bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conjugated polymers for pure UV light emission: Poly(meta‐phenylenes)
Authors: Patel Dinesh G. “Dan” , Ohnishi Yu‐ya , Yang Yixing , Eom Sang‐Hyun , Farley Richard T. , Graham Kenneth R. , Xue Jiangeng , Hirata So , Schanze Kirk S. , Reynolds John R. 
Published: March 2011

AbstractWe report the synthesis of a 3‐ethylhexyloxy substituted poly(meta‐phenylene), EHO‐PMP that shows absorption and solid state photoluminescence exclusively in the UV region of the electromagnetic spectrum with an emission maximum of 345 nm. Computational analysis of model oligomers by DFT methods indicates that EHO‐PMP is a wide bandgap polymer with the HOMO being localized on a dimeric (biphenyl) unit and with the LUMO being more delocalized. The energy of the LUMO, however, suggests that inefficient electron injection would occur from currently available cathode materials in standard light‐emitting device architectures, and this was observed experimentally. The computational results, coupled with experimental observation, lead us to believe that efficient electroluminescence from organic polymer UV emitters requires advances in electron transport layers and cathode materials. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011
The multidimensionality of spiritual wellbeing: peace, meaning, and faith and their association with quality of life and coping in oncology
Authors: Whitford Hayley S. , Olver Ian N. 
Published: March 2011

AbstractObjectiveThis study explored associations between the recently proposed three‐factor structure of the 12‐item Functional Assessment of Chronic Illness Therapy—Spiritual Well‐being (FACIT‐Sp) subscale (Peace, Meaning, and Faith), quality of life (QoL), and coping in an oncology population.MethodsA total of 999 newly diagnosed, study eligible, consecutive cancer patients completed the FACIT‐Sp and the Mental Adjustment to Cancer (MAC) scale.ResultsHierarchical multiple regressions revealed that Peace alone added 3% to the prediction of QoL and accounted for 15.8% of the overlap in Total Functional Assessment of Cancer Therapy—General (FACT‐G) scores (both p<0.001). Meaning alone added 1.3% to QoL prediction and accounted for 5.8% in overlap (both p<0.001). Faith did not significantly contribute to the unique prediction or overlap of QoL. Correlational analyses revealed that Peace was most prominently associated with the QoL subscales of Functional (r = 0.64) and Emotional Wellbeing (r = 0.61) and the coping styles of Helpless/Hopeless (r = −0.53), Fighting Spirit (r = 0.47), and Anxious Preoccupation (r = −0.34). Meaning was also highly associated with Functional Wellbeing (r = 0.56), Helpless/Hopeless (r = −0.53), and Fighting Spirit (r = 0.54), but in addition, Social Wellbeing (r = 0.49).ConclusionsThe three‐factor model of spiritual wellbeing appears psychometrically superior to previous models as it further discriminates between which components are most highly associated with improved QoL facets and coping styles. This study provides normative data on newly diagnosed patients with cancer and further highlights the clinical contribution of such detailed assessment.Copyright © 2011 John Wiley & Sons, Ltd.
One‐step Fabrication of π‐Conjugated Polymer Thin Films from Naphthalenes via Plasma Polymerization for Efficient Optoelectronic Devices: White Polymer Light‐emitting Diodes
Authors: Chang Chun‐Chih , Chang Yi‐Hsin , Hwang Kuo‐Chu , Jou Jwo‐Huei , Yang Arnold C.‐M. 
Published: March 2011

AbstractWe describe a facile one‐step fabrication process of thin film conjugated polymers for efficient optoelectronic devices from naphthalenes by plasma polymerization through a new monomer feeding method. The resulting 3‐D aromatic chain networks of the polymerized films were in good agreement with the predictions based on monomer bond rupture routes analysis. The photoluminescence (PL) spectra of plasma‐polymerized films featured short‐lived inter‐molecular emissions arising from self‐assembly of the naphthalene units in the crosslinked architectures. When functioning between the electrodes for light emitting, the plasma films manifested electroluminescence (EL) spectra that showed a steep rise at the threshold wavelength red‐shifted relative to the PL spectra, indicating prevailing charge tunneling to lower excited states by the accumulated interfacial charges. The wide distribution of conjugation lengths in the plasma films provided the subsequent energy transfer routes and gave rise to the broad EL emission band that produced stable pure white light of CIE coordinates of (0.34, 0.33) with excellent efficiencies. This dry deposition process allows the use of multiple monomers for property tailoring and may be used for large‐area depositions. magnified image
Structural modeling and molecular dynamics simulation of the actin filament
Authors: Splettstoesser Thomas , Holmes Kenneth C. , Noé Frank , Smith Jeremy C. 
Published: March 2011

AbstractActin is a major structural protein of the eukaryotic cytoskeleton and enables cell motility. Here, we present a model of the actin filament (F‐actin) that not only incorporates the global structure of the recently published model by Oda et al. but also conserves internal stereochemistry. A comparison is made using molecular dynamics simulation of the model with other recent F‐actin models. A number of structural determents such as the protomer propeller angle, the number of hydrogen bonds, and the structural variation among the protomers are analyzed. The MD comparison is found to reflect the evolution in quality of actin models over the last 6 years. In addition, simulations of the model are carried out in states with both ADP or ATP bound and local hydrogen‐bonding differences characterized. Proteins 2011; © 2011 Wiley‐Liss, Inc.
A parameterized, continuum electrostatic model for predicting protein pKa values
Authors: Burger Steven K. , Ayers Paul W. 
Published: March 2011

AbstractRecognizing the limits of trying to achieve chemical accuracy for pKa calculations with a purely electrostatic model, we include empirical corrections into the Poisson–Boltzmann solver macroscopic electrostatics with atomic detail (Bashford, Biochemistry 1990;29:10219–10225), to improve the reliability and accuracy of the model. The total number of parameters is kept to a minimum to maximize the robustness of the model for compounds outside of the fitting dataset. The parameters are based on: (a) the electrostatic interaction between functional groups close to the titratable site, (b) the electrostatic work required to desolvate the residue, and (c) the site‐to‐site interactions. These interactions are straightforward to calculate once the electrostatic field has been solved for each residue using the linearized Poisson–Boltzmann equation and are assumed to be linearly related to the intrinsic pKa. Two hundred and eighty‐six residues from 30 proteins are used to determine the empirical parameters, which result in a root mean square error (RMSE) of 0.70 for the entire set. Eight proteins with 46 experimentally known values were excluded from the parameterization to test the model. This test set had a RMSE of 1.08. We show that the parameterized model improves the results over other models, although like other models the error is strongly correlated with the degree to which a residue is buried. The parameters themselves indicate that local effects are most important for determining the pKa, whereas site‐to‐site interactions are found to be less significant. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Structure‐based identification of catalytic residues
Authors: Yahalom Ran , Reshef Dan , Wiener Ayana , Frankel Sagiv , Kalisman Nir , Lerner Boaz , Keasar Chen 
Published: March 2011

AbstractThe identification of catalytic residues is an essential step in functional characterization of enzymes. We present a purely structural approach to this problem, which is motivated by the difficulty of evolution‐based methods to annotate structural genomics targets that have few or no homologs in the databases. Our approach combines a state‐of‐the‐art support vector machine (SVM) classifier with novel structural features that augment structural clues by spatial averaging andZscoring. Special attention is paid to the class imbalance problem that stems from the overwhelming number of non‐catalytic residues in enzymes compared to catalytic residues. This problem is tackled by: (1) optimizing the classifier to maximize a performance criterion that considers both Type I and Type II errors in the classification of catalytic and non‐catalytic residues; (2) under‐sampling non‐catalytic residues before SVM training; and (3) during SVM training, penalizing errors in learning catalytic residues more than errors in learning non‐catalytic residues. Tested on four enzyme datasets, one specifically designed by us to mimic the structural genomics scenario and three previously evaluated datasets, our structure‐based classifier is never inferior to similar structure‐based classifiers and comparable to classifiers that use both structural and evolutionary features. In addition to the evaluation of the performance of catalytic residue identification, we also present detailed case studies on three proteins. This analysis suggests that many false positive predictions may correspond to binding sites and other functional residues. A web server that implements the method, our own‐designed database, and the source code of the programs are publicly available athttp://www.cs.bgu.ac.il/∼meshi/functionPrediction. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Progress in the structural prediction of G protein‐coupled receptors: D3 receptor in complex with eticlopride
Authors: Obiol‐Pardo Cristian , López Laura , Pastor Manuel , Selent Jana 
Published: March 2011

AbstractPredicting the three‐dimensional structure of ligand–receptor complexes involving G protein‐coupled receptors (GPCRs) is still a challenging task in rational drug design. To evaluate the reliability of the GPCR structural prediction, only a couple of community‐wide assessments have been carried out. Our participation in the last edition, DOCK2010, involved the blind prediction of the dopaminergic D3 receptor in complex with the D2/D3 selective antagonist eticlopride for which the crystal structure has been recently released. Here, we describe a methodology that succeeded to produce a correctly predicted eticlopride‐D3 receptor complex out of three submitted models. Ranking the obtained models in the correct order is the main challenge due to subtle structural differences in the complex that are not sufficiently captured by conventional scoring functions. Importantly, our work reveals that a correct ranking is obtained by including a more sophisticated description of conformational ligand energy on binding. All in all, this case study highlights the current progress in modeling GPCR complexes and underlines that in silico modeling can be a valuable complement in GPCR drug discovery. Proteins 2011; © 2011 Wiley‐Liss, Inc.
X‐ray, ESR, and quantum mechanics studies unravel a spin well in the cofactor‐less urate oxidase
Authors: Gabison Laure , Chopard Claude , Colloc'h Nathalie , Peyrot Fabienne , Castro Bertrand , Hajji Mohamed El , Altarsha Muhannad , Monard Gerald , Chiadmi Mohamed , Prangé Thierry 
Published: March 2011

AbstractUrate oxidase (EC 1.7.3.3 or UOX) catalyzes the conversion of uric acid using gaseous molecular oxygen to 5‐hydroxyisourate and hydrogen peroxide in absence of any cofactor or transition metal. The catalytic mechanism was investigated using X‐ray diffraction, electron spin resonance spectroscopy (ESR), and quantum mechanics calculations. The X‐ray structure of the anaerobic enzyme–substrate complex gives credit to substrate activation before the dioxygen fixation in the peroxo hole, where incoming and outgoing reagents (dioxygen, water, and hydrogen peroxide molecules) are handled. ESR spectroscopy establishes the initial monoelectron activation of the substrate without the participation of dioxygen. In addition, both X‐ray structure and quantum mechanic calculations promote a conserved base oxidative system as the main structural features in UOX that protonates/deprotonates and activate the substrate into the doublet state now able to satisfy the Wigner's spin selection rule for reaction with molecular oxygen in its triplet ground state. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Fabrication and study of porous PbTe layers on silicon substrates
Authors: Zimin Sergey , Vasin Vladimir , Gorlachev Egor , Naumov Viktor , Petrakov Anatoly , Shilov Sergey 
Published: March 2011

AbstractFabrication of porous PbTe layers on Si substrates using a developed technique based on anodic electrochemical etching of PbTe/CaF2/Si(111) heteroepitaxial structures in a Norr electrolyte with anodizing current density 2‐4 mA/cm2 is reported. The structural and morphological parameters of such layers are investigated with x‐ray reflectometry and diffractometry methods and with high‐resolution scanning electron microscopy. The influence of anodizing conditions on the parameters of the layers is discussed, as well as the morphological peculiarities of the anodized structures. The presence of cylindrical mesopores with diameter of 7‐26 nm inclined at the angle of ∼35° to the surface normal is shown. The value of the porosity for the near‐surface layer of lead telluride films is in the interval of 41‐68% and depends on the anodic electrochemical treatment conditions. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Ultra thin porous silicon films investigated by X‐ray reflectometry
Authors: Ennejah Nessima , Aouida Selma , Bessais Brahim 
Published: March 2011

AbstractIn this study, we report on structural variation of ultrathin of p‐type Porous Silicon (PS) films during the early stage growth process using X‐Ray Reflectometry (XRR). The PS samples were firstly characterized by Fourier Transform Infrared spectroscopy (FTIR) measurements. The homogeneity and surface roughness of the PS films, which enable characterizing the PS films by XRR, were investigated by UV‐visible spectroscopy and atomic force microscopy (AFM) measurements. The PS layers were then analyzed by specular X‐Ray Reflectivity (XRR). XRR reveals a linear thickness behavior as a function of etching time, while the porosity increases before reaching a constant value around 72%. These results were compared to those obtained from other characterization. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Correlation between spin density and photoluminescence intensity in thermally oxidized porous silicon
Authors: Pavlikov Alexander , Konstantinova Elizaveta , Timoshenko Victor 
Published: March 2011

AbstractWe have investigated the optoelectronic properties of thermally oxidized meso ‐PS layers. The correlation between photoluminescence (PL) intensity in the visible spectral ranges and defect density detected by electron spin resonance method has been established. The observed PL is explained by the radiative recombination of excitons trapped on the electronic states (Si=O bonds) in Si nanocrystals. The thermal treatment of meso ‐PS results in both the oxidation and coalescence of Si nanocrystals. Then, the simultaneous increase of both Si=O bond concentration and the density of Pb‐like centers at Si/SiO2 interfaces takes place. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Combination of silicon nitride and porous silicon induced optoelectronic features enhancement of multicrystalline silicon solar cells
Authors: Rabha Mohamed Ben , Dimassi Wissem , Gaidi Mounir , Ezzaouia Hatem , Bessais Brahim 
Published: March 2011

AbstractThe effects of antireflection (ARC) and surface passivation films on optoelectronic features of multicrystalline silicon (mc‐Si) were investigated in order to perform high efficiency solar cells. A double layer consisting of Plasma Enhanced Chemical Vapor Deposition (PECVD) of silicon nitride (SiNx) on porous silicon (PS) was achieved on mc‐Si surfaces. It was found that this treatment decreases the total surface reflectivity from about 25% to around 6% in the 450‐1100 nm wavelength range. As a result, the effective minority carrier diffusion length, estimated from the Laser‐beam‐induced current (LBIC) method, was found to increase from 312 µm for PS‐treated cells to about 798 µm for SiNx/PS‐treated ones. The deposition of SiNx was found to impressively enhance the minority carrier diffusion length probably due to hydrogen passivation of surface, grain boundaries and bulk defects. Fourier Transform Infrared Spectroscopy (FTIR) shows that the vibration modes of the highly suitable passivating Si‐H bonds exhibit frequency shifts toward higher wavenumber, depending on the x ratio of the introduced N atoms neighbors. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
On the origin of photoluminescence from silicon nanostructures: a new perspective
Authors: Sa'ar Amir 
Published: March 2011

AbstractThis review is aimed at describing recent developments in the field of silicon nanostructures, particularly those properties and phenomena that are connected with the room‐temperature, photoluminescence (PL) from these nanostructures. Two classes of models are the most notable ones: the quantum confinement model that assigns the PL to quantum size effects in the nanocrystalline silicon core, and the surface chemistry model that assigns the PL to surface phenomena at the interface between the crystalline core and the host matrix that wrap the nanostructures. In recent years, with the improvement in growth techniques and methods to control dimensionality and shape, it has been suggested that none of the above models alone can explain the entire spectrum of optical phenomena in silicon nanostructures. Instead, a refined model that takes into accounts both phenomena should be considered. This review describes some of these recent developments in the field of silicon nanostructures, particularly those experiments and models that indicate the mutual role of quantum confinement and surface chemistry in shaping the optical properties of these nanostructures. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
State and parameter estimation with the extended Kalman filter: an alternative formulation of the model error dynamics
Authors: Carrassi Alberto , Vannitsem Stéphane 
Published: March 2011

AbstractAn alternative formulation of the extended Kalman filter for state and parameter estimation is presented, referred to as Short‐Time Augmented Extended Kalman Filter (ST‐AEKF). In this algorithm, the evolution of the model error generated by the uncertain parameters is described using a truncated short‐time Taylor expansion within the assimilation interval. This allows for a simplification of the forward propagation of the augmented error covariance matrix with respect to the classical state augmented approach. The algorithm is illustrated in the case of a scalar unstable dynamics and is then more extensively analyzed in the context of the Lorenz 36‐variable model. The results demonstrate the ability of the ST‐AEKF to provide accurate estimate of both the system's state and parameters with a skill comparable to that of the full state augmented approach and in some cases close to the EKF in a perfect model scenario. The performance of the filter is analyzed for different initial parametric errors and assimilation intervals, and for the estimates of one or more model parameters. The filter accuracy is sensitive to the nature of the estimated parameter but more importantly to the assimilation interval, a feature connected to the short‐time approximation on which the filter formulation relies. The conditions and the context of applications of the present approach are also discussed. Copyright © 2011 Royal Meteorological Society
Does needle rotation improve lesion targeting?
Authors: Badaan Shadi , Petrisor Doru , Kim Chunwoo , Mozer Pierre , Mazilu Dumitru , Gruionu Lucian , Patriciu Alex , Cleary Kevin , Stoianovici Dan 
Published: March 2011

AbstractBackgroundImage‐guided robots are manipulators that operate based on medical images. Perhaps the most common class of image‐guided robots are robots for needle interventions. Typically, these robots actively position and/or orient a needle guide, but needle insertion is still done by the physician. While this arrangement may have safety advantages and keep the physician in control of needle insertion, actuated needle drivers can incorporate other useful features.MethodsWe first present a new needle driver that can actively insert and rotate a needle. With this device we investigate the use of needle rotation in controlled in‐vitro experiments performed with a specially developed revolving needle driver.ResultsThese experiments show that needle rotation can improve targeting and may reduce errors by as much as 70%.ConclusionThe new needle driver provides a unique kinematic architecture that enables insertion with a compact mechanism. Perhaps the most interesting conclusion of the study is that lesions of soft tissue organs may not be perfectly targeted with a needle without using special techniques, either manually or with a robotic device. The results of this study show that needle rotation may be an effective method of reducing targeting errors. Copyright © 2011 John Wiley & Sons, Ltd.
Nanoparticles: Well Shaped Mn3O4 Nano‐octahedra with Anomalous Magnetic Behavior and Enhanced Photodecomposition Properties (Small 4/2011)
Authors: Li Yu , Tan Haiyan , Yang Xiao‐Yu , Goris Bart , Verbeeck Jo , Bals Sara , Colson Pierre , Cloots Rudi , Van Tendeloo Gustaaf , Su Bao‐Lian 
Published: March 2011

AbstractVery uniform and well shaped Mn3O4 nano‐octahedra are synthesized using a simple hydrothermal method under the help of polyethylene glycol (PEG200) as a reductant and shape‐directing agent. The nano‐octahedra formation mechanism is monitored. The shape and crystal orientation of the nanoparticles is reconstructed by scanning electron microscopy and electron tomography, which reveals that the nano‐octahedra only selectively expose {101} facets at the external surfaces. The magnetic testing demonstrates that the Mn3O4 nano‐octahedra exhibit anomalous magnetic properties: the Mn3O4 nano‐octahedra around 150 nm show a similar Curie temperature and blocking temperature to Mn3O4 nanoparticles with 10 nm size because of the vertical axis of [001] plane and the exposed {101} facets. With these Mn3O4 nano‐octahedra as a catalyst, the photodecomposition of rhodamine B is evaluated and it is found that the photodecomposition activity of Mn3O4 nano‐octahedra is much superior to that of commercial Mn3O4 powders. The anomalous magnetic properties and high superior photodecomposition activity of well shaped Mn3O4 nano‐octahedra should be related to the special shape of the nanoparticles and the abundantly exposed {101} facets at the external surfaces. Therefore, the shape preference can largely broaden the application of the Mn3O4 nano‐octahedra.
Sonographic ‘molar tooth’ sign in the diagnosis of Joubert syndrome
Authors: Pugash D. , Oh T. , Godwin K. , Robinson A. J. , Byrne A. , Van Allen M. I. , Osiovich H. 
Published: March 2011

AbstractThe characteristic imaging finding common to Joubert syndrome and related disorders is the ‘molar tooth’ sign. The prenatal diagnosis of Joubert syndrome using both ultrasound and fetal magnetic resonance imaging (MRI) in families with an affected child has been reported previously. We report two cases in which the molar tooth sign was identified by sonography at 26 + 4 weeks and at 20 + 6 weeks, respectively, prior to fetal MRI or genetic testing. In both cases the finding was subsequently confirmed on fetal MRI. As definitive prenatal genetic testing may not be conclusive in Joubert syndrome, the ability to identify the molar tooth sign sonographically before 24 weeks provides a valuable adjunct to prenatal diagnosis. Copyright © 2011 ISUOG. Published by John Wiley & Sons, Ltd.