bluuebunny/crossref_metadata_2025 huggingface dataset:
Honors
Authors: Anonymous
Published: November 2011

Two AGU members are principal investigators on a project at the University of Colorado's National Snow and Ice Data Center (NSIDC) that recently received the 2011 Governor's Award for High‐Impact Research from Colorado governor John Hickenlooper. NSIDC technical services manager David Gallaher and NSIDC director Mark Serreze have been involved with the center's Green Data Center, which has saved significant energy. Cornell University astronomy professorSteven Squyres is the new chairman of the NASA Advisory Council, which offers guidance and policy advice to the NASA administrator, the agency announced on 2 November. Squyres previously served on the council during the 1990s and also served as chairman of the former NASA Space Science Advisory Committee.
Interviews with survivors of Tohoku earthquake provide insights into fatality rate
Authors: Ando Masataka , Ishida Mizuho , Hayashi Yoshinori , Mizuki Chiharu
Published: November 2011

The 11 March 2011 Tohoku earthquake and tsunami devastated northeastern Japan, causing thousands of deaths and widespread destruction. Many people in the zones affected by the tsunami evacuated to safety, but others were not so fortunate. Why did some people evacuate immediately and others wait until it was too late? In interviews with survivors, we sought to find answers to that question. These interviews revealed that many residents did not get accurate warnings, and many chose to stay in dangerous locations in part because they misunderstood the risks. Better communication of warnings and improved education about the science behind earthquakes and tsunamis could help save lives in the future.
Atmospheric waves break on the Moon's shadow
Authors: Schultz Colin
Published: November 2011

During a solar eclipse the Moon's passage overhead blocks out the majority of the Sun's light, casting a wide swath of the Earth into darkness. The land under the Moon's shadow receives less incoming energy than the surrounding regions, causing it to cool. In the early 1970s, researchers proposed that this temperature difference could set off slow moving waves in the upper atmosphere. They hypothesized that the waves, moving more slowly than the traveling temperature disparity from which they spawned, would pile up along the leading edge of the Moon's path—like slow moving waves breaking on a ship's bow. The dynamic was shown theoretically and in early computer simulations, but it was not until a total solar eclipse on 22 July 2009 that researchers were able to observe the behavior.
Terannual variation in the F2 layer peak electron density (NmF2) at middle latitudes
Authors: Xu Jiyao , Ma Ruiping , Wang Wenbin
Published: November 2011

Ionosonde data from 33 stations in three longitude sectors from 1969 to 1986 have been used to study the seasonal variations of ionospheric F2 layer peak electron densities (NmF2). We found that there is a periodic oscillation in daytime NmF2 with a period of 4 months (terannual). Our analysis shows that there is a very good phase match between the annual and semiannual oscillations and the terannual oscillations. These three oscillations vary with solar activity in the same way: large amplitudes during solar maximum. The amplitude of the terannual oscillation is also correlated with the product of the amplitudes of annual and semiannual oscillations. These suggest that the terannual oscillation might be related to the nonlinear interaction between the annual and semiannual oscillations. In addition, the terannual oscillation is stronger in the midlatitude region in the Northern Hemisphere than in the Southern Hemisphere. Furthermore, there are large differences in the ionospheric seasonal variations between daytime and nighttime. No obvious terannual oscillation signature is seen in the nighttime F2 layer.
On the relationship between azimuthal anisotropy from shear wave splitting and surface wave tomography
Authors: Becker T. W. , Lebedev S. , Long M. D.
Published: November 2011

Seismic anisotropy provides essential constraints on mantle dynamics and continental evolution. One particular question concerns the depth distribution and coherence of azimuthal anisotropy, which is key for understanding force transmission between the lithosphere and asthenosphere. Here, we reevaluate the degree of coherence between the predicted shear wave splitting derived from tomographic models of azimuthal anisotropy and that from actual observations of splitting. Significant differences between the two types of models have been reported, and such discrepancies may be due to differences in averaging properties or due to approximations used in previous comparisons. We find that elaborate, full waveform methods to estimate splitting from tomography yield generally similar results to the more common, simplified approaches. This validates previous comparisons and structural inversions. However, full waveform methods may be required for regional studies, and they allow exploiting the back‐azimuthal variations in splitting that are expected for depth‐variable anisotropy. Applying our analysis to a global set ofSKSsplitting measurements and two recent surface wave models of upper‐mantle azimuthal anisotropy, we show that the measures of anisotropy inferred from the two types of data are in substantial agreement. Provided that the splitting data is spatially averaged (so as to bring it to the scale of long‐wavelength tomographic models and reduce spatial aliasing), observed and tomography‐predicted delay times are significantly correlated, and global angular misfits between predicted and actual splits are relatively low. Regional anisotropy complexity notwithstanding, our findings imply that splitting and tomography yield a consistent signal that can be used for geodynamic interpretation.
Three‐dimensional oceanic eddy analysis in the Southern California Bight from a numerical product
Authors: Dong Changming , Lin Xiayan , Liu Yu , Nencioli Francesco , Chao Yi , Guan Yuping , Chen Dake , Dickey Tommy , McWilliams James C.
Published: November 2011

With eight islands, complex coastlines and bottom topography, strong wind curls, and frequent upwelling fronts, the Southern California Bight (SCB) is an area with strong eddy activity. By applying an automated eddy detection scheme to a 12 year high‐resolution numerical product of the oceanic circulation in the SCB, a three‐dimensional eddy data set is developed. It includes information for each eddy's location, polarity, intensity, size, boundary, and moving path at nine vertical levels. Through a series of statistical analyses applied to the eddy data set, three‐dimensional statistical characteristics of mesoscale and submeoscale eddy variations in the SCB are elucidated; these shed light on how eddies are generated, evolve, and terminate. A significant percentage of eddies is found to be generated around islands and headlands along the coastline, which indicates that islands in the SCB play a vital role in eddy generation. Three types of eddies, based on shape, are identified from the numerical product: bowl, lens, and cone. A dynamic analysis shows that some submesoscale eddies with finite local Rossby numbers tend to be ageostrophic balanced while mesoscale eddies are in geostrophic balance. The present research results are useful for the interpretation of data sets obtained during the interdisciplinary Santa Barbara Channel Radiance in a Dynamic Ocean (RaDyo) field experiment conducted on September 3–25, 2008.
Effective pore‐scale dispersion upscaling with a correlated continuous time random walk approach
Authors: Le Borgne T. , Bolster D. , Dentz M. , de Anna P. , Tartakovsky A.
Published: November 2011

We investigate the upscaling of dispersion from a pore‐scale analysis of Lagrangian velocities. A key challenge in the upscaling procedure is to relate the temporal evolution of spreading to the pore‐scale velocity field properties. We test the hypothesis that one can represent Lagrangian velocities at the pore scale as a Markov process in space. The resulting effective transport model is a continuous time random walk (CTRW) characterized by a correlated random time increment, here denoted as correlated CTRW. We consider a simplified sinusoidal wavy channel model as well as a more complex heterogeneous pore space. For both systems, the predictions of the correlated CTRW model, with parameters defined from the velocity field properties (both distribution and correlation), are found to be in good agreement with results from direct pore‐scale simulations over preasymptotic and asymptotic times. In this framework, the nontrivial dependence of dispersion on the pore boundary fluctuations is shown to be related to the competition between distribution and correlation effects. In particular, explicit inclusion of spatial velocity correlation in the effective CTRW model is found to be important to represent incomplete mixing in the pore throats.
Over‐extraction from shallow bedrock versus deep alluvial aquifers: Reliability versus sustainability considerations for India's groundwater irrigation
Authors: Fishman Ram Mukul , Siegfried Tobias , Raj Pradeep , Modi Vijay , Lall Upmanu
Published: November 2011

The excessive exploitation of groundwater aquifers is emerging as a worldwide problem, but it is nowhere as dramatic and consequential as it is in India, the world's largest consumer, where hundreds of millions of people depend on it. Usually the problem is framed in terms of a long‐term decline in water tables and its consequence for extraction costs, resource depletion, and the sustainability of irrigated agriculture. Here a comparative analysis is provided of coupled groundwater, energy, and irrigation dynamics in two groundwater intensive regions in India that differ in their underlying hydrogeology—the Indian Punjab with its deep alluvial aquifers and the Telangana region in south‐central India with its shallow hard rock aquifers. Using a simple modeling framework and piezometric and agricultural time series, we show that in shallow aquifers the sense in which extraction is excessive is different, and is related to the short‐term reliability of water supply rather than long‐term sustainability. This has important repercussions for irrigated agricultural economies.
Infrared thermography of evaporative fluxes and dynamics of salt deposition on heterogeneous porous surfaces
Authors: Nachshon Uri , Shahraeeni Ebrahim , Or Dani , Dragila Maria , Weisbrod Noam
Published: November 2011

Evaporation of saline solutions from porous media, common in arid areas, involves complex interactions between mass transport, energy exchange and phase transitions. We quantified evaporation of saline solutions from heterogeneous sand columns under constant hydraulic boundary conditions to focus on effects of salt precipitation on evaporation dynamics. Mass loss measurements and infrared thermography were used to quantify evaporation rates. The latter method enables quantification of spatial and temporal variability of salt precipitation to identify its dynamic effects on evaporation. Evaporation from columns filled with texturally‐contrasting sand using different salt solutions revealed preferential salt precipitation within the fine textured domains. Salt precipitation reduced evaporation rates from the fine textured regions by nearly an order of magnitude. In contrast, low evaporation rates from coarse‐textured regions (due to low capillary drive) exhibited less salt precipitation and consequently less evaporation rate suppression. Experiments provided insights into two new phenomena: (1) a distinct increase in evaporation rate at the onset of evaporation; and (2) a vapor pumping mechanism related to the presence of a salt crust over semidry media. Both phenomena are related to local vapor pressure gradients established between pore water and the surface salt crust. Comparison of two salts: NaCl and NaI, which tend to precipitate above the matrix surface and within matrix pores, respectively, shows a much stronger influence of NaCl on evaporation rate suppression. This disparity reflects the limited effect of NaI precipitation on matrix resistivity for solution and vapor flows.
Basis set convergence of the coupled-cluster correction, $\delta _{\text{MP2}}^{\text{CCSD(T)}}$δMP2CCSD(T): Best practices for benchmarking non-covalent interactions and the attendant revision of the S22, NBC10, HBC6, and HSG databases
Authors: Marshall Michael S. , Burns Lori A. , Sherrill C. David
Published: November 2011

In benchmark-quality studies of non-covalent interactions, it is common to estimate interaction energies at the complete basis set (CBS) coupled-cluster through perturbative triples [CCSD(T)] level of theory by adding to CBS second-order perturbation theory (MP2) a “coupled-cluster correction,” \documentclass[12pt]{minimal}\begin{document}$\delta _{\text{MP2}}^{\text{CCSD(T)}}$\end{document}δMP2CCSD(T), evaluated in a modest basis set. This work illustrates that commonly used basis sets such as 6-31G*(0.25) can yield large, even wrongly signed, errors for \documentclass[12pt]{minimal}\begin{document}$\delta _{\text{MP2}}^{\text{CCSD(T)}}$\end{document}δMP2CCSD(T) that vary significantly by binding motif. Double-ζ basis sets show more reliable results when used with explicitly correlated methods to form a \documentclass[12pt]{minimal}\begin{document}$\delta _{\text{MP2}-{\rm F}12}^{\text{CCSD(T}^*)-{\rm F}12}$\end{document}δMP2−F12CCSD(T*)−F12 correction, yielding a mean absolute deviation of 0.11 kcal mol−1 for the S22 test set. Examining the coupled-cluster correction for basis sets up to sextuple-ζ in quality reveals that \documentclass[12pt]{minimal}\begin{document}$\delta _{\text{MP2}}^{\text{CCSD(T)}}$\end{document}δMP2CCSD(T) converges monotonically only beyond a turning point at triple-ζ or quadruple-ζ quality. In consequence, CBS extrapolation of \documentclass[12pt]{minimal}\begin{document}$\delta _{\text{MP2}}^{\text{CCSD(T)}}$\end{document}δMP2CCSD(T) corrections before the turning point, generally CBS (aug-cc-pVDZ,aug-cc-pVTZ), are found to be unreliable and often inferior to aug-cc-pVTZ alone, especially for hydrogen-bonding systems. Using the findings of this paper, we revise some recent benchmarks for non-covalent interactions, namely the S22, NBC10, HBC6, and HSG test sets. The maximum differences in the revised benchmarks are 0.080, 0.060, 0.257, and 0.102 kcal mol−1, respectively.
Determination of depolarization temperature of (Bi1/2Na1/2)TiO3-based lead-free piezoceramics
Authors: Anton Eva-Maria , Jo Wook , Damjanovic Dragan , Rödel Jürgen
Published: November 2011

The depolarization temperature Td of piezoelectric materials is an important figure of merit for their application at elevated temperatures. Until now, there are several methods proposed in the literature to determine the depolarization temperature of piezoelectrics, which are based on different physical origins. Their validity and inter-correlation have not been clearly manifested. This paper applies the definition of depolarization temperature as the temperature of the steepest decrease of remanent polarization and evaluates currently used methods, both in terms of this definition and practical applicability. For the investigations, the lead-free piezoceramics (1–y)(Bi1/2Na1/2TiO3–xBi1/2K1/2TiO3)−yK0.5Na0.5NbO3 in a wide compositional range were chosen. Results were then compared to those for BaTiO3 and a commercial Pb(Zr,Ti)O3-based material as references. Thermally stimulated depolarization current and in situ temperature-dependent piezoelectric coefficient d33 are recommended to determine Td according to the proposed definition. Methods based on inflection point of the real part of permittivity or the peak in dielectric loss give consistently higher temperature values.
Observation of spectral and temporal polarization oscillations of optical pulses in a silicon nanowaveguide
Authors: Daniel Brian A. , Lee Jonathan Y. , Fauchet Philippe M. , Agrawal Govind P.
Published: November 2011

We observe both spectral and temporal oscillations in the polarization state of optical pulses propagating through a silicon nanowaveguide. The spectral oscillations are linear in nature and result from polarization-mode dispersion (PMD). The temporal oscillations are nonlinear in nature, and theoretical simulations clarify that they result from the combined effects of two-photon absorption generated free carriers and PMD.
Effects of solvation shells and cluster size on the reaction of aluminum clusters with water
Authors: Mou Weiwei , Ohmura Satoshi , Hemeryck Anne , Shimojo Fuyuki , Kalia Rajiv K. , Nakano Aiichiro , Vashishta Priya
Published: November 2011

Reaction of aluminum clusters, Aln (n = 16, 17 and 18), with liquid water is investigated using quantum molecular dynamics simulations, which show rapid production of hydrogen molecules assisted by proton transfer along a chain of hydrogen bonds (H-bonds) between water molecules, i.e. Grotthuss mechanism. The simulation results provide answers to two unsolved questions: (1) What is the role of a solvation shell formed by non-reacting H-bonds surrounding the H-bond chain; and (2) whether the high size-selectivity observed in gas-phase Aln-water reaction persists in liquid phase? First, the solvation shell is found to play a crucial role in facilitating proton transfer and hence H2 production. Namely, it greatly modifies the energy barrier, generally to much lower values (< 0.1 eV). Second, we find that H2 production by Aln in liquid water does not depend strongly on the cluster size, in contrast to the existence of magic numbers in gas-phase reaction. This paper elucidates atomistic mechanisms underlying these observations.
Localized subsurface modification of materials using micro-low-energy multiple ion beamlets
Authors: Chowdhury Abhishek , Bhattacharjee Sudeep
Published: November 2011

Generation of focused multiple ion beamlets from an intense microwave plasma source is investigated for the creation of localized subsurface modification of materials. Unlike conventional single element focused ion beam (FIB) systems, the plasma source is capable of providing ion beams of multiple elements. Two types of plasma electrodes (PE) are employed, one with a honeycomb structure with notched apertures and another with a 5×5 array of through apertures, both attached to the plasma source and are capable of generating focused ion beamlets (50 - 100 μm diameter) in a patterned manner. Measurements of ion saturation current near the PE indicate that the plasma is uniform over an area of ∼ 7 cm2, which is further confirmed by uniformity in extracted beam current through the apertures. The ion beams are applied to investigate change in electrical sheet resistance Rs of metallic thin films in a controlled manner by varying the ionic species and beam energy. Results indicate a remarkable increase in Rs with beam energy (∼ 50 % at 1 keV for Ar ions), and with ionic species (∼ 90% for Krypton ions at 0.6 keV), when 80 nm thick copper films are irradiated by ∼2 cm diameter ion beams. Ion induced surface roughness is considered as the main mechanism for this change as confirmed by atomic force microscopy (AFM) measurements. Predictions for micro-beamlet induced change in Rs are discussed. The experimental results are verified using TRIM and AXCEL-INP simulations.
Preparation and Properties of (Hydroxymethyl)boronic Acid and its Pinanediol Ester
Authors: Matteson Donald S.
Published: November 2011

Hydrolysis of diisopropyl (bromomethyl)boronate followed by reaction with pinanediol provides an efficient route to pinanediol (hydroxymethyl)boronate (12), a useful intermediate for asymmetric synthesis. The stability of (hydroxymethyl)boronic acid (10) and its ester 12 have been examined by NMR spectroscopy. Heating for 1 h in acidic D2O does not degrade 10 and only affects the pinanediol moiety of 12. Base does not degrade 10 or 12 in several days at 20–25°C, but converts either to DCH2OD and CH3OD in a few h at 90–98°C, with a large H/D isotope effect. Pinanediol (bromomethyl)boronate with sodium hydroxide in D2O yields a gross mixture of products.
Using Quenching Kinetics and Thermodynamics of Amino-Fluorophores as Empirical Tools for Predicting Boronic Acid Sensors Suitable for Use in Physiological Conditions
Authors: McGregor Nicholas , Pardin Christophe , Skene W. G.
Published: November 2011

A series of water-soluble 1-amino-naphthalenes and 2-amino-fluorenes are prepared. These serve as model fluorophores for measuring the thermodynamics and kinetics of fluorescence quenching with phenylboronic acids and aliphatic amines. Steady-state and time-resolved fluorescence quenching kinetics are investigated using the Stern–Volmer method. Diffusion limited quenching constants and exergonic thermodynamics of electron transfer are derived for the 5-amino-1-napthol and 2-aminofluorene derivatives with phenylboronic acid and/or an aliphatic imine. No quenching and endergonic thermodynamics or electron transfer are observed for 5-sulfonamide, 5-sulfonic acid, or 5-hydroxy-7-sulfonic acid aminonaphthalene derivatives. Boronic acid sensors synthesized from these aminofluorophores by reductive amination with 2-formylphenylboronic acid undergo fluorescence revival in the presence of saccharides only when the fluorophore demonstrates diffusion limited quenching kinetics and exergonic thermodynamics of electron transfer with the boronic acid or imine quenchers. Thus, these two properties are suitable empirical tools for predicting saccharide-induced fluorescence revival of boronic acid sensors.
High levels of mitochondrial heteroplasmy modify the development of ovine - bovine interspecies nuclear transferred embryos
Authors: Hua Song , Lu Chenglong , Song Yakun , Li Ruizhe , Liu Xu , Quan Fusheng , Wang Yongsheng , Liu Jun , Su Feng , Zhang Yong
Published: November 2011

To investigate the effect of mitochondrial heteroplasmy on embryo development, cloned embryos produced using bovine oocytes as the recipient cytoplasm and ovine granulosa cells as the donor nuclei were complemented with 2 pL mitochondrial suspension isolated from ovine (BOOMT embryos) or bovine (BOBMT embryos) granulosa cells; cloned embryos without mitochondrial injection served as the control group (BO embryos). Reverse transcription–quantitative polymerase chain reaction (RT-qPCR) and sodium bisulfite genomic sequencing were used to analyse mRNA and methylation levels of pluripotency genes (OCT4, SOX2) and mitochondrial genes (TFAM, POLRMT) in the early developmental stages of cloned embryos. The number of mitochondrial DNA copies in 2 pL ovine-derived and bovine-derived mitochondrial suspensions was 960 ± 110 and 1000 ± 120, respectively. The blastocyst formation rates were similar in BOBMT and BO embryos (P > 0.05), but significantly higher than in BOOMT embryos (P < 0.01). Expression of OCT4 and SOX2, as detected by RT-qPCR, decreased significantly in BOOMT embryos (P < 0.05), whereas the expression of TFAM and POLRMT increased significantly, compared with expression in BOOMT and BO embryos (P < 0.05). In addition, methylation levels of OCT4 and SOX2 were significantly greater (P < 0.05), whereas those of TFAM and POLRMT were significantly lower (P < 0.01), in BOOMT embryos compared with BOBMT and BO embryos. Together, the results of the present study suggest that the degree of mitochondrial heteroplasmy may affect embryonic development.
Reduced impact logging minimally alters tropical rainforest carbon and energy exchange
Authors: Miller Scott D. , Goulden Michael L. , Hutyra Lucy R. , Keller Michael , Saleska Scott R. , Wofsy Steven C. , Figueira Adelaine Michela Silva , da Rocha Humberto R. , de Camargo Plinio B.
Published: November 2011

We used eddy covariance and ecological measurements to investigate the effects of reduced impact logging (RIL) on an old-growth Amazonian forest. Logging caused small decreases in gross primary production, leaf production, and latent heat flux, which were roughly proportional to canopy loss, and increases in heterotrophic respiration, tree mortality, and wood production. The net effect of RIL was transient, and treatment effects were barely discernable after only 1 y. RIL appears to provide a strategy for managing tropical forest that minimizes the potential risks to climate associated with large changes in carbon and water exchange.
On a characterization of bilinear forms on the Dirichlet space
Authors: Cascante Carme , Ortega Joaquin
Published: November 2011

Arcozzi, Rochberg, Sawyer and Wick obtained a characterization of the holomorphic functions

b
b

such that the Hankel type bilinear form
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="upper T Subscript b Baseline left-parenthesis f comma g right-parenthesis equals integral Underscript double-struck upper D Endscripts left-parenthesis upper I plus upper R right-parenthesis left-parenthesis f g right-parenthesis left-parenthesis z right-parenthesis ModifyingAbove left-parenthesis upper I plus upper R right-parenthesis b left-parenthesis z right-parenthesis With bar d v left-parenthesis z right-parenthesis">

T

b

(
f
,
g
)
=

∫

D

(
I
+
R
)
(
f
g
)
(
z
)

(
I
+
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)
b
(
z
)

¯

d
v
(
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)

T_{b}(f,g)= \int _{{\mathbb D}}(I+R)(fg)(z) \overline {(I+R)b(z)}dv(z)

is bounded on

D

×

D

{\mathcal D}\times {\mathcal D}

, where

D

{\mathcal D}

is the Dirichlet space. In this paper we give an alternative proof of this characterization which tries to understand the similarity with the results of Maz

′

’

ya and Verbitsky relative to the Schrödinger forms on the Sobolev spaces

L
2
1

(

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n

)

L_2^1(\mathbb {R}^n)

.
Characterization of a Unique “Super Soft” Kernel Trait in Wheat
Authors: Morris Craig F. , Anderson James A. , King G. E. , Bettge Arthur D. , Garland‐Campbell Kimberly , Allan R. E. , Fuerst E. Patrick , Beecher Brian S.
Published: November 2011

Kernel texture in wheat (Triticum sp.) is central to end‐use quality and utilization. Here we report the discovery of a novel soft kernel trait in soft white winter wheat (T. aestivum L.). Two heritable kernel phenotypes were selected among F3‐derived sibs, hereafter designated “normal soft” (wild‐type) and “super soft.” Normal soft lines exhibited single kernel characterization system (SKCS) hardness index (HI) values typical of soft wheat (HI ≈ 20), whereas the super soft lines were unusually soft (HI ≈ 5). Under some environments, individual super soft lines exhibited HI values as low as HI = –4. The super soft trait was manifested in reduced SKCS kernel texture and higher break flour yields, with some increase in sodium carbonate SRC (solvent retention capacity) values and sponge cake volumes. Straight‐grade flour yield, flour ash, milling score, and cookie diameter were largely unaffected. With the possible exception of the sodium carbonate SRC values, we observed no indication that the super soft trait conferred any negative aspects to commercial soft wheat quality. As such, the super soft trait may provide wheat breeders with new opportunities to modify the end‐use quality of wheat.
Characterization of CbCyp51 from Field Isolates of Cercospora beticola
Authors: Bolton Melvin D. , Birla Keshav , Rivera-Varas Viviana , Rudolph Kurt D. , Secor Gary A.
Published: November 2011

The hemibiotrophic fungus Cercospora beticola causes leaf spot of sugar beet. Leaf spot control measures include the application of sterol demethylation inhibitor (DMI) fungicides. However, reduced sensitivity to DMIs has been reported recently in the Red River Valley sugar beet-growing region of North Dakota and Minnesota. Here, we report the cloning and molecular characterization of CbCyp51, which encodes the DMI target enzyme sterol P450 14α-demethylase in C. beticola. CbCyp51 is a 1,632-bp intron-free gene with obvious homology to other fungal Cyp51 genes and is present as a single copy in the C. beticola genome. Five nucleotide haplotypes were identified which encoded three amino acid sequences. Protein variant 1 composed 79% of the sequenced isolates, followed by protein variant 2 that composed 18% of the sequences and a single isolate representative of protein variant 3. Because resistance to DMIs can be related to polymorphism in promoter or coding sequences, sequence diversity was assessed by sequencing >2,440 nucleotides encompassing CbCyp51 coding and flanking regions from isolates with varying EC50 values (effective concentration to reduce growth by 50%) to DMI fungicides. However, no mutations or haplotypes were associated with DMI resistance or sensitivity. No evidence for alternative splicing or differential methylation of CbCyp51 was found that might explain reduced sensitivity to DMIs. However, CbCyp51 was overexpressed in isolates with high EC50 values compared with isolates with low EC50 values. After exposure to tetraconazole, isolates with high EC50 values responded with further induction of CbCyp51, with a positive correlation of CbCyp51 expression and tetraconazole concentration up to 2.5 μg ml–1.
The H/ACA RNP assembly factor SHQ1 functions as an RNA mimic
Authors: Walbott Hélène , Machado-Pinilla Rosario , Liger Dominique , Blaud Magali , Réty Stéphane , Grozdanov Petar N. , Godin Kate , van Tilbeurgh Herman , Varani Gabriele , Meier U. Thomas , Leulliot Nicolas
Published: November 2011

SHQ1 is an essential assembly factor for H/ACA ribonucleoproteins (RNPs) required for ribosome biogenesis, pre-mRNA splicing, and telomere maintenance. SHQ1 binds dyskerin/NAP57, the catalytic subunit of human H/ACA RNPs, and this interaction is modulated by mutations causing X-linked dyskeratosis congenita. We report the crystal structure of the C-terminal domain of yeast SHQ1, Shq1p, and its complex with yeast dyskerin/NAP57, Cbf5p, lacking its catalytic domain. The C-terminal domain of Shq1p interacts with the RNA-binding domain of Cbf5p and, through structural mimicry, uses the RNA–protein-binding sites to achieve a specific protein–protein interface. We propose that Shq1p operates as a Cbf5p chaperone during RNP assembly by acting as an RNA placeholder, thereby preventing Cbf5p from nonspecific RNA binding before association with an H/ACA RNA and the other core RNP proteins.
Anterior thalamic lesions alter both hippocampal-dependent behavior and hippocampal acetylcholine release in the rat
Authors: Savage Lisa M. , Hall Joseph M. , Vetreno Ryan P.
Published: November 2011

The anterior thalamic nuclei (ATN) are important for learning and memory as damage to this region produces a persistent amnestic syndrome. Dense connections between the ATN and the hippocampus exist, and importantly, damage to the ATN can impair hippocampal functioning. Acetylcholine (ACh) is a key neurotransmitter in the hippocampus, and in vivo measures of ACh are correlated to learning and memory performance. In the present study, complete lesions of the ATN impaired performance on two measures of hippocampal-dependent learning and memory (spontaneous alternation and delayed alternation) and severely disrupted behaviorally evoked ACh efflux within the hippocampus of adult male rats. In contrast, incomplete ATN lesions did not impair spontaneous alternation performance but did impair delayed alternation performance while blunting hippocampal ACh efflux. Interestingly, ATN lesions of any size did not affect basal concentrations of ACh in the hippocampus. These results demonstrate that the ATN have the capacity to modulate behaviorally relevant neuronal transmission within the hippocampus.
O-Acetylation ofArabidopsisHemicellulose Xyloglucan Requires AXY4 or AXY4L, Proteins with a TBL and DUF231 Domain
Authors: Gille Sascha , de Souza Amancio , Xiong Guangyan , Benz Monique , Cheng Kun , Schultink Alex , Reca Ida-Barbara , Pauly Markus
Published: November 2011

In an Arabidopsis thaliana forward genetic screen aimed at identifying mutants with altered structures of their hemicellulose xyloglucan (axy mutants) using oligosaccharide mass profiling, two nonallelic mutants (axy4-1 and axy4-2) that have a 20 to 35% reduction in xyloglucan O-acetylation were identified. Mapping of the mutation in axy4-1 identified AXY4, a type II transmembrane protein with a Trichome Birefringence-Like domain and a domain of unknown function (DUF231). Loss of AXY4 transcript results in a complete lack of O-acetyl substituents on xyloglucan in several tissues, except seeds. Seed xyloglucan is instead O-acetylated by the paralog AXY4like, as demonstrated by the analysis of the corresponding T-DNA insertional lines. Wall fractionation analysis of axy4 knockout mutants indicated that only a fraction containing xyloglucan is non-O-acetylated. Hence, AXY4/AXY4L is required for the O-acetylation of xyloglucan, and we propose that these proteins represent xyloglucan-specific O-acetyltransferases, although their donor and acceptor substrates have yet to be identified. An Arabidopsis ecotype, Ty-0, has reduced xyloglucan O-acetylation due to mutations in AXY4, demonstrating that O-acetylation of xyloglucan does not impact the plant's fitness in its natural environment. The relationship of AXY4 with another previously identified group of Arabidopsis proteins involved in general wall O-acetylation, reduced wall acetylation, is discussed.
Phase II multicenter, randomized, double‐blind study of recombinant mutated human tumor necrosis factor‐α in combination with chemotherapies in cancer patients
Authors: Li Meng , Xu Tianjiao , Zhang Zhao , Xue Xiaochang , Zhang Cun , Qin Xin , Li Weina , Hao Qiang , Zhang Wei , Zhang Yingqi
Published: November 2011

We previously prepared a tumor necrosis factor (TNF)‐α mutant (rmhTNF‐α) that showed higher antitumor activity and lower systemic toxicity compared with native TNF‐α. The safety profile and the pharmacokinetic characteristics of rmhTNF‐α were suited for clinical use according to biological Investigational New Drug application, a standard guideline for new drug investigation in China. Here, we evaluate the activity and safety of rmhTNF‐α combined with chemotherapies in head/neck, lung, colorectal, stomach, and renal cancer patients. Ninety‐five eligible patients received i.m. rmhTNF‐α treatment combined with standard chemotherapies. Another 95 patients were treated with standard chemotherapies. After two treatment cycles, one patient achieved a complete response and 24 patients had partial response, yielding an overall response rate (complete response + partial response) of 27.47% in the rmhTNF‐α plus chemotherapy cohort. The chemotherapy alone group acquired only a 11.39% response rate (P < 0.05). When compared between different cancers, a 48.89% response rate was detected in the 45 lung cancer patients of the combination cohort. The most common grade 1–2 adverse events of rmhTNF‐α were drug‐related fever, allergy, flu‐like symptoms, and myalgia. No significant difference was found in grade 3–4 toxicities between the two cohorts. Based on the results of this research, rmhTNF‐α can significantly enhance the effectiveness of chemotherapy. An extended phase III trial of rmhTNF‐α combined with standard chemotherapy is warranted for evaluating its antitumor activity and toxicity in a larger cohort of tumor patients. The studies in this paper were registered with the State Food and Drug Administration of China (No. 2003S00692). (Cancer Sci 2012; 103: 288–295)
Would vaccination against nicotine be a cost‐effective way to prevent smoking uptake in adolescents?
Authors: Gartner Coral E. , Barendregt Jan J. , Wallace Angela , Hall Wayne D.
Published: November 2011

Aims We used epidemiological modelling to assess whether nicotine vaccines would be a cost‐effective way of preventing smoking uptake in adolescents.

Design, Setting, Participants and Measurements We built an epidemiological model using Australian data on age‐specific smoking prevalence; smoking cessation and relapse rates; life‐time sex‐specific disability‐adjusted life years lived for cohorts of 100 000 smokers and non‐smokers; government data on the costs of delivering a vaccination programme by general practitioners; and a range of plausible and optimistic estimates of vaccine cost, efficacy and immune response rates based on clinical trial results. We first estimated the smoking uptake rates for Australians aged 12–19 years. We then used these estimates to predict the expected smoking prevalence in a birth cohort aged 12 in 2003 by age 20 under (i) current policy and (ii) different vaccination scenarios that varied in cost, initial vaccination uptake, yearly re‐vaccination rates, efficacy and a favourable vaccine immune response rate.

Findings Under the most optimistic assumptions, the cost to avert a smoker at age 20 was $44 431 [95% confidence interval (CI) $40 023–49 250]. This increased to $296 019 (95% CI $252 307–$355 930) under more plausible scenarios. The vaccine programme was not cost‐effective under any scenario.

Conclusions A preventive nicotine vaccination programme is unlikely to be cost‐effective. The total cost of a universal vaccination programme would be high and its impact on population smoking prevalence negligible. For these reasons, such a programme is unlikely to be publicly funded in Australia or any other developed country.
Identification of a Dau c PRPlike protein (Dau c 1.03) as a new allergenic isoform in carrots (cultivar Rodelika)
Authors: Wangorsch A. , Weigand D. , Peters S. , Mahler V. , Fötisch K. , Reuter A. , Imani J. , DeWitt Å. M. , Kogel K.‐H. , Lidholm J. , Vieths S. , Scheurer S.
Published: November 2011

Background

Up to 25% of food allergic subjects in central Europe suffer from carrot allergy. Until now, two isoforms of the major carrot (Daucus carota) allergen Dau c 1 have been described: Dau c 1.01, comprising five variants (Dau c 1.0101–Dau c 1.0105) and Dau c 1.02.

Objective

To investigate potential allergenic properties of a Dau c PRPlike protein, a novel isoform of the PR‐10 protein family in carrot.

Methods

Dau c PRPlike cDNA from carrot roots (cv Rodelika) was cloned after RT‐PCR and 5′RACE. Dau c PRPlike protein was expressed in E. coli, purified under native conditions by Ni‐NTA chromatography and analysed by CD spectroscopy. Immuno‐reactivity of the rDau c PRPlike protein was compared with rDau c 1.0104 and rDau c 1.0201 in terms of IgE binding (immunoblotting, ImmunoCAP™), IgE cross‐reactivity (ELISA inhibition) and in vitro mediator release with sera from carrot allergic patients. mRNA expression of Dau c PRPlike protein in wild‐type and transgenic carrot roots was analysed by qRT‐PCR.

Results

The Dau c PRPlike protein was identified as a new allergenic isoform, Dau c 1.03, in carrot roots. 68% of carrot allergic patients were sensitized to rDau c 1.03. The IgE‐reactivity of rDau c 1.03 strongly correlated with reactivity to rDau c 1.0104, but not to rDau c 1.0201. The extent of IgE cross‐reactivity and allergenic potency of Dau c 1 isoforms varied between the individual sera tested. Dau c 1.03 mRNA transcripts were up‐regulated in Dau c 1.01 and Dau c 1.02 gene‐silenced carrot roots.

Conclusion and clinical relevance

Dau c 1 isoforms display distinct IgE epitope heterogeneity. Dau c 1.03 appears to contribute to the allergenicity of carrots and the manifestation of carrot allergy. The epitope diversity of different Dau c 1 isoforms should be considered for component‐resolved diagnosis and gene silencing of carrot allergens.
The psychological impact of diagnostic food challenges to confirm the resolution of peanut or tree nut allergy
Authors: Knibb R. C. , Ibrahim N. F. , Stiefel G. , Petley R. , Cummings A. J. , King R. M. , Keeton D. , Brown L. , Erlewyn‐Lajeunesse M. , Roberts G. , Lucas J. S. A.
Published: November 2011

Background

Twenty percent of children outgrow peanut allergy and 10% outgrow tree nut allergy. Resolution can be confirmed by a food challenge. Little is known about the psychosocial impact of the challenge. We aimed to investigate effects of a food challenge on anxiety, stress and quality of life (QoL) in children and their mothers on the day of a food challenge to peanuts or nuts, and in the months following the challenge.

Methods

One hundred and three families participated. Forty children undergoing food challenges to access resolution of allergy, and their mothers, completed validated questionnaires to measure generic and food specific quality of life, stress and anxiety prior to challenge, on the day of investigation and 3–6 months later. Sixty‐three children with no clinical indication to challenge (i.e. in the opinion of the allergist had persistent allergy) acted as comparison group completing questionnaires 3–6 months apart.

Results

Mothers reported raised anxiety on the day of challenge (P = 0.007), but children were less anxious. The children (P = 0.01) and mothers (P = 0.01) had improved food‐related, but not general, QoL 3–6 months following challenge. Children reported lower anxiety levels following the challenge (P = 0.02), but anxiety remained unchanged in mothers. The improvements in maternal and children's QoL and anxiety levels were irrespective of the challenge outcome and despite co‐existing food allergies in 50% of children.

Conclusions

Mothers experienced increased anxiety on the day of food challenge, unlike the children, perhaps reflecting the differences in their perceived risks. Food challenges are associated with improved food‐related QoL in the following months even in those with a positive challenge.
Impact of clear and cloudy sky conditions on the vertical distribution of photosynthetic CO2 uptake within a spruce canopy
Authors: Urban Otmar , Klem Karel , Ač Alexander , Havránková Kateřina , Holišová Petra , Navrátil Martin , Zitová Martina , Kozlová Klára , Pokorný Radek , Šprtová Mirka , Tomášková Ivana , Špunda Vladimír , Grace John
Published: November 2011

1. Cloud cover affects carbon exchange between biota and the atmosphere. Recent studies have demonstrated that an increase in the diffuse radiation fraction enhances the photosynthetic efficiency of canopies. Although the exact mechanism behind this effect is not clear, a more even distribution of light among leaves across the vertical profile of the canopy is considered to be the most important cause of this difference.

2. To test this hypothesis, the net ecosystem production (NEP) of a Norway spruce forest (30‐year‐old) was measured under cloudy and sunny skies by the eddy covariance method. In parallel, measurements of the diurnal courses of gas exchange and chlorophyll fluorescence parameters were made in the upper sun (5th whorl; 1‐year‐old needles), middle (8th and 10th whorl; 1‐ and 2‐year‐old needles) and lower shade (15th whorl; >2‐year‐old needles) shoots.

3. The higher diffuse radiation fraction during cloudy days resulted in significantly higher ecosystem carbon uptake than at corresponding incident photosynthetic photon flux density on sunny days. Our shoot‐level data show that shoots from deep within the canopy contribute substantially to the overall carbon balance during cloudy days. But, although shade‐adapted shoots had a markedly positive carbon balance over a 24‐h period on cloudy days, their performance was impaired on sunny days contributing only a marginal or even negative carbon balance from the middle and shaded parts of the canopy. The uppermost sun shoots contributed 78% of the total carbon assimilated during a sunny day, but only 43% during a cloudy day.

4. In addition, afternoon depression of canopy NEP and CO2 assimilation rates of the uppermost shoots (5th and 8th whorl) occurred in response to irradiance on sunny days, characterized by significant decreases in CO2 uptake and apparent quantum yield; however, this depression did not occur under cloudy conditions. Stomatal and non‐stomatal regulations of carbon assimilation in the afternoon are discussed.
NaV1.8, but not NaV1.9, is upregulated in the inflamed dental pulp tissue of human primary teeth
Authors: Suwanchai A. , Theerapiboon U. , Chattipakorn N. , Chattipakorn S. C.
Published: November 2011

Suwanchai A, Theerapiboon U, Chattipakorn N, Chattipakorn SC. NaV1.8, but not NaV1.9, is upregulated in the inflamed dental pulp tissue of human primary teeth. International Endodontic Journal, 45, 372–378, 2012.

Aim  To investigate alterations in NaV1.8 and NaV1.9 expression within inflamed dental pulp tissue of human primary teeth.

Methodology  Dental pulp tissue obtained from both normal and inflamed pulps in primary teeth as well as pulps from normal and inflamed permanent teeth was used. The quantity of NaV1.8 and NaV1.9 expression in the dental pulp tissue was investigated using Western blot analysis. General neuron marker (PGP9.5) was used to quantify for neural density, and an increase in metalloproteinase‐9 was used to indicate pulpal inflammation in inflamed teeth. Statistically significant differences for each determined parameter between normal and inflamed teeth of both primary and permanent teeth were tested using the Mann–Whitney rank sum test.

Results  There was no significant difference in neural density of normal and inflamed dental pulp tissue, although degrees of inflammation were increased in the inflamed dental pulp of both permanent and primary teeth (P < 0.05). NaV1.8 and NaV1.9 expression in inflamed pulps of permanent teeth increased significantly compared with normal permanent teeth (P < 0.05). However, only NaV1.8 expression was increased significantly in the inflamed dental pulp of primary teeth (P < 0.05).

Conclusions  NaV1.8 alone may be the therapeutic target for treatment of painful pulpitis in primary teeth.
Tadalafil once daily and extracorporeal shock wave therapy in the management of patients with Peyronie’s disease and erectile dysfunction: results from a prospective randomized trial
Authors: Palmieri A. , Imbimbo C. , Creta M. , Verze P. , Fusco F. , Mirone V.
Published: November 2011

Extracorporeal shock wave therapy improves erectile function in patients with Peyronie’s disease. However, erectile dysfunction still persists in many cases. We aimed to investigate the effects of extracorporeal shock wave therapy plus tadalafil 5 mg once daily in the management of patients with Peyronie’s disease and erectile dysfunction not previously treated. One hundred patients were enrolled in a prospective, randomized, controlled study. Patients were randomly allocated to receive either extracorporeal shock wave therapy alone for 4 weeks (n = 50) or extracorporeal shock wave therapy plus tadalafil 5 mg once daily for 4 weeks (n = 50). Main outcome measures were: erectile function (evaluated through the shortened version of the International Index of Erectile Function), pain during erection (evaluated through a Visual Analog Scale), plaque size, penile curvature and quality of life (evaluated through an internal questionnaire). Follow‐up evaluations were performed after 12 and 24 weeks. In both groups, at 12 weeks follow‐up, mean Visual Analog Scale score, mean International Index of Erectile Function score and mean quality of life score ameliorated significantly while mean plaque size and mean curvature degree were unchanged. Intergroup analysis revealed a significantly higher mean International Index of Erectile Function score and quality of life score in patients receiving the combination. After 24 weeks, intergroup analysis revealed a significantly higher mean International Index of Erectile Function score and mean quality of life score in patients that received extracorporeal shock wave therapy plus tadalafil. In conclusion extracorporeal shock wave therapy plus tadalafil 5 mg once daily may represent a valid conservative strategy for the management of patients with Peyronie’s disease and erectile dysfunction.