bluuebunny/crossref_metadata_2025 huggingface dataset:
Transport properties of carbon dioxide and methane from molecular dynamics simulations
Authors: Aimoli C. G. , Maginn E. J. , Abreu C. R. A.
Published: October 2014

Transport properties of carbon dioxide and methane are predicted for temperatures between (273.15 and 573.15) K and pressures up to 800 MPa by molecular dynamics simulations. Viscosities and thermal conductivities were obtained through the Green–Kubo formalism, whereas the Einstein relation was used to provide self-diffusion coefficient estimates. The differences in property predictions due to the force field nature and parametrization were investigated by the comparison of seven different CO2 models (two single-site models, three rigid three-site models, and two fully flexible three-site models) and three different CH4 models (two single-site models and one fully flexible five-site model). The simulation results show good agreement with experimental data, except for thermal conductivities at low densities. The molecular structure and force field parameters play an important role in the accuracy of the simulations, which is within the experimental deviations reported for viscosities and self-diffusion coefficients considering the most accurate CO2 and CH4 models studied. On the other hand, the molecular flexibility does not seem to improve accuracy, since the explicit account of vibrational and bending degrees of freedom in the CO2 flexible models leads to slightly less accurate results. Nonetheless, the use of a correctional term to account for vibrational modes in rigid models generally improves estimations of thermal conductivity values. At extreme densities, the caging effect observed with single-site representations of the molecules restrains mobility and leads to an unphysical overestimation of viscosities and, conversely, to the underestimation of self-diffusion coefficients. This result may help to better understand the limits of applicability of such force fields concerning structural and transport properties of dense systems.
First principles transport coefficients and reaction rates of ${\rm Ar}_2^+$ Ar 2+ ions in argon for cold plasma jet modeling
Authors: Chicheportiche Alexandre , Stachoň Martin , Benhenni Malika , Gadéa Florent Xavier , Kalus René , Yousfi Mohammed
Published: October 2014

Momentum-transfer collision cross-sections and integral collision cross-sections for the collision-induced dissociation are calculated for collisions of ionized argon dimers with argon atoms using a nonadiabatic semiclassical method with the electronic Hamiltonian calculated on the fly via a diatomics-in-molecules semiempirical model as well as inverse-method modeling based on simple isotropic rigid-core potential. The collision cross-sections are then used in an optimized Monte Carlo code for evaluations of the \documentclass[12pt]{minimal}\begin{document}${\rm Ar}_2^+$\end{document} Ar 2+ mobility in argon gas, longitudinal diffusion coefficient, and collision-induced dissociation rates. A thorough comparison of various theoretical calculations as well as with available experimental data on the \documentclass[12pt]{minimal}\begin{document}${\rm Ar}_2^+$\end{document} Ar 2+ mobility and collision cross-sections is performed. Good agreement is found between both theoretical approaches and the experiment. Analysis of the role of inelastic processes in \documentclass[12pt]{minimal}\begin{document}${\rm Ar}_2^+$\end{document} Ar 2+/Ar collisions is also provided.
The HD molecule in small and medium cages of clathrate hydrates: Quantum dynamics studied by neutron scattering measurements and computation
Authors: Colognesi Daniele , Powers Anna , Celli Milva , Xu Minzhong , Bačić Zlatko , Ulivi Lorenzo
Published: October 2014

We report inelastic neutron scattering (INS) measurements on molecular hydrogen deuteride (HD) trapped in binary cubic (sII) and hexagonal (sH) clathrate hydrates, performed at low temperature using two different neutron spectrometers in order to probe both energy and momentum transfer. The INS spectra of binary clathrate samples exhibit a rich structure containing sharp bands arising from both the rotational transitions and the rattling modes of the guest molecule. For the clathrates with sII structure, there is a very good agreement with the rigorous fully quantum simulations which account for the subtle effects of the anisotropy, angular and radial, of the host cage on the HD microscopic dynamics. The sH clathrate sample presents a much greater challenge, due to the uncertainties regarding the crystal structure, which is known only for similar crystals with different promoter, but nor for HD (or H2) plus methyl tert-butyl ether (MTBE-d12).
Electronic and thermoelectric properties of Ce3Te4 and La3Te4 computed with density functional theory with on-site Coulomb interaction correction
Authors: Vo Trinh , von Allmen Paul , Huang Chen-Kuo , Ma James , Bux Sabah , Fleurial Jean-Pierre
Published: October 2014

The electronic properties and Seebeck coefficients of Ce3Te4 and La3Te4 are computed using Density Functional Theory with on-site Coulomb interaction correction. We found that the Seebeck coefficients of Ce3Te4 and La3Te4 are almost equal at temperatures larger than the Curie temperature of Ce3Te4, and in good agreement with the measurements reported by May et al. [Phys. Rev. B 86, 035135 (2012)]. At temperatures below the Curie temperature, the Seebeck coefficient of Ce3Te4 increases due to the ferromagnetic ordering, which leads the f-electron of Ce to contribute to the Seebeck coefficient in the relevant range of electron concentration.
Vacancy-oxygen defects in p-type Si1−xGex
Authors: Sgourou E. N. , Londos C. A. , Chroneos A.
Published: October 2014

Oxygen-vacancy defects and, in particular, the VO pairs (known as A-centers) are common defects in silicon (Si) with a deleterious impact upon its properties. Although oxygen-vacancy defects have been extensively studied in Si there is far less information about their properties in p-type doped silicon germanium (Si1−xGex). Here, we use Fourier transform infrared spectroscopy to determine the production and evolution of oxygen-vacancy defects in p-type Si1−xGex. It was determined that the increase of Ge content affects the production and the annealing behavior of the VO defect as well as its conversion to the VO2 defect. In particular, both the VO production and the VO annealing temperature are reduced with the increase of Ge. The conversion ratio [VO2]/[VO] also decreases with the increase of x, although the ratios [VO3]/[VO2] and [VO4]/[VO3] show a tendency to increase for larger Ge contents. The results are discussed in view of recent experimental and theoretical studies in Si and Si1−xGex.
Nanosecond laser-induced phase transitions in pulsed laser deposition-deposited GeTe films
Authors: Sun Xinxing , Thelander Erik , Lorenz Pierre , Gerlach Jürgen W. , Decker Ulrich , Rauschenbach Bernd
Published: October 2014

Phase transformations between amorphous and crystalline states induced by irradiation of pulsed laser deposition grown GeTe thin films with nanosecond laser pulses at 248 nm and pulse duration of 20 ns are studied. Structural and optical properties of the Ge-Te phase-change films were studied by X-ray diffraction and optical reflectivity measurements as a function of the number of laser pulses between 0 and 30 pulses and of the laser fluence up to 195 mJ/cm2. A reversible phase transition by using pulse numbers ≥ 5 at a fluence above the threshold fluence between 11 and 14 mJ/cm2 for crystallization and single pulses at a fluence between 162 and 182 mJ/cm2 for amorphization could be proved. For laser fluences from 36 up to 130 mJ/cm2, a high optical contrast of 14.7% between the amorphous and crystalline state is measured. A simple model is used that allows the discussion on the distribution of temperature in dependency on the laser fluence.
Growth, strain relaxation properties and high-κ dielectric integration of mixed-anion GaAs1-ySby metamorphic materials
Authors: Zhu Y. , Clavel M. , Goley P. , Hudait M. K.
Published: October 2014

Mixed-anion, GaAs1-ySby metamorphic materials with a wide range of antimony (Sb) compositions extending from 15% to 62%, were grown by solid source molecular beam epitaxy (MBE) on GaAs substrates. The impact of different growth parameters on the Sb composition in GaAs1-ySby materials was systemically investigated. The Sb composition was well-controlled by carefully optimizing the As/Ga ratio, the Sb/Ga ratio, and the substrate temperature during the MBE growth process. High-resolution x-ray diffraction demonstrated a quasi-complete strain relaxation within each composition of GaAs1-ySby. Atomic force microscopy exhibited smooth surface morphologies across the wide range of Sb compositions in the GaAs1-ySby structures. Selected high-κ dielectric materials, Al2O3, HfO2, and Ta2O5 were deposited using atomic layer deposition on the GaAs0.38Sb0.62 material, and their respective band alignment properties were investigated by x-ray photoelectron spectroscopy (XPS). Detailed XPS analysis revealed a valence band offset of >2 eV for all three dielectric materials on GaAs0.38Sb0.62, indicating the potential of utilizing these dielectrics on GaAs0.38Sb0.62 for p-type metal-oxide-semiconductor (MOS) applications. Moreover, both Al2O3 and HfO2 showed a conduction band offset of >2 eV on GaAs0.38Sb0.62, suggesting these two dielectrics can also be used for n-type MOS applications. The well-controlled Sb composition in several GaAs1-ySby material systems and the detailed band alignment analysis of multiple high-κ dielectric materials on a fixed Sb composition, GaAs0.38Sb0.62, provides a pathway to utilize GaAs1-ySby materials in future microelectronic and optoelectronic applications.
Ejecta production from shocked Pb surface via molecular dynamics
Authors: Ren Guowu , Chen Yongtao , Tang Tiegang , Li Qingzhong
Published: October 2014

Molecular dynamics simulations are employed to examine the relation between ejecta production and shock-breakout pressure for single crystal Pb subjected to a decaying shockwave loading. To better understand the physical mechanism of ejecta formation, a surface with multiple triangular grooves representing the imperfections left from machining finish is taken into consideration. It is found that the ejecta volume density distribution displays a smooth nature and the amount of ejecta increases significantly after melting on release or shock. Additionally, the ejecta particle mass distribution is captured by a power law scaling, revealing the self-similarity. These results are in reasonable agreement with the characteristics of experimentally diagnosed findings.
Combustion-process derived comparable performances of Zn-(In:Sn)-O thin-film transistors with a complete miscibility
Authors: Jiang Qingjun , Lu Jianguo , Cheng Jipeng , Li Xifeng , Sun Rujie , Feng Lisha , Dai Wen , Yan Weichao , Ye Zhizhen
Published: October 2014

Amorphous zinc-indium-tin oxide (a-ZITO) thin-film transistors (TFTs) have been prepared using a low-temperature combustion process, with an emphasis on complete miscibility of In and Sn contents. The a-ZITO TFTs were comparatively studied in detail, especially for the working stability. The a-ZITO TFTs all exhibited acceptable and excellent behaviors from Sn-free TFTs to In-free TFTs. The obtained a-ZTO TFTs presented a field-effect mobility of 1.20 cm2 V−1 s−1, an on/off current ratio of 4.89 × 106, and a long-term stability under positive bias stress, which are comparable with those of the a-ZIO TFTs. The In-free a-ZTO TFTs are very potential for electrical applications with a low cost.
Magnetic and transport properties of epitaxial stepped Fe3O4(100) thin films
Authors: Wu Han-Chun , Syrlybekov Askar , Mauit Ozhet , Mouti Anas , Coileáin Cormac Ó , Abid Mourad , Abid Mohamed , Shvets Igor V.
Published: October 2014

We investigate the magnetic and transport properties of epitaxial stepped Fe3O4 thin films grown with different thicknesses. Magnetization measurements suggest that the steps induce additional anisotropy, which has an easy axis perpendicular to steps and the hard axis along the steps. Separate local transport measurements, with nano-gap contacts along a single step and perpendicular to a single step, suggest the formation of a high density of anti-phase boundaries (APBs) at the step edges are responsible for the step induced anisotropy. Our local transport measurements also indicate that APBs distort the long range charge-ordering of magnetite.
Delayed Ras/PKA signaling augments the unfolded protein response
Authors: Pincus David , Aranda-Díaz Andrés , Zuleta Ignacio A. , Walter Peter , El-Samad Hana
Published: October 2014

Significance

The unfolded protein response (UPR) maintains protein-folding homeostasis in the endoplasmic reticulum (ER). The UPR is involved in diseases such as triple-negative breast cancer, developmental processes such as B-cell activation, and the decision to commit to apoptosis. In principle, the UPR could restore homeostasis to the ER by increasing folding capacity or reducing the load of newly synthesized proteins. Here we report that budding yeast augments the UPR with PKA signaling and reduces the load of newly synthesized proteins, a role functionally analogous to the PKR-like ER kinase (PERK) and regulated inositol-requiring enzyme 1 (IRE1)-dependent mRNA decay (RIDD) pathways in other organisms. Accounting for all the pathways that contribute to stress resistance is necessary to understand how perturbations, including targeted therapies, propagate through the cell.
Investigating the role of a backbone to substrate hydrogen bond in OMP decarboxylase using a site-specific amide to ester substitution
Authors: Desai Bijoy J. , Goto Yuki , Cembran Alessandro , Fedorov Alexander A. , Almo Steven C. , Gao Jiali , Suga Hiroaki , Gerlt John A.
Published: October 2014

Significance

Orotidine 5′-monophosphate decarboxylase has attracted intense enzymological interest, because it achieves a very large rate enhancement (∼10
17
) without the use of cofactors. Previous studies provided evidence that substrate destabilization and vinyl anion intermediate stabilization contribute to the rate enhancement. Using in vitro translation, we generated a backbone amide to ester substitution to evaluate the importance of the hydrogen bond between a backbone amide and the substrate in intermediate stabilization. The hydrogen bond contributes modestly (≤10
2
), suggesting that the intermediate is primarily stabilized by electrostatic interactions with the active site. This study establishes a versatile method for generation of backbone amide to ester substitutions in sufficient quantities to investigate the importance of backbone amide hydrogen bonding interactions in enzyme-catalyzed reactions.
Measurement of Patient Hand Hygiene in Multiorgan Transplant Units Using a Novel Technology: An Observational Study
Authors: Srigley Jocelyn A. , Furness Colin D. , Gardam Michael
Published: October 2014

Objective.

Healthcare worker hand hygiene is known to prevent healthcare-associated infections, but there are few data on patient hand hygiene despite the fact that nosocomial pathogens may be acquired by patients via their own unclean hands. The purpose of this study was to measure patient hand hygiene behavior in the hospital after visiting a bathroom, before eating, and on entering and leaving their rooms

Design.

Cross-sectional study.

Setting.

Acute care teaching hospital in Canada.

Patients.

Convenience sample of 279 adult patients admitted to 3 multiorgan transplant units between July 2012 and March 2013.

Methods.

Patient use of alcohol-based hand rub and soap dispensers was measured using an ultrasound-based real-time location system during visits to bathrooms, mealtimes, kitchen visits, and on entering and leaving their rooms.

Results.

Overall, patients performed hand hygiene during 29.7% of bathroom visits, 39.1% of mealtimes, 3.3% of kitchen visits, 2.9% of room entries, and 6.7% of room exits.

Conclusions.

Patients appear to perform hand hygiene infrequently, which may contribute to transmission of pathogens from the hospital environment via indirect contact or fecal-oral routes.

Infect Control Hosp Epidemiol 2014;35(11):1336–1341
Effectiveness of a Dental Care Intervention in the Prevention of Lower Respiratory Tract Nosocomial Infections among Intensive Care Patients: A Randomized Clinical Trial
Authors: Bellissimo-Rodrigues Wanessa T. , Menegueti Mayra G. , Gaspar Gilberto G. , Nicolini Edson A. , Auxiliadora-Martins Maria , Basile-Filho Anibal , Martinez Roberto , Bellissimo-Rodrigues Fernando
Published: October 2014

Objective.

To evaluate whether dental treatment may enhance oral antisepsis, thus preventing more effectively lower respiratory tract infections (LRTIs) among critically ill patients

Design.

Observer-blind randomized clinical trial.

Setting.

General intensive care unit (ICU) for adult patients.

Patients.

We analyzed data from 254 adult patients who stayed for at least 48 hours in the ICU.

Intervention.

Patients were randomized by means of rolling dice. The experimental group (n = 127) had access to dental care provided by a dental surgeon, 4–5 times a week. Besides routine oral hygiene, care also included teeth brushing, tongue scraping, removal of calculus, atraumatic restorative treatment of caries, and tooth extraction. The control group (n = 127) had access to routine oral hygiene only, which included the use of chlorhexidine as a mouth rinse, which was performed by the ICU nurse staff.

Results.

The primary study outcome was the LRTI incidence, which was 8.7% in the experimental group and 18.1% in the control group (adjusted relative risk [RR], 0.44 [95% confidence interval (CI), 0.20–0.96]; P = .04). Ventilator-associated pneumonia rates per 1,000 ventilator-days were 16.5 (95% CI, 9.8–29.5) in the control group and 7.6 (95% CI, 3.3–15.0) in the experimental group (P < .05). Mortality rates were similar between both study groups: 31.5% in the control group versus 29.1% in the experimental group (adjusted RR, 0.93 [95% CI, 0.52–1.65]; P = .796). No severe adverse events related to oral care were observed during the study.

Conclusion.

Dental treatment was safe and effective in the prevention of LRTI among critically ill patients who were expected to stay at least 48 hours in the ICU.

Trial registration.

Brazilian Clinical Trials Registry, affiliated with the World Health Organization’s International Clinical Trial Registry Platform: U1111-1152-2671.

Infect Control Hosp Epidemiol 2014;35(11):1342–1348
Induction of focal adhesions and motility inDrosophilaS2 cells
Authors: Ribeiro Susana A. , D'Ambrosio Michael V. , Vale Ronald D.
Published: October 2014

Focal adhesions are dynamic structures that interact with the extracellular matrix on the cell exterior and actin filaments on the cell interior, enabling cells to adhere and crawl along surfaces. We describe a system for inducing the formation of focal adhesions in normally non–ECM-adherent, nonmotile Drosophila S2 cells. These focal adhesions contain the expected molecular markers such as talin, vinculin, and p130Cas, and they require talin for their formation. The S2 cells with induced focal adhesions also display a nonpolarized form of motility on vitronectin-coated substrates. Consistent with findings in mammalian cells, the degree of motility can be tuned by changing the stiffness of the substrate and was increased after the depletion of PAK3, a p21-activated kinase. A subset of nonmotile, nonpolarized cells also exhibited focal adhesions that rapidly assembled and disassembled around the cell perimeter. Such cooperative and dynamic fluctuations of focal adhesions were decreased by RNA interference (RNAi) depletion of myosin II and focal adhesion kinase, suggesting that this behavior requires force and focal adhesion maturation. These results demonstrate that S2 cells, a cell line that is well studied for cytoskeletal dynamics and readily amenable to protein manipulation by RNAi, can be used to study the assembly and dynamics of focal adhesions and mechanosensitive cell motility.
Predicting interactome network perturbations in human cancer: application to gene fusions in acute lymphoblastic leukemia
Authors: Hajingabo Leon Juvenal , Daakour Sarah , Martin Maud , Grausenburger Reinhard , Panzer-Grümayer Renate , Dequiedt Franck , Simonis Nicolas , Twizere Jean-Claude
Published: October 2014

Genomic variations such as point mutations and gene fusions are directly or indirectly associated with human diseases. They are recognized as diagnostic, prognostic markers and therapeutic targets. However, predicting the functional effect of these genetic alterations beyond affected genes and their products is challenging because diseased phenotypes are likely dependent of complex molecular interaction networks. Using as models three different chromosomal translocations—ETV6-RUNX1 (TEL-AML1), BCR-ABL1, and TCF3-PBX1 (E2A-PBX1)—frequently found in precursor-B-cell acute lymphoblastic leukemia (preB-ALL), we develop an approach to extract perturbed molecular interactions from gene expression changes. We show that the MYC and JunD transcriptional circuits are specifically deregulated after ETV6-RUNX1 and TCF3-PBX1 gene fusions, respectively. We also identified the bulk mRNA NXF1-dependent machinery as a direct target for the TCF3-PBX1 fusion protein. Through a novel approach combining gene expression and interactome data analysis, we provide new insight into TCF3-PBX1 and ETV6-RUNX1 acute lymphoblastic leukemia.
God: A Very Short Introduction
Authors: Bowker John
Published: October 2014

Who or what is God? How can we know God? Many people believe in God; not just throughout history but also in the present day. But who or what is it they believe in? Many different and sometimes conflicting answers have been suggested to this question. God: A Very Short Introduction explores some of the answers provided by philosophers, poets, and theologians, and considers why some people believe in God and others do not. It considers how each major religion established their own distinctive beliefs about God and how they each interpret His existence, and concludes by looking at how our understanding of God continues to evolve.
Inference of protein kinetics by stochastic modeling and simulation of fluorescence recovery after photobleaching experiments
Authors: Rapsomaniki Maria Anna , Cinquemani Eugenio , Giakoumakis Nickolaos Nikiforos , Kotsantis Panagiotis , Lygeros John , Lygerou Zoi
Published: October 2014

Motivation : Fluorescence recovery after photobleaching (FRAP) is a functional live cell imaging technique that permits the exploration of protein dynamics in living cells. To extract kinetic parameters from FRAP data, a number of analytical models have been developed. Simplifications are inherent in these models, which may lead to inexhaustive or inaccurate exploitation of the experimental data. An appealing alternative is offered by the simulation of biological processes in realistic environments at a particle level. However, inference of kinetic parameters using simulation-based models is still limited.

Results : We introduce and demonstrate a new method for the inference of kinetic parameter values from FRAP data. A small number of in silico FRAP experiments is used to construct a mapping from FRAP recovery curves to the parameters of the underlying protein kinetics. Parameter estimates from experimental data can then be computed by applying the mapping to the observed recovery curves. A bootstrap process is used to investigate identifiability of the physical parameters and determine confidence regions for their estimates. Our method circumvents the computational burden of seeking the best-fitting parameters via iterative simulation. After validation on synthetic data, the method is applied to the analysis of the nuclear proteins Cdt1, PCNA and GFPnls. Parameter estimation results from several experimental samples are in accordance with previous findings, but also allow us to discuss identifiability issues as well as cell-to-cell variability of the protein kinetics.

Implementation : All methods were implemented in MATLAB R2011b. Monte Carlo simulations were run on the HPC cluster Brutus of ETH Zurich.

Contact : lygeros@control.ee.ethz.ch or lygerou@med.upatras.gr

Supplementary information:  Supplementary data are available at Bioinformatics online.
OrthoInspector 2.0: Software and database updates
Authors: Linard Benjamin , Allot Alexis , Schneider Raphaël , Morel Can , Ripp Raymond , Bigler Marc , Thompson Julie D. , Poch Olivier , Lecompte Odile
Published: October 2014

Summary: We previously developed OrthoInspector, a package incorporating an original algorithm for the detection of orthology and inparalogy relations between different species. We have added new functionalities to the package. While its original algorithm was not modified, performing similar orthology predictions, we facilitated the prediction of very large databases (thousands of proteomes), refurbished its graphical interface, added new visualization tools for comparative genomics/protein family analysis and facilitated its deployment in a network environment. Finally, we have released three online databases of precomputed orthology relationships.

Availability: Package and databases are freely available at http://lbgi.fr/orthoinspector with all major browsers supported.

Contact:  odile.lecompte@unistra.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
PFP/ESG: automated protein function prediction servers enhanced with Gene Ontology visualization tool
Authors: Khan Ishita K. , Wei Qing , Chitale Meghana , Kihara Daisuke
Published: October 2014

Summary : Protein function prediction (PFP) is an automated function prediction method that predicts Gene Ontology (GO) annotations for a protein sequence using distantly related sequences and contextual associations of GO terms. Extended similarity group (ESG) is another GO prediction algorithm that makes predictions based on iterative sequence database searches. Here, we provide interactive web servers for the PFP and ESG algorithms that are equipped with an effective visualization of the GO predictions in a hierarchical topology.

Availability : PFP/ESG servers are freely available at http://kiharalab.org/web/pfp.php and http://kiharalab.org/web/esg.php , or access both at http://kiharalab.org/pfp_esg.php

Contact : dkihara@purdue.edu

Supplementary information : Supplementary data are available at Bioinformatics online.
Physicochemical and Thermal Characteristics of Starch Isolated from a Waxy Wheat Genotype Exhibiting Partial Expression of Wx Proteins
Authors: Jung Taek‐Hee , Kim Jae Yoon , Baik Byung‐Kee , Park Chul Soo
Published: October 2014

A unique wheat genotype carrying waxy‐type allelic composition at the Wx loci, Gunji‐1, was developed, and its starch properties were evaluated in comparison to parental waxy and wild‐type wheat varieties. Gunji‐1 was null in all three of the Wx genes but exhibited a lower level of Wx proteins than the wild‐type. Starch amylose content and cold water retention capacity were 10.1 and 70.5% for Gunji‐1, 4.2 and 76.6% for waxy, and 27.9 and 65.0% for wild‐type, respectively. No significant differences were observed in microstructure, granule size distribution, and X‐ray diffractograms of the starch granules isolated from Gunji‐1 compared with those of waxy and wild‐type wheat varieties. Starch pasting peak, breakdown, and setback viscosities and peak temperature of Gunji‐1 were intermediate between waxy and wild‐type wheat. In starch gel hardness, Gunji‐1 (1.1 N) was more similar to waxy wheat (0.5 N) than to the wild‐type variety (17.6 N). Swelling power, swelling volume, paste transmittance during storage, and gelatinization enthalpy of Gunji‐1 were lower than those of waxy wheat but greater than those of wild‐type wheat. Retrogradation of starch stored for one week at 4°C expressed with DSC endothermic enthalpy was absent in the waxy wheat variety, whereas Gunji‐1 exhibited both retrogradation of amylopectin and amylose‐lipid complex melting similar to the wild‐type parent, even though enthalpies of Gunji‐1 were much smaller than the wild‐type parent.
NOTE: Hydrolysis Temperature Affects the Phloroglucinol Assay for Arabinoxylan Quantification in Wheat Flour
Authors: Laidlaw Hunter K. C. , Kooij‐Liu Peggy , Jobling Stephen A.
Published: October 2014

Phloroglucinol has a long history of use for the determination of pentose monomer content. Its application to cereal chemistry has been developed over several decades; however, no studies on the potential influence of hydrolysis temperature have yet been reported. We demonstrate the effect of hydrolysis temperature on the phloroglucinol assay for the measurement of pentosans in both refined and wholemeal wheat flours. In refined flour, monosaccharide degradation and interfering reactions from starch appear to effectively reduce the absorbance difference used to determine pentosan content. The presence of glucose in the reaction is also shown to provide stability to the reaction products. The potential impact of these factors on the determination of pentosan content needs to be considered when interpreting the results obtained using phloroglucinol‐based methods.
Screening Questions for Nonsteroidal Anti-inflammatory Drug Risk Knowledge
Authors: van den Bogert Cornelis A. , Miller Michael J. , Cobaugh Daniel J. , Chen Lang , Allison Jeroan J. , Saag Kenneth G.
Published: October 2014

Objective

The aim of this study was to evaluate screening questions for estimating nonsteroidal anti-inflammatory drug (NSAID) risk knowledge.

Methods

Cross-sectional data from a telephone interview of NSAID users 50 years or older from 39 physician practices in Alabama were used. Patient-reported awareness of prescription NSAID risk and health literacy were the independent variables, and a cumulative index score of objectively tested knowledge of 4 prominent NSAID risks was the dependent variable. General linearized latent and mixed model ordered logistic regression was used to estimate associations among the independent variables, covariates, and objectively tested NSAID risk knowledge. Population-averaged probabilities for levels of objectively tested NSAID risk knowledge were subsequently estimated.

Results

Subjective awareness of any prescription NSAID risk (adjusted odds ratio [AOR], 2.40; 95% confidence interval [CI], 1.55–3.74), adequate health literacy (AOR, 1.71; 95% CI, 1.04–2.83), and physician counseling about 1 or more NSAID risks (AOR, 1.69; 95% CI, 1.09–2.61) were significantly and positively associated with NSAID risk knowledge. The probability of correctly answering at least 1 of the 4 NSAID risk knowledge questions was 70% in the absence of any subjective risk awareness and in less than adequate health literacy. Whereas the probability of correctly answering at least 1 of the 4 NSAID risk knowledge questions increased to 86% in the presence of subjective awareness of any prescription NSAID risk and adequate health literacy.

Conclusions

Screening questions for subjective NSAID risk awareness and health literacy are predictive of objectively tested NSAID knowledge and can be used to triage patients as well as subsequently initiate and direct a conversation about NSAID risk.
Deciphering the complex three-way interaction between the non-integrin laminin receptor, galectin-3 andNeisseria meningitidis
Authors: Alqahtani Fulwah , Mahdavi Jafar , Wheldon Lee M. , Vassey Matthew , Pirinccioglu Necmettin , Royer Pierre-Joseph , Qarani Suzan M. , Morroll Shaun , Stoof Jeroen , Holliday Nicholas D. , Teo Siew Y. , Oldfield Neil J. , Wooldridge Karl G. , Ala'Aldeen Dlawer A. A.
Published: October 2014

The non-integrin laminin receptor (LAMR1/RPSA) and galectin-3 (Gal-3) are multi-functional host molecules with roles in diverse pathological processes, particularly of infectious or oncogenic origins. Using bimolecular fluorescence complementation and confocal imaging, we demonstrate that the two proteins homo- and heterodimerize, and that each isotype forms a distinct cell surface population. We present evidence that the 37 kDa form of LAMR1 (37LRP) is the precursor of the previously described 67 kDa laminin receptor (67LR), whereas the heterodimer represents an entity that is distinct from this molecule. Site-directed mutagenesis confirmed that the single cysteine (C173) of Gal-3 or lysine (K166) of LAMR1 are critical for heterodimerization. Recombinant Gal-3, expressed in normally Gal-3-deficient N2a cells, dimerized with endogenous LAMR1 and led to a significantly increased number of internalized bacteria (Neisseria meningitidis), confirming the role of Gal-3 in bacterial invasion. Contact-dependent cross-linking determined that, in common with LAMR1, Gal-3 binds the meningococcal secretin PilQ, in addition to the major pilin PilE. This study adds significant new mechanistic insights into the bacterial–host cell interaction by clarifying the nature, role and bacterial ligands of LAMR1 and Gal-3 isotypes during colonization.
Evolution: are the monkeys’ typewriters rigged?
Authors: Garvin Michael R. , Gharrett Anthony J.
Published: October 2014

Evolution is presumed to proceed by random mutations, which increase an individual’s fitness. Increased fitness produces a higher survival rate for those individuals within populations and drives the variants to fixation over large timescales to produce new species. We recently identified positively selected sites in mitochondrial complex I in numerous, diverse taxa. In one taxon, a simple sequence repeat (SSR) encompassed the positively selected sites. We hypothesized a model in which: (i) slip-strand mis-pairing during replication due to the SSR increases the mutation rate at these sites, and (ii) a functional constraint at the protein level maintains the SSR and therefore a higher mutation rate at this site over large time scales to drive evolution. We tested this model by identifying SSRs in a mitochondrial-encoded protein in species from our previous work and determined that nearly all of the positively selected sites encompass an SSR. Furthermore, we show that our proposed model accounts for most of the mutations at neutral sites but it is probably the predominant mechanism at positively selected sites. This suggests that evolution does not proceed by simple random processes but is guided by physical properties of the DNA itself and functional constraint of the proteins encoded by the DNA.
Continuum mechanics beyond the second law of thermodynamics
Authors: Ostoja-Starzewski M. , Malyarenko A.
Published: October 2014

The results established in contemporary statistical physics indicating that, on very small space and time scales, the entropy production rate may be negative, motivate a generalization of continuum mechanics. On account of the fluctuation theorem, it is recognized that the evolution of entropy at a material point is stochastically (not deterministically) conditioned by the past history, with an increasing trend of average entropy production. Hence, the axiom of Clausius–Duhem inequality is replaced by a submartingale model, which, by the Doob decomposition theorem, allows classification of thermomechanical processes into four types depending on whether they are conservative or not and/or conventional continuum mechanical or not. Stochastic generalizations of thermomechanics are given in the vein of either thermodynamic orthogonality or primitive thermodynamics, with explicit models formulated for Newtonian fluids with, respectively, parabolic or hyperbolic heat conduction. Several random field models of the martingale component, possibly including spatial fractal and Hurst effects, are proposed. The violations of the second law are relevant in those situations in continuum mechanics where very small spatial and temporal scales are involved. As an example, we study an acceleration wavefront of nanoscale thickness which randomly encounters regions in the medium characterized by a negative viscosity coefficient.
Chryseobacterium takakiae sp. nov., a member of the phylum Bacteroidetes isolated from Takakia lepidozioides
Authors: Zhao Ran , Chen Xin Yao , Li Xue Dong , Chen Zhi Ling , Li Yan Hong
Published: October 2014

A Gram-stain-negative, rod-shaped and non-endospore-forming bacterium, designated strain AG1-2T, was isolated from Takakia lepidozioides collected from the Gawalong glacier in Tibet, China and characterized using a polyphasic taxonomic approach. The predominant fatty acids of strain AG1-2T were iso-C15 : 0 (36.0 %), iso-C17 : 0 3-OH (20.2 %), summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl, 16.4 %) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 11.1 %). The major polar lipids were phosphatidylethanolamine, three unidentified aminolipids and two unidentified lipids. Strain AG1-2T contained MK-6 as the dominant menaquinone, and the genomic DNA G+C content was 37.3 mol%. The phylogenetic analysis based on the 16S rRNA gene sequences showed that strain AG1-2T was affiliated to species of the genus

Chryseobacterium

, and its closest related species were

Chryseobacterium taiwanense

Soil-3-27T,

Chryseobacterium hispalense

AG13T,

Chryseobacterium camelliae

THG C4-1T and

Chryseobacterium taeanense

PHA3-4T with a sequence similarity of 98.0, 97.8, 97.3 and 97.1 %, respectively. However, the DNA–DNA relatedness values between these strains and strain AG1-2T were 29, 21, 21 and 45 %, respectively. Based on phylogenetic inference and phenotypic data, strain AG1-2T is considered to represent a novel species of the genus

Chryseobacterium

, for which the name Chryseobacterium
takakiae sp. nov. is proposed. The type strain is AG1-2T ( = CGMCC 1.12488T = DSM 26898T).
Managing the life cycle of Java Card applets in other Java virtual machines
Authors: Roland Michael , Langer Josef , Mayrhofer Rene
Published: October 2014

Purpose

– The purpose of this paper is to address the design, implementation, performance and limitations of an environment that emulates a secure element for rapid prototyping and debugging. Today, it is difficult for developers to get access to a near field communication (NFC)-secure element in current smartphones. Moreover, the security constraints of smartcards make in-circuit emulation and debugging of applications impractical. Therefore, an environment that emulates a secure element brings significant advantages for developers.

Design/methodology/approach

– The authors' approach to such an environment is the emulation of Java Card applets on top of non-Java Card virtual machines (e.g. Android Dalvik VM), as this would facilitate the use of existing debugging tools. As the operation principle of the Java Card VM is based on persistent memory technology, the VM and applications running on top of it have a significantly different life cycle compared to other Java VMs. The authors evaluate these differences and their impact on Java VM-based Java Card emulation. They compare possible strategies to overcome the problems caused by these differences, propose a possible solution and create a prototypical implementation to verify the practical feasibility of such an emulation environment.

Findings

– While the authors found that the Java Card inbuilt persistent memory management is not available on other Java VMs, they present a strategy to model this persistence mechanism on other VMs to build a complete Java Card run-time environment on top of a non-Java Card VM. Their analysis of the performance degradation in a prototypical implementation caused by additional effort put into maintaining persistent application state revealed that the implementation of such an emulation environment is practically feasible.

Originality/value

– This paper addresses the problem of emulating a complete Java Card run-time environment on top of non-Java Card virtual machines which could open and significantly ease the development of NFC secure element applications.
A crowdsourcing framework for the management of mobile multimedia nature observations
Authors: Skevakis Giannis , Tsinaraki Chrisa , Trochatou Ioanna , Christodoulakis Stavros
Published: October 2014

Purpose

– This paper aims to describe MoM-NOCS, a Framework and a System that support communities with common interests in nature to capture and share multimedia observations of nature objects or events using mobile devices.

Design/methodology/approach

– The observations are automatically associated with contextual metadata that allow them to be visualized on top of 2D or 3D maps. The observations are managed by a multimedia management system, and annotated by the same and/or other users with common interests. Annotations made by the crowd support the knowledge distillation of the data and data provenance processes in the system.

Findings

– MoM-NOCS is complementary and interoperable with systems that are managed by natural history museums like MMAT (Makris et al., 2013) and biodiversity metadata management systems like BIOCASE (BioCASE) and GBIF (GBIF) so that they can link to interesting observations in the system, and the statistics of the observations that they manage can be visualized by the software.

Originality/value

– The Framework offers rich functionality for visualizing the observations made by the crowd as function of time.
MTAPIN: multi-touch key input enhances security of PIN authentication while keeping usability
Authors: Takada Tetsuji , Kokubun Yuki
Published: October 2014

Purpose

– The aim of the research is to realize a better form of personal identification number (PIN) authentication for a mobile phone without lowering usability and acceptability.

Design/methodology/approach

– The authors’ approach is to extend the input operation of PIN authentication by allowing more than one number at a time using a multi-touch-enabled screen. The authors also introduced substitution keys to be able to type any combination of a PIN value and an input pattern by multi-touch typing.

Findings

– The authors conducted a user evaluation study using a Web-based prototype system. The results of the study indicate that PIN input time, input errors and secret memorability of the proposed scheme were no worse than those of conventional PIN authentication. The theoretical security level of the proposed scheme is almost three and a half times than that of the conventional scheme.

Originality/value

– The paper introduced a multi-touch-allowed secret input operation into a PIN authentication. Though the introduction affected not only an input operation but also a PIN input interface and secret information, it makes possible to realize a better security level without a drastic change of a user interface and taking a longer input time.
High‐Volume Postdilution Hemodiafiltration Is a Feasible Option in Routine Clinical Practice
Authors: Marcelli Daniele , Scholz Caecilia , Ponce Pedro , Sousa Tânia , Kopperschmidt Pascal , Grassmann Aileen , Pinto Bruno , Canaud Bernard
Published: October 2014

Hemodiafiltration (HDF) with 20–22 L of substitution fluid is increasingly recognized as associated with significant benefits regarding patient outcome. However, some doubt exists as to whether these high volumes can be achieved in routine clinical practice. A total of 4176 sessions with 366 patients on postdilution HDF were analyzed in this 1‐month observational cohort study with prospective data collection. All dialysis machines were equipped with AutoSub plus signal analysis software that automatically and continuously adapts the substitution fluid flow according to the blood flow, blood viscosity, and dialyzer characteristics. Percentages of sessions with different types of vascular access were compared regarding achievement of ≥21 L substitution fluid. Logistic regression analysis was conducted to study the independent relationship of selected variables with achievement of ≥21 L substitution volume. Patient‐ and dialysis‐related variables that showed an association with the convection volume were entered in a multivariable model that included hematocrit up front. Respectively, 87%, 84%, and 33% of routine sessions conducted with fistulas, grafts, and catheters qualified as high‐volume HDF. Serum albumin levels ≥4.2 g/dL were positively associated with the achievement of at least 21 L substitution volume. Positive associations were also observed for blood flows in the ranges 350–399 and ≥400 mL/min compared with the reference range (300–350 mL/min), for longer treatment time, for fistula versus catheter, for higher filtration fraction, and for dialysis conducted at the end of the week versus Monday. It can be concluded that implementation and sustainability of high‐volume HDF is possible in routine clinical practice for almost all patients treated with fistulas and grafts.
Stability of parent‐reported food allergy in six and 7‐year‐old children: the first 5 years of the Finnish allergy programme
Authors: Järvenpää Johanna , Paassilta Marita , Salmivesi Susanna , Sannisto Tuire , Niitty Siina , Korppi Matti
Published: October 2014

Aim

The Finnish national allergy programme was introduced in 2008 to decrease the burden of allergy in the population. This study, carried out in 2013, evaluated the prevalence of parent‐reported food allergies, treated with an avoidance diet until early school age, and discussed the rates in relation to those found in an identical study in 2009.

Methods

School health nurses used a structured questionnaire to interview the parents of 1653 children aged of six or seven in the first year of elementary school. The criterion for a parent‐reported food allergy was that the parents considered it necessary for their child to follow an avoidance diet at school.

Results

In 2013, 6.1% of the children were allergic to at least one food and 2.5% of the children were allergic to basic foods, such as cows' milk, eggs and wheat, compared with 2.7% in 2009. A significant decrease was seen in allergies to nuts, fruits and vegetables.

Conclusion

Parent‐reported allergies to basic foods, such as cow's milk, eggs and wheat, remained rather stable in first graders of elementary schools during the first 5 years of the Finnish national allergy programme, but allergies to nuts, fruits and vegetables decreased.
Recent Trends in Sinus Lift Surgery and Their Clinical Implications
Authors: Al‐Dajani Mahmoud
Published: October 2014

Background

Sinus lift procedures are used to allow residual bone to accommodate functional implants in atrophic posterior maxilla. Numerous anatomical and surgical advancements in sinus lift surgery are still inspiring clinicians.

Purpose

The purpose of this study was to describe the recent trends in sinus lift surgery focusing on implant survival, bone grafting, anatomical and surgical considerations, and their clinical implications on the practice of implant dentistry in atrophic posterior maxilla.

Materials and Methods

We performed an extensive search in MEDLINE, Embase, Scopus, Web of Science, Trip, Cochrane Oral Health Group's Trials Register, Cochrane Central Register of Controlled Trials, and ProQuest Dissertations & Theses. Articles were critically reviewed to determine the level of evidence as per the Canadian Task Force on Preventive Health Care.

Results

Comprehensive assessment of sinus septa, sinus pathology, and bone quality and quantity using three‐dimensional cone beam computed tomography radiographs is important before placing implants in posterior maxilla. With a residual bone height of less than 5 mm, the survival rate of implant decreases substantially. Lateral window approach can increase the vertical bone height to greater than 9 mm, while osteotome approach can increase this height from 3 to 9 mm. The perforation of Schneiderian membrane doubles the risk for the incidence of sinusitis or infection. The use of piezoelectric surgery allows adequate sinus lift while protecting soft tissues and minimizing patient discomfort.

Conclusions

Although both osteotome and lateral window procedures can help clinicians in overcoming the challenges of placing implants in atrophic posterior maxilla, pre‐implant residual bone height is crucial in determining the survival of these implants. Future research directions should consider study designs grounded on longitudinal randomized controlled trials of large sample size.