bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantification of physical (roughness) and chemical (dielectric constant) leaf surface properties relevant to wettability and adhesion
Authors: Nairn Justin J , Forster W Alison , van Leeuwen Rebecca M
Published: June 2011

BACKGROUND: Spray droplet adhesion is dependent not only on formulation and droplet parameters but also on the surface properties (physical and chemical) of the leaf. Quantifying these leaf surface properties would aid understanding and modelling of adhesion, helping to optimise spray formulations. Fractal dimensions (FDs) were used to quantify the relative leaf surface roughness of ten plant species. Static droplet contact angles were measured on each leaf surface, and wetting tension was calculated. Chemical profiles of the leaf surfaces were developed by evaluating contact angle behaviour relative to solution dielectric constants.

RESULTS: The FDs of Cryo‐SEM micrographs taken at 300× magnification gave the best correlation with adhesion. The wetting tension intercept had a strong relationship with mean adhesion, and successfully accounted for the wettability of the outlier species.

CONCLUSIONS: The microroughness of the leaf surface, as revealed by Cryo‐SEM, can be quantified by fractal dimension analysis. However, the wetting tension intercept is a more useful universal measure of the surface properties of the leaf (including roughness) as they pertain to adhesion. The slope of the wetting tension versus dielectric constant plot allowed preliminary quantification of the chemical contribution of leaf surface dielectric behaviour to adhesion. Copyright © 2011 Society of Chemical Industry
Optical absorption related to Fe impurities in TlGaSe2
Authors: Grivickas Vytautas , Gavryushin Vladimir , Grivickas Paulius , Galeckas Augustinas , Bikbajevas Vitalijus , Gulbinas Karolis
Published: June 2011

Absorption measurements of TlGaSe2 crystals intentionally doped with Fe show growing optical transitions below the band gap energies as impurity concentration increase. The comprehensive theoretical analysis is performed for elucidation of subband absorption spectra by using valence band‐to‐Fe centre optical transitions. We identify three deep donor levels at 1.33, 1.475, and 1.77 eV, respectively, with rather similar doping and temperature dependences. Energy position of levels follows temperature shrinkage of the lowest direct band gap rather than of the indirect band gap. Electron–phonon and static structural broadening is evaluated and the corresponding configurational coordinate diagram of Fe centres is constructed. Subtraction of calculated band‐to‐Fe centre absorption from the total absorption spectrum shows that the fundamental absorption edge structure of the TlGaSe2 crystal remains almost unchanged at least to the doping level of Fe = 0.5%. However, Fe impurities cancel low‐temperature photoluminescence.
Microstructure of Sn1–xPbxS grown by hot‐wall technique
Authors: Wagner Gerald , Kaden Ronny , Lazenka Vera , Bente Klaus
Published: June 2011

Orthorhombic Sn1–xPbxS (x ≈ 0.1) was grown on glass substrates by hot‐wall technique. The entire deposited material is subdivided into a more or less continuous layer and whiskers grown on it. The former one consists of stacked blocks with their c‐axis always parallel to growth direction. However, each block is alternately rotated 90° around the [001] against its underlying and following one. Therefore, the boundaries between them are twist boundaries having an orthogonal network of pure screw dislocations due to plastic relaxation. On these blocks Sn1–xPbxS whiskers of the same composition grow via a VLS mechanism. Especially, these whiskers consist of either thicker misaligned blocks, too (at 300 °C), or at higher growth temperatures (e.g., 320 °C) they contain many 90°‐twisted very thin strained sequences being intergrown pseudomorphically. Based on α‐SnS (Herzenbergite) a structural model is presented which is sufficient to describe the defects observed and to simulate the corresponding HRTEM images.
A new rapid and micro‐scale hydrolysis, using triethylamine citrate, for lipopolysaccharide characterization by mass spectrometry
Authors: Chafchaouni‐Moussaoui Imane , Novikov Alexey , Bhrada Fatiha , Perry Malcolm B. , Filali‐Maltouf Abdelkarim , Caroff Martine
Published: June 2011

Endotoxin (lipopolysaccharide, LPS) is, in general, composed of two moieties: a hydrophilic polysaccharide linked to a hydrophobic lipid A terminal unit and forms a major surface component of Gram‐negative bacteria. The structural features of LPS moieties play a role in pathogenesis and also involve immunogenicity and diagnostic serology. The major toxic factor of LPS resides in the lipid A moiety, anchored in the outer layer of the bacterium, and its relative biological activity is critically related to fine structural features within the molecule. In establishing relationships between structural features and biological activities of LPS it is of the utmost importance to develop new analytical methods that can be applied to the complete unambiguous characterization of a specific LPS molecule. Herein is presented a practical rapid and sensitive analytical procedure for the mass spectral screening of LPS using triethylamine citrate as an agent for both disaggregation and mild hydrolysis of LPS. It provides improved matrix‐assisted laser desorption/ionization (MALDI) mass spectra and, in particular, affords the identification of fragments retaining labile substituents present in the native macromolecular LPS structures. The methods were developed and applied using purified LPS of Escherichia coli and Salmonella enterica, as well as more complex LPS of Actnobacillus pleuropneumoniae. Copyright © 2011 John Wiley & Sons, Ltd.
Anodic Deposition of Colloidal Iridium Oxide Thin Films from Hexahydroxyiridate(IV) Solutions
Authors: Zhao Yixin , Vargas‐Barbosa Nella M. , Hernandez‐Pagan Emil A. , Mallouk Thomas E.
Published: June 2011

A facile, in‐situ deposition route to stable iridium oxide (IrOx·nH2O) nanoparticle thin films from [Ir(OH)6]2− solutions is reported. The [Ir(OH)6]2− solution, made by alkaline hydrolysis of [IrCl6]2−, is colorless and stable near neutral pH, and forms blue IrOx·nH2O nanoparticle suspensions once it is adjusted to acidic or basic conditions. IrOx·nH2O nanoparticle thin films are grown anodically on glassy carbon, fluorine‐doped tin oxide, and gold electrodes by electrolyzing [Ir(OH)6]2− solutions at +1.0–1.3 V versus Ag/AgCl. The thickness of the IrOx·nH2O films can be controlled by varying the concentration of [Ir(OH)6]2−, the deposition potential, and/or the deposition time. These thin films are stable between pH 1 and 13 and have the lowest overpotential (η) for the oxygen evolution reaction (OER) of any yet reported. Near neutral pH, the Tafel slope for the OER at a IrOx·nH2O film/Au rotating disk electrode was 37–39 mV per decade. The exchange current density for the OER was 4–8 × 10−10 A cm−2 at a 4 mC cm−2 coverage of electroactive Ir.
Preparation of granular cold‐water‐soluble corn starch by surface modification with poly(ethylene glycol)
Authors: Wang Jiwen , Zhai Wentao , Zheng Wenge
Published: June 2011

The main target of this study is to synthesize one kind of granular cold‐water‐soluble (GCWS) starch by grafting poly(ethylene glycol) (PEG) segments onto the surface of native starch granules. It is found that the grafting process could introduce long PEG chains onto the granule surface, resulting in the presence of special micropits on the granule surface, as characterized by SEM. The cold water solution test verified that the resultant PEG‐grafted corn starches exhibited excellent cold‐water‐solubility. The XRD analysis and further polar optical micrograph (POM) observation indicated that the crystallites structure inside the PEG‐grafted corn starches was fully preserved, since no gelatinization process was involved. The present study provides a new train of thought that we can adjust the physiochemical properties of starch granules with proper surface modification.
Design of floor structures against human‐induced vibrations
Authors: Hicks Stephen J. , Smith Andrew L.
Published: June 2011

A simple method for designing floor structures against humaninduced vibrations is presented in a joint JRC‐ECCS publication, which was developed from two major European research projects supported by the Research Fund for Coal and Steel (RFCS). The simple method is appropriate for floors where the response is dominated by the first eigenmode being excited by walking. This paper presents a general design method that was also developed within the scope of these RFCS projects and is based on a modal superposition approach. The method has a wider range of application as it may be applied to any floor type and, in addition to walking, other human activities can be readily included. The general design methodology has been successfully used in the UK since 2004 on a variety of steel‐framed floors, which have included office, hospital, residential and dance floors.
Valorization of Beef Tallow by Lipase‐Catalyzed Interesterification with High Oleic Sunflower Oil
Authors: Segura Nadia , da Silva Roberta Claro , de M. Soares Fabiana A. Schäfer , Gioielli Luiz Antonio , Jachmanián Iván
Published: June 2011

Although beef tallow (BT) has been considered a hard low‐trans fat convenient to be used in several bakery applications, it has some undesirable characteristics like fatty acid composition, crystallization behavior, graininess formation and poor plastic range. This work studied the modification of BT by blending at different percentages with high oleic sunflower oil (HOSFO) followed by the enzyme‐catalyzed interesterification of the blends. The reduction in the solid fat content achieved by the simple blending was enhanced by the interesterification process, as a result of the increase in the concentration of the diunsaturated monosaturated type triacylglycerols. Interesterification strongly impacted too on the crystallization behavior of the blends, since products showed more homogeneous and regular crystals than the starting mixture. Results show that lipase catalyzed interesterification of BT with HOSFO offers a useful tool for the design of fats with adjustable physicochemical properties, improved with respect to that of the starting fats.
Three-dimensional instabilities in the boundary-layer flow over a long rectangular plate
Authors: CHAURASIA HEMANT K. , THOMPSON MARK C.
Published: June 2011

A detailed numerical study of the separating and reattaching flow over a square leading-edge plate is presented, examining the instability modes governing transition from two- to three-dimensional flow. Under the influence of background noise, experiments show that the transition scenario typically is incompletely described by either global stability analysis or the transient growth of dominant optimal perturbation modes. Instead two-dimensional transition effectively can be triggered by the convective Kelvin–Helmholtz (KH) shear-layer instability; although it may be possible that this could be described alternatively in terms of higher-order optimal perturbation modes. At least in some experiments, observed transition occurs by either: (i) KH vortices shedding downstream directly and then almost immediately undergoing three-dimensional transition or (ii) at higher Reynolds numbers, larger vortical structures are shed that are also three-dimensionally unstable. These two paths lead to distinctly different three-dimensional arrangements of vortical flow structures. This paper focuses on the mechanisms underlying these three-dimensional transitions. Floquet analysis of weakly periodically forced flow, mimicking the observed two-dimensional quasi-periodic base flow, indicates that the two-dimensional vortex rollers shed from the recirculation region become globally three-dimensionally unstable at a Reynolds number of approximately 380. This transition Reynolds number and the predicted wavelength and flow symmetries match well with those of the experiments. The instability appears to be elliptical in nature with the perturbation field mainly restricted to the cores of the shed rollers and showing the spatial vorticity distribution expected for that instability type. Indeed an estimate of the theoretical predicted wavelength is also a good match to the prediction from Floquet analysis and theoretical estimates indicate the growth rate is positive. Fully three-dimensional simulations are also undertaken to explore the nonlinear development of the three-dimensional instability. These show the development of the characteristic upright hairpins observed in the experimental dye visualisations. The three-dimensional instability that manifests at lower Reynolds numbers is shown to be consistent with an elliptic instability of the KH shear-layer vortices in both symmetry and spanwise wavelength.
Endochronic Fatigue Life Prediction of SN/3.5AG/0.75CU BGA Solder Joints Under Oblique Displacement Cyclic Tests
Authors: Lee C. F. , Lin T. T. , Tsai P. S.
Published: June 2011

In this paper, cyclic damage behavior of cyclically load drop curves and their fatigue initiation life of Sn/3.5 Ag/0.75Cu BGA solder joint specimens under oblique displacement cyclic tests were investigated by the theory of damage — coupled endochronic viscoplasticity.

By linearly unloading with damage elastic modulus and the linearly damage-free behavior of grip system, the damage loops of force-Φ angle oblique displacement of BGA solder joint specimen were converted successfully into damage loops of the representative solder ball under cyclically proportional straining, which can be predicted by the endochronic constitutive equations. These results established the relationship of the BGA oblique displacement amplitudes da(Φ) and the effective inelastic strain amplitudes of solder ball: da (Φ)= . Based on the phenomena of cyclic damage and its fatigue life, a Φ dependent degree of damage in the evolution equation of damage under proportional strain path was proposed to depend positively on and N cycles. Using this parameter in the damage per cycle computed by the endochronic theory, a Φ modified cycles N(Φ)/β(Φ) can be defined and then derive the Φ modified Lee-Coffin-Manson (Φ-LCM) equation for the fatigue initiation life of solder ball:

Finally, a Φ modified Lee's BGA (Φ LBGA) equation for BGA solder joint specimens can be derived:

This equation can predict quite well the life data of Sn/3.5Ag/0.75Cu solder joint specimens under Φ ϵ [0π/2]. As a consequence, a vehicle to study the fatigue initiation life of BGA solder joint specimens is constructed completely by the workable methodology and the theory discussed in the paper.
Cinematographic Analysis of Counter Jet Formation in a Single Cavitation Bubble Collapse Flow
Authors: Yang S.-H. , Jaw S.-Y. , Yeh K.-C.
Published: June 2011

This study utilized a U-shape platform device to generate a single cavitation bubble for the detail analysis of the flow field characteristics and the cause of the counter jet during the process of bubble collapse induced by pressure wave. A series of bubble collapse flows induced by pressure waves of different strengths are investigated by positioning the cavitation bubble at different stand-off distances to the solid boundary. It is found that the Kelvin-Helmholtz vortices are formed when the liquid jet induced by the pressure wave penetrates the bubble surface. If the bubble center to the solid boundary is within one to three times the bubble's radius, a stagnation ring will form on the boundary when impacted by the penetrated jet. The liquid inside the stagnation ring is squeezed toward the center of the ring to form a counter jet after the bubble collapses. At the critical position, where the bubble center from the solid boundary is about three times the bubble's radius, the bubble collapse flows will vary. Depending on the strengths of the pressure waves applied, either just the Kelvin-Helmholtz vortices form around the penetrated jet or the penetrated jet impacts the boundary directly to generate the stagnation ring and the counter jet flow. This phenomenon used the particle image velocimetry method can be clearly revealed the flow field variation of the counter jet. If the bubble surface is in contact with the solid boundary, the liquid jet can only splash radially without producing the stagnation ring and the counter jet. The complex phenomenon of cavitation bubble collapse flows are clearly manifested in this study.
Performance Analysis of a Hybrid Solar Energy Storage System
Authors: Mohamadi Zaeem Moosavi , Zohoor Hassan , Assadi Morteza Khalaji , Hamidi Ali A.
Published: June 2011

In this work, a method for increasing the storage capability of a solar thermal energy system has been discussed. The system includes two tanks with the flexibility in choosing the best storage medium on the basis of the solar collector's outlet temperature. The results show that using such a hybrid storage system, the storable energy can be increased. Comparing the results with those for simple common storage systems, the extent of improvement was calculated.

For verification of the results, a small pilot system was assembled. The test apparatus operated during 2008-2009 cold months and the parameters were recorded. Comparison of the theoretical and experimental results showed a good agreement.
ON COLLINEAR CLOSED ONE-FORMS
Authors: GELBUKH IRINA
Published: June 2011

We study one-forms with zero wedge-product, which we call collinear, and their foliations. We characterise the set of forms that define a given foliation, with special attention to closed forms and forms with small singular sets. We apply the notion of collinearity to give a criterion for the existence of a compact leaf and to study homological properties of compact leaves.
ON MINIMAL SURFACES SATISFYING THE OMORI–YAU PRINCIPLE
Authors: BORBÉLY ALBERT
Published: June 2011

Complete minimal immersions satisfying the Omori–Yau maximum principle are investigated. It is shown that the limit set of a proper immersion into a convex set must be the whole boundary of the convex set. In case of a nonproper and nonplanar immersion we prove that the convex hull of the immersion is a half-space or ℝ3.
I Introduction
Authors: Sparkes Brian A.
Published: June 2011

The study of Greek art is always on the move. New discoveries, made in Greece or in the various regions of the ancient world with which the Greeks were in contact, add to and/or alter the overall picture. However, renewed investigation of the material already known, seen in the light of the fresh evidence, and the reinterpretation that may follow – whether of sculpture, architecture, pottery, texts, and so forth – can be of equal, if not greater, importance.
IV Luxury Items
Authors: Sparkes Brian A.
Published: June 2011

The uneven survival of material evidence from Greek antiquity has tended to guide interest and research towards the diferent forms and functions of sculpture (Chapters II and III) and of vase-painting (Chapters V and VI). They have been preserved in such numbers that, although we have only a fraction of the total output, we can study the ways in which they developed over the centuries against the social, economic, and political background and in the diferent parts of the Greek world. This has encouraged a tendency towards positivism and has had the unfortunate outcome of considering them as the exclusive elements of Greek art, with a concomitant emphasis on the aspects of restraint, simplicity, and so forth that were highlighted by the Neoclassical attitudes to Greek art that emerged in the eighteenth century. This approach has led scholars to demean the more lavish products that, by the very nature of their intrinsic value, have failed to survive in any numbers – gold, silver, ivory, and the like. Recent excavations, particularly those in cemeteries situated in the outlying areas of the Greek world and in the regions bordering on ancient Greece, have brought to light some of those expensive objects that are now missing from the Greek heartlands. Meanwhile, investigations into the more flamboyant aspects of Greek art have shown that buildings and architectural and freestanding sculpture were lavishly coloured. A nineteenth-century drawing by Donaldson shows coloured glass beads set into a column capital of the Erechtheion (Figure 21).
A 160-GHz low-noise downconversion receiver front-end in a SiGe HBT technology
Authors: Öjefors Erik , Pourchon Franck , Chevalier Pascal , Pfeiffer Ullrich R.
Published: June 2011

A 160-GHz SiGe-HBT (Heterojunction Bipolar Transistor) down-conversion receiver front-end for use in active millimeter-wave imaging arrays and D-band communication applications is presented. The monolithic front-end consists of a three-stage low-noise amplifier providing 24 dB of gain and a Gilbert-cell mixer capable of operating from a −8-dBm LO signal. A fully differential architecture compatible with balanced on or off-chip antennas is used to avoid the need for on-chip baluns in antenna-integrated applications. The implemented downconversion front-end consumes 50 mA from a 3.3 V supply and requires a 0.1 mm2 die area (excl. pads) per channel. With a 160-GHz input signal and an Intermediate Frequency (IF) of 1 GHz, the implemented front-end yields a 25-dB conversion gain, a −30-dBm input compression point, and a 9-dB/7-dB (with/without auxiliary on-chip input balun) system noise figure.
Signatures of spatial organizations – From the universe of proteins to the universe in general
Authors: Mittal Aditya
Published: June 2011

Pattern generation and recognition in 3-D space have been of wide interest in fields varying from atomic and molecular structures to organization of celestial objects. Our thoughts towards investigating patterns (and elucidation of geometrical rules) followed by a known number of points with specific or specified coordinates are guided by the assumption/belief that there must be some thermodynamic and/or kinetic basis leading to the organization of coordinates of the known points. In terms of biomolecular structures, the DNA double helix is one of the strongest examples of such structures with coordinates of atoms in the phosphate backbone and the side-chains provide a helical geometrical configuration. It needs to be appreciated (and emphasized) that, regardless of the system in consideration (e.g. molecular structures or celestial objects), the sample space of known points utilized to investigate underlying patterns is comprised of only remnants or subsets of a larger distribution of points that is either too large to sample, or presence of which has been indicated but not conclusively detected, or presence of which is known to have occurred at an earlier time and some data exists to show disappearance of some points in the sample space due to certain events leading to their deletion. For example, it is now well established that all DNA is not double helical and there are a variety of forms of DNA structures. In this work, I show conclusively it is possible to decipher the origin of apparently random points in space that assemble to give a diversity of structures. I have developed spatial maps for distinguishing different clusters of coordinates originating from well defined geometries. Utilizing the maps, I mathematically prove the existence of a recently discovered universal spatial organization of naturally occurring folded proteins, regardless of their fold or function as categorized by the SCOP classification system. Development of the spatial maps in this work could prove to be a major step in not just advancing our understanding of biomolecular structures, but also arrangement of spatial objects that are apparent in their present coordinate space following some major reorganizing events in the history of our universe.
A New BIA Equation Estimating the Body Composition of Young Children
Authors: Clasey Jody L. , Bradley Kelly D. , Bradley James W. , Long Douglas E. , Griffith Joan R.
Published: June 2011

Bioelectric impedance analyses (BIA) provides a valid and reliable measure of body composition in field, clinical, and research settings if standard protocol procedures are followed, and population‐specific equations are available and utilized. The objective of this study was to create and cross‐validate a new BIA body composition equation with representative healthy weight (HW), overweight (OW), and obese (OB) young children. Participants were 436 children who were 5–11 years of age. Dual‐energy absorptiometry fat‐free mass (FFM) was used as the criterion measure and a single frequency tetra‐polar BIA device was used to create the new BIA equation. The new BIA equation explained 95.2% of the variance in FFM with no statistical shrinkage upon cross‐validation. The use of this equation may help to identify effective intervention strategies to prevent or combat childhood obesity, and may assist in additional conditions or treatments where information concerning body composition measures would provide greater accuracy and sensitivity measures for preventing or combating disease.
State-to-state dynamics at the gas-liquid metal interface: Rotationally and electronically inelastic scattering of NO[2Π1/2(0.5)] from molten gallium
Authors: Ziemkiewicz Michael P. , Roscioli Joseph R. , Nesbitt David J.
Published: June 2011

Jet cooled NO molecules are scattered at 45° with respect to the surface normal from a liquid gallium surface at Einc from 1.0(3) to 20(6) kcal/mol to probe rotationally and electronically inelastic scattering from a gas-molten metal interface (numbers in parenthesis represent 1σ uncertainty in the corresponding final digits). Scattered populations are detected at 45° by confocal laser induced fluorescence (LIF) on the γ(0-0) and γ(1-1) A2Σ ← X2ΠΩ bands, yielding rotational, spin-orbit, and λ-doublet population distributions. Scattering of low speed NO molecules results in Boltzmann distributions with effective temperatures considerably lower than that of the surface, in respectable agreement with the Bowman-Gossage rotational cooling model [J. M. Bowman and J. L. Gossage, Chem. Phys. Lett. 96, 481 (1983)] for desorption from a restricted surface rotor state. Increasing collision energy results in a stronger increase in scattered NO rotational energy than spin-orbit excitation, with an opposite trend noted for changes in surface temperature. The difference between electronic and rotational dynamics is discussed in terms of the possible influence of electron hole pair excitations in the conducting metal. While such electronically non-adiabatic processes can also influence vibrational dynamics, the γ(1-1) band indicates <2.6 × 10−4 probability for collisional formation of NO(v = 1) at surface temperatures up to 580 K. Average translational to rotational energy transfer is compared from a hard cube model perspective with previous studies of NO scattering from single crystal solid surfaces. Despite a lighter atomic mass (70 amu), the liquid Ga surface is found to promote translational to rotational excitation more efficiently than Ag(111) (108 amu) and nearly as effectively as Au(111) (197 amu). The enhanced propensity for Ga(l) to transform incident translational energy into rotation is discussed in terms of temperature-dependent capillary wave excitation of the gas-liquid metal interface.
Pound-Drever-Hall-locked, frequency-stabilized cavity ring-down spectrometer
Authors: Cygan A. , Lisak D. , Masłowski P. , Bielska K. , Wójtewicz S. , Domysławska J. , Trawiński R. S. , Ciuryło R. , Abe H. , Hodges J. T.
Published: June 2011

We describe a high sensitivity and high spectral resolution laser absorption spectrometer based upon the frequency-stabilized cavity ring-down spectroscopy (FS-CRDS) technique. We used the Pound-Drever-Hall (PDH) method to lock the probe laser to the high-finesse ring-down cavity. We show that the concomitant narrowing of the probe laser line width leads to dramatically increased ring-down event acquisition rates (up to 14.3 kHz), improved spectrum signal-to-noise ratios for weak O2 absorption spectra at λ = 687 nm and substantial increase in spectrum acquisition rates compared to implementations of FS-CRDS that do not incorporate high-bandwidth locking techniques. The minimum detectable absorption coefficient and the noise-equivalent absorption coefficient for the spectrometer are about \documentclass[12pt]{minimal}\begin{document}$2\times 10^{-10}\ \rm {cm}^{-1}$\end{document}2×10−10 cm −1 and \documentclass[12pt]{minimal}\begin{document}$7.5\times 10^{-11}\ \rm {cm}^{-1}\rm {Hz}^{-1/2}$\end{document}7.5×10−11 cm −1 Hz −1/2, respectively.
Experimental study of graphitic nanoribbon films for ammonia sensing
Authors: Johnson Jason L. , Behnam Ashkan , An Yanbin , Pearton S. J. , Ural Ant
Published: June 2011

We fabricate and study the ammonia sensing properties of graphitic nanoribbon films consisting of multi-layer graphene nanoribbons. These films show very good sensitivity to parts-per-million (ppm) level concentrations of ammonia, which is further enhanced by platinum functionalization, resulting in a relative resistance response of ∼70% when exposed to 50 ppm ammonia. In addition, the sensing response exhibits excellent repeatability and full recovery in air. We also study in detail the dependence of the sensing response on ammonia concentration and temperature. We find that the relative resistance response of the graphitic nanoribbon films shows a power-law dependence on the ammonia concentration, which can be explained based on the Freundlich isotherm. The activation energy obtained from an Arrhenius plot of the temperature-dependent measurements is ∼50 meV, which is consistent with the theoretical calculations of the adsorption energies of ammonia on large graphene sheets and nanoribbons. Their simple and low-cost fabrication process and good sensing response open up the possibility of using graphitic nanoribbon films for large-scale sensing applications.
Multiple-mode excitation in spin-transfer nanocontacts with dynamic polarizer
Authors: Wang N. , Wang X. L. , Qin W. , Yeung S. H. , Kwok D. T. K. , Wong H. F. , Xue Q. , Chu P. K. , Leung C. W. , Ruotolo A.
Published: June 2011

We report our study on the emission response of a magnetic nanocontact with dynamic polarizer in perpendicular magnetic field. In this configuration three modes are accessible, two of which correspond to the precessional motion of a vortex in one of the two ferromagnetic layers with the other working as a static polarizer. At high currents a third mode can be observed that is ascribed to the simultaneous precession of two vortices, one in each layer, with the other layer working as a dynamic polarizer.
On the extension of ℎ^{𝑝}-CR distributions defined on rough tubes
Authors: Hoepfner G. , Hounie J. , dos Santos L.
Published: June 2011

We consider rough tubes

X
+
i

R

m

⊂

C

m

X+i\mathbb R^m\subset \mathbb {C}^m

and generalized

C
R

CR

functions in

L
∞

(
X
,

h
p

(

R

m

)
)

L^\infty (X,h^p(\mathbb R^m))

, where

h
p

(

R

m

)

h^p(\mathbb R^m)

,

0
>
p
>
∞

0>p>\infty

, is Goldberg’s semilocal Hardy space. We show that if

X
X

is arcwise connected by rectifiable arcs, then all such

C
R

CR

functions can be extended to the convex hull of the tube as

C
R

CR

functions
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="element-of upper L Superscript normal infinity Baseline left-parenthesis normal c normal h left-parenthesis upper X right-parenthesis comma h Superscript p Baseline left-parenthesis double-struck upper R Superscript m Baseline right-parenthesis right-parenthesis">

∈

L
∞

(

c
h

(
X
)
,

h
p

(

R

m

)
)

\in L^\infty (\mathrm {ch}(X),h^p(\mathbb R^m))

. This extends previous work of the authors.
On the irreducible components of the singular locus of 𝐴_{𝑔}. II
Authors: González-Aguilera V. , Munoz-Porras J. , Zamora A.
Published: June 2011

In our earlier paper it was proved that the singular locus of

A

g

A_{g}

(coarse moduli space of principally polarized abelian varieties over

C

\mathbb {C}

) is expressed as the union of irreducible varieties

A

g

(
p
,
α
)

A_{g}(p,\alpha )

representing abelian varieties with an order

p
p

automorphism of fixed entire representation. In this paper we prove that

A

g

(
p
,
α
)

A_{g}(p,\alpha )

is an irreducible component of

Sing

A

g

\text {Sing} A_{g}

if and only if for a general element of this variety its automorphism group modulo

{
±
1
}

\{\pm 1\}

,

G

+

G_{+}

, satisfies the equivalent conditions:

G

+

=
⟨
α
⟩

G_{+}=\langle \alpha \rangle

or

N

G

+

(
⟨
α
⟩
)
=
⟨
α
⟩

N_{G_{+}}(\langle \alpha \rangle )=\langle \alpha \rangle

. We illustrate how these results can be used by studying the case

g
=
4

g=4

and

p
=
5

p=5

.
Role for casein kinase 1 in the phosphorylation of Claspin on critical residues necessary for the activation of Chk1
Authors: Meng Zheng , Capalbo Luisa , Glover David M. , Dunphy William G.
Published: June 2011

The mediator protein Claspin is critical for the activation of the checkpoint kinase Chk1 during checkpoint responses to stalled replication forks. This function involves the Chk1-activating domain (CKAD) of Claspin, which undergoes phosphorylation on multiple conserved sites. These phosphorylations promote binding of Chk1 to Claspin and ensuing activation of Chk1 by ATR. However, despite the importance of this regulatory process, the kinase responsible for these phosphorylations has remained unknown. By using a multifaceted approach, we have found that casein kinase 1 gamma 1 (CK1γ1) carries out this function. CK1γ1 phosphorylates the CKAD of Claspin efficiently in vitro, and depletion of CK1γ1 from human cells by small interfering RNA (siRNA) results in dramatically diminished phosphorylation of Claspin. Consequently, the siRNA-treated cells display impaired activation of Chk1 and resultant checkpoint defects. These results indicate that CK1γ1 is a novel component of checkpoint responses that controls the interaction of a key checkpoint effector kinase with its cognate mediator protein.
Discovering and visualizing indirect associations between biomedical concepts
Authors: Tsuruoka Yoshimasa , Miwa Makoto , Hamamoto Kaisei , Tsujii Jun'ichi , Ananiadou Sophia
Published: June 2011

Motivation: Discovering useful associations between biomedical concepts has been one of the main goals in biomedical text-mining, and understanding their biomedical contexts is crucial in the discovery process. Hence, we need a text-mining system that helps users explore various types of (possibly hidden) associations in an easy and comprehensible manner.

Results: This article describes FACTA+, a real-time text-mining system for finding and visualizing indirect associations between biomedical concepts from MEDLINE abstracts. The system can be used as a text search engine like PubMed with additional features to help users discover and visualize indirect associations between important biomedical concepts such as genes, diseases and chemical compounds. FACTA+ inherits all functionality from its predecessor, FACTA, and extends it by incorporating three new features: (i) detecting biomolecular events in text using a machine learning model, (ii) discovering hidden associations using co-occurrence statistics between concepts, and (iii) visualizing associations to improve the interpretability of the output. To the best of our knowledge, FACTA+ is the first real-time web application that offers the functionality of finding concepts involving biomolecular events and visualizing indirect associations of concepts with both their categories and importance.

Availability: FACTA+ is available as a web application at http://refine1-nactem.mc.man.ac.uk/facta/, and its visualizer is available at http://refine1-nactem.mc.man.ac.uk/facta-visualizer/.

Contact:  tsuruoka@jaist.ac.jp
Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs
Authors: Kam-Thong Tony , Pütz Benno , Karbalai Nazanin , Müller−Myhsok Bertram , Borgwardt Karsten
Published: June 2011

Motivation: In recent years, numerous genome-wide association studies have been conducted to identify genetic makeup that explains phenotypic differences observed in human population. Analytical tests on single loci are readily available and embedded in common genome analysis software toolset. The search for significant epistasis (gene–gene interactions) still poses as a computational challenge for modern day computing systems, due to the large number of hypotheses that have to be tested.

Results: In this article, we present an approach to epistasis detection by exhaustive testing of all possible SNP pairs. The search strategy based on the Hilbert–Schmidt Independence Criterion can help delineate various forms of statistical dependence between the genetic markers and the phenotype. The actual implementation of this search is done on the highly parallelized architecture available on graphics processing units rendering the completion of the full search feasible within a day.

Availability:The program is available at http://www.mpipsykl.mpg.de/epigpuhsic/.

Contact:  tony@mpipsykl.mpg.de
Environment specific substitution tables improve membrane protein alignment
Authors: Hill Jamie R. , Kelm Sebastian , Shi Jiye , Deane Charlotte M.
Published: June 2011

Motivation: Membrane proteins are both abundant and important in cells, but the small number of solved structures restricts our understanding of them. Here we consider whether membrane proteins undergo different substitutions from their soluble counterparts and whether these can be used to improve membrane protein alignments, and therefore improve prediction of their structure.

Results: We construct substitution tables for different environments within membrane proteins. As data is scarce, we develop a general metric to assess the quality of these asymmetric tables. Membrane proteins show markedly different substitution preferences from soluble proteins. For example, substitution preferences in lipid tail-contacting parts of membrane proteins are found to be distinct from all environments in soluble proteins, including buried residues. A principal component analysis of the tables identifies the greatest variation in substitution preferences to be due to changes in hydrophobicity; the second largest variation relates to secondary structure. We demonstrate the use of our tables in pairwise sequence-to-structure alignments (also known as ‘threading’) of membrane proteins using the FUGUE alignment program. On average, in the 10–25% sequence identity range, alignments are improved by 28 correctly aligned residues compared with alignments made using FUGUE's default substitution tables. Our alignments also lead to improved structural models.

Availability: Substitution tables are available at: http://www.stats.ox.ac.uk/proteins/resources.

Contact:  deane@stats.ox.ac.uk
A method for probing the mutational landscape of amyloid structure
Authors: O'Donnell Charles W. , Waldispühl Jérôme , Lis Mieszko , Halfmann Randal , Devadas Srinivas , Lindquist Susan , Berger Bonnie
Published: June 2011

Motivation: Proteins of all kinds can self-assemble into highly ordered β-sheet aggregates known as amyloid fibrils, important both biologically and clinically. However, the specific molecular structure of a fibril can vary dramatically depending on sequence and environmental conditions, and mutations can drastically alter amyloid function and pathogenicity. Experimental structure determination has proven extremely difficult with only a handful of NMR-based models proposed, suggesting a need for computational methods.

Results: We present AmyloidMutants, a statistical mechanics approach for de novo prediction and analysis of wild-type and mutant amyloid structures. Based on the premise of protein mutational landscapes, AmyloidMutants energetically quantifies the effects of sequence mutation on fibril conformation and stability. Tested on non-mutant, full-length amyloid structures with known chemical shift data, AmyloidMutants offers roughly 2-fold improvement in prediction accuracy over existing tools. Moreover, AmyloidMutants is the only method to predict complete super-secondary structures, enabling accurate discrimination of topologically dissimilar amyloid conformations that correspond to the same sequence locations. Applied to mutant prediction, AmyloidMutants identifies a global conformational switch between Aβ and its highly-toxic ‘Iowa’ mutant in agreement with a recent experimental model based on partial chemical shift data. Predictions on mutant, yeast-toxic strains of HET-s suggest similar alternate folds. When applied to HET-s and a HET-s mutant with core asparagines replaced by glutamines (both highly amyloidogenic chemically similar residues abundant in many amyloids), AmyloidMutants surprisingly predicts a greatly reduced capacity of the glutamine mutant to form amyloid. We confirm this finding by conducting mutagenesis experiments.

Availability: Our tool is publically available on the web at http://amyloid.csail.mit.edu/.

Contact:  lindquist_admin@wi.mit.edu; bab@csail.mit.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin
Authors: Savol Andrej J. , Burger Virginia M. , Agarwal Pratul K. , Ramanathan Arvind , Chennubhotla Chakra S.
Published: June 2011

Motivation: Molecular dynamics (MD) simulations have dramatically improved the atomistic understanding of protein motions, energetics and function. These growing datasets have necessitated a corresponding emphasis on trajectory analysis methods for characterizing simulation data, particularly since functional protein motions and transitions are often rare and/or intricate events. Observing that such events give rise to long-tailed spatial distributions, we recently developed a higher-order statistics based dimensionality reduction method, called quasi-anharmonic analysis (QAA), for identifying biophysically-relevant reaction coordinates and substates within MD simulations. Further characterization of conformation space should consider the temporal dynamics specific to each identified substate.

Results: Our model uses hierarchical clustering to learn energetically coherent substates and dynamic modes of motion from a 0.5 μs ubiqutin simulation. Autoregressive (AR) modeling within and between states enables a compact and generative description of the conformational landscape as it relates to functional transitions between binding poses. Lacking a predictive component, QAA is extended here within a general AR model appreciative of the trajectory's temporal dependencies and the specific, local dynamics accessible to a protein within identified energy wells. These metastable states and their transition rates are extracted within a QAA-derived subspace using hierarchical Markov clustering to provide parameter sets for the second-order AR model. We show the learned model can be extrapolated to synthesize trajectories of arbitrary length.

Contact:  ramanathana@ornl.gov; chakracs@pitt.edu
Dynamics of Pseudoperonospora cubensis Sporangia in Commercial Cucurbit Fields in Michigan
Authors: Granke L. L. , Hausbeck M. K.
Published: June 2011

Major outbreaks of cucurbit downy mildew have been observed since 2005 in Michigan, the top state for pickling cucumber production in the United States. Airborne concentrations of Pseudoperonospora cubensis sporangia were monitored from 2006 to 2009 in a commercial cucurbit field in each of five Michigan counties. Temperature, relative humidity, leaf wetness, and rainfall were recorded on site in 2008 and 2009. Seasonal and daily trends for sporangial concentrations were examined using loess regression to determine when sporangia were present throughout the growing season. Airborne sporangia were detected from June through September, and concentrations increased during this period. Peak airborne sporangial concentrations occurred between 8:00 and 13:00 h. Airborne sporangial concentrations were positively correlated with temperature (r = 0.17 to 0.38, P < 0.0001) and negatively correlated with relative humidity (r = –0.16 to –0.45, P ≤ 0.0046) and leaf wetness (r = –0.14 to –0.39, P ≤ 0.0001) in 2008 and 2009 at all sites. In autoregressive moving average models, sporangial concentrations were negatively related to relative humidity (slope = –0.03 to –1.34, P < 0.0496) at three of five sites in 2008 and four of five sites in 2009. Hence, sporangia are likely to be airborne above the crop canopy during periods with high temperatures and low relative humidity and leaf wetness.
Host Status of False Brome Grass to the Leaf Rust Fungus Puccinia brachypodii and the Stripe Rust Fungus P. striiformis
Authors: Barbieri Mirko , Marcel Thierry C. , Niks Rients E.
Published: June 2011

Purple false brome grass (Brachypodium distachyon) has recently emerged as a model system for temperate grasses and is also a potential model plant to investigate plant interactions with economically important pathogens such as rust fungi. We determined the host status of five Brachypodium species to three isolates of Puccinia brachypodii, the prevalent rust species on Brachypodium sylvaticum in nature, and to one isolate each of three formae speciales of the stripe rust fungus P. striiformis. Two P. striiformis isolates produced sporulating lesions, both in only one of the tested interactions, suggesting a marginal host status of B. distachyon. P. brachypodii formed sporulating uredinia on the five Brachypodium species tested, and a range of reactions was observed. Surprisingly, the B. sylvaticum–derived rust isolates were more frequently pathogenic to B. distachyon than to their original host species. The B. distachyon diploid inbred lines, developed and distributed as reference material to the Brachypodium research community, include susceptible and resistant genotypes to at least three of the four P. brachypodii isolates tested. This creates the opportunity to use B. distachyon/P. brachypodii as a model pathosystem. In one B. distachyon accession, heavy infection by the loose smut fungus Ustilago bromivora occurred. That pathogen could also serve as a model pathogen of Brachypodium.
Parenting conditions in the midst of suspicion of child sexual abuse (CSA)
Authors: Søftestad Siri , Toverud Ruth
Published: June 2011

This paper presents the findings of an exploratory study on parenting in the midst of suspicion of child sexual abuse (CSA). Data were drawn from in‐depth interviews with 19 parents. Five of these had been accused of CSA. Study methods followed guidelines of grounded theory approaches. Specific parenting conditions during CSA suspicion were identified. Six analytic categories were developed: uncertainty concerning abuse, dilemmas on protection, changes in parent–child relationships, changes in the natural support network, dependency upon professional competence and severe emotional strain. The results are suggested as a tool for identifying themes in order to support and strengthen parenting in ensuring the safety and well‐being of children in these kinds of situations. The current paper contributes to the field by exploring the perspectives of both suspected and non‐suspected parents.