bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational dynamics of recoverin's Ca2+‐myristoyl switch probed by 15N NMR relaxation dispersion and chemical shift analysis
Authors: Xu Xianzhong , Ishima Rieko , Ames James B. 
Published: February 2011

AbstractRecoverin, a member of the neuronal calcium sensor (NCS) branch of the calmodulin superfamily, serves as a calcium sensor in retinal rod cells. Ca2+‐induced conformational changes in recoverin promote extrusion of its covalently attached myristate, known as the Ca2+‐myristoyl switch. Here, we present nuclear magnetic resonance (NMR) relaxation dispersion and chemical shift analysis on 15N‐labeled recoverin to probe main chain conformational dynamics. 15N NMR relaxation data suggest that Ca2+‐free recoverin undergoes millisecond conformational dynamics at particular amide sites throughout the protein. The addition of trace Ca2+ levels (0.05 equivalents) increases the number of residues that show detectable relaxation dispersion. The Ca2+‐dependent chemical shifts and relaxation dispersion suggest that recoverin has an intermediate conformational state (I) between the sequestered apo state (T) and Ca2+ saturated extruded state (R): T ↔ I ↔ R. The first step is a fast conformational equilibrium ([T]/[I] < 100) on the millisecond time scale (τexδω < 1). The final step (I ↔ R) is much slower (τexδω > 1). The main chain structure of I is similar in part to the structure of half‐saturated E85Q recoverin with a sequestered myristoyl group. We propose that millisecond dynamics during T ↔ I may transiently increase the exposure of Ca2+‐binding sites to initiate Ca2+ binding that drives extrusion of the myristoyl group during I ↔ R. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Innate factors causing differences in gene flow frequency from transgenic rice to different weedy rice biotypes
Authors: Zuo Jiao , Zhang Lianju , Song Xiaoling , Dai Weimin , Qiang Sheng 
Published: February 2011

AbstractBACKGROUND: The compatibility and outcrossing rates between transgenic rice and weedy rice biotypes have been studied in some previous cases. However, few studies have addressed the reasons for these differences. The present study compared the compatibility and outcrossing rates between transgenic rice and selected weedy rice biotypes using manual and natural crossing experiments to elucidate the key innate factors causing the different outcrossing rates.RESULTS: Hybrid seed sets from manual crossing between transgenic rice and weedy rice varied from 31.8 to 82.7%, which correlated directly with genetic compatibility. Moreover, the significant differences in the quantity of germinated donor pollens and pollen tubes entering the weedy rice ovule directly contributed to the different seed sets. The natural outcrossing rates varied from 0 to 6.66‰. The duration of flowering overlap was the key factor influencing natural outcrossing. Plant and panicle height also affected outcrossing success.CONCLUSION: From this study, it is concluded that the likelihood of gene flow between transgenic rice and weedy rice biotypes is primarily determined by floral synchronisation and secondarily influenced by genetic compatibility and some morphological characteristics. Copyright © 2011 Society of Chemical Industry
Nanocoax solar cells based on aligned multiwalled carbon nanotube arrays
Authors: Paudel T. , Rybczynski J. , Gao Y. T. , Lan Y. C. , Peng Y. , Kempa K. , Naughton M. J. , Ren Z. F. 
Published: February 2011

AbstractWe fabricated and studied solar cells based on a distributed nanocoax architecture by depositing amorphous silicon as photovoltaic medium on arrays of aligned multiwalled carbon nanotubes. These inexpensive cells demonstrate an initial efficiency of 6.1% that can be further enhanced by increasing the nanocoax density per unit area and improving the amorphous silicon quality.
Numerical investigation of the coupling between microdisk modes and quantum dots
Authors: Declair S. , Meier T. , Förstner J. 
Published: February 2011

AbstractWe numerically investigate the coupling between circular resonators and study strong light‐matter coupling of single as well as multiple circular resonators to quantum‐mechanical resonators in two dimensional model simulations. For all cases, the computed resonances of the coupled system as function of the detuning show anti‐crossings.The obtained mode splittings of coupled optical resonators are strongly depending on distance and cluster in almost degenerate eigenstates for large distances, as is known from coupled resonator optical waveguides. Vacuum Rabi splitting is observed for a quantum dot strongly coupled to eigenmodes of single perfectly cylindrical resonators. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Microcavity mode structure investigations with high spatial resolution
Authors: Ahrens Thomas , Burau Gerolf K.G. , Stolz Heinrich , Reitzenstein Stephan , Forchel Alfred 
Published: February 2011

AbstractMicropillar cavities of different diameters have been excited optically. The photoluminescence spectra of the top face emission have been measured while studying their intensity profile with high spatial resolution through the use of microscope objectives within the cryostat.The “donut”‐shape of the cavity mode with the second highest intensity is shown for the 2.3 µm pillar. A transfer matrix method has been applied to estimate the spatial and spectral profile of the individual cavity modes for comparison with the experimental results. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Cross sectional evaluation of boron doping and defect distribution in homoepitaxial diamond layers
Authors: Araújo Daniel , Paz Alegre M. A. , García Antonio J. , Pilar Villar M. , Bustarret Etienne , Achatz Philipp , Volpe Pierre N. , Omnès Franck 
Published: February 2011

AbstractIn some diamond‐based semiconducting devices, large variations of doping level are required over short distances. Tools to determine doping level and defects distribution should therefore be developed. The present contribution shows the capabilities of electron microscopy in this field. Focused ion beam (FIB‐dual beam) cross section preparations allowed evaluating doping level in highly boron doped sample with doping transition down to some nm by diffraction contrast mode of transmission electron microscopy (CTEM) and by high angle annular dark field mode of scanning transmission electron microscopy (HAADF‐STEM). The sensibility of the latter is around 1019cm‐3 and, thus, cathodoluminescence (CL) is required for lower doping levels. Cross sectional analysis on FIB prepared lamella allowed to separate the epilayer behaviour from that of the substrate. Mid‐gap centers involving boron, hydrogen and, for some peaks, also nitrogen are revealed. sp2 bonds are also present in the grown epilayer. These transitions make difficult the observation of excitonic recombinations in the cross section configuration. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Efficient methods for detection of SiC and Si3N4 precipitates and filaments in multi‐crystalline silicon wafers and solar cells
Authors: Bakowskie R. , Petter K. , Eiternick S. , Lausch D. , Müller G. 
Published: February 2011

AbstractTwo easy and efficient methods are demonstrated to detect SiC and Si3N4 filaments and precipitates in multi‐crystalline silicon (mc‐Si) wafers and solar cells by Optical Light (OLM) Microscopy and Scanning Electron Microscopy (SEM). In the case of OLM the image is created in the dark field mode which clearly visualizes the grain boundaries decorated by filaments in acidic etched silicon solar cells. In the case of SEM the image is created by a combination of Secondary Electrons (SE) imaging and Back Scattered Electrons (BSE) imaging. By using this method a clear discrimination of precipitates with different chemical compositions is possible. Note that both methods make it possible to investigate and analyze relatively large sample areas in a comparatively short period of time. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Si+ ion implantation in silica and ion beam mixing in SiO2/Si interfaces
Authors: Fitting Hans‐Joachim , Zatsepin Dmitry A. , Fitting Kourkoutis Lena , Schmidt Bernd 
Published: February 2011

AbstractScanning transmission electron microscopy (STEM) in combination with electron energy loss spectroscopy (EELS), energy filtered transmission electron microscopy (EFTEM), soft X‐ray emission spectroscopy (SXES), and cathodoluminescence (CL) have been used to investigate Si nanocluster formation in amorphous silicon dioxide layers implanted with Si+ ions. As samples we have used amorphous, thermally grown SiO2 layers, 20 and 500 nm thick on Si substrate. The layers are doped by Si+ ions with energies of 12 and 150 keV and doses of 1016 and 5×1016 ions/cm2 leading to atomic dopant fractions of about 7 and 4 at% at mean depths of 20 and 200 nm, respectively. After high fluence Si+ ion implantation into and around the interface of the thin 20 nm a ‐SiO2 layer on c‐Si the formation of an ion‐beam mixed buffer layer SiOx in this region was detected by means of SXES and compared with a TRIDYN computer simulation. This buffer layer is extended over about 20 nm and consists mainly of an understoichiometric SiOx matrix with 2 > x > 0 and gradually decreasing of x into the Si substrate. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Intensity‐dependent ultrafast dynamics of injection currents in unbiased GaAs quantum wells
Authors: Pochwała Michał , Duc Huynh Thanh , Förstner Jens , Meier Torsten 
Published: February 2011

AbstractThe intensity dependence of optically‐induced injection currents in unbiased GaAs semiconductor quantum wells grown in [110] direction is investigated theoretically for a number of well widths. Our microscopic analysis is based on a 14 × 14 band k · p method in combination with the multisubband semiconductor Bloch equations. An oscillatory dependence of the injection current transients as function of intensity and time is predicted and explained. It is demonstrated that optical excitations involving different subbands and Rabi flopping are responsible for this complex dynamics. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The H‐Bond activation mechanism and enantioselectivity in stepwise conjugate amine addition promoted by hydroxyl‐thiourea catalyst
Authors: Lu Nan , Chen Dezhan , Mi Shizhen , Zhang Guiqiu , Zhang Honghong 
Published: February 2011

AbstractThe H‐bond activation mechanism and enantioselectivity of hydroxyl‐thiourea catalyst in conjugate amine addition of O‐benzyl hydroxylamine to pyrazole crotonate is investigated using density functional theory (DFT) calculations. Two competing activation models are explored in detail. CN bond formation is stepwise in both of the two models. The enantioselective (S)‐channel is more favorable than (R)‐channel via the calculated barriers. The enantioselectivity originated from si face preferable than re face can be attributed to the H‐bonded network provided by thiourea and hydroxyl groups in rate‐determining step. The enantiomeric excess (ee) values predicted through ONIOM calculations are in line with the experiment. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Static and dynamic dipole polarizabilities and electron density at origin: Ground and excited states of hydrogen atom confined in multiwalled fullerenes
Authors: Motapon O. , Ndengue S. A. , Sen K. D. 
Published: February 2011

AbstractWe report accurate computations of static and dynamic dipole polarizabilities for the ground and excited states of hydrogen atom confined at the center of either a single and/or multiwalled fullerene cage, using the Galerkin variational method developed on a B‐spline basis set. The results obtained in the cage‐free case are in good agreement with other numerical techniques such as the mapped Fourier grid method. It is shown that the addition of new walls does not modify the polarizability of the ground state, but changes significantly those of the excited states. A condition on the ratio of the scaled second derivative of density to the scaled density evaluated at the nuclear position is tested in case of the cage confined atoms for the first time, and the significance of such numerical results are discussed. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
The role of hydrogen bonds in protein–ligand interactions. DFT calculations in 1,3‐dihydrobenzimidazole‐2 thione derivatives with glycinamide as model HIV RT inhibitors
Authors: Kretschmer Robert , Kinzel Daniel , González Leticia 
Published: February 2011

AbstractThe structures, redshifts, binding energies, Bader analysis, and shared‐electron numbers (SENs) of 1,3‐dihydrobenzimidazole‐2‐thione (DBS) derivatives hydrogen bonded to glycinamide were calculated by the means of DFT methods. The DBS–glycinamide complex serves as a model for human immunodeficiency virus reverse transcriptase inhibitors of theN‐dimethylallyl‐6‐methyl‐4,5,6,7‐tetrahydroimidazo‐[4,5,1‐jk][1,4]‐benzodiazepin‐2(1H)‐thione family. A correlation between experimental Gibbs free energies, associated biological activities and the energy of the hydrogen bond obtained with the SEN method showed a linear relationship for different substitution patterns. Our results suggest that efficient inhibitors are those substituted in the 8‐position with electron‐withdrawing small substituents. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem 112:1786–1795, 2012
Quantum chemical modeling of 1,1‐proton transfer reaction catalyzed by a cofactor‐independent α‐methylacyl‐CoA racemase
Authors: Li Xue , Zheng Qing‐Chuan , Zhang Hong‐Xing 
Published: February 2011

Abstractα‐Methylacyl‐CoA racemases (AMACR) are essential enzymes for branched‐chain lipids and drugs metabolism. AMACR catalyzes the chiral inversion of (2R) and (2S)‐methylacyl‐CoA esters in both directions. In this study, we investigated the catalytic mechanism of Mycobacterium tuberculosis (MCR) α‐methylacyl‐CoA racemase by using the density functional theory with the hybrid functional B3LYP. Our calculations elucidate and support the mechanism proposed by Prasenjit Bhaumik. His126 and Asp156 serve as the acid/base‐pair residues in the 1,1‐proton transfer catalytic reaction. From the optimized structures, it can be seen that an enolate intermediate is formed and the possibility of forming a ketene or a carbanion intermediate is excluded. By comparing the energy barriers, we could consider that the deprotonation step is the rate‐determined step in the invert direction from (S)‐ to (R)‐enantiomer. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Molecular and Functional Characterizations of Gastrula Organizer Cells Derived from Human Embryonic Stem Cells
Authors: Sharon Nadav , Mor Ishay , Golan-lev Tamar , Fainsod Abraham , Benvenisty Nissim 
Published: February 2011

Abstract
The Spemann-Mangold organizer is the structure that provides the signals, which initiate pattern formation in the developing vertebrate embryo, affecting the main body axes. Very little is known about axial induction in the gastrulating human embryo, as research is hindered by obvious ethical restrictions. Human embryonic stem cells (hESCs) are pluripotent cells derived from the pregastrula embryo that can differentiate in culture following a program similar to normal embryonic development but without pattern formation. Here, we show that in hESC-derived embryoid bodies, we can induce differentiation of cells that harbor markers and characteristics of the gastrula-organizer. Moreover, genetic labeling of these cells enabled their purification, and the discovery of a comprehensive set of their secreted proteins, cell surface receptors, and nuclear factors characteristic of the organizer. Remarkably, transplantation of cell populations enriched for the putative human organizer into frog embryos induced a secondary axis. Our research demonstrates that the human organizer can be induced in vitro and paves the way for the study of pattern formation and the initial regulation of body axis establishment in humans.
Model Based Systems Engineering with Department of Defense Architectural Framework
Authors: Piaszczyk Chris 
Published: February 2011

AbstractThis paper presents a methodology for Model Based Systems Engineering (MBSE) utilizing the guidelines provided by the Department of Defense Architectural Framework (DoDAF). MBSE focuses the system engineering process on system modeling. Thus, requirements derivation, system design, integration, verification, and validation activities all center around the model of the system. System models can be built in many ways. This paper presents an approach using DoDAF. Visual accessibility of the DoDAF views facilitates full participation by all system stakeholders, including the customers, developers, and implementers, and enables the necessary dialogue. The approach promotes communications among the members of the development team and speeds up the iterations of the systems engineering process. The paper illustrates the utility of the DoDAF artifacts by means of a simplified but comprehensive, easy to follow, illustrative example. © 2011 Wiley Periodicals, Inc. Syst Eng
An architectural systems engineering methodology for addressing cyber security
Authors: Bayuk Jennifer L. , Horowitz Barry M. 
Published: February 2011

AbstractThis paper discusses important shortcomings of current approaches to systems security engineering. The value and limitations of perimeter security designs are examined. An architectural approach to systems security engineering is introduced as a complementary means for strengthening current approaches. Accordingly, this paper outlines a methodology to identify classes of new reusable system security solutions and an architectural framework based on reuse of the patterns of solutions. It also introduces a new methodology for security metrics intended to stimulate critical solution design tradeoff analyses as part of security design reuse considerations. Examples of problems, potential architectural solutions, and corresponding security metrics are provided. © 2011 Wiley Periodicals, Inc. Syst Eng
Mining large medical claims database to identify high‐risk patients: The case of antidepressant utilization
Authors: Huang Samuel H. , Li Hua , Mo Dengyao , Wulsin Lawson R. 
Published: February 2011

AbstractData mining techniques have been applied to discover knowledge from large observational data sets. In this paper, we focus on mining large medical claims databases to identify high‐risk patients. Patient selection, feature extraction, and feature selection are three important processing steps before popular data mining techniques are successfully applied. Both patient selection and feature extraction require domain knowledge. The episode treatment group methodology is a useful tool for organizing medical claims data. It is used for patient selection and feature extraction in this paper. The specific goal of the study is to identify patients with major depression who have a high risk of receiving inadequate antidepressant medication. A nationwide medical claims database covering a 5‐year period is used for this study. The records of 31,721 high‐risk patients and 50,022 comparison patients were examined for 18 features that include patient demographics, episode factors, and comorbidity factors. After supervised feature selection, three features were selected and analyzed using the classification and regression tree method. The result showed that it is possible to use two of the features (number of non‐antidepressant medications used and average number of claims during an episode of major depression) to identify a group of high‐risk patients. These patients are 2.67 times more likely to have inadequate antidepressant medication than the comparison patients. © 2011 John Wiley & Sons, Inc. WIREs Data Mining Knowl Discov 2011 1 154‐163 DOI: 10.1002/widm.5This article is categorized under:

Application Areas > Health Care
Fundamental Concepts of Data and Knowledge > Knowledge Representation
Substrate Pretreatment can Reduce the Alcohol Requirement During Biodiesel Production Via in Situ Transesterification
Authors: Haas Michael J. , Wagner Karen M. 
Published: February 2011

AbstractThe ability of physical pretreatment of the feedstock to reduce the alcohol requirement for high yield fatty acid methyl esters (FAME) production during the in situ transesterification of soybeans was investigated. Four physical treatments were studied: (a) dehulling and flaking, (b) dehulling, flaking and passage through a twin screw extruder, (c) passage through an expander type extruder, or (d) conversion to a flour‐like consistency (1–10 μm particles) via disruption in a Pulsewave disintegrator. Following drying, optimal reaction conditions for high yield, room temperature, in situ transesterification of the lipid‐linked fatty acids resident in these materials were determined. Expander and Pulsewave pretreatment did not substantially reduce the amount of methanol required for high level FAME production below that required for flaked soybeans. However, the combination of flaking, extrusion and drying achieved a minimum nearly threefold reduction in the methanol requirement compared with that for soybeans that had been only flaked and dried. The flaking/extrusion/drying regime resulted in a minimum optimal molar ratio for (methanol/substrate fatty acid) of 9:1 for effective in situ transesterification. This is a 20‐fold reduction in methanol usage compared to the previously reported ratio of 181:1 for the use of flaked‐only soybeans. (Haas et al. in J Am Oil Chem Soc 81:83–89, 2004).
Dissection of the thoracic aorta following cardiopulmonary resuscitation
Authors: Oren-Grinberg Achikam , Shahul Sajid , Sarge Todd 
Published: February 2011

Abstract
An 86-year-old patient was admitted to the ICU with multiple trauma injury following a fall down ten stairs. Shortly after ICU admission the patient went into cardiac arrest and resuscitation efforts, including cardiopulmonary resuscitation (CPR), were initiated. Transesophageal echocardiogram was performed to guide therapy and, after regaining heart rhythm and blood pressure, the echocardiogram exam demonstrated critical aortic stenosis and type-B aortic dissection. The aortic dissection was not present on initial chest computerized tomography done on admission to the hospital. The aortic dissection appears to have resulted from the CPR performed to revive the patient.
Further insights into the strange role of bacterial endosymbionts in whitefly, Bemisia tabaci: Comparison of secondary symbionts from biotypes B and Q in China
Authors: Chu D. , Gao C.S. , De Barro P. , Zhang Y.J. , Wan F.H. , Khan I.A. 
Published: February 2011

AbstractThe percentage infection of secondary symbionts (SS) (Wolbachia, Arsenophonus, Rickettsia, Hamiltonella, Fritschea and Cardinium) in the exotic Bemisia tabaci (Genn.) invaders, commonly known as biotypes B and Q from China, were determined by PCR. In total, 373 biotype B and 1830 biotype Q individuals were screened for the presence of SS. Biotype B was more abundant than biotype Q from 2005 to 2006, and biotype Q was more abundant from 2007 to 2009. Each of the SS, with the exception of Fritschea, was detected in both biotypes B and Q; Fritschea was found in none of the samples examined. For biotype B, the percentage infection of Hamiltonella was the highest (92.0%) followed by Rickettsia (70.2%). For biotype Q, the percentage infection of Hamiltonella was again the highest (73.3%). Arsenophonus was the least common of the SS observed in both biotypes B and Q. The percentage infection of Wolbachia, Rickettsia and Hamiltonella in biotype B was each significantly higher than in biotype Q, whereas the percentage infection of Cardinium in biotype B was significantly lower than in biotype Q. The percentage infection of SS in biotypes B and Q varied from year to year over the period 2005–2009. Furthermore, within biotype Q, two distinct subgroups were identified which differ from each other in terms of their SS complement. We discuss these results in the light of the potentially influential factors and roles of the SS.