bluuebunny/crossref_metadata_2025 huggingface dataset:
Evidence for the uptake of atmospheric acetone and methanol by the Arctic Ocean during late summer DMS‐Emission plumes
Authors: Sjostedt S. J. , Leaitch W. R. , Levasseur M. , Scarratt M. , Michaud S. , Motard‐Côté J. , Burkhart J. H. , Abbatt J. P. D.
Published: May 2012

Mixing ratios of gas‐phase dimethyl sulfide (DMS), acetone and methanol were measured for the first time in the Canadian Archipelago using a proton‐transfer‐reaction mass spectrometer (PTR‐MS) onboard the CCGSAmundsen from 23 August 2008 to 12 September 2008. For the entire measurement period, there existed moderate negative correlations between both acetone (R = 0.37, p < 10−4) and methanol (R = 0.26, p < 10−4) with DMS. When elevated DMS mixing ratios were observed on a transect between Kugaaruk and Resolute, during which elevated oceanic DMS was also observed, the anticorrelations of acetone and methanol mixing ratios with DMS were stronger (R = 0.61, p < 10−4 and 0.45, p < 10−4 respectively). There were no significant correlations of the aromatic species (benzene and toluene) with DMS, and the relatively low values of benzene (mean = 12 pptv) and toluene (mean = 4 pptv) indicate little significant local or regional influence of anthropogenic sources on these observations. When the recent air parcel history was predominantly of marine influence, the DMS mixing ratios were positively correlated with wind speed whereas acetone and methanol were negatively correlated. These observations suggest that biologically active waters in the high Arctic act as a sink for acetone and methanol. While speculative, continued changes in the Arctic climate have the potential to affect levels of acetone and methanol in the polar atmosphere, either through increased levels of open ocean or increased biological productivity.
Catastrophic impact of typhoon waves on coral communities in the Ryukyu Islands under global warming
Authors: Hongo Chuki , Kawamata Hideki , Goto Kazuhisa
Published: May 2012

Typhoon‐generated storm waves generally cause mechanical damage to coral communities on present‐day reefs, and the magnitude and extent of damage is predicted to increase in the near future as a result of global warming. Therefore, a comprehensive understanding of potential future scenarios of reef ecosystems is of prime interest. This study assesses the current status of coral communities on Ibaruma reef, Ryukyu Islands, on the basis of field observations, engineering and fluid dynamic models, and calculations of wave motion, and predicts the potential effects of a super‐extreme typhoon (incident wave height,H = 20 m; wave period, T = 20 s) on the reef. On the present‐day reef, massive corals occur in shallow lagoons and tabular corals occur from the reef crest to the reef slope. The observed distribution of corals, which is frequently attacked by moderate (H = 10 m, T = 10 s) and extreme (H = 10 m, T = 15 s) typhoons, is consistent with the predictions of engineering models. Moreover, this study indicates that if a super‐extreme typhoon attacks the reef in the near future, massive corals will survive in the shallow lagoons but tabular corals on the reef crest and reef slope will be severely impacted. The findings imply that super‐extreme typhoons will cause a loss of species diversity, as the tabular corals are important reef builders and are critical to the maintenance of reef ecosystems. Consequently, reef restoration is a key approach to maintaining reef ecosystems in the wake of super‐extreme typhoons.
Reply to J.N. Perry et al
Authors: Wynne Brian , Wickson Fern
Published: May 2012

The authors of “The anglerfish deception” respond to the criticism of their article.
Charge instability of atomic-layer deposited TaSiOx insulators on Si, InP, and In0.53Ga0.47As
Authors: Afanas’ev V. V. , Chou H.-Y. , Thoan N. H. , Adelmann C. , Lin H. C. , Houssa M. , Stesmans A.
Published: May 2012

Low barriers for electrons are found to be the reason for significant charge instability at interfaces of (100)InP and (100)In0.53Ga0.47As with atomic-layer deposited TaSiOx insulators. The formation of these reduced barriers is associated with the growth of a narrow-bandgap interlayer between the semiconductor and TaSiOx, which enables electron tunneling at low electric fields and subsequent trapping in the insulator. A wide-gap passivation layer may be required to improve the performance of TaSiOx as gate insulator.
Constrained dynamics of localized excitations causes a non-equilibrium phase transition in an atomistic model of glass formers
Authors: Speck Thomas , Chandler David
Published: May 2012

Recent progress has demonstrated that trajectory space for both kinetically constrained lattice models and atomistic models can be partitioned into a liquid-like and an inactive basin with a non-equilibrium phase transition separating these behaviors. Recent work has also established that excitations in atomistic models have statistics and dynamics like those in a specific class of kinetically constrained models. But it has not been known whether the non-equilibrium phase transitions occurring in the two classes of models have similar origins. Here, we show that the origin is indeed similar. In particular, we show that the number of excitations identified in an atomistic model serves as the order parameter for the inactive–active phase transition for that model. In this way, we show that the mechanism by which excitations are correlated in an atomistic model – by dynamical facilitation – is the mechanism from which the active–inactive phase transition emerges. We study properties of the inactive phase and show that it is amorphous lacking long-range order. We also discuss the choice of dynamical order parameters.
Semiflexible polymers grafted to a solid planar substrate: Changing the structure from polymer brush to “polymer bristle”
Authors: Milchev A. , Binder Kurt
Published: May 2012

Monte Carlo simulations are presented for a coarse-grained model of polymer brushes with polymers having a varying degree of stiffness. Both linear chains and ring polymers grafted to a flat structureless non-adsorbing substrate surface are considered. Applying good solvent conditions, it is shown that with growing polymer stiffness the brush height increases significantly. The monomer density profiles for the case of ring polymers (chain length NR = 64) are very similar to the case of corresponding linear chains (NL = 32, grafting density larger by a factor of two) in the case of flexible polymers, while slight differences appear with increasing stiffness. Evidence is obtained that the chain dynamics in brushes is slowed down dramatically with increasing stiffness. Very short stiff rings (NR ⩽ 16) behave like disks, grafted to the substrate such that the vector, perpendicular to the disk plane, is oriented parallel to the substrate surface. It is suggested that such systems can undergo phase transitions to states with liquid crystalline order.
Distribution of transverse chain fluctuations in harmonically confined semiflexible polymers
Authors: Sharma Rati , Cherayil Binny J.
Published: May 2012

Two different experimental studies of polymer dynamics based on single-molecule fluorescence imaging have recently found evidence of heterogeneities in the widths of the putative tubes that surround filaments of F-actin during their motion in concentrated solution. In one [J. Glaser, D. Chakraborty, K. Kroy, I. Lauter, M. Degawa, N. Kirchesner, B. Hoffmann, R. Merkel, and M. Giesen, Phys. Rev. Lett. 105, 037801 (2010)]10.1103/PhysRevLett.105.037801, the observations were explained in terms of the statistics of a worm-like chain confined to a potential determined self-consistently by a binary collision approximation, and in the other [B. Wang, J. Guan, S. M. Anthony, S. C. Bae, K. S. Schweizer, and S. Granick, Phys. Rev. Lett. 104, 118301 (2010)]10.1103/PhysRevLett.104.118301, they were explained in terms of the scaling properties of a random fluid of thin rods. In this paper, we show, using an exact path integral calculation, that the distribution of the length-averaged transverse fluctuations of a harmonically confined weakly bendable rod (one possible realization of a semiflexible chain in a tube), is in good qualitative agreement with the experimental data, although it is qualitatively different in analytic structure from the earlier theoretical predictions. We also show that similar path integral techniques can be used to obtain an exact expression for the time correlation function of fluctuations in the tube cross section.
Comparisons of classical chemical dynamics simulations of the unimolecular decomposition of classical and quantum microcanonical ensembles
Authors: Manikandan Paranjothy , Hase William L.
Published: May 2012

Previous studies have shown that classical trajectory simulations often give accurate results for short-time intramolecular and unimolecular dynamics, particularly for initial non-random energy distributions. To obtain such agreement between experiment and simulation, the appropriate distributions must be sampled to choose initial coordinates and momenta for the ensemble of trajectories. If a molecule's classical phase space is sampled randomly, its initial decomposition will give the classical anharmonic microcanonical (RRKM) unimolecular rate constant for its decomposition. For the work presented here, classical trajectory simulations of the unimolecular decomposition of quantum and classical microcanonical ensembles, at the same fixed total energy, are compared. In contrast to the classical microcanonical ensemble, the quantum microcanonical ensemble does not sample the phase space randomly. The simulations were performed for CH4, C2H5, and Cl−---CH3Br using both analytic potential energy surfaces and direct dynamics methods. Previous studies identified intrinsic RRKM dynamics for CH4 and C2H5, but intrinsic non-RRKM dynamics for Cl−---CH3Br. Rate constants calculated from trajectories obtained by the time propagation of the classical and quantum microcanonical ensembles are compared with the corresponding harmonic RRKM estimates to obtain anharmonic corrections to the RRKM rate constants. The relevance and accuracy of the classical trajectory simulation of the quantum microcanonical ensemble, for obtaining the quantum anharmonic RRKM rate constant, is discussed.
Highly efficient accelerator of dense matter using laser-induced cavity pressure acceleration
Authors: Badziak J. , Jabłoński S. , Pisarczyk T. , Rączka P. , Krousky E. , Liska R. , Kucharik M. , Chodukowski T. , Kalinowska Z. , Parys P. , Rosiński M. , Borodziuk S. , Ullschmied J.
Published: May 2012

Acceleration of dense matter to high velocities is of high importance for high energy density physics, inertial confinement fusion, or space research. The acceleration schemes employed so far are capable of accelerating dense microprojectiles to velocities approaching 1000 km/s; however, the energetic efficiency of acceleration is low. Here, we propose and demonstrate a highly efficient scheme of acceleration of dense matter in which a projectile placed in a cavity is irradiated by a laser beam introduced into the cavity through a hole and then accelerated in a guiding channel by the pressure of a hot plasma produced in the cavity by the laser beam or by the photon pressure of the ultra-intense laser radiation trapped in the cavity. We show that the acceleration efficiency in this scheme can be much higher than that achieved so far and that sub-relativisitic projectile velocities are feasible in the radiation pressure regime.
Silicon germanium tin alloys formed by pulsed laser induced epitaxy
Authors: Stefanov S. , Conde J. C. , Benedetti A. , Serra C. , Werner J. , Oehme M. , Schulze J. , Buca D. , Holländer B. , Mantl S. , Chiussi S.
Published: May 2012

Pulsed lased induced epitaxy is used to obtain heteroepitaxial Ge1−xSnx and Si1−x−yGexSny alloys with graded composition on Si(001) substrates. The transition from Ge1−xSnx to Si1−x−yGexSny was achieved by varying the number of laser pulses accordingly with the level of intermixing between Si, Ge, and Sn. Melt duration, predicted by numerical methods, is experimentally confirmed by "in-situ" reflectivity measurements and relates, like the end reflectivity value, to the level of intermixing. The possibility to adjust concentration profiles through laser processing of Sn films on virtual germanium buffer layers for lattice engineering of Ge1−xSnx and Si1−x−yGexSny alloys on silicon substrates is demonstrated.
Combined microscopies study of the C-contamination induced by extreme-ultraviolet radiation: A surface-dependent secondary-electron-based model
Authors: Prezioso S. , Donarelli M. , Bisti F. , Palladino L. , Santucci S. , Spadoni S. , Avaro L. , Liscio A. , Palermo V. , Ottaviano L.
Published: May 2012

SiO2 and Al2O3 surfaces exposed to periodically modulated extreme ultraviolet (EUV) light (λ = 46.9 nm) have been investigated at the μm scale by optical microscopy, scanning electron microscopy, scanning Auger microscopy, atomic force microscopy, and Kelvin probe force microscopy. The formation of a carbon contamination layer preserving the same periodical modulation of the EUV dose has been observed. The mechanisms of hydrocarbon molecules deposition have been studied with the help of correlation plots between the modulated Auger signal and the corresponding EUV dose. A surface-dependent secondary-electron-based model has been proposed.
Resonant inelastic x-ray scattering of CeB6 at the Ce L1- and L3-edges
Authors: Liu Lijia , Sham Tsun-Kong , Hayashi Hisashi , Kanai Noriko , Takehara Yuki , Kawamura Naomi , Mizumaki Masaichiro , Gordon Robert A.
Published: May 2012

We report a resonant inelastic x-ray scattering (RIXS) study of crystalline CeB6. Ce Lα1,2 RIXS was measured with excitation energies resonant with the Ce L3-edge. A lifetime-broadening suppressed x-ray absorption near-edge structure (LBS-XANES), which successfully reproduced the Lα1,2 RIXS spectra over wide ranges of excitation and emission energies, was simulated using the SIM-RIXS program. A pre-edge structure in the LBS-XANES can be resolved, and many-body effects were suggested in the Lα1,2 RIXS around the Ce L3-edge energy. No convincing signs of Ce (II) or Ce (IV) states were observed in the LBS-XANES. Ce Lγ4 RIXS was measured at 302 K and 28 K with excitation energies across the Ce L1-edge. The interactions of p-valence electrons between Ce and B6 were found to be considerably small, regardless of temperature. Thus, the electronic state of CeB6 was concluded to be suitably described as a nominally Ce(4f 1)3+(e−)(B6)2− system with some hybridization among all valence orbitals of Ce and B.
First-principles study on the half-metallicity of full-Heusler alloy Co2VGa (111) surface
Authors: Han Hongpei , Gao G. Y. , Yao K. L.
Published: May 2012

A recent experimental study indicates that full-Heusler alloy Co2VGa exhibits half-metallic ferromagnetism and the magnetic moment measured at 5 K is independent of high pressure up to 12.1 kbar [T. Kanomata et al. Phys. Rev. B 82, 144415 (2010)]. Using the full potential linearized augmented plane-wave method, we here further investigate the structural, electronic, and magnetic properties of all possible (111) surfaces of Co2VGa. Both structural relaxation and calculated surface energy reveal that Ga-terminated surface is more stable than other terminations. From the analysis of the spin-polarized density of states, we find that the half-metallicity confirmed in bulk Co2VGa is lost at the Co-terminated surface but still maintained at the V- and Ga-terminated surfaces. Moreover, we also find that the atomic magnetic moments at the (111) surfaces are greatly different from the bulk values.
A master-equation approach to simulate kinetic traps during directed self-assembly
Authors: Lakerveld Richard , Stephanopoulos George , Barton Paul I.
Published: May 2012

Robust directed self-assembly of non-periodic nanoscale structures is a key process that would enable various technological breakthroughs. The dynamic evolution of directed self-assemblies towards structures with desired geometries is governed by the rugged potential energy surface of nanoscale systems, potentially leading the system to kinetic traps. To study such phenomena and to set the framework for the directed self-assembly of nanoparticles towards structures with desired geometries, the development of a dynamic model involving a master equation to simulate the directed self-assembly process is presented. The model describes the probability of each possible configuration of a fixed number of nanoparticles on a domain, including parametric sensitivities that can be used for optimization, as a function of time during self-assembly. An algorithm is presented that solves large-scale instances of the model with linear computational complexity. Case studies illustrate the influence of several degrees of freedom on directed self-assembly. A design approach that systematically decomposes the ergodicity of the system to direct self-assembly of a targeted configuration with high probability is illustrated. The prospects for extending such an approach to larger systems using coarse graining techniques are also discussed.
A pressure gauge based on gas density measurement from analysis of the thermal noise of an atomic force microscope cantilever
Authors: Seo Dongjin , Paul Mark R. , Ducker William A.
Published: May 2012

We describe a gas-density gauge based on the analysis of the thermally-driven fluctuations of an atomic force microscope (AFM) cantilever. The fluctuations are modeled as a ring-down of a simple harmonic oscillator, which allows fitting of the resonance frequency and damping of the cantilever, which in turn yields the gas density. The pressure is obtained from the density using the known equation of state. In the range 10–220 kPa, the pressure readings from the cantilever gauge deviate by an average of only about 5% from pressure readings on a commercial gauge. The theoretical description we use to determine the pressure from the cantilever motion is based upon the continuum hypothesis, which sets a minimum pressure for our analysis. It is anticipated that the cantilever gauge could be extended to measure lower pressures given a molecular theoretical description. Alternatively, the gauge could be calibrated for use in the non-continuum range. Our measurement technique is similar to previous AFM cantilever measurements, but the analysis produces improved accuracy.
Relief of surface stress at steps during displacive adsorption of As on Si(111)
Authors: Zheng C. X. , Tang W. X. , Jesson D. E.
Published: May 2012

The displacive adsorption of As on 1 × 1 Si(111) is examined using surface electron microscopy. High temperature adsorption experiments are used to reduce the As chemical potential and identify regions of enhanced As incorporation in the vicinity of steps. This is explained by a reduction in tensile surface stress associated with 1 × 1 As:Si(111). Cycling the incident As flux on and off creates surface roughening via respective displacive adsorption and evaporation of As. This roughness facilitates increased 1 × 1 As:Si(111) coverage during As deposition due to surface stress relief at steps.
Shear-mode magnetostrictive/piezoelectric composite with an enhanced magnetoelectric coefficient
Authors: Wang Yaojin , Hasanyan D. , Li Jiefang , Viehland D. , Luo Haosu
Published: May 2012

A magnetoelectric (ME) laminate heterostructure consisting of two shear-mode piezoelectric Pb(Mg1/3Nb2/3)O3-30PbTiO3 (PMN-PT) single crystal layers, a longitudinally magnetized magnetostrictive Tb0.3Dy0.7Fe1.92 alloy plate, and a mechanical clamping brass substrate has been demonstrated that has a notably superior ME effect relative to previous laminate configurations of these two materials. A giant ME coefficient of 7.5 V/(cm Oe) at low frequencies under an optimal dc magnetic bias of ∼400 Oe was found. The superior ME effects originate from the nature of heterostructure design, which allows the PMN-PT single crystals to operate in a shear mode that has maximum electro-mechanical coupling (i.e., d15 = 6800 pC/N).
Communication: A minimal model for the diffusion-relaxation backbone dynamics of proteins
Authors: Kneller Gerald R. , Hinsen Konrad , Calligari Paolo
Published: May 2012

We present a model for the local diffusion-relaxation dynamics of the Cα-atoms in proteins describing both the diffusive short-time dynamics and the asymptotic long-time relaxation of the position autocorrelation functions. The relaxation rate spectra of the latter are represented by shifted gamma distributions, where the standard gamma distribution describes anomalous slow relaxation in macromolecular systems of infinite size and the shift accounts for a smallest local relaxation rate in macromolecules of finite size. The resulting autocorrelation functions are analytic for any time t ⩾ 0. Using results from a molecular dynamics simulation of lysozyme, we demonstrate that the model fits the position autocorrelation functions of the Cα-atoms exceptionally well and reveals moreover a strong correlation between the residue's solvent-accessible surface and the fitted model parameters.
Dispersal will limit ability of mammals to track climate change in the Western Hemisphere
Authors: Schloss Carrie A. , Nuñez Tristan A. , Lawler Joshua J.
Published: May 2012

As they have in response to past climatic changes, many species will shift their distributions in response to modern climate change. However, due to the unprecedented rapidity of projected climatic changes, some species may not be able to move their ranges fast enough to track shifts in suitable climates and associated habitats. Here, we investigate the ability of 493 mammals to keep pace with projected climatic changes in the Western Hemisphere. We modeled the velocities at which species will likely need to move to keep pace with projected changes in suitable climates. We compared these velocities with the velocities at which species are able to move as a function of dispersal distances and dispersal frequencies. Across the Western Hemisphere, on average, 9.2% of mammals at a given location will likely be unable to keep pace with climate change. In some places, up to 39% of mammals may be unable to track shifts in suitable climates. Eighty-seven percent of mammalian species are expected to experience reductions in range size and 20% of these range reductions will likely be due to limited dispersal abilities as opposed to reductions in the area of suitable climate. Because climate change will likely outpace the response capacity of many mammals, mammalian vulnerability to climate change may be more extensive than previously anticipated.
G-protein–mediated inhibition of the Trp channel TRPM1 requires the Gβγ dimer
Authors: Shen Yin , Rampino Melissa Ann F. , Carroll Reed C. , Nawy Scott
Published: May 2012

ON bipolar cells are critical for the function of the ON pathway in the visual system. They express a metabotropic glutamate receptor (mGluR6) that, when activated, couples to the G
o
class of G protein. The channel that is primarily responsible for the synaptic response has been recently identified as the transient receptor potential cation channel subfamily M member 1 (TRPM1); TRPM1 is negatively coupled to the mGluR6/Go cascade such that activation of the cascade results in closure of the channel. Light indirectly opens TRPM1 by reducing transmitter release from presynaptic photoreceptors, resulting in a decrease in mGluR6 activation. Conversely, in the dark, binding of synaptic glutamate to mGluR6 inhibits TRPM1 current. Closure of TRPM1 by G-protein activation in the dark is a critical step in the process of ON bipolar cell signal transduction, but the precise pathway linking these two events is not understood. To address this question, we measured TRPM1 activity in retinal bipolar cells, in human ependymal melanocytes (HEMs) that endogenously express TRPM1, and in HEK293 cells transfected with TRPM1. Dialysis of the Gβγ subunit dimer, but not Gα
o
, closed TRPM1 channels in every cell type that we tested. In addition, activation of an endogenous G-protein–coupled receptor pathway in HEK293 cells that releases Gβγ without activating Go protein also closed TRPM1 channels. These results suggest a model in which the Gβγ dimer that is released as a result of the dissociation from Gα
o
upon activation of mGluR6 closes the TRPM1 channel, perhaps via a direct interaction.
Regulatory changes contribute to the adaptive enhancement of thermogenic capacity in high-altitude deer mice
Authors: Cheviron Zachary A. , Bachman Gwendolyn C. , Connaty Alex D. , McClelland Grant B. , Storz Jay F.
Published: May 2012

In response to hypoxic stress, many animals compensate for a reduced cellular O
2
supply by suppressing total metabolism, thereby reducing O
2
demand. For small endotherms that are native to high-altitude environments, this is not always a viable strategy, as the capacity for sustained aerobic thermogenesis is critical for survival during periods of prolonged cold stress. For example, survivorship studies of deer mice (
Peromyscus maniculatus
) have demonstrated that thermogenic capacity is under strong directional selection at high altitude. Here, we integrate measures of whole-organism thermogenic performance with measures of metabolic enzyme activities and genomic transcriptional profiles to examine the mechanistic underpinnings of adaptive variation in this complex trait in deer mice that are native to different elevations. We demonstrate that highland deer mice have an enhanced thermogenic capacity under hypoxia compared with lowland conspecifics and a closely related lowland species,
Peromyscus leucopus
. Our findings suggest that the enhanced thermogenic performance of highland deer mice is largely attributable to an increased capacity to oxidize lipids as a primary metabolic fuel source. This enhanced capacity for aerobic thermogenesis is associated with elevated activities of muscle metabolic enzymes that influence flux through fatty-acid oxidation and oxidative phosphorylation pathways in high-altitude deer mice and by concomitant changes in the expression of genes in these same pathways. Contrary to predictions derived from studies of humans at high altitude, our results suggest that selection to sustain prolonged thermogenesis under hypoxia promotes a shift in metabolic fuel use in favor of lipids over carbohydrates.
Repair complexes of FEN1 endonuclease, DNA, and Rad9-Hus1-Rad1 are distinguished from their PCNA counterparts by functionally important stability
Authors: Querol-Audí Jordi , Yan Chunli , Xu Xiaojun , Tsutakawa Susan E. , Tsai Miaw-Sheue , Tainer John A. , Cooper Priscilla K. , Nogales Eva , Ivanov Ivaylo
Published: May 2012

Processivity clamps such as proliferating cell nuclear antigen (PCNA) and the checkpoint sliding clamp Rad9/Rad1/Hus1 (9-1-1) act as versatile scaffolds in the coordinated recruitment of proteins involved in DNA replication, cell-cycle control, and DNA repair. Association and handoff of DNA-editing enzymes, such as flap endonuclease 1 (FEN1), with sliding clamps are key processes in biology, which are incompletely understood from a mechanistic point of view. We have used an integrative computational and experimental approach to define the assemblies of FEN1 with double-flap DNA substrates and either proliferating cell nuclear antigen or the checkpoint sliding clamp 9-1-1. Fully atomistic models of these two ternary complexes were developed and refined through extensive molecular dynamics simulations to expose their conformational dynamics. Clustering analysis revealed the most dominant conformations accessible to the complexes. The cluster centroids were subsequently used in conjunction with single-particle electron microscopy data to obtain a 3D EM reconstruction of the human 9-1-1/FEN1/DNA assembly at 18-Å resolution. Comparing the structures of the complexes revealed key differences in the orientation and interactions of FEN1 and double-flap DNA with the two clamps that are consistent with their respective functions in providing inherent flexibility for lagging strand DNA replication or inherent stability for DNA repair.
PKCα is genetically linked to memory capacity in healthy subjects and to risk for posttraumatic stress disorder in genocide survivors
Authors: de Quervain Dominique J.-F. , Kolassa Iris-Tatjana , Ackermann Sandra , Aerni Amanda , Boesiger Peter , Demougin Philippe , Elbert Thomas , Ertl Verena , Gschwind Leo , Hadziselimovic Nils , Hanser Edveena , Heck Angela , Hieber Petra , Huynh Kim-Dung , Klarhöfer Markus , Luechinger Roger , Rasch Björn , Scheffler Klaus , Spalek Klara , Stippich Christoph , Vogler Christian , Vukojevic Vanja , Stetak Attila , Papassotiropoulos Andreas
Published: May 2012

Strong memory of a traumatic event is thought to contribute to the development and symptoms of posttraumatic stress disorder (PTSD). Therefore, a genetic predisposition to build strong memories could lead to increased risk for PTSD after a traumatic event. Here we show that genetic variability of the gene encoding PKCα (PRKCA) was associated with memory capacity—including aversive memory—in nontraumatized subjects of European descent. This finding was replicated in an independent sample of nontraumatized subjects, who additionally underwent functional magnetic resonance imaging (fMRI). fMRI analysis revealedPRKCAgenotype-dependent brain activation differences during successful encoding of aversive information. Further, the identified genetic variant was also related to traumatic memory and to the risk for PTSD in heavily traumatized survivors of the Rwandan genocide. Our results indicate a role for PKCα in memory and suggest a genetic link between memory and the risk for PTSD.
Functional intestinal stem cells after Paneth cell ablation induced by the loss of transcription factor Math1 (Atoh1)
Authors: Durand Aurélie , Donahue Bridgitte , Peignon Grégory , Letourneur Franck , Cagnard Nicolas , Slomianny Christian , Perret Christine , Shroyer Noah F. , Romagnolo Béatrice
Published: May 2012

Intestinal epithelium has the capacity to self-renew and generate differentiated cells through the existence of two types of epithelial stem cells: active crypt base columnar cells (CBCs) and quiescent +4 cells. The behaviors of these cells are regulated both by intrinsic programs and by extrinsic signals sent by neighboring cells, which define the niche. It is clear that the β-catenin pathway acts as an essential intrinsic signal for the maintenance and proliferation of CBC, and it was recently proposed that Paneth cells provide a crucial niche by secreting Wingless/Int (Wnt) ligands. Here, we examined the effect of disrupting the intestinal stem cell niche by inducible deletion of the transcription factor Math1 (Atoh1), an essential driver of secretory cell differentiation. We found that complete loss of Paneth cells attributable to Math1 deficiency did not perturb the crypt architecture and allowed the maintenance and proliferation of CBCs. Indeed, Math1-deficient crypt cells tolerated in vivo Paneth cell loss and maintained active β-catenin signaling but could not grow ex vivo without exogenous Wnt, implying that, in vivo, underlying mucosal cells act as potential niche. Upon irradiation, Math1-deficient crypt cells regenerated and CBCs continued cycling. Finally, CBC stem cells deficient in adenomatous polyposis coli (Apc) and Math1 were able to promote intestinal tumorigenesis. We conclude that in vivo, Math1-deficient crypts counteract the absence of Paneth cell-derived Wnts and prevent CBC stem cell exhaustion.
LPS remodeling is an evolved survival strategy for bacteria
Authors: Li Yanyan , Powell Daniel A. , Shaffer Scott A. , Rasko David A. , Pelletier Mark R. , Leszyk John D. , Scott Alison J. , Masoudi Ali , Goodlett David R. , Wang Xiaoyuan , Raetz Christian R. H. , Ernst Robert K.
Published: May 2012

Maintenance of membrane function is essential and regulated at the genomic, transcriptional, and translational levels. Bacterial pathogens have a variety of mechanisms to adapt their membrane in response to transmission between environment, vector, and human host. Using a well-characterized model of lipid A diversification (
Francisella
), we demonstrate temperature-regulated membrane remodeling directed by multiple alleles of the lipid A-modifying
N
-acyltransferase enzyme, LpxD. Structural analysis of the lipid A at environmental and host temperatures revealed that the LpxD1 enzyme added a 3-OH C18 acyl group at 37 °C (host), whereas the LpxD2 enzyme added a 3-OH C16 acyl group at 18 °C (environment). Mutational analysis of either of the individual
Francisella lpxD
genes altered outer membrane (OM) permeability, antimicrobial peptide, and antibiotic susceptibility, whereas only the
lpxD1
-null mutant was attenuated in mice and subsequently exhibited protection against a lethal WT challenge. Additionally, growth-temperature analysis revealed transcriptional control of the
lpxD
genes and posttranslational control of the LpxD1 and LpxD2 enzymatic activities. These results suggest a direct mechanism for LPS/lipid A-level modifications resulting in alterations of membrane fluidity, as well as integrity and may represent a general paradigm for bacterial membrane adaptation and virulence-state adaptation.
Linking agent-based models and stochastic models of financial markets
Authors: Feng Ling , Li Baowen , Podobnik Boris , Preis Tobias , Stanley H. Eugene
Published: May 2012

It is well-known that financial asset returns exhibit fat-tailed distributions and long-term memory. These empirical features are the main objectives of modeling efforts using (i) stochastic processes to quantitatively reproduce these features and (ii) agent-based simulations to understand the underlying microscopic interactions. After reviewing selected empirical and theoretical evidence documenting the behavior of traders, we construct an agent-based model to quantitatively demonstrate that “fat” tails in return distributions arise when traders share similar technical trading strategies and decisions. Extending our behavioral model to a stochastic model, we derive and explain a set of quantitative scaling relations of long-term memory from the empirical behavior of individual market participants. Our analysis provides a behavioral interpretation of the long-term memory of absolute and squared price returns: They are directly linked to the way investors evaluate their investments by applying technical strategies at different investment horizons, and this quantitative relationship is in agreement with empirical findings. Our approach provides a possible behavioral explanation for stochastic models for financial systems in general and provides a method to parameterize such models from market data rather than from statistical fitting.
Fluorescence lifetime snapshots reveal two rapidly reversible mechanisms of photoprotection in live cells of
Chlamydomonas reinhardtii
Authors: Amarnath Kapil , Zaks Julia , Park Samuel D. , Niyogi Krishna K. , Fleming Graham R.
Published: May 2012

Photosynthetic organisms avoid photodamage to photosystem II (PSII) in variable light conditions via a suite of photoprotective mechanisms called nonphotochemical quenching (NPQ), in which excess absorbed light is dissipated harmlessly. To quantify the contributions of different quenching mechanisms to NPQ, we have devised a technique to measure the changes in chlorophyll fluorescence lifetime as photosynthetic organisms adapt to varying light conditions. We applied this technique to measure the fluorescence lifetimes responsible for the predominant, rapidly reversible component of NPQ, qE, in living cells of
Chlamydomonas reinhardtii
. Application of high light to dark-adapted cells of
C. reinhardtii
led to an increase in the amplitudes of 65 ps and 305 ps chlorophyll fluorescence lifetime components that was reversed after the high light was turned off. Removal of the pH gradient across the thylakoid membrane linked the changes in the amplitudes of the two components to qE quenching. The rise times of the amplitudes of the two components were significantly different, suggesting that the changes are due to two different qE mechanisms. We tentatively suggest that the changes in the 65 ps component are due to charge-transfer quenching in the minor light-harvesting complexes and that the changes in the 305 ps component are due to aggregated light-harvesting complex II trimers that have detached from PSII. We anticipate that this technique will be useful for resolving the various mechanisms of NPQ and for quantifying the timescales associated with these mechanisms.
HCS-Analyzer: open source software for high-content screening data correction and analysis
Authors: Ogier Arnaud , Dorval Thierry
Published: May 2012

Motivation: High-throughput screening is a powerful technology principally used by pharmaceutical industries allowing the identification of molecules of interest within large libraries. Originally target based, cellular assays provide a way to test compounds (or other biological material such as small interfering RNA) in a more physiologically realistic in vitro environment. High-content screening (HCS) platforms are now available at lower cost, giving the opportunity for universities or research institutes to access those technologies for research purposes. However, the amount of information extracted from each experiment is multiplexed and hence difficult to handle. In such context, there is an important need for an easy-to-use, but still powerful software able to manage multidimensional screening data by performing adapted quality control and classification. HCS-analyzer includes: a user-friendly interface specifically dedicated to HCS readouts, an automated approach to identify systematic errors potentially occurring during screening and a set of tools to classify, cluster and identify phenotypes of interest among large and multivariate data.

Availability: The application, the C# .Net source code, as well as detailed documentation, are freely available at the following URL: http://hcs-analyzer.ip-korea.org.

Contact:  dorvalt@ip-korea.org

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Incorporating Global Health and International Experience into Your Career
Authors: Pettigrew Luisa , Ramsay Robin
Published: May 2012

There is a great deal of enthusiasm among future and new GPs wishing to engage in global health-related activities and gain international experience. Altruism and idealism to advocate for greater worldwide equality in health, as well as a passion to learn and share experiences, are key motivating factors behind this. Yet, despite enthusiasm, incorporating global health and international experiences into your career can be challenging and may be met with resistance. This article will emphasize that incorporating global health and acquiring international experience throughout your career as a GP is both relevant and achievable. It will then go on to provide the information required in order to help take enthusiasm a stage further into action.
A mechanism for the coordination of proliferation and differentiation by spatial regulation of Fus2p in budding yeast
Authors: Kim Junwon , Rose Mark D.
Published: May 2012

Yeast cells induce the genes required for mating prior to the completion of mitosis. To ensure proper cell cycle progression prior to mating differentiation, a key cytoplasmic regulator of cell fusion, Fus2p, is sequestered in the nucleus by cyclin-dependent kinase (Cdk). In response to pheromone signaling, the mitogen-activated protein kinase Fus3p phosphorylates Ser 84 in Fus2p to drive nuclear export. We found that Fus3p becomes active and phosphorylates S84 as early as S phase, raising the question of how Cdk prevents inappropriate activation of Fus2p. Countering Fus3p, Cdk and a p21-activated kinase, Cla4p, maintain Fus2p's nuclear localization by phosphorylating Ser 67, which drives nuclear import and inhibits nuclear export. When Cdk and Cla4p activities drop after cell division, Fus3p promotes Fus2p export both via S84 phosphorylation and by down-regulating S67 phosphorylation. Thus, potential premature activation of Fus2p in mitosis is prevented by cell cycle-dependent phosphorylation that overrides the mating pheromone-induced phosphorylation that drives nuclear export.
Recruitment of sphingosine kinase to presynaptic terminals by a conserved muscarinic signaling pathway promotes neurotransmitter release
Authors: Chan Jason P. , Hu Zhitao , Sieburth Derek
Published: May 2012

Sphingolipids are potent lipid second messengers that regulate cell differentiation, migration, survival, and secretion, and alterations in sphingolipid signaling have been implicated in a variety of diseases. However, how sphingolipid levels are regulated, particularly in the nervous system, remains poorly understood. Here, we show that the generation of sphingosine-1-phosphate by sphingosine kinase (SphK) promotes neurotransmitter release. Electrophysiological, imaging, and behavioral analyses ofCaenorhabditis elegansmutants lacking sphingosine kinasesphk-1indicate that neuronal development is normal, but there is a significant defect in neurotransmitter release from neuromuscular junctions. SPHK-1 localizes to discrete, nonvesicular regions within presynaptic terminals, and this localization is critical for synaptic function. Muscarinic agonists cause a rapid increase in presynaptic SPHK-1 abundance, whereas reduction of endogenous acetylcholine production results in a rapid decrease in presynaptic SPHK-1 abundance. Muscarinic regulation of presynaptic SPHK-1 abundance is mediated by a conserved presynaptic signaling pathway composed of the muscarinic acetylcholine receptor GAR-3, the heterotrimeric G protein Gαq, and its effector, Trio RhoGEF. SPHK-1 activity is required for the effects of muscarinic signaling on synaptic transmission. This study shows that SPHK-1 promotes neurotransmitter release in vivo and identifies a novel muscarinic pathway that regulates SphK abundance at presynaptic terminals.
syn-5,10,15-Tris(dichloromethyl)-5,10,15-trihydroxy-5H-diindeno[1,2-a:1′,2′-c]fluorene dichloromethane 0.82-solvate
Authors: Morrison Gregory W. , Fronczek Frank R. , Watkins Steven F.
Published: May 2012

The title compound, C30H18Cl6O3·0.82CH2Cl2, consists of a slightly cup-shaped seven-ring truxene nucleus with hydroxy and dichloromethyl substituents at stereocenters 5R/S, 10R/S and 15R/S. C—Cl distances are in the range 1.759 (4)–1.783 (3) Å. Solvent channels parallel to the b axis appear to be partially occupied by highly disordered dichloromethane solvent molecules, the contribution of which were removed from the refinement with the SQUEEZE procedure in PLATON [Spek (2009). Acta Cryst. D65, 148–155]. Only one of the OH groups forms a hydrogen bond, which is intermolecular to another OH group, forming centrosymmetric dimers in the crystal.
Pure acoustic wave propagation in transversely isotropic media by the pseudospectral method
Authors: Chu Chunlei , Macy Brian K. , Anno Phil D.
Published: May 2012

Seismic wave propagation in transversely isotropic (TI) media is commonly described by a set of coupled partial differential equations, derived from the acoustic approximation. These equations produce pure P‐wave responses in elliptically anisotropic media but generate undesired shear‐wave components for more general TI anisotropy. Furthermore, these equations suffer from instabilities when the anisotropy parameter ε is less than δ. One solution to both problems is to use pure acoustic anisotropic wave equations, which can produce pure P‐waves without any shear‐wave contaminations in both elliptical and anelliptical TI media. In this paper, we propose a new pure acoustic transversely isotropic wave equation, which can be conveniently solved using the pseudospectral method. Like most other pure acoustic anisotropic wave equations, our equation involves complicated pseudo‐differential operators in space which are difficult to handle using the finite difference method. The advantage of our equation is that all of its model parameters are separable from the spatial differential and pseudo‐differential operators; therefore, the pseudospectral method can be directly applied. We use phase velocity analysis to show that our equation, expressed in a summation form, can be properly truncated to achieve the desired accuracy according to anisotropy strength. This flexibility allows us to save computational time by choosing the right number of summation terms for a given model. We use numerical examples to demonstrate that this new pure acoustic wave equation can produce highly accurate results, completely free from shear‐wave artefacts. This equation can be straightforwardly generalized to tilted TI media.
Guidelines adherence and hypertension control at a tertiary hospital in Malaysia
Authors: Ahmad Nafees , Hassan Yahaya , Tangiisuran Balamurugan , Meng Ong Loke , Aziz Noorizan Abd , Ahmad Fiaz‐ud‐Din , Atif Muhammad
Published: May 2012

Rationale, aims and objectives  Existing literature suggests that doctors' poor adherence with guidelines is one of the major contributing factors to suboptimal control of hypertension. This study aims to evaluate doctors' adherence with Malaysian clinical practice guideline (CPG 2008) in a tertiary care hospital, and factors associated with guideline adherence and hypertension control.

Methods  This was a cross‐sectional study conducted at Hospital Pulau Pinang, Penang, Malaysia. Prescriptions written by 26 enrolled doctors to 650 established hypertensive outpatients (25 prescriptions per enrolled doctor) were noted on visit 1 along with patients' demographic and clinical data. The noted prescriptions were classified either as compliant or non‐compliant to CPG (2008). Five hundred twenty (80%) of the enrolled patients (20 patients per enrolled doctor) were followed for one more visit. Blood pressure (BP) noted on visit 2 was related to the prescription written on visit 1. SPSS 16 (SPSS Inc., Chicago, IL, USA) was used for data analysis.

Results  Three hundred forty‐nine (67.1%) patients received guidelines compliant pharmacotherapy. In multivariate analysis, hypertension clinic had significant negative association with guidelines adherence. Two hundred sixty‐five patients (51%) were at goal BP on visit 2. In multivariate analysis, angiotensin‐converting enzyme inhibitors and guidelines adherence had significant positive, while renal disease, diabetes mellitus and diabetic clinic had significant negative association with hypertension control.

Conclusions  An overall fair level of adherence with guidelines and better control of hypertension was observed. Guidelines compliant practices resulted in better control of hypertension. The gaps between what guidelines recommend and clinical practice were especially seen in the pharmacotherapy of uncomplicated hypertension and hypertension with diabetes mellitus and renal disease.