyme-proximity synergy, and cellulose–enzyme–cell synergy were analyzed, and the length of anchoring miniscaffoldin was optimized. The engineered
S. cerevisiae
was applied in fermentation of carboxymethyl cellulose (CMC), phosphoric acid-swollen cellulose (PASC), or Avicel. It showed a significant hydrolytic activity toward microcrystalline cellulose, with an ethanol titer of 1,412 mg/L. This indicates that simultaneous saccharification and fermentation of crystalline cellulose to ethanol can be accomplished by the yeast, engineered with minicellulosome.
A microRNA network regulates expression and biosynthesis of wild-type and ΔF508 mutant cystic fibrosis transmembrane conductance regulator
Authors: Ramachandran Shyam , Karp Philip H. , Jiang Peng , Ostedgaard Lynda S. , Walz Amy E. , Fisher John T. , Keshavjee Shaf , Lennox Kim A. , Jacobi Ashley M. , Rose Scott D. , Behlke Mark A. , Welsh Michael J. , Xing Yi , McCray Paul B.
Published: August 2012

Production of functional proteins requires multiple steps, including gene transcription and posttranslational processing. MicroRNAs (miRNAs) can regulate individual stages of these processes. Despite the importance of the cystic fibrosis transmembrane conductance regulator (CFTR) channel for epithelial anion transport, how its expression is regulated remains uncertain. We discovered that miRNA-138 regulates
CFTR
expression through its interactions with the transcriptional regulatory protein SIN3A. Treating airway epithelia with an miR-138 mimic increased
CFTR
mRNA and also enhanced CFTR abundance and transepithelial Cl
−
permeability independent of elevated mRNA levels. An miR-138 anti-miR had the opposite effects. Importantly, miR-138 altered the expression of many genes encoding proteins that associate with CFTR and may influence its biosynthesis. The most common
CFTR
mutation, ΔF508, causes protein misfolding, protein degradation, and cystic fibrosis. Remarkably, manipulating the miR-138 regulatory network also improved biosynthesis of CFTR-ΔF508 and restored Cl
−
transport to cystic fibrosis airway epithelia. This miRNA-regulated network directs gene expression from the chromosome to the cell membrane, indicating that an individual miRNA can control a cellular process more broadly than recognized previously. This discovery also provides therapeutic avenues for restoring CFTR function to cells affected by the most common cystic fibrosis mutation.
Approaches to the Futures of Research (Based on the Conference Keynote, British Association of Dramatherapists Conference 2011, Measure for Measures, Researching, Re-Viewing and Re-Framing Dramatherapy in Practice)
Authors: Jones Phil
Published: August 2012

This article, delivered in two parts, identifies and examines factors affecting the development of dramatherapy research. Drawing on qualitative research with Dramatherapists in a number of countries, it identifies three related challenges as a way of responding to the question, ‘What is the next developmental phase of dramatherapy research?’ The three challenges are: ‘impact’; ‘reviewing dramatherapy's relationship with qualitative and quantitative methodologies’; and ‘in depth: increasing the field's research capacity’.
Fluid balance of cyclists during a 387‐km race
Authors: Black Katherine Elizabeth , Skidmore Paula , Brown Rachel Claire
Published: August 2012

Current hydration guidelines are designed to address the fine balance between minimising dehydration while reducing the risk of hyponatremia. During prolonged cycling events small discrepancies between drinking behaviour and fluid requirements may be detrimental to health and performance. The present study aimed to investigate the hydration practices of competitors in a 387 km cycle race in order to evaluate the effect on fluid balance and monitor the prevalence of dysnatremia. Eighteen participants provided blood and urine samples pre‐ and post‐race to measure sodium and fluid balance. Sweat samples were collected via patches for analysis of sodium concentration. Body weight was measured at the start and end of the race. On average participants consumed 0.58 L h−1 of fluid. Upon completion of the race 7 of the 18 (39%) cyclists had blood sodium concentrations of 135 mmol L−1 or lower with one cyclist recording a value of 132 mmol L−1. Only two cyclists appeared to be moderately dehydrated. A post‐race questionnaire indicated cyclists were most concerned with preventing dehydration. It appears that cyclists taking part in prolonged endurance events are at more risk of hyponatremia than dehydration and do not readily change their drinking behaviour to match their sweat losses.
Explaining between-group differences in performance on timing tasks
Authors: Wearden John H. , Jones Luke A.
Published: August 2012

The article discusses interpretation of between-group differences in performance on timing tasks. First, it is shown that differences in internal clock “pacemaker speed” cannot normally be used as a coherent explanation of obtained effects, even if such differences in pacemaker speed exist. Secondly, it is shown how, in theory, modelling of performance on commonly used timing tasks like bisection and temporal generalization can illuminate between-group effects. Thirdly, the article discusses some examples of such modelling from published work and shows how some between-group differences—for example, between children of different ages, or between patients and controls—have been explained. Finally, some ambiguities in modelling are discussed—for example, the fact that different explanations of differences in performance on timing tasks between groups may be difficult or impossible to distinguish in practice.
A peculiar prevalence of p values just below .05
Authors: Masicampo E.J. , Lalande Daniel R.
Published: August 2012

In null hypothesis significance testing (NHST), p values are judged relative to an arbitrary threshold for significance (.05). The present work examined whether that standard influences the distribution of p values reported in the psychology literature. We examined a large subset of papers from three highly regarded journals. Distributions of p were found to be similar across the different journals. Moreover, p values were much more common immediately below .05 than would be expected based on the number of p values occurring in other ranges. This prevalence of p values just below the arbitrary criterion for significance was observed in all three journals. We discuss potential sources of this pattern, including publication bias and researcher degrees of freedom.
Film deposition on the inner surface of tubes using atmospheric-pressure Ar–CH4, Ar–C2H2 and Ar–C2H2–H2 plasmas: interpretation of film properties from plasma-chemical kinetics
Authors: Pothiraja Ramasamy , Engelhardt Max , Bibinov Nikita , Awakowicz Peter
Published: August 2012

A hard hydrocarbon film is deposited on the inner surface of glass tubes using a filamentary discharge at atmospheric pressure in Ar–C2H2–H2 and Ar–CH4 mixtures. Under similar conditions, a soft film is deposited with a high deposition rate in an Ar–C2H2 mixture. These differences in film hardness and deposition rate are interpreted on the basis of carbon and hydrogen elemental composition in the plasma.

The deposition rate is varied along the axis of the tubes in the Ar–C2H2–H2 plasma. This can be controlled by controlling the substrate (tube) temperature. Chemical erosion of the deposited film by hydrogen atoms is the probable reason for this effect.

The plasma conditions (gas temperature, electron distribution function and electron density) are characterized by applying optical emission spectroscopy (OES), microphotography and numerical simulation for all three gas mixtures. The density of hydrogen atoms in the inter-electrode region of the tube is determined by applying OES in all gas mixtures. The rates of precursor molecule excitation and follow-up plasma-chemical reactions are calculated on the basis of the determined plasma parameters. Correlations between plasma conditions and film properties are discussed.
Identification and quantification of the dissipative mechanisms involved in the radial permanent deformation of carbon nanotubes
Authors: Souier Tewfik , Santos Sergio , Gadelrab Karim , Al Ghaferi Amal , Chiesa Matteo
Published: August 2012

Recent advances in atomic force microscopy (AFM) are used here to determine, decouple and quantify the dissipative processes involved in the interaction between a silicon tip and a carbon nanotube (CNT). The energy dissipated per atom due to hysteretic contact processes on the CNT remains constant with increasing cantilever stored energy. The energy dissipated due to viscoelasticity, however, increases in the order of several eV nm−2 per nm of free amplitude until the CNT eventually laterally deforms. This trend is general in amplitude modulation AFM and could be used to determine the nature and effects of dissipation for other relevant nanostructures.
BiP prevents rod opsin aggregation
Authors: Athanasiou Dimitra , Kosmaoglou Maria , Kanuga Naheed , Novoselov Sergey S. , Paton Adrienne W. , Paton James C. , Chapple J. Paul , Cheetham Michael E.
Published: August 2012

Mutations in rod opsin—the light-sensitive protein of rod cells—cause retinitis pigmentosa. Many rod opsin mutations lead to protein misfolding, and therefore it is important to understand the role of molecular chaperones in rod opsin biogenesis. We show that BiP (HSPA5) prevents the aggregation of rod opsin. Cleavage of BiP with the subtilase cytotoxin SubAB results in endoplasmic reticulum (ER) retention and ubiquitylation of wild-type (WT) rod opsin (WT–green fluorescent protein [GFP]) at the ER. Fluorescence recovery after photobleaching reveals that WT-GFP is usually mobile in the ER. By contrast, depletion of BiP activity by treatment with SubAB or coexpression of a BiP ATPase mutant, BiP(T37G), decreases WT-GFP mobility to below that of the misfolding P23H mutant of rod opsin (P23H-GFP), which is retained in the ER and can form cytoplasmic ubiquitylated inclusions. SubAB treatment of P23H-GFP–expressing cells decreases the mobility of the mutant protein further and leads to ubiquitylation throughout the ER. Of interest, BiP overexpression increases the mobility of P23H-GFP, suggesting that it can reduce mutant rod opsin aggregation. Therefore inhibition of BiP function results in aggregation of rod opsin in the ER, which suggests that BiP is important for maintaining the solubility of rod opsin in the ER.
SRSF1 regulates the assembly of pre-mRNA processing factors in nuclear speckles
Authors: Tripathi Vidisha , Song David Y. , Zong Xinying , Shevtsov Sergey P. , Hearn Stephen , Fu Xiang-Dong , Dundr Miroslav , Prasanth Kannanganattu V.
Published: August 2012

The mammalian cell nucleus is compartmentalized into nonmembranous subnuclear domains that regulate key nuclear functions. Nuclear speckles are subnuclear domains that contain pre-mRNA processing factors and noncoding RNAs. Many of the nuclear speckle constituents work in concert to coordinate multiple steps of gene expression, including transcription, pre-mRNA processing and mRNA transport. The mechanism that regulates the formation and maintenance of nuclear speckles in the interphase nucleus is poorly understood. In the present study, we provide evidence for the involvement of nuclear speckle resident proteins and RNA components in the organization of nuclear speckles. SR-family splicing factors and their binding partner, long noncoding metastasis-associated lung adenocarcinoma transcript 1 RNA, can nucleate the assembly of nuclear speckles in the interphase nucleus. Depletion of SRSF1 in human cells compromises the association of splicing factors to nuclear speckles and influences the levels and activity of other SR proteins. Furthermore, on a stably integrated reporter gene locus, we demonstrate the role of SRSF1 in RNA polymerase II–mediated transcription. Our results suggest that SR proteins mediate the assembly of nuclear speckles and regulate gene expression by influencing both transcriptional and posttranscriptional activities within the cell nucleus.
Association of Lis1 with outer arm dynein is modulated in response to alterations in flagellar motility
Authors: Rompolas Panteleimon , Patel-King Ramila S. , King Stephen M.
Published: August 2012

The cytoplasmic dynein regulatory factor Lis1, which induces a persistent tight binding to microtubules and allows for transport of cargoes under high-load conditions, is also present in motile cilia/flagella. We observed that Lis1 levels in flagella of Chlamydomonas strains that exhibit defective motility due to mutation of various axonemal substructures were greatly enhanced compared with wild type; this increase was absolutely dependent on the presence within the flagellum of the outer arm dynein α heavy chain/light chain 5 thioredoxin unit. To assess whether cells might interpret defective motility as a “high-load environment,” we reduced the flagellar beat frequency of wild-type cells through enhanced viscous load and by reductive stress; both treatments resulted in increased levels of flagellar Lis1, which altered the intrinsic beat frequency of the trans flagellum. Differential extraction of Lis1 from wild-type and mutant axonemes suggests that the affinity of outer arm dynein for Lis1 is directly modulated. In cytoplasm, Lis1 localized to two punctate structures, one of which was located near the base of the flagella. These data reveal that the cell actively monitors motility and dynamically modulates flagellar levels of the dynein regulatory factor Lis1 in response to imposed alterations in beat parameters.
GATA-6 promotes cell survival by up-regulating BMP-2 expression during embryonic stem cell differentiation
Authors: Rong Li , Liu Jie , Qi Yanmei , Graham Alan M. , Parmacek Michael S. , Li Shaohua
Published: August 2012

GATA-6 is a zinc-finger transcription factor essential for early embryogenesis. Ablation of GATA-6 in mice impairs endoderm differentiation and causes apoptosis of epiblast cells. The endoderm defects have been attributed to the loss of HNF4, disabled-2, and GATA-4. However, the mechanisms underlying epiblast apoptosis are unclear. In this study we used mouse embryonic stem cell–derived embryoid bodies (EBs) as a model for peri-implantation development and found that ablation of GATA-6 causes massive apoptosis during EB differentiation. Endoderm grafting experiments and ectopic basement membrane (BM) assembly suggest that both BM and non-BM factors contribute to cell survival. Furthermore, the increased cell death in mutant EBs is accompanied by reduced expression of bone morphogenetic protein 2 (BMP-2). Chromatin immunoprecipitation reveals direct binding of GATA-6 to the Bmp2 promoter. Treatment of the mutant EBs with BMP-2 markedly suppresses apoptosis, whereas stable overexpression of the BMP antagonist noggin or a dominant-negative BMP receptor in normal EBs leads to increased apoptosis. Last, activation of SMAD1/5 by phosphorylation is significantly inhibited in the absence of GATA-6, and this is reversed by exogenous BMP-2. Treatment of normal EBs with SMAD phosphorylation inhibitor increases apoptosis. Collectively these results suggest that GATA-6 promotes cell survival by regulating endoderm expression of BMP-2 and BM during embryonic epithelial morphogenesis.
Sialylation of N-linked glycans mediates apical delivery of endolyn in MDCK cells via a galectin-9–dependent mechanism
Authors: Mo Di , Costa Simone A. , Ihrke Gudrun , Youker Robert T. , Pastor-Soler Nuria , Hughey Rebecca P. , Weisz Ora A.
Published: August 2012

The sialomucin endolyn is implicated in adhesion, migration, and differentiation of various cell types. Along rat kidney tubules, endolyn is variously localized to the apical surface and endosomal/lysosomal compartments. Apical delivery of newly synthesized rat endolyn predominates over direct lysosomal delivery in polarized Madin–Darby canine kidney cells. Apical sorting depends on terminal processing of a subset of lumenal N-glycans. Here we dissect the requirements of N-glycan processing for apical targeting and investigate the underlying mechanism. Modulation of glycan branching and subsequent polylactosamine elongation by knockdown of N-acetylglucosaminyltransferase III or V had no effect on apical delivery of endolyn. In contrast, combined but not individual knockdown of sialyltransferases ST3Gal-III, ST3Gal-IV, and ST6Gal-I, which together are responsible for addition of α2,3- and α2,6-linked sialic acids on N-glycans, dramatically decreased endolyn surface polarity. Endolyn synthesized in the presence of kifunensine, which blocks terminal N-glycan processing, reduced its interaction with several recombinant canine galectins, and knockdown of galectin-9 (but not galectin-3, -4, or -8) selectively disrupted endolyn polarity. Our data suggest that sialylation enables recognition of endolyn by galectin-9 to mediate efficient apical sorting. They raise the intriguing possibility that changes in glycosyltransferase expression patterns and/or galectin-9 distribution may acutely modulate endolyn trafficking in the kidney.
The kinesin-3 family motor KLP-4 regulates anterograde trafficking of GLR-1 glutamate receptors in the ventral nerve cord ofCaenorhabditis elegans
Authors: Monteiro Michael I. , Ahlawat Shikha , Kowalski Jennifer R. , Malkin Emily , Koushika Sandhya P. , Juo Peter
Published: August 2012

The transport of glutamate receptors from the cell body to synapses is essential during neuronal development and may contribute to the regulation of synaptic strength in the mature nervous system. We previously showed that cyclin-dependent kinase-5 (CDK-5) positively regulates the abundance of GLR-1 glutamate receptors at synapses in the ventral nerve cord (VNC) of Caenorhabditis elegans. Here we identify a kinesin-3 family motor klp-4/KIF13 in a cdk-5 suppressor screen for genes that regulate GLR-1 trafficking. klp-4 mutants have decreased abundance of GLR-1 in the VNC. Genetic analysis of klp-4 and the clathrin adaptin unc-11/AP180 suggests that klp-4 functions before endocytosis in the ventral cord. Time-lapse microscopy indicates that klp-4 mutants exhibit decreased anterograde flux of GLR-1. Genetic analysis of cdk-5 and klp-4 suggests that they function in the same pathway to regulate GLR-1 in the VNC. Interestingly, GLR-1 accumulates in cell bodies of cdk-5 but not klp-4 mutants. However, GLR-1 does accumulate in klp-4–mutant cell bodies if receptor degradation in the multivesicular body/lysosome pathway is blocked. This study identifies kinesin KLP-4 as a novel regulator of anterograde glutamate receptor trafficking and reveals a cellular control mechanism by which receptor cargo is targeted for degradation in the absence of its motor.
The essential iron-sulfur protein Rli1 is an important target accounting for inhibition of cell growth by reactive oxygen species
Authors: Alhebshi Alawiah , Sideri Theodora C. , Holland Sara L. , Avery Simon V.
Published: August 2012

Oxidative stress mediated by reactive oxygen species (ROS) is linked to degenerative conditions in humans and damage to an array of cellular components. However, it is unclear which molecular target(s) may be the primary “Achilles’ heel” of organisms, accounting for the inhibitory action of ROS. Rli1p (ABCE1) is an essential and highly conserved protein of eukaryotes and archaea that requires notoriously ROS-labile cofactors (Fe-S clusters) for its functions in protein synthesis. In this study, we tested the hypothesis that ROS toxicity is caused by Rli1p dysfunction. In addition to being essential, Rli1p activity (in nuclear ribosomal-subunit export) was shown to be impaired by mild oxidative stress in yeast. Furthermore, prooxidant resistance was decreased by RLI1 repression and increased by RLI1 overexpression. This Rlip1 dependency was abolished during anaerobicity and accentuated in cells expressing a FeS cluster–defective Rli1p construct. The protein's FeS clusters appeared ROS labile during in vitro incubations, but less so in vivo. Instead, it was primarily55FeS-cluster supply to Rli1p that was defective in prooxidant-exposed cells. The data indicate that, owing to its essential nature but dependency on ROS-labile FeS clusters, Rli1p function is a primary target of ROS action. Such insight could help inform new approaches for combating oxidative stress–related disease.
A robust approach to extract biomedical events from literature
Authors: Bui Quoc-Chinh , Sloot Peter M.A.
Published: August 2012

Motivation: The abundance of biomedical literature has attracted significant interest in novel methods to automatically extract biomedical relations from the literature. Until recently, most research was focused on extracting binary relations such as protein–protein interactions and drug–disease relations. However, these binary relations cannot fully represent the original biomedical data. Therefore, there is a need for methods that can extract fine-grained and complex relations known as biomedical events.

Results: In this article we propose a novel method to extract biomedical events from text. Our method consists of two phases. In the first phase, training data are mapped into structured representations. Based on that, templates are used to extract rules automatically. In the second phase, extraction methods are developed to process the obtained rules. When evaluated against the Genia event extraction abstract and full-text test datasets (Task 1), we obtain results with F-scores of 52.34 and 53.34, respectively, which are comparable to the state-of-the-art systems. Furthermore, our system achieves superior performance in terms of computational efficiency.

Availability: Our source code is available for academic use at http://dl.dropbox.com/u/10256952/BioEvent.zip

Contact: bqchinh@gmail.com
HSP90α deficiency does not affect immunoglobulin gene hypermutation and class switch but causes enhanced MHC class II antigen presentation
Authors: Li Yingqian , Li Shuyin , Hoshino Mari , Ishikawa Rikiya , Kajiwara Chiaki , Gao Xiang , Zhao Yaofeng , Ishido Satoshi , Udono Heiichiro , Wang Ji-Yang
Published: August 2012

Heat shock protein 90 (HSP90) is a molecular chaperone required for efficient antigen presentation and cross-presentation. In addition, HSP90 was recently reported to interact with and stabilize the activation-induced cytidine deaminase (AID) and plays a critical role in immunoglobulin gene hypermutation and class switch recombination. In mice and humans, there are two HSP90 isoforms, HSP90α and HSP90β, but the in vivo role of each isoform remains largely unknown. Here we have analyzed humoral immune responses in HSP90α-deficient mice. We found that HSP90α deficiency did not affect AID protein expression. B cell development and maturation, as well as immunoglobulin gene hypermuation and class switch, occurred normally in HSP90α-deficient mice. However, antibody production to a T-dependent antigen was elevated in the mutant mice and this was associated with enhanced MHC class II antigen presentation to T helper cells by dendritic cells. Our results reveal a previously unidentified inhibitory role for HSP90α isoform in MHC class II antigen presentation and the humoral immune response. Along with our recent finding that HSP90α is required for antigen cross-presentation, these results suggest that HSP90α controls the balance of humoral and cellular immunity by dictating the fate of presentation of exogenous antigen.