bluuebunny/crossref_metadata_2025 huggingface dataset:
Micro‐topography creates biogeochemical hot spots in wetlands
Authors: Bhattacharya Atreyee
Published: October 2012

Interventions in wetlands could improve water quality, as wetlands regulate not only nutrients such as nitrogen and sulfur but also pollutants in the waters that flow through them. Biological and chemical processes maintain conditions for redox reactions in the wetlands that control the concentration of certain solutes, including nutrients and pollutants. But such biogeochemical processes are not evenly distributed and often are localized in “hot spots” or take place in bouts known as “hot moments.” How these hot spots or hot moments arise remains poorly understood and is often explained by simply evoking variations in soil properties in the wetlands.
Constraints on the Venusian crustal thickness variations in the isostatic stagnant lid approximation
Authors: Orth C. P. , Solomatov V. S.
Published: October 2012

The isostatic stagnant lid (ISL) approximation is applied to the long‐wavelength Venusian topography and geoid to place constraints on the thickness of the crust and lithosphere. Previous studies showed that a purely thermal isostasy model of the lithosphere (the “stagnant lid”) accounts for a significant portion of the topography and geoid anomalies. Here we assume that the remaining discrepancy between the observed and model geoid is due to crustal thickness variations and that the crust, the lithosphere and the mantle are in a state of double isostatic equilibrium: the lithosphere is isostatically floating on top of the mantle and the crust is isostatically floating on top of the lithosphere. The addition of another variable, the crustal thickness, allows an exact fit to the observed topography and geoid. This also makes the solution non‐unique: an exact fit to topography and geoid can be achieved in a broad range of average lithospheric and crustal thicknesses. Additional constraints such as the gabbro‐eclogite phase transition and the existence of relatively young volcanism limit this range to some extent. The inferred variations in the crustal thickness are less sensitive to model assumptions and generally agree with the results obtained in previous studies.
Nonlocal component of radiative flux perturbation
Authors: Ming Yi , Ramaswamy V.
Published: October 2012

Radiative flux perturbation (RFP) is defined as the top‐of‐the‐atmosphere (TOA) radiative imbalance after the atmosphere‐land system adjusts fully to an external perturbation, and serves as a useful metric for quantifying climate forcing. This paper presents an effort to address the issue of whether a forcing imposed persistently over a specific region may alter the radiative balance elsewhere through atmospheric circulation, thus giving rise to a nonlocal component of RFP. We perturb the climate simulated with an atmospheric general circulation model (AGCM) solely by increasing the cloud droplet number concentration over the land, and observe widespread positive (warming) RFP over the ocean, along with the expected negative (cooling) RFP over the land. A detailed analysis suggests that the oceanic (or nonlocal) RFP is closely associated with a reduction in low cloud amount, which can be attributed primarily to the horizontal advection of drier land boundary layer air and to the oceanic boundary layer top entrainment of drier free troposphere air. By examining how the land surface and atmospheric energy balances are re‐established, we are able to identify the physical mechanisms behind the strong hydrological impact of a tropical land shortwave (SW) forcing (the multiplier effect). In contrast, the hydrological cycle is relatively insensitive to an extratropical forcing.
An empirical model of magnetospheric chorus amplitude using solar wind and geomagnetic indices
Authors: Golden D. I. , Spasojevic M. , Li W. , Nishimura Y.
Published: October 2012

Magnetospheric chorus is an Extremely Low Frequency/Very Low Frequency (ELF/VLF, 0.3–30 kHz) electromagnetic wave phenomenon which plays an important role in the acceleration and loss of energetic electrons in the Earth's radiation belts. One must therefore possess accurate estimates of chorus amplitudes in order to model radiation belt dynamics. The goal of this study is to design an empirical model of chorus amplitude, the output of which can be used as input to models of radiation belt dynamics. In pursuit of this goal, we compare two related empirical models of chorus amplitude that we have developed based on THEMIS data from June 2008 through December 2011 which use multiple regression to predict equatorial chorus amplitudes as a function of L and MLT. One model uses only AE* and Kp as model inputs, and the other model utilizes solar wind measurements and geomagnetic indices. The models perform similarly, with each one achieving a median RMS prediction error of 0.39 log10 pT (a factor of 2.5 in amplitude). The coefficients of determination of chorus amplitude for the full model and the AE*/Kp model are 0.034 and 0.026, respectively, meaning that these models explain 3.4 and 2.6 percent of the variance of chorus amplitude. We present a parametric analysis, showing the expected effects on chorus amplitude from a modeled substorm and solar wind pressure pulse, as well as modeled chorus amplitude over the course of the month of September 2008. The model outputs give important insight into the global evolution of equatorial chorus amplitude as a function of geomagnetic storm and substorm phase.
Numerical analysis using WRF‐SBM for the cloud microphysical structures in the C3VP field campaign: Impacts of supercooled droplets and resultant riming on snow microphysics
Authors: Iguchi Takamichi , Matsui Toshihisa , Shi Jainn J. , Tao Wei‐Kuo , Khain Alexander P. , Hou Arthur , Cifelli Robert , Heymsfield Andrew , Tokay Ali
Published: October 2012

Two distinct snowfall events are observed over the region near the Great Lakes during 19–23 January 2007 under the intensive measurement campaign of the Canadian CloudSat/CALIPSO validation project (C3VP). These events are numerically investigated using the Weather Research and Forecasting model coupled with a spectral bin microphysics (WRF‐SBM) scheme that allows a smooth calculation of riming process by predicting the rimed mass fraction on snow aggregates. The fundamental structures of the observed two snowfall systems are distinctly characterized by a localized intense lake‐effect snowstorm in one case and a widely distributed moderate snowfall by the synoptic‐scale system in another case. Furthermore, the observed microphysical structures are distinguished by differences in bulk density of solid‐phase particles, which are probably linked to the presence or absence of supercooled droplets. The WRF‐SBM coupled with Goddard Satellite Data Simulator Unit (G‐SDSU) has successfully simulated these distinctive structures in the three‐dimensional weather prediction run with a horizontal resolution of 1 km. In particular, riming on snow aggregates by supercooled droplets is considered to be of importance in reproducing the specialized microphysical structures in the case studies. Additional sensitivity tests for the lake‐effect snowstorm case are conducted utilizing different planetary boundary layer (PBL) models or the same SBM but without the riming process. The PBL process has a large impact on determining the cloud microphysical structure of the lake‐effect snowstorm as well as the surface precipitation pattern, whereas the riming process has little influence on the surface precipitation because of the small height of the system.
Information Overload, Professionalization, and the Origins of the Publication Manual of the American Psychological Association
Authors: Sigal Matthew J. , Pettit Michael
Published: October 2012

This article examines the origins of psychology's adoption of a standardized style and format for its publications and the controversies that this decision engendered. The present account draws on perspectives derived from the history of reading and the sociology of professions to explain the historical appeal of such standards. Archival documents are used to trace the events that led to the drafting of the first set of publication standards in 1929. Where previous historical accounts of the publication manual have stressed the influence of behaviorism, the discipline's leaders embraced these instructions because of the perception of information overload resulting from the rapid expansion and professionalization of psychology following World War I. Under the auspices of the National Research Council, a committee on publication practices surveyed scientists, editors, and publishers in the hopes of making more efficient the communication of psychological knowledge within an increasingly large and anonymous discipline. Archival documents also reveal an animated debate over whether the progress of psychology as a science required the adoption of universally followed rules trusted by all or the cultivation of the scientist's creativity and individuality of expression.
A Regression Framework for Effect Size Assessments in Longitudinal Modeling of Group Differences
Authors: Feingold Alan
Published: October 2012

The use of growth modeling analysis (GMA)–particularly multilevel analysis and latent growth modeling—to test the significance of intervention effects has increased exponentially in prevention science, clinical psychology, and psychiatry over the past 15 years. Model-based effect sizes for differences in means between 2 independent groups in GMA can be expressed in the same metric (Cohen's d) commonly used in classical analysis and meta-analysis. This article first reviews conceptual issues regarding calculation of d for findings from GMA and then introduces an integrative framework for effect size assessments that subsumes GMA. The new approach uses the structure of the linear regression model, from which effect sizes for findings from diverse cross-sectional and longitudinal analyses can be calculated with familiar statistics, such as the regression coefficient, the standard deviation of the dependent measure, and study duration.
Breath figure in non-aqueous vapor
Authors: Ding Jianyun , Zhang Aijuan , Bai Hua , Li Lei , Li Jian , Ma Zhi
Published: October 2012

The breath figure process was implemented in an atmosphere of methanol and ethanol vapors, producing porous polymer films with different features.
Erlotinib binds both inactive and active conformations of the EGFR tyrosine kinase domain
Authors: Park Jin H. , Liu Yingting , Lemmon Mark A. , Radhakrishnan Ravi
Published: October 2012

Erlotinib and gefitinib, tyrosine kinase inhibitors used to block EGFR (epidermal growth factor receptor) signalling in cancer, are thought to bind only the active conformation of the EGFR-TKD (tyrosine kinase domain). Through parallel computational and crystallographic studies, we show in the present study that erlotinib also binds the inactive EGFR-TKD conformation, which may have significant implications for its use in EGFR-mutated cancers.
The influence of dietary lipid composition on liver mitochondria from mice following 1 month of calorie restriction
Authors: Chen Yana , Hagopian Kevork , Bibus Douglas , Villalba José M. , López-Lluch Guillermo , Navas Plácido , Kim Kyoungmi , McDonald Roger B. , Ramsey Jon J.
Published: October 2012

To investigate the role mitochondrial membrane lipids play in the actions of CR (calorie restriction), C57BL/6 mice were assigned to four groups (control and three 40% CR groups) and the CR groups were fed diets containing soya bean oil (also in the control diet), fish oil or lard. The fatty acid composition of the major mitochondrial phospholipid classes, proton leak and H2O2 production were measured in liver mitochondria following 1 month of CR. The results indicate that mitochondrial phospholipid fatty acids reflect the PUFA (polyunsaturated fatty acid) profile of the dietary lipid sources. CR significantly decreased the capacity of ROS (reactive oxygen species) production by Complex III but did not markedly alter proton leak and ETC (electron transport chain) enzyme activities. Within the CR regimens, the CR-fish group had decreased ROS production by both Complexes I and III, and increased proton leak when compared with the other CR groups. The CR-lard group showed the lowest proton leak compared with the other CR groups. The ETC enzyme activity measurements in the CR regimens showed that Complex I activity was decreased in both the CR-fish and CR-lard groups. Moreover, the CR-fish group also had lower Complex II activity compared with the other CR groups. These results indicate that dietary lipid composition does influence liver mitochondrial phospholipid composition, ROS production, proton leak and ETC enzyme activities in CR animals.
Formation and magnetic manipulation of periodically aligned microchains in thin plastic membranes
Authors: Lorenzo Daniela , Fragouli Despina , Bertoni Giovanni , Innocenti Claudia , Anyfantis George C. , Davide Cozzoli P. , Cingolani Roberto , Athanassiou Athanassia
Published: October 2012

We demonstrate the fabrication of polymeric membranes that incorporate a few layers of periodically aligned magnetic microchains formed upon the application of variable magnetic fields. A homogeneous solution containing an elastomeric polymer and a small amount of colloidal magnetic nanoparticles is spin coated on glass slides, thereby forming thin magnetic membranes of ca. 10 μm thickness. Subsequent application of a homogeneous magnetic field results in the orientation of the magnetic clusters and their further motion into the matrix along the field lines forming layers of aligned chains. The study of the kinetics of alignment demonstrates that the chains are formed in the first hour of exposure to the magnetic field. Above all, a detailed microscopy study reveals that the dimensions and the periodicity of the microchains are effectively controlled by the intensity of the magnetic field, in good agreement with the theoretical simulations. This ability to form and manipulate the size and the distribution of chains into the polymeric matrix gives the opportunity to develop multifunctional composite materials ready to be used in various applications such as electromagnetic shielding, or multifunctional magnetic membranes etc.
Trapped disturbances and finite amplitude downstream wavetrains on the f-plane
Authors: Stastna Marek , Subich Christopher , Soontiens Nancy
Published: October 2012

We consider the generation and evolution of finite amplitude internal waves over, and downstream of, small-amplitude topography. We demonstrate that in addition to a large amplitude, non-hydrostatic wave trapped over the topography, a finite amplitude wavetrain of Poincaré waves is generated. This wavetrain is nearly hydrostatic over the majority of its extent, but can lead to the generation of non-hydrostatic undular bores, weak shear instability, and large secondary solitary-like waves downstream. The secondary waves are non-hydrostatic, and unlike the undular bores, achieve steady state. For parameters corresponding to a high latitude, coastal ocean secondary waves are generated well over 100 km downstream of the topography. The hydrostatic Poincaré waves thus serve as a bridge for strong energy transfer from the forcing region to distant regions downstream.
Mushy-layer dynamics in micro and hyper gravity
Authors: O'Rourke J. G. , Riggs A. J. E. , Guertler C. A. , Miller P. W. , Padhi C. M. , Popelka M. M. , Wells A. J. , West A. C. , Zhong J.-Q. , Wettlaufer J. S.
Published: October 2012

We describe the results of experiments on mushy layers grown from aqueous ammonium chloride solution in normal, micro, and hyper gravity environments. In the fully developed chimney state, the chimney plume dynamics differ strikingly when conditions change from micro to hyper gravity. In microgravity, we find fully arrested plume motion and suppressed convection. As gravity exceeds Earth conditions, we observe a host of phenomena, ranging from arched plumes that undergo forced Rayleigh-Taylor instabilities to in-phase multiple plume oscillatory behavior. For the same initial solute concentrations and fixed boundary cooling temperatures, we find that, in runs of over two hours, the averaged effects of microgravity and hypergravity result in suppressed growth of the mushy layers, a phenomenon caused by a net enhancement of convective heat and solute transport from the liquid to the mushy layers. These behaviors are placed in the context of the theory of convecting mushy layers as studied under normal laboratory conditions.
Visualization of the structural response of a hypersonic turbulent boundary layer to convex curvature
Authors: Humble R. A. , Peltier S. J. , Bowersox R. D. W.
Published: October 2012

The effects of convex curvature on the outer structure of a Mach 4.9 turbulent boundary layer (Reθ = 4.7 × 104) are investigated using condensate Rayleigh scattering and analyzed using spatial correlations, intermittency, and fractal theory. It is found that the post-expansion boundary layer structure morphology appears subtle, but certain features exhibit a more obvious response. The large-scale flow structures survive the initial expansion, appearing to maintain the same physical size. However, due to the nature of the expansion fan, a differential acceleration effect takes place across the flow structures, causing them to be reoriented, leaning farther away from the wall. The onset of intermittency moves closer towards the boundary layer edge and the region of intermittent flow decreases. It is likely that this reflects the less frequent penetration of outer irrotational fluid into the boundary layer, consistent with a boundary layer that is losing its ability to entrain freestream fluid. The fractal dimension of the turbulent/nonturbulent interface decreases with increasing favorable pressure gradient, indicating that the interface's irregularity decreases. Because fractal scale similarity does not encompass the largest scales, this suggests that the change in fractal dimension is due to the action of the smaller-scales, consistent with the idea that the small-scale flow structures are quenched during the expansion in response to bulk dilatation.
Analysis of wavelength deviation of guided waves with electromagnetic acoustic transducers
Authors: Zhai Guofu , Jiang Tao , Kang Lei
Published: October 2012

It is usually considered that the wavelength of guided waves propagating in plates is equal to the double spacing interval of the meander-line coil of electromagnetic acoustic transducers (EMATs). However, the actual value of the wavelength might deviate from the double spacing. This paper takes Shear Horizontal (SH) waves for instance to study the relationship between the wavelength deviation and the parameters of EMATs. It is shown that the wavelength deviation occurs when the operating point of EMATs does not locate on the dispersion curves of a certain SH mode. A wavelength measurement method is proposed to evaluate the deviation by the time-frequency analysis of detected wave signals. Experiments are set up to study the phenomenon of wavelength deviation and verify the validity of the proposed method.
Raman spectroscopy and crystal-field split rotational states of photoproducts CO and H2 after dissociation of formaldehyde in solid argon
Authors: Lindgren Johan , Olbert-Majkut Adriana , Pettersson Mika , Kiljunen Toni
Published: October 2012

Raman signal is monitored after 248 nm photodissociation of formaldehyde in solid Ar at temperatures of 9–30 K. Rotational transitions J = 2 ← 0 for para-H2 fragments and J = 3 ← 1 for ortho-H2 are observed as sharp peaks at 347.2 cm−1 and 578.3 cm−1, respectively, which both are accompanied by a broader shoulder band that shows a split structure. The rovibrational spectrum of CO fragments has transitions at 2136.5 cm−1, 2138.3 cm−1, 2139.9 cm−1, and 2149 cm−1. To explain the observations, we performed adiabatic rotational potential calculations to simulate the Raman spectrum. The simulations indicate that the splitting of rotational transitions is a site effect, where H2 molecules can reside in a substitution site, in addition to an interstitial site. In the former site, rotational motion is unperturbed by the electrostatic field of the host atoms, while the latter site splits the excited rotational manifolds, J = 2 and 3, into doublet and triplet structures, respectively. For CO, the spectrum can be ascribed to monomeric species in single- and double-substitution sites, to a dimeric species (CO)2, and to a CO–H2O complex. The simulations show that a nearest-neighbor molecular complex CO–H2 is not responsible for any of the observed spectral fingerprints. The cause of the exit of the molecular hydrogen from the initial cage can be traced to high translational energy of the fragment after the photodissociation. After the matrix has reached a thermal equilibrium, a diffusion driven formation of the complex is possibly hindered by the high rotational zero-point energy developed upon complexation.
Quantum spin transport through magnetic superatom dimer (Cs8V-Cs8V)
Authors: Zhu Lin , Khanna Shiv N.
Published: October 2012

Theoretical studies of the spin transport through a magnetic superatom dimer (Cs8V)-(Cs8V) have been carried out within a density functional theory combined with nonequilibrium Green's-function formalism. It is shown that the electronic transport is sensitive to the binding site as well as the contact distance between the dimer and the electrode, and that the conductance at zero bias exhibits an oscillatory behavior as a function of the contact distance. The conductance in ferromagnetic state shows an unusually high spin polarization that exceeds 80% at large separations. The I–V curve shows negative differential resistance for specific contact distances, whose origin lies in the shift of frontier energy levels as well as the charged state of the superatom, under external bias.
Capillary-driven flow induced by a stepped perturbation atop a viscous film
Authors: Salez Thomas , McGraw Joshua D. , Bäumchen Oliver , Dalnoki-Veress Kari , Raphaël Elie
Published: October 2012

Thin viscous liquid films driven by capillarity are well described in the lubrication theory through the thin film equation. In this article, we present an analytical solution of this equation for a particular initial profile: a stepped perturbation. This initial condition allows a linearization of the problem making it amenable to Fourier analysis. The solution is obtained and characterized. As for a temperature step in the heat equation, self-similarity of the first kind of the full evolution is demonstrated and a long-term expression for the excess free energy is derived. In addition, hydrodynamical fields are described. The solution is then compared to experimental profiles from a model system: a polystyrene nanostep above the glass transition temperature which flows due to capillarity. The excellent agreement enables a precise measurement of the capillary velocity for this polymeric liquid, without involving any numerical simulation. More generally, as these results hold for any viscous system driven by capillarity, the present solution may provide a useful tool in hydrodynamics of thin viscous films.
Hot-electron generation by “cavitating” Langmuir turbulence in the nonlinear stage of the two-plasmon–decay instability
Authors: Vu H. X. , DuBois D. F. , Russell D. A. , Myatt J. F.
Published: October 2012

The kinetic reduced-description particle-in-cell simulation technique has been applied to study the nonlinear stage of two-plasmon–decay (TPD) instability in an inhomogeneous plasma driven by crossed laser beams. The TPD instability is found to be a prolific generator of “cavitating” Langmuir turbulence. Langmuir “cavitons”—localized longitudinal electric fields, oscillating near the local electron plasma frequency, trapped in ponderomotive density depressions—collapse to dimensions of a few electron Debye lengths, where the electric field energy is collisionlessly transferred to electron kinetic energy. The resulting hot electrons can attain instantaneous temperatures up to 100 keV with net suprathermal heat flux out of the system of up to a few percent of the input laser energy. Scaling laws for this hot-electron generation by TPD, in regimes motivated by recent experiments on the Omega laser, were presented recently by Vu et al. (H. X. Vu, D. F. DuBois, D. A. Russell, and J. F. Myatt, Phys. Plasmas 19, 102703 (2012)). This paper concentrates on the microscopic mechanisms for hot-electron generation. The spatial distribution of the maxima of the electric field envelope modulus is found to be very spiky, with the distribution of electric field envelope maxima obeying Gaussian statistics. The cavitons are produced in density-depletion trenches produced by the combined ponderomotive interference of the crossed laser beams and the ponderomotive beats of the primary backward-going TPD Langmuir waves (LWs) resulting from the crossed beams. The Langmuir turbulence is strongest in the electron-density region near 0.241× the laser's critical density, where the forward LWs from the crossed-beam TPD are degenerate. Nucleation of cavitons is assisted by the modulation of the electron density in the trenches, which in turn is caused by the beating of the common forward-going LW and the pair of backward-going LWs. The autocorrelation function of the LW envelope field provides a near-universal shape for intense cavitons—in the neighborhood of the local field maxima. The hot-electron temperature is found to be approximately a linear function of the “caviton temperature” determined from the Gaussian distribution of caviton maxima. These diagnostics provide strong evidence for the importance of Langmuir caviton collapse in the generation of hot electrons by TPD. Extended Zakharov model predictions for TPD exhibit the same qualitative phenomena.
Note: Effective diffusion coefficient in heterogeneous media
Authors: Kalnin Juris R. , Kotomin Eugene
Published: October 2012

A closed formula for the effective diffusion coefficient in a heterogeneous medium with periodically distributed inclusions is derived using the extended effective medium theory. It is shown that the expression for the effective diffusion coefficient is an exact result, since it is identical to the expression obtained using the Lifson-Jackson formula.
Note: Controlled fabrication of suspended metallic vacuum tunneling gaps
Authors: Günay-Demirkol Anıl , Kaya İsmet İ.
Published: October 2012

We developed a new fabrication technique for the realization of nanogaps using conventional lithography and in situ controlled thermal evaporation. A 20–40 nm gap between two suspended metallic electrodes is shrunk down to about 1 nm using controlled thermal evaporation. It is demonstrated that with this technique rigid and stable metallic vacuum tunneling junctions can be consistently produced. The fabricated nanogaps were characterized by I-V measurements and their gap sizes and barrier heights were interrogated using the Simmons’ model.
Amplitude equation for a diffusion-reaction system: The reversible Sel'kov model
Authors: Dutt A. K.
Published: October 2012

For a model glycolytic diffusion-reaction system, an amplitude equation has been derived in the framework of a weakly nonlinear theory. The linear stability analysis of this amplitude equation interprets the structural transitions and stability of various forms of Turing structures. This amplitude equation also conforms to the expectation that time-invariant amplitudes in Turing structures are independent of complexing reaction with the activator species, whereas complexing reaction strongly influences Hopf-wave bifurcation.
Molecular dynamics simulations of gas flow in nanochannel with a Janus interface
Authors: Hui Xie , Chao Liu
Published: October 2012

It is interesting to investigate fluid flow in nanochannel with a Janus interface (NCJI), especially when considering the asymmetric situations of wettability in the biology. The simulation results show that the temperature has a significant influence on the particle number near the hydrophilic surface because the desorption increases with the fluid temperature, while the external force has a little influence on the mass distribution. Because the viscosity of gas increases with temperature, the flow velocity of gas in NCJI decreases as the wall temperature increases. The flow in NCJI is neither Poiseuille-like nor plug-flow behaviors. This particular form of flow may be able to help us invent new nano-devices.
Effects of spin-polarized current on pulse field-induced precessional magnetization reversal
Authors: Zhang Guang-fu , Guo Guang-hua , Wang Xi-guang , Nie Yao-zhuang , Li Zhi-xiong
Published: October 2012

We investigate effects of a small DC spin-polarized current on the pulse field-induced precessional magnetization reversal in a thin elliptic magnetic element by micromagnetic simulations. We find that the spin-polarized current not only broadens the time window of the pulse duration, in which a successful precessional reversal is achievable, but also significantly suppresses the magnetization ringing after the reversal. The pulse time window as well as the decay rate of the ringing increase with increasing the current density. When a spin-polarized current with 5 MA/cm2 is applied, the time window increases from 80 ps to 112 ps, and the relaxation time of the ringing decreases from 1.1 ns to 0.32 ns. Our results provide useful information to achieve magnetic nanodevices based on precessional switching.
Structure of Regenerated Celluloses Treated with Ionic Liquids and Comparison of their Enzymatic Digestibility by Purified Cellulase Components
Authors: Mizuno Masahiro , Kachi Shuji , Togawa Eiji , Hayashi Noriko , Nozaki Kouichi , Itoh Toshiyuki , Amano Yoshihiko
Published: October 2012

In this study, regenerated celluloses were prepared from microcrystalline cellulose (MCC) by treatment with three ionic liquids (ILs) having 1-ethyl-3-methylimidazolium (Emim) as the cation, and the IL N-(2-methoxyethyl)-N,N-diethyl-N-methylammonium alanine ([N221ME][Ala]), where the amino acid moiety is the anion. The crystal form of cellulose was transformed from cellulose I to cellulose II by dissolution with an IL and regeneration with anti-solvent. However, the crystallinity of the regenerated cellulose was different; the disordered chain region was increased in the order of [N221ME][Ala] < [Emim][OAc] < [Emim][DEP] < [Emim][Cl]. The monocomponent cellulase, especially endoglucanase, showed high hydrolyzing activity for regenerated cellulose compared with untreated cellulose. Furthermore, the degree of increase of hydrolyzing activity was almost coincident with the order of crystallinity. For the effective hydrolysis of cellulose treated with an IL, it is necessary to prepare the cellulase mixture containing an adequate ratio of each cellulase component according to crystal allomorph and the crystallinity of regenerated cellulose.
Progress in Microwave-Aided Chemical Synthesis
Authors: Hassan Hani Mutlak A. , Harakeh Steve , Sakkaf Kaltoom A. , Denetiu Iuliana
Published: October 2012

The continuing use of microwave (µwave) energy in chemical synthesis has been impressive over the past decade, with many reports incorporating µwave-based reactions. Two of the major benefits of using µwave heating are the remarkable decrease in reaction times and often high yield of products in comparison with classical heating, an ideal technology for synthetic chemists. Herein, we highlight some exciting examples of its recent utility in organic, medicinal, and natural product synthetic endeavours.
Drought adversely affects tuber development and nutritional quality of the staple crop cassava (Manihot esculenta Crantz)
Authors: Vandegeer Rebecca , Miller Rebecca E. , Bain Melissa , Gleadow Roslyn M. , Cavagnaro Timothy R.
Published: October 2012

Cassava (Manihot esculenta Crantz) is the staple food source for over 850 million people worldwide. Cassava contains cyanogenic glucosides and can be toxic to humans, causing paralysing diseases such as konzo, and even death if not properly processed. Konzo epidemics are often associated with times of drought. This may be due to a greater reliance on cassava as it is drought tolerant, but it may also be due to an increase in cyanogenic glucosides. Episodic droughts are forecast to become more common in many cassava-growing regions. We therefore sought to quantify the effect of water-stress on both yield and cyanogenic glucoside concentration (CNc) in the developing tubers of cassava. Five-month-old plants were grown in a glasshouse and either well watered or droughted for 28 days. A subset of droughted plants was re-watered half way through the experiment. Droughted plants had 45% fewer leaves and lower tuber yield, by 83%, compared with well-watered plants. CNc was 2.9-fold higher in the young leaves of droughted plants, whereas CNc in tubers from droughted plants was 4-fold greater than in tubers from well-watered plants. Re-watered plants had a similar biomass to control plants, and lower CNc than droughted plants. These findings highlight the important link between food quality and episodic drought.
Fumiyo Ikeda: Ubiquitin lines up for action
Authors: Sedwick Caitlin
Published: October 2012

Ikeda is studying the biological significance of linear ubiquitin chains.
Observing force-regulated conformational changes and ligand dissociation from a single integrin on cells
Authors: Chen Wei , Lou Jizhong , Evans Evan A. , Zhu Cheng
Published: October 2012

As adhesion molecules, integrins connect a cell to its environment and transduce signals across the membrane. Their different functional states correspond to distinct conformations. Using a biomembrane force probe, we observed real-time reversible switches between bent and extended conformations of a single integrin, αLβ2, on the surface of a living cell by measuring its nanometer-scale headpiece displacements, bending and unbending frequencies, and molecular stiffness changes. We determined the stabilities of these conformations, their dynamic equilibrium, speeds and rates of conformational changes, and the impact of divalent cations and tensile forces. We quantified how initial and subsequent conformations of αLβ2 regulate the force-dependent kinetics of dissociation from intercellular adhesion molecule 1. Our findings provide new insights into how integrins function as nanomachines to precisely control cell adhesion and signaling.
Discovering the first microRNA-targeted drug
Authors: Lindow Morten , Kauppinen Sakari
Published: October 2012

MicroRNAs (miRNAs) are important post-transcriptional regulators of nearly every biological process in the cell and play key roles in the pathogenesis of human disease. As a result, there are many drug discovery programs that focus on developing miRNA-based therapeutics. The most advanced of these programs targets the liver-expressed miRNA-122 using the locked nucleic acid (LNA)–modified antisense oligonucleotide miravirsen. Here, we describe the discovery of miravirsen, which is currently in phase 2 clinical trials for treatment of hepatitis C virus (HCV) infection.
Modeling-independent elucidation of inactivation pathways in recombinant and native A-type Kv channels
Authors: Fineberg Jeffrey D. , Ritter David M. , Covarrubias Manuel
Published: October 2012

A-type voltage-gated K+ (Kv) channels self-regulate their activity by inactivating directly from the open state (open-state inactivation [OSI]) or by inactivating before they open (closed-state inactivation [CSI]). To determine the inactivation pathways, it is often necessary to apply several pulse protocols, pore blockers, single-channel recording, and kinetic modeling. However, intrinsic hurdles may preclude the standardized application of these methods. Here, we implemented a simple method inspired by earlier studies of Na+ channels to analyze macroscopic inactivation and conclusively deduce the pathways of inactivation of recombinant and native A-type Kv channels. We investigated two distinct A-type Kv channels expressed heterologously (Kv3.4 and Kv4.2 with accessory subunits) and their native counterparts in dorsal root ganglion and cerebellar granule neurons. This approach applies two conventional pulse protocols to examine inactivation induced by (a) a simple step (single-pulse inactivation) and (b) a conditioning step (double-pulse inactivation). Consistent with OSI, the rate of Kv3.4 inactivation (i.e., the negative first derivative of double-pulse inactivation) precisely superimposes on the profile of the Kv3.4 current evoked by a single pulse because the channels must open to inactivate. In contrast, the rate of Kv4.2 inactivation is asynchronous, already changing at earlier times relative to the profile of the Kv4.2 current evoked by a single pulse. Thus, Kv4.2 inactivation occurs uncoupled from channel opening, indicating CSI. Furthermore, the inactivation time constant versus voltage relation of Kv3.4 decreases monotonically with depolarization and levels off, whereas that of Kv4.2 exhibits a J-shape profile. We also manipulated the inactivation phenotype by changing the subunit composition and show how CSI and CSI combined with OSI might affect spiking properties in a full computational model of the hippocampal CA1 neuron. This work unambiguously elucidates contrasting inactivation pathways in neuronal A-type Kv channels and demonstrates how distinct pathways might impact neurophysiological activity.
Rare variant discovery and calling by sequencing pooled samples with overlaps
Authors: Wang Wenhui , Yin Xiaolin , Soo Pyon Yoon , Hayes Matthew , Li Jing
Published: October 2012

Motivation: For many complex traits/diseases, it is believed that rare variants account for some of the missing heritability that cannot be explained by common variants. Sequencing a large number of samples through DNA pooling is a cost-effective strategy to discover rare variants and to investigate their associations with phenotypes. Overlapping pool designs provide further benefit because such approaches can potentially identify variant carriers, which is important for downstream applications of association analysis of rare variants. However, existing algorithms for analysing sequence data from overlapping pools are limited.

Results: We propose a complete data analysis framework for overlapping pool designs, with novelties in all three major steps: variant pool and variant locus identification, variant allele frequency estimation and variant sample decoding. The framework can be used in combination with any design matrix. We have investigated its performance based on two different overlapping designs and have compared it with three state-of-the-art methods, by simulating targeted sequencing and by pooling real sequence data. Results on both datasets show that our algorithm has made significant improvements over existing ones. In conclusion, successful discovery of rare variants and identification of variant carriers using overlapping pool strategies critically depend on many steps, from generation of design matrixes to decoding algorithms. The proposed framework in combination with the design matrixes generated based on the Chinese remainder theorem achieves best overall results.

Availability: Source code of the program, termed VIP for Variant Identification by Pooling, is available at http://cbc.case.edu/VIP.

Contact:  jingli@cwru.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Unusual case of new‐onset heart failure due to cor triatriatum sinister
Authors: Méndez Ana Belén , Colchero Teresa , Garcia‐Picart Joan , Vila Montserrat , Subirana Maria Teresa , Sionis Alessandro
Published: October 2012

We report the case of a 30‐year old man who came to the emergency department of our hospital with acute left heart failure, and was diagnosed with a rare congenital anomaly (cor triatriatrum sinister), which can mimic a severe mitral stenosis. Cor triatriatum sinister is a rare anomaly (0.1% of all cases of congenital heart disease) that is seldom diagnosed in adult patients. The hallmark of this congenital defect is the presence of a fibromuscular membrane that divides the left atrium (LA) into two chambers: a postero‐superior chamber into which the pulmonary veins drain and an infero‐anterior chamber (true LA) containing the mitral valve and atrial appendage. Both chambers communicate through a membrane in which one or more drain holes can be found. When the hole is significantly obstructive, it results in increased venous and arterial pressures. Even though the definitive treatment of cor triatriatum is the surgical excision of the membrane, we present a balloon dilatation case with a good response to percutaneous therapy, both initially and in the ensuing months.
Union Recognition in Britain: The End of Legally Induced Voluntarism?
Authors: Gall Gregor
Published: October 2012

The enactment of a third statutory union recognition procedure in Britain in 2000 led to a sharp rise and then fall in the number of new, largely voluntary, union recognition agreements being signed. This article examines and explains this trajectory, finding that the interaction of a weak procedure with its wider environment has led to a situation where the outcome of a reflexive law is heavily determined by the external balance of power in employment relations.
Central Nervous System Vasculopathy in HIV-Infected Children Enrolled in the Pediatric AIDS Clinical Trials Group 219/219C Study
Authors: Schieffelin John S. , Williams Paige L. , Djokic Divna , Anderson Jeffrey P. , Nachman Sharon , Oleske James M. , Seage George R. , Van Dyke Russell B.
Published: October 2012

Background

Central nervous system (CNS) vasculopathy has been reported in human immunodeficiency virus–infected (HIV+) adults and children. In children, it often presents with HIV encephalopathy, stroke, or intracerebral aneurysms. The etiology, incidence, and risk factors of HIV-associated CNS vasculopathy in children are unknown.

Methods

We identified HIV+ children with a diagnosis of vasculopathy or other cerebrovascular events among children enrolled between 1993 and 2004 in 2 prospective, multicenter cohort studies. Demographic and laboratory data, history of antiretroviral use, and signs, symptoms, and diagnostic studies pertaining to the CNS event were reviewed.

Results

Among the 3338 HIV+ children, 51 had diagnoses that suggested CNS vasculopathy. Of these, 12 (24%) were included in this analysis, after excluding those with alternative diagnoses and those from closed sites. Among these 12, 4 (33%) were female, 4 (33%) were white, and 10 (83%) had perinatal HIV. Their average age at the event was 10.8 years with a median CD4 count of 22 cells/mm3 and median HIV-1 viral load of 94 304 copies/mL. Fifty-eight percent of subjects had a history of opportunistic infections before the CNS event. Fifty percent had cerebral aneurysms on imaging. The overall incidence among HIV+ subjects was 3.4 cases per 10 000 person-years (95% confidence interval, 1.8–6.0).

Conclusions

CNS vasculopathy in HIV+ children is uncommon but more common than in the general pediatric population. Cerebral aneurysms are the most common manifestation. Although the pathogenesis remains unclear, older children and those with low CD4 counts and high HIV viral loads are at the highest risk.
Autozygome-guided exome sequencing in retinal dystrophy patients reveals pathogenetic mutations and novel candidate disease genes
Authors: Abu-Safieh Leen , Alrashed May , Anazi Shamsa , Alkuraya Hisham , Khan Arif O. , Al-Owain Mohammed , Al-Zahrani Jawahir , Al-Abdi Lama , Hashem Mais , Al-Tarimi Salwa , Sebai Mohammed-Adeeb , Shamia Ahmed , Ray-zack Mohamed D. , Nassan Malik , Al-Hassnan Zuhair N. , Rahbeeni Zuhair , Waheeb Saad , Alkharashi Abdullah , Abboud Emad , Al-Hazzaa Selwa A.F. , Alkuraya Fowzan S.
Published: October 2012

Retinal dystrophy (RD) is a heterogeneous group of hereditary diseases caused by loss of photoreceptor function and contributes significantly to the etiology of blindness globally but especially in the industrialized world. The extreme locus and allelic heterogeneity of these disorders poses a major diagnostic challenge and often impedes the ability to provide a molecular diagnosis that can inform counseling and gene-specific treatment strategies. In a large cohort of nearly 150 RD families, we used genomic approaches in the form of autozygome-guided mutation analysis and exome sequencing to identify the likely causative genetic lesion in the majority of cases. Additionally, our study revealed six novel candidate disease genes (C21orf2, EMC1, KIAA1549, GPR125, ACBD5, and DTHD1), two of which (ACBD5 and DTHD1) were observed in the context of syndromic forms of RD that are described for the first time.
In situX-ray data collection from highly sensitive crystals ofPseudomonas putidaPtxS in complex with DNA
Authors: Pineda-Molina E. , Daddaoua A. , Krell T. , Ramos J. L. , García-Ruiz J. M. , Gavira J. A.
Published: October 2012

Pseudomonas putidaPtxS is a member of the LacI protein family of transcriptional regulators involved in glucose metabolism. All genes involved in this pathway are clustered into two operons,kguandgad. PtxS controls the expression of thekguandgadoperons as well as its own transcription. The PtxS operator is a perfect palindrome, 5′-TGAAACCGGTTTCA-3′, which is present in all three promoters. Crystallization of native PtxS failed, and PtxS–DNA crystals were finally produced by the counter-diffusion technique. A portion of the capillary used for crystal growth was attached to the end of a SPINE standard cap and directly flash-cooled in liquid nitrogen for diffraction tests. A full data set was collected with a beam size of 10 × 10 µm. The crystal belonged to the trigonal space groupP3, with unit-cell parametersa=b= 213.71,c = 71.57 Å. Only unhandled crystals grown in capillaries of 0.1 mm inner diameter diffracted X-rays to 1.92 Å resolution.
Crystallization and preliminary X-ray analysis of the FliH–FliI complex responsible for bacterial flagellar type III protein export
Authors: Uchida Yumiko , Minamino Tohru , Namba Keiichi , Imada Katsumi
Published: October 2012

The bacterial flagellar proteins are translocated into the central channel of the flagellum by a specific protein-export apparatus for self-assembly at the distal growing end. FliH and FliI are soluble components of the export apparatus and form an FliH2–FliI heterotrimer in the cytoplasm. FliI is an ATPase and the FliH2–FliI complex delivers export substrates from the cytoplasm to an export gate made up of six integral membrane proteins of the export apparatus. In this study, an FliHCfragment consisting of residues 99–235 was co-purified with FliI and the FliHC2–FliI complex was crystallized. Crystals were obtained using the hanging-drop vapour-diffusion technique with PEG 400 as a precipitant. The crystals belonged to the orthorhombic space groupP212121, with unit-cell parametersa= 133.7,b= 147.3,c= 164.2 Å, and diffracted to 3.0 Å resolution.
Ellman's reagent in promoting crystallization and structure determination ofAnabaenaCcbP
Authors: Fan Xue-Xin , Zhou Yan-Feng , Liu Xiang , Li Lan-Fen , Su Xiao-Dong
Published: October 2012

Obtaining crystals presented a bottleneck in the structural study ofAnabaenacyanobacterial Ca2+-binding protein (CcbP). In this report, the promoting effect of Ellman's reagent [5,5′-dithiobis(2-nitrobenzoic acid); DTNB] on the crystallization of CcbP is described. CcbP contains one free cysteine. A quick and simple oxidation reaction with DTNB blocked the free cysteine in purified CcbP and generated a homogenous monomeric protein for crystallization. The crystal structure of DTNB-modified CcbP was determined by the single-wavelength anomalous diffraction method. Structure analysis indicated that DTNB modification facilitated crystallization of CcbP by inducing polar interactions in the crystal lattice. DTNB-mediated cysteine modification was demonstrated to have little effect on the overall structure and the Ca2+binding of CcbP. Thus, DTNB modification may provide a simple and general approach for protein modification to improve the success of crystallization screening.