bluuebunny/crossref_metadata_2025 huggingface dataset:
Legume consumption and severe depressed mood, the modifying roles of gender and menopausal status
Authors: Li Yanfeng , Dai Qi , Tedders Stuart H , Arroyo Cassandra , Zhang Jian
Published: January 2010

Objective

Legumes have been recommended as staple foods in the anticipation of disease prevention. However, the scientific evidence of their benefits, particularly on mental well-being, remains preliminary. We longitudinally assessed the association between legume consumption and the risk of severe depressed mood (SDM) among a national cohort.

Design

The study included adults aged 25–74 years who were examined in 1971–1975 as a part of the National Health and Nutrition Examination Survey. Legume consumption at baseline was obtained from a 3-month FFQ and categorised as infrequent (<1 time/week), moderate (1–2 times/week) and frequent (≥3 times/week). SDM was defined as Center for Epidemiologic Studies Depression Scale score ≥22 or taking anti-depression medication after an average of 10·6 years of follow-up (from 8·0 to 12·5 years).

Results

Among women, the proportion of individuals with SDM was 17·75 %. For premenopausal women (n1778), a significant linear trend of deleterious effect from legume consumption was observed (Pfor trend = 0·0148). The relative risks (RR) for infrequent, moderate and frequent consumptions were 1 (reference), 1·24 (95 % CI = 0·91, 1·70) and 1·75 (1·12, 2·75), respectively. However, moderate consumption showed a significant protective effect (RR = 0·52 (0·27, 1·00)) among women undergoing the menopausal transition (n454). No association was obtained from either postmenopausal women (n601) or men (n2036).

Conclusions

These findings suggest that gender and menopausal status were effect modifiers of the association between legume consumption and SDM. Detrimental effects of frequent consumption of legumes may exist among premenopausal women; moderate consumption, however, may protect perimenopausal women against SDM.
BMI ≥ 50 kg/m2is associated with a younger age of onset of overweight and a high prevalence of adverse metabolic profiles
Authors: O’Connell Jean , Kieran Phillip , Gorman Kathleen , Ahern Tomas , Cawood Tom J , O’Shea Donal
Published: January 2010

Objective

To study the demographic and clinical parameters of three different categories of obesity, with particular focus on a cohort of individuals with BMI ≥ 50 kg/m2, the fastest growing category of obesity.

Design

Over 700 obese individuals were studied (186 with BMI = 30–39 kg/m2, 316 with BMI = 40–49 kg/m2and 290 with BMI ≥ 50 kg/m2).

Results

Median BMI was 51 kg/m2for patients who reported onset of overweight before 15 years of age, 47 kg/m2for patients who reported onset between 15 and 30 years, and 42 kg/m2for patients who became overweight after 30 years of age. The BMI ≥ 50 kg/m2group was notably younger than the group with BMI = 30–39 kg/m2(44 (sd11) yearsv. 50 (sd15) years;P< 0·0001). Eighteen per cent of obese patients studied were considered metabolically healthy according to standard cut-off points for blood pressure, fasting glucose and lipid profiles. However, the proportion of metabolically healthy individuals was significantly higher in the BMI = 30–39 kg/m2group than in the BMI = 40–49 kg/m2and BMI ≥ 50 kg/m2groups (31 %v. 17 % and 12 % respectively;P< 0·05 andP< 0·005). When compared with people of similar age in the general population, individuals with BMI ≥ 50 kg/m2had lower rates of marriage (51 %v. 72 %) and a higher prevalence of unemployment (14 %v. 5 %).

Conclusions

The current study suggests that the increasing prevalence of childhood obesity worldwide will lead to many more individuals achieving a higher BMI at a younger age. Furthermore, an earlier onset of overweight does not appear to prevent the adverse metabolic health outcomes associated with extreme obesity.
Bacterial and Mineral Elements in an Arctic Biofilm: A Correlative Study Using Fluorescence and Electron Microscopy
Authors: Clarke Samuel , Mielke Randall E. , Neal Andrea , Holden Patricia , Nadeau Jay L.
Published: January 2010

Few simple labeling methods exist for simultaneous fluorescence and electron microscopy of bacteria and biofilms. Here we describe the synthesis, characterization, and application of fluorescent nanoparticle quantum dot (QD) conjugates to target microbial species, including difficult to label Gram-negative strains. These QD conjugates impart contrast for both environmental scanning electron microscopy (ESEM) and fluorescence microscopy, permitting observation of living and fixed bacteria and biofilms. We apply these probes for studying biofilms extracted from perennial cold springs in the Canadian High Arctic, which is a particularly challenging system. In these biofilms, sulfur-metabolizing bacteria live in close association with unusual sulfur mineral formations. Following simple labeling protocols with the QD conjugates, we are able to image these organisms in fully-hydrated samples and visualize their relationship to the sulfur minerals using both ESEM and fluorescence microscopy. We then use scanning transmission electron microscopy to observe precipitated sulfur around individual cells and within the biofilm lattice. All combined, this information sheds light on the possible mechanisms of biofilm and mineral structure formation. These new QD conjugates and techniques are highly transferable to many other microbiological applications, especially those involving Gram-negative bacteria, and can be used for correlated fluorescence and electron microscopy.
A Comparison between Bright Field and Phase-Contrast Image Analysis Techniques in Activated Sludge Morphological Characterization
Authors: Mesquita D.P. , Dias O. , Amaral A.L. , Ferreira E.C.
Published: January 2010

Different approaches using microscopy image analysis procedures were employed for characterization of activated sludge systems. The approaches varied mainly on the type of visualization and acquisition method used for collection of data. In this context, this study focused on the comparison of the two most common acquisition methods: bright field and phase-contrast microscopy. Images were acquired from seven different wastewater treatment plants for a combined period of two years. Advantages and disadvantages of each acquisition technique and the results are discussed. Bright field microscopy proved to be more simple and inexpensive and provided the best overall results.
Mercury mobilization and episodic stream acidification during snowmelt: Role of hydrologic flow paths, source areas, and supply of dissolved organic carbon
Authors: Demers Jason D. , Driscoll Charles T. , Shanley James B.
Published: January 2010

We quantified hydrologic source areas and flow paths, acid‐base and aluminum chemistry, dissolved organic carbon dynamics, and mercury mobilization during snowmelt at the Hubbard Brook Experimental Forest (HBEF), New Hampshire, USA. Here we show (1) episodic acidification during snowmelt at the HBEF is controlled by multiple mechanisms (base cation dilution, nitrate and aluminum acidity, and natural organic acids) and persists despite long‐term decreases in acidic deposition; (2) episodic acidification continues to result in mobilization of inorganic monomeric aluminum to concentrations toxic to fish; (3) DOC mobilized from shallow organic soils during snowmelt results in the mobilization of mercury from these same sources; (4) methyl mercury may be produced in the forest floor over winter and flushed from soils during snowmelt; (5) the amount of mercury released during snowmelt likely represents a large portion of annual mercury export; and (6) hydrologic source areas and flow paths, as well as DOC dynamics, strongly influence episodic acidification and the mobilization of mercury, even in a watershed with low stream water DOC concentrations and export.
Nature of crustal terranes and the Moho in northern Costa Rica from receiver function analysis
Authors: Linkimer Lepolt , Beck Susan L. , Schwartz Susan Y. , Zandt George , Levin Vadim
Published: January 2010

The Central American subduction zone in northern Costa Rica shows along‐strike variations in both the incoming and overriding plates. By analyzing the subducting oceanic Moho (M1) and the upper plate Moho (M2) with receiver functions, we investigate the variability in the hydration state of the subducting Cocos Plate and the nature of crustal terranes within the overriding Caribbean Plate. We calculate high‐qualityPandPPwave receiver functions using broadband data of the Global Seismology Network; Geoscope Project; and the CRSEIZE, Pocosol, and Corisubmod experiments. In addition, we estimate the depth (H) and vertically averagedVp/Vs(κ) to Moho and present a sensitivity study to explore the effects of a dipping interface on receiver functions and theHand κ estimates. Our results are consistent with a drier oceanic mantle subducting beneath the southernmost part of the Nicoya Peninsula, as compared to a serpentinized oceanic mantle subducting beneath the northern part. In the Caribbean Plate, we describe the nature of the Mesquito, Nicoya, and Chorotega terranes by integrating new and publishedVp/Vsestimates. Both the Nicoya and Chorotega terranes display highVp/Vs(1.80–1.92) consistent with their oceanic character. In contrast, the oceanic Mesquito Terrane mostly displays lowerVp/Vs(1.62–1.80) more compatible with continental crust, which may indicate that subduction zone magmatism is modifying the crust to display continental character. Our estimates show that the deepest M2 (∼42 km) is observed in the volcanic arc region whereas the shallowest M2 (∼27–33 km) is observed in parts of the fore‐arc and back‐arc regions.
ENSO modulation of the upwelling season off southern‐central Chile
Authors: Montecinos Aldo , Gomez Fabian
Published: January 2010

Southern‐central Chile (35°–41°S) is characterized by strong seasonality of coastal upwelling. At these latitudes, El Niño‐Southern Oscillation (ENSO) forces climatic changes mainly through atmospheric teleconnections. Here we show that ENSO also modulates the timing, i.e. onset and end, of the upwelling season. In order to study the ENSO related wind‐driven upwelling changes, compositing analysis was applied to coastal winds and to other atmospheric fields. During El Niño (La Niña) austral spring conditions, delayed (earlier‐normal) onset of the upwelling season is associated with a meridional dipole characterized by weaken (stronger) South Pacific subtropical anticyclone and blocking (cyclonic) systems in the Amundsen‐Bellingshausen Seas. During austral fall season, similar meridional dipole pattern described for spring La Niña conditions is related to delayed end of the upwelling season. Accordingly, shorter (longer) duration and weaker (stronger) intensity of upwelling season occurs during El Niño (La Niña) events off southern‐central Chile.
Transition from complex craters to multi‐ringed basins on terrestrial planetary bodies: Scale‐dependent role of the expanding melt cavity and progressive interaction with the displaced zone
Authors: Head J. W.
Published: January 2010

The observed differences between complex craters and multi‐ringed basins are described and a combined “transient cavity/displaced zone/melt cavity” model is explored to account for the observations. In this “nested melt‐cavity model”, the increasing influence of the percentage of the target undergoing impact melting at the sub‐impact point with increasing size (the differential melt scaling of Cintala and Grieve [1998]) causes fundamental changes in the nature of the transient cavity, its relationship to the displaced zone, and its short‐term collapse behavior. The transition from complex craters to two‐ring basins involves expansion of the melting front into the displaced zone, formation of a two‐component excavation cavity, and a concomitant radial expansion outward of the zone of maximum elastic rebound. The short‐term modification stage is then dominated by the strength differences between the fluid melt in the inner cavity and rocks of the displaced zone; the highly shocked rocks at the outer margin of the expanded parabolic melting front rebound to form the expanded peak ring, moving upward and laterally inward, easily displacing fluid melt filling the inner depression. At larger sizes, differential melt scaling causes the peak ring diameter to expand relatively more rapidly than the basin rim, and upon collapse, the increased volume of melt ponds in the rebounded melt cavity inside the expanding peak ring. As the transient melt cavity further increases proportionally in size, it penetrates through the base of the displaced zone with significant consequences. The resulting modification stage now incorporates into the collapse process inward and upward movement along the base of the displaced zone; listric failure occurs inward into the fluid melt cavity beginning at the edge of the melt cavity and extending out along the base of the displaced zone up to the base of the rim structural uplift (at ∼1.5 crater radii). This forms an additional outer ring and a resulting megaterrace, modifying the radial ejecta on the collapsed rim to form a domical facies. At multi‐ring basin scales, the significantly deeper penetration that occurs in the expanding melt cavity accounts for the maximum crustal thickness decrease that occurs inside the peak ring in the final basin. Early onset and higher density of peak ring basins on Mercury is predicted by higher mean impact velocity and differential melt scaling.
Vertical transport of surface fire emissions observed from space
Authors: Gonzi Siegfried , Palmer Paul I.
Published: January 2010

We use optimal estimation to infer the vertical distribution of surface emissions lofted from boreal and tropical biomass burning during June–October (JJASO) 2006. We use satellite observations of CO, a tracer of incomplete combustion, at thermal infrared and microwave wavelengths from Aura Tropospheric Emission Spectrometer (TES) and Microwave Limb Sounder (MLS), respectively. TES and MLS together typically provide two to three pieces of information. We use a maximum a posteriori (MAP) methodology to estimate emitted CO mass in five vertical regions spanning the troposphere and lower stratosphere, equivalent to estimating surface emissions. Correlations between neighboring vertical regions, due to vigorous mixing induced by surface heating, reduce the inversion to the information content provided by the data. We use a total of 1785 TES profile measurements, of which 672 are colocated with MLS. We define an injection height based on MAP statistics. We find that 10%–20% of boreal and tropical fire emissions, depending on the region, reach the free and upper troposphere during JJASO 2006. Our injection height estimates during two key pyroconvective events, Siberia (July) and Indonesia (October), qualitatively agree with measurements of aerosol index and attenuated backscatter from Aura Ozone Monitoring Instrument (OMI) and CALIPSO, respectively. Surface emissions inferred from our mass estimates agree with the Global Fire Emission Database biomass burning emission inventory to within ±10%. The small percentage of emissions injected above the boundary layer result in disproportionate changes in CO concentrations of more than 2–25 ppb and 15–160 ppb over boreal and tropical regions, respectively.
Fitting bivariate copulas to the dependence structure between storm characteristics: A detailed analysis based on 105 year 10 min rainfall
Authors: Vandenberghe S. , Verhoest N. E. C. , De Baets B.
Published: January 2010

The use of copulas as flexible tools for constructing marginal‐free distribution functions for multivariate phenomena, such as rainfall, recently enjoys substantial attention by researchers in hydrology. In this study, commonly used bivariate copulas and techniques for fitting such bivariate copulas are applied to different couples of storm variables based on an extensive data set of 105 years of 10 min rainfall, observed at Uccle, Belgium. In the analysis, various problems that can occur are highlighted, and opportunities for further research are outlined. After selecting storms and introducing a meaningful solution to circumvent the presence of abundant ties in the data, a detailed seasonal dependence analysis is provided, together with a study on tail dependence. Further, different existing parameter estimation techniques and goodness‐of‐fit methods for selecting the most appropriate bivariate copulas are applied and compared. Finally, attention is given to the presence of asymmetric dependence and nonexchangeability.
Cobalt-catalyzed regio- and stereoselective intermolecular enyne coupling: an efficient route to 1,3-diene derivatives
Authors: Mannathan Subramaniyan , Cheng Chien-Hong
Published: January 2010

The reaction of alkynes with vinyl arenes or vinyl trimethyl silane in the presence of a cobalt(ii) complex, Zn and ZnI2 in CH2Cl2 at rt to 50 °C for 12–36 h provides 1,3-dienes in good to excellent yields.
Chiral molecules containing the pyrrole framework
Authors: Thirumalairajan Srinath , Pearce Beth M. , Thompson Alison
Published: January 2010

Synthetic routes to chiral molecules containing a pyrrolic ring are discussed: strategies include formation of the pyrrole ring using starting materials appended with chirality, as well as the attachment of chirality to a pre-formed pyrrole.
Chemistry‐based protein modification strategy for endocytic pathway analysis
Authors: Christiano Romain , Amessou Mohamed , Shi Getao , Azoulay Michel , Blanpain Annick , Drobecq Hervé , Melnyk Oleg , Florent Jean‐Claude , Johannes Ludger
Published: January 2010

Background information. The integrated analysis of intracellular trafficking pathways is one of the current challenges in the field of cell biology, and functional proteomics has become a powerful technique for the large‐scale identification of proteins or lipids and the elucidation of biological processes in their natural contexts. For this, new dynamic strategies must be devised to trace proteins that follow a specific pathway such that their initial and final destinations can be detected by automated means.

Results. Here, we report a novel vectorial strategy for trafficking pathway analysis. This strategy is based on a chemical modification of plasma membrane proteins with a bSuPeR (biotinylated sulfation site peptide reagent) and metabolic labelling in the Golgi apparatus, such that plasma membrane proteins that traffic via the retrograde route become detectable in complex mixtures. Efficient synthesis schemes are presented for tailor‐made chemical tools that are then applied to the step‐by‐step validation of the strategy, using a known retrograde cargo protein: the STxB (Shiga toxin B‐subunit). bSuPeR modification at the plasma membrane does not affect STxB transport to the Golgi apparatus, where the protein is metabolically labelled, allowing its detection in cell lysates.

Conclusions. Our vectorial concept proposes a new chemical approach for traffic‐based profiling of proteins that may prove to be applicable to the analysis of diverse endocytic pathways.
Decreased cytochrome c mediates an age-related decline of oxidative phosphorylation in rat kidney mitochondria
Authors: O'Toole John F. , Patel Hiral V. , Naples Colin J. , Fujioka Hisashi , Hoppel Charles L.
Published: January 2010

Kidney function declines with advancing age and mitochondria have been implicated. In the present study we have examined the integrated function of mitochondria isolated from kidneys of 6- and 24-month-old Fischer 344 rats. OXPHOS (oxidative phosphorylation) of intact mitochondria and cytochrome c oxidase activity in permeabilized mitochondria were determined with polarographic assays. The activities of the ETC (electron transport chain) complexes and the cytochrome content in solubilized mitochondria were measured using spectrophotometric methods. The respiratory complexes were evaluated with blue native gel electrophoresis. Mitochondrial preparations were evaluated by immunoblotting for cytochrome c, Smac/Diablo and VDAC (voltage-dependent anion channel). Mitochondrial morphology was examined by electron microscopy. OXPHOS of mitochondria isolated from 24-month-old animals was decreased 15–25% with complexes I, II, III and IV, and fatty acid substrates. The electron microscopic appearance of mitochondria, the activity of the ETC complexes and the protein abundance of individual complexes and supercomplexes were unchanged. The content of cytochrome c was decreased by 37% in aged mitochondria, as determined by spectrophotometric methods and confirmed with immunoblotting. Polarographic determination of cytochrome c oxidase activity with endogenous cytochrome c demonstrated a 23% reduction in aged mitochondria, which was corrected with the addition of exogenous cytochrome c. Renal mitochondrial OXPHOS decreased with aging in the Fischer 344 rat. Decreased mitochondrial cytochrome c content is a major factor contributing to the OXPHOS defect of mitochondria isolated from kidneys of elderly animals.
Overexpression of xCT induces up-regulation of 14-3-3β in Kaposi's sarcoma
Authors: Zeng Yan , Li Yan , Chen Ri-Sheng , He Xin , Yang Lei , Li Wei
Published: January 2010

KSHV (Kaposi's sarcoma-associated herpesvirus), or HHV-8 (human herpesvirus 8), is associated with the pathogenesis of KS, the most common AIDS-related malignancy. xCT (functional subunit of the cystine/glutamate transporter xc− system) is known as the HHV-8 fusion-entry receptor as well as an oncogenic protein. How the xCT triggers the signal transduction of HHV-8 infection and the cell proliferation remains incomplete. We found that xCT was overexpressed in KS tissues and HHV-8-positive BCBL-1 cells. When xCT cDNA plasmids were transfected into the HHV-8-negative BJAB cells, the expression of 14-3-3β and cell growth rate were increased. In contrast, the expression of 14-3-3β and the cell growth rate of HHV-8-positive BCBL-1 cells were suppressed by either xCT siRNA (short interfering RNA) or an xCT inhibitor, sulfsalazine. These results suggest that 14-3-3β is a downstream effector of xCT in KS to mediate the cell proliferation.
Electronic and thermal generation of vibrations of optically excited cantilevers
Authors: Todorović D. M. , Cretin B. , Song Y. Q. , Vairac P.
Published: January 2010

The results of the theoretical analysis of the dynamic effects in the optically excited cantilevers were given. Theoretical model for dynamic elastic bending for two-layer cantilevers was derived including electronic and thermal elastic deformation effects which have the main influence on the dynamics of the cantilevers. The influence of the carrier transport characteristics (the carrier diffusion coefficient, the lifetime of photogenerated carriers, and the carrier recombination velocities) to the elastic vibrations of cantilevers was analyzed. Theoretical model was verified by comparing with the experimental results. The results of these investigations are important for sensors, actuators, and resonators based on the cantilevers.
Observing two stage recovery of gate oxide damage created under negative bias temperature stress
Authors: Aichinger Thomas , Nelhiebel Michael , Einspieler Sascha , Grasser Tibor
Published: January 2010

We study the hysteresis in threshold voltage shift during alternating gate bias ramps (drain current vs gate voltage (IdVg) sweeps) after negative bias temperature stress and compare the results with carefully recorded charge pumping measurements. This allows us to clearly identify three different types of defects. All defect types have in common that their charge state depends on the position of the Fermi level and that they introduce a broad density of states (DOS) in the vicinity or within of the silicon band gap. Defect I is fully recoverable, defect II is similar to defect I in terms of DOS but does not recover, while defect III can be attributed to the conventional interface states. With a precise microstructural model in mind, and by using specific test chips, which allow us to vary stress bias and temperature quasiarbitrarily, we come to the conclusion that the carrier trapping and detrapping characteristics of stress induced defects can be controlled by temperature and electric field in a similar way, but that irrevocable structural relaxation is mainly influenced by temperature. Based on these ideas, we present a measurement method which can be used to energetically profile the relaxation of stress induced oxide defects.
High contrast, depth-resolved thermoreflectance imaging using a Nipkow disk confocal microscope
Authors: Summers J. A. , Yang T. , Tuominen M. T. , Hudgings J. A.
Published: January 2010

We have developed a depth-resolved confocal thermal imaging technique that is capable of measuring the temperature distribution of an encapsulated or semi-obstructed device. The technique employs lock-in charge coupled device-based thermoreflectance imaging via a Nipkow disk confocal microscope, which is used to eliminate extraneous reflections from above or below the imaging plane. We use the confocal microscope to predict the decrease in contrast and dynamic range due to an obstruction for widefield thermoreflectance, and we demonstrate the ability of confocal thermoreflectance to maintain a high contrast and thermal sensitivity in the presence of large reflecting obstructions in the optical path.
Interaction of weakly compressible isotropic turbulence with planar expansion waves: Flow anisotropy and vorticity alignment
Authors: Xanthos Savvas , Gong Minwei , Andreopoulos Yiannis
Published: January 2010

Further analysis of the experimental data of the velocity gradient tensor first published by Xanthos et al. [J. Fluid Mech. 584, 301 (2007)] has been carried out and new results are reported here to provide additional insights on the effects of expansion waves interacting with isotropic turbulence. The flow field was generated by the reflection of an incoming shock wave at the open end of a large scale shock tube facility which interacted with the induced flow behind the incident shock wave which passed through a turbulence generating grid. In the present configuration the interaction is free from streamline curvature effects, which cause additional effects on turbulence. The strength of the applied expansive straining was 240 s−1. Rectangular pattern grids of different mesh sizes were used to generate isotropic and homogeneous turbulence with turbulent Reynolds number Reλ based on Taylor’s microscale between 450 and 488. Lateral vorticity fluctuations and fluctuations of enstrophy and all stretching vector components are drastically reduced during the interaction. Residual attenuation in the postinteraction flow field was found only in the lateral vorticity fluctuations and in the longitudinal stretching term S11Ω1. Helicity and the helicity angle were computed from the data and the orientation angle of the vorticity vector in reference to the velocity vector was determined. Large fluctuations of the helicity angle were observed which extend from 0° to 180° with most probable values close to 30° and 130° and a mean value of 85°. Rotational dissipation rate was found to be high at these angles. The time-dependent signals of enstrophy, vortex stretching/tilting vector, and dissipation rate were found to exhibit a rather strong intermittent behavior which is characterized by high amplitude bursts followed by low level activities. It was found that the observed strong dissipative events are mostly associated with strong activities in the longitudinal stretching S11Ω1 rather than with events in the lateral components.
Beta-induced Alfvén-acoustic eigenmodes in stellarator plasmas with low shear
Authors: Eremin D. Yu. , Könies A.
Published: January 2010

The coupling of low-frequency Alfvénic modes with acoustic oscillations due to curvature of the background magnetic field is considered for stellarator plasmas with low shear. Magnetohydrodynamic (MHD) analysis demonstrates that the interaction between these branches can generate gaps in the continua with a width proportional to beta as well as the magnitude of the Fourier harmonics of the magnetic field strength which cause the coupling. The gaps can provide a habitat for beta-induced Alfvén-acoustic eigenmodes (BAAEs). Using the causality principle, a technique is developed to resolve the singular behavior of the MHD BAAE eigenmode equation at the points of resonance with the acoustic continuum. Alternatively, the singularities arising in the reduced MHD description can be resolved by accounting for the finite parallel electrical field. Both approaches yield consistent continuum damping rate, which proves to be small. Numerical calculations for analytically fitted experimental profiles of electron-dominated plasma in Helically Symmetric eXperiment (HSX) facility yield two weakly damped BAAE modes with different frequencies: one is close to the maximum of the lower-frequency Alfvén-acoustic continuum, and the other is located well within the BAAE gap. The numerically found BAAEs have frequencies in the same range as the experimentally observed electromagnetic modes in HSX, even when the finite diamagnetic frequency effects are considered.
Sharp low frequency dissipative effects in tetragonal BaTiO3 ceramics
Authors: Dong Liang , Stone Donald S. , Lakes Roderic S.
Published: January 2010

Mechanical anomalies (damping peaks sharper than Debye peaks, in contrast to a broad relaxation peak) were observed in tetragonal barium titanate ceramic via broadband viscoelastic spectroscopy at low frequencies (<10 Hz) at ambient temperature after aging at 90 °C for 15 h. The sharp peaks disappear after aging above the Curie point (150 °C for 10 h). Mechanical anomalies are tentatively attributed to negative stiffness heterogeneity, the mechanism of which is proposed based upon the theory of symmetry-conforming short-range order property of point defects.
Anisotropic strain-stress state and intermixing in epitaxial Mo(110)/Ni(111) multilayers: An x-ray diffraction study
Authors: Abadias G. , Debelle A. , Michel A. , Jaouen C. , Martin F. , Pacaud J.
Published: January 2010

The present study deals with the analysis of elastic strains and stresses in high-quality heteroepitaxial Mo/Ni superlattices with periods Λ lying in the range 4.8–27.6 nm. The strain-stress state in this lattice-mismatched system grown under energetic deposition conditions (ion beam sputtering) is rather complex, resulting from three contributions: (i) intrinsic (growth) stress due to atomic peening, (ii) coherency stresses of opposite sign in the two elemental layers due to the observed Nishiyama–Wassermann epitaxial relationship Ni[11¯0](111)∥Mo[001](110), and (iii) interfacial mixing. The measurement of the lattice parameters of Mo and Ni sublayers in various crystallographic directions was performed by x-ray diffraction, using the sin2 ψ method adapted for epitaxial layers. A large anisotropy of elastic strain and associated in-plane coherency stresses is revealed in the Mo sublayers, while for Ni sublayers no such behavior could be detected due to the superimposition of growth variants with threefold symmetry. Postgrowth ion irradiation with Ar ions at very low dose (∼0.2 dpa) was employed as a powerful tool to modify the intrinsic stress, thus providing additional data to be implemented in a triaxial strain-stress model, which enabled us to separate the different stress sources (intrinsic and coherency stresses) as well as to quantify the intermixing occurring during growth. This model, which has been successfully applied previously to Mo thin films, yields in the case of multilayer systems to the determination of the “stress-free and defect-free” lattice parameter, a0, i.e., solely linked to chemical mixing. The linear dependence of a0 with Λ observed in both sublayers reveals an interface-mediated chemical mixing mechanism, the extent of this interfacial mixing being much more pronounced in Mo sublayers than in Ni ones.
On Landauer versus Boltzmann and full band versus effective mass evaluation of thermoelectric transport coefficients
Authors: Jeong Changwook , Kim Raseong , Luisier Mathieu , Datta Supriyo , Lundstrom Mark
Published: January 2010

Using a full band description of electronic bandstructure, the Landauer approach to diffusive transport is mathematically related to the solution of the Boltzmann transport equation, and expressions for the thermoelectric parameters in both formalisms are presented. Quantum mechanical and semiclassical techniques to obtain from a full description of the bandstructure, E(k), the density of modes in the Landauer approach or the transport distribution in the Boltzmann solution are compared and thermoelectric transport coefficients are evaluated. Several example calculations for representative bulk materials are presented and the full band results are related to the more common effective mass formalism. Finally, given a full E(k) for a crystal, a procedure to extract an accurate, effective mass level description is presented.
First-order nonadiabatic couplings from time-dependent hybrid density functional response theory: Consistent formalism, implementation, and performance
Authors: Send Robert , Furche Filipp
Published: January 2010

First-order nonadiabatic coupling matrix elements (NACMEs) are key for phenomena such as nonradiative transitions and excited-state decay, yet a consistent and practical first principles treatment has been elusive for molecules with more than a few heavy atoms. Here we present theory, implementation using Gaussian basis sets, and benchmarks of first-order NACMEs between ground and excited states in the framework of time-dependent hybrid density functional theory (TDDFT). A time-dependent response approach to NACMEs which avoids explicit computation of excited-state wave functions is outlined. In contrast to previous approaches, the present treatment produces exact analytical derivative couplings between time-dependent Kohn–Sham (TDKS) determinants in a finite atom-centered basis set. As in analytical gradient theory, derivative molecular orbital coefficients can be eliminated, making the computational cost independent of the number of nuclear degrees of freedom. Our expression reduces to the exact Chernyak–Mukamel formula for first-order NACMEs in the complete basis-set limit, but greatly improves basis-set convergence in finite atom-centered basis sets due to additional Pulay type terms. The Chernyak–Mukamel formula is shown to be equivalent to the Hellmann–Feynman contribution in analytical gradient theory. Our formalism may be implemented in TDDFT analytical excited-state gradient codes with minor modifications. Tests for systems with up to 147 atoms show that evaluation of first-order NACMEs causes total computation times to increase by an insignificant 10% on average. The resolution-of-the-identity approximation for the Coulomb energy (RI-J) reduces the computational cost by an order of magnitude for nonhybrid functionals, while errors are insignificant with standard auxiliary basis sets. We compare the computed NACMEs to full configuration interaction (FCI) in benchmark results for diatomic molecules; hybrid TDDFT and FCI are found to be in agreement for regions of the potential energy curve where the Kohn–Sham ground-state reference is stable and the character of the excitation is properly captured by the present functionals. With these developments, nonadiabatic molecular dynamics simulations of molecular systems in the 100 atoms regime are within reach.
Surface segregation at the aluminum interface of poly(3-hexylthiophene)/fullerene solar cells
Authors: Orimo Akiko , Masuda Kohji , Honda Satoshi , Benten Hiroaki , Ito Shinzaburo , Ohkita Hideo , Tsuji Hiroshi
Published: January 2010

The effects of thermal annealing before and after Al deposition on poly(3-hexylthiophene) (P3HT)/[6,6]-phenyl-C61 butyric acid methyl ester (PCBM) blend solar cells were investigated by current density-voltage measurements and x-ray photoelectron spectroscopy (XPS). Compared to the preannealed device, the postannealed device exhibited enhanced open-circuit voltage (VOC), which is ascribed to the decrease in the reverse saturation current density J0. The XPS measurements demonstrated that P3HT is dominant at the Al interface in the preannealed device while PCBM is instead dominant in the postannealed device. This surface-segregated PCBM formed in the postannealed device can serve as a hole-blocking layer at the Al interface to reduce J0, and therefore improve VOC.
Triply-resonant optical parametric oscillator by four-wave mixing with rubidium vapor inside an optical cavity
Authors: Yu Xudong , Xiao Min , Zhang Jing
Published: January 2010

We present an experimental demonstration of simultaneous above-threshold oscillations of the Stokes and anti-Stokes fields together with the single pumping beam with rubidium atoms inside an optical standing-wave cavity. The triple resonant conditions can be achieved easily by making use of the large dispersions due to two-photon transitions in the three-level atomic system. This work provides a way to achieve high efficient nonlinear frequency conversion and the generated bright Stokes and anti-Stokes cavity output beams are potential resource for applications in quantum information science.
Suppression of Landau damping via electron band gap
Authors: Son S. , Ku S.
Published: January 2010

The pondermotive potential in the x-ray Raman compression can generate an electron band gap, which suppresses the Landau damping. The regime is identified where a Langmuir wave can be driven without damping in the stimulated Raman compression. It is shown that the partial wave breaking and the frequency detuning due to the trapped particles would be greatly reduced.
A wave-function based approach for polarizable charge model: Systematic comparison of polarization effects on protic, aprotic, and ionic liquids
Authors: Nakano Hiroshi , Yamamoto Takeshi , Kato Shigeki
Published: January 2010

We first describe a wave-function based formalism of polarizable charge model by starting from the Hartree product ansatz for the total wave function and making the second-order expansion of individual molecular energies with the use of partial charge operators. The resulting model is shown to be formally equivalent to the charge response kernel model that starts from the linear-response approximation to partial charges, and also closely related to a family of fluctuating charge models that are based on the electronegativity equalization principle. We then apply the above model to a systematic comparison of polarization effects on qualitatively different liquids, namely, protic solvents (water and methanol), an aprotic polar solvent (acetonitrile), and imidazolium-based ionic liquids. Electronic polarization is known to decelerate molecular motions in conventional solvents while it accelerates them in ionic liquids. To obtain more insights into these phenomena, we consider an effective decomposition of total polarization energy into molecular contributions, and show that their statistical distribution is well-correlated with the acceleration/deceleration of molecular motions. In addition, we perform effective nonpolarizable simulations based on mean polarized charges, and compare them with fully polarizable simulations. The result shows that the former can reproduce structural properties of conventional solvents rather accurately, while they fail qualitatively to reproduce acceleration of molecular motions in ionic liquids.
Response to “Comment on ‘Comparison between solutions of the general dynamic equation and the kinetic equation for nucleation and droplet growth’ ” [J. Chem. Phys. 132, 047101 (2010)]
Authors: Holten V. , van Dongen M. E. H.
Published: January 2010

The analytical results presented in the comment of Shneidman for the droplet size distribution, the thickness of the distribution front, and the location of the stationary source are compared to our earlier numerical results. The agreement is very good in the case of the size distribution and the source location, but the analytical result for the thickness of the front deviates from the numerical result at high supersaturations.
Layered structure in compatible binary polymer brushes with high graft density: A computer simulation study
Authors: Xue Yao-Hong , Liu Hong , Lu Zhong-Yuan , Liang Xue-Zhang
Published: January 2010

We focus on highly grafted binary polymer brushes with compatible components in the cases of different chain lengths. Layered structures parallel to the surface that indicating “phase separation” are observed in a series of dissipative particle dynamics simulations. The stretch parameters indicate that the short chains are suppressed in the lower layer of the film, whereas the longer chains are much stretched in the region dominated by the short chains (lower layer) but possess relaxed conformations in the upper layer. By slightly changing the solvent selectivity to prefer the short chains, we find a reversion of the layered structure. Such a sensitive switch of film property implies its potential application as tuning the wettability and adhesion of the surface in industry.
Coordination of plant cell division and expansion in a simple morphogenetic system
Authors: Dupuy Lionel , Mackenzie Jonathan , Haseloff Jim
Published: January 2010

Morphogenesis in plants arises from the interplay of genetic and physical interactions within a growing network of cells. The physical aspects of cell proliferation and differentiation are genetically regulated, but constrained by mechanical interactions between the cells. Higher plant tissues consist of an elaborate three-dimensional matrix of active cytoplasm and extracellular matrix, where it is difficult to obtain direct measurements of geometry or cell interactions. To properly understand the workings of plant morphogenesis, it is necessary to have biological systems that allow simple and direct observation of these processes. We have adopted a highly simplified plant system to investigate how cell proliferation and expansion is coordinated during morphogenesis.
Coleocheate scutata
is a microscopic fresh-water green alga with simple anatomical features that allow for accurate quantification of morphogenetic processes. Image analysis techniques were used to extract precise models for cell geometry and physical parameters for growth. This allowed construction of a deformable finite element model for growth of the whole organism, which incorporated cell biophysical properties, viscous expansion of cell walls, and rules for regulation of cell behavior. The study showed that a simple set of autonomous, cell-based rules are sufficient to account for the morphological and dynamic properties of
Coleochaete
growth. A variety of morphogenetic behavior emerged from the application of these local rules. Cell shape sensing is sufficient to explain the patterns of cell division during growth. This simplifying principle is likely to have application in modeling and design for engineering of higher plant tissues.
Cross-cultural recognition of basic emotions through nonverbal emotional vocalizations
Authors: Sauter Disa A. , Eisner Frank , Ekman Paul , Scott Sophie K.
Published: January 2010

Emotional signals are crucial for sharing important information, with conspecifics, for example, to warn humans of danger. Humans use a range of different cues to communicate to others how they feel, including facial, vocal, and gestural signals. We examined the recognition of nonverbal emotional vocalizations, such as screams and laughs, across two dramatically different cultural groups. Western participants were compared to individuals from remote, culturally isolated Namibian villages. Vocalizations communicating the so-called “basic emotions” (anger, disgust, fear, joy, sadness, and surprise) were bidirectionally recognized. In contrast, a set of additional emotions was only recognized within, but not across, cultural boundaries. Our findings indicate that a number of primarily negative emotions have vocalizations that can be recognized across cultures, while most positive emotions are communicated with culture-specific signals.
PDR-type ABC transporter mediates cellular uptake of the phytohormone abscisic acid
Authors: Kang Joohyun , Hwang Jae-Ung , Lee Miyoung , Kim Yu-Young , Assmann Sarah M. , Martinoia Enrico , Lee Youngsook
Published: January 2010

Abscisic acid (ABA) is a ubiquitous phytohormone involved in many developmental processes and stress responses of plants. ABA moves within the plant, and intracellular receptors for ABA have been recently identified; however, no ABA transporter has been described to date. Here, we report the identification of the ATP-binding cassette (ABC) transporter Arabidopsis thaliana Pleiotropic drug resistance transporter PDR12 (AtPDR12)/ABCG40 as a plasma membrane ABA uptake transporter. Uptake of ABA into yeast and BY2 cells expressing AtABCG40 was increased, whereas ABA uptake into protoplasts of
atabcg40
plants was decreased compared with control cells. In response to exogenous ABA, the up-regulation of ABA responsive genes was strongly delayed in
atabcg40
plants, indicating that ABCG40 is necessary for timely responses to ABA. Stomata of loss-of-function
atabcg40
mutants closed more slowly in response to ABA, resulting in reduced drought tolerance. Our results integrate ABA-dependent signaling and transport processes and open another avenue for the engineering of drought-tolerant plants.
Structural basis of the oxidative activation of the carboxysomal γ-carbonic anhydrase, CcmM
Authors: Peña Kerry L. , Castel Stephane E. , de Araujo Charlotte , Espie George S. , Kimber Matthew S.
Published: January 2010

Cyanobacterial RuBisCO is sequestered in large, icosahedral, protein-bounded microcompartments called carboxysomes. Bicarbonate is pumped into the cytosol, diffuses into the carboxysome through small pores in its shell, and is then converted to CO
2
by carbonic anhydrase (CA) prior to fixation. Paradoxically, many β-cyanobacteria, including
Thermosynechococcus elongatus
BP-1, lack the conventional carboxysomal β-CA,
ccaA
. The N-terminal domain of the carboxysomal protein CcmM is homologous to γ-CA from
Methanosarcina thermophila
(Cam) but recombinant CcmM derived from
ccaA
-containing cyanobacteria show no CA activity. We demonstrate here that either full length CcmM from
T. elongatus
, or a construct truncated after 209 residues (CcmM209), is active as a CA—the first catalytically active bacterial γ-CA reported. The 2.0 Å structure of CcmM209 reveals a trimeric, left-handed β-helix structure that closely resembles Cam, except that residues 198–207 form a third α-helix stabilized by an essential Cys194-Cys200 disulfide bond. Deleting residues 194–209 (CcmM193) results in an inactive protein whose 1.1 Å structure shows disordering of the N- and C-termini, and reorganization of the trimeric interface and active site. Under reducing conditions, CcmM209 is similarly partially disordered and inactive as a CA. CcmM protein in fresh
E. coli
cell extracts is inactive, implying that the cellular reducing machinery can reduce and inactivate CcmM, while diamide, a thiol oxidizing agent, activates the enzyme. Thus, like membrane-bound eukaryotic cellular compartments, the β-carboxysome appears to be able to maintain an oxidizing interior by precluding the entry of thioredoxin and other endogenous reducing agents.