bluuebunny/crossref_metadata_2025_split huggingface dataset:
Covalent attachment of P15 peptide to titanium surfaces enhances cell attachment, spreading, and osteogenic gene expression
Authors: Liu Qinyi , Limthongkul Worawat , Sidhu Gursukhmandeep , Zhang Jun , Vaccaro Alexander , Shenck Ryan , Hickok Noreen , Shapiro Irving , Freeman Theresa 
Published: April 2012

AbstractP15, a synthetic 15 amino acid peptide, mimics the cell‐binding domain within the alpha‐1 chain of human collagen is being tested in clinical trials to determine if it enhances bone formation in spinal fusions. We hypothesize that covalent attachment of P15 to titanium implants may also serve to promote osseointegration. To test this hypothesis, we measured osteoblast and mesenchymal cell adhesion, proliferation, and maturation on P15 tethered to a titanium (Ti‐P15) surface. P15 peptide was covalently bonded to titanium alloy surfaces and incubated with osteoblast like cells. Cell toxicity, adhesion, spreading, and differentiation was then evaluated. Real‐time quantitative PCR, Western blot analysis, and fluorescent immunohistochemistry was performed to measure osteoblast gene expression and differentiation. There was no evidence of toxicity. Significant increases in early cell attachment, spreading, and proliferation were observed on the Ti‐P15 surface. Increased filapodial attachments, α2 integrin expression, and phosphorylated focal adhesion kinase immunostaining indicated activation of integrin signaling pathways. qRT‐PCR analysis indicated there was significant increase in osteogenic differentiation markers in cells grown on Ti‐P15 compared to control‐Ti. Western blotting confirmed these findings. Surface modification of titanium with P15 significantly increased cell attachment, spreading, osteogenic gene expression, and differentiation. Results of this study suggest that Ti‐P15 has the potential to safely enhance bone formation and promote osseointegration of titanium implants. © 2012 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 30:1626–1633, 2012
An investigation of the transmission and attenuation of intense pulsed light on samples of human Achilles tendon and surrounding tissue
Authors: Hutchison A.M. , Beard D.J. , Bishop J. , Pallister I. , Davies W. 
Published: April 2012

AbstractBackgroundLight therapy is a common mode of treatment for musculoskeletal injuries but the depth of penetration of light radiation is controversial. Evidence exists for the efficacy of intense pulsed light (IPL) treatment for the rejuvenation of skin (superficial tissue) but it is not known if the IPL can penetrate deeper. If the IPL can penetrate to the depth of the Achilles tendon it may provide a potential management options in the treatment of a chronic mid‐body Achilles tendinopathy.ObjectivesTo examine if any optical radiation produced by an IPL transmits to the depth of the Achilles tendon when applied cutaneously to excised samples of human Achilles tissue. A secondary aim was to establish the relative amount of optical radiation that was attenuated within the tendon.Materials and MethodsThree samples of human Achilles tendon and surrounding tissue were harvested following elective lower limb amputation operations. Each sample was irradiated 2–6 cm above the insertion into the calcaneus (area of an Achilles tendinopathy) with IPL (model iPulse; Cyden Ltd, Wales, UK) set at a single pulse of 25 millisecond, wavelength range 530–1,110 nm and fluence of 13 J/cm2. The transmission of light radiation was evaluated using (a) standard SLR digital camera, (b) spectrometer, and (c) an external energy meter.ResultsLight radiation was found to have transmitted through each of the three tissue samples by all three instruments. There were observable differences in the color of light detected for the control photo and the IPL irradiated tissue samples photographs. The percentage of fluence that was detected to have transmitted through the tissue samples by the energy meter was 4–8.1% and wavelengths between 645 and 843 nm were detected to have transmitted through the tissue by the spectrometer. In addition, the percentage of light radiation that attenuated with the tendon was 10.2–17.32%.ConclusionThe results of this study provides evidence that IPL penetrates to the depth of the Achilles tendon and attenuates with the tendon. IPL has potential to produce physiological effects in the treatment of patients with a chronic mid‐body Achilles tendinopathy. Lasers Surg. Med. 44: 397–405, 2012. © 2012 Wiley Periodicals, Inc.
Proofs with monotone cuts
Authors: Jeřábek Emil 
Published: April 2012

AbstractAtserias, Galesi, and Pudlák have shown that the monotone sequent calculus MLK quasipolynomially simulates proofs of monotone sequents in the full sequent calculus LK (or equivalently, in Frege systems). We generalize the simulation to the fragment MCLK of LK which can prove arbitrary sequents, but restricts cut‐formulas to be monotone. We also show that MLK as a refutation system for CNFs quasipolynomially simulates LK.
Chemical shift encoded water–fat separation using parallel imaging and compressed sensing
Authors: Sharma Samir D. , Hu Houchun H. , Nayak Krishna S. 
Published: April 2012

AbstractChemical shift encoded techniques have received considerable attention recently because they can reliably separate water and fat in the presence of off‐resonance. The insensitivity to off‐resonance requires that data be acquired at multiple echo times, which increases the scan time as compared to a single echo acquisition. The increased scan time often requires that a compromise be made between the spatial resolution, the volume coverage, and the tolerance to artifacts from subject motion. This work describes a combined parallel imaging and compressed sensing approach for accelerated water–fat separation. In addition, the use of multiscale cubic B‐splines for B0 field map estimation is introduced. The water and fat images and the B0 field map are estimated via an alternating minimization. Coil sensitivity information is derived from a calculated k‐space convolution kernel and l1‐regularization is imposed on the coil‐combined water and fat image estimates. Uniform water–fat separation is demonstrated from retrospectively undersampled data in the liver, brachial plexus, ankle, and knee as well as from a prospectively undersampled acquisition of the knee at 8.6x acceleration. Magn Reson Med, 2013. © 2012 Wiley Periodicals, Inc.
Selective homonuclear polarization transfer for spectroscopic imaging of GABA at 7T
Authors: Pan J. W. , Duckrow R. B. , Spencer D. D. , Avdievich N. I. , Hetherington H. P. 
Published: April 2012

AbstractWe develop and implement a selective homonuclear polarization transfer method for the detection of 3.0 ppm C‐4 GABA resonance by spectroscopic imaging in the human brain at 7T. This single shot method is demonstrated with simulations and phantoms, which achieves comparable efficiency of detection to that of J‐difference editing. The macromolecule resonance that commonly co‐edits with GABA is suppressed at 7T through use of a narrow band preacquisition suppression pulse. This technique is implemented in humans with an eight channel transceiver array and high degree B0 shimming to measure supplementary motor area and thalamic GABA in controls (n = 8) and epilepsy patients (n = 8 total). We find that the GABA/N‐acetyl aspartate ratio in the thalamus of control volunteers, well controlled and poorly controlled epilepsy patients are 0.053 ± 0.012 (n = 8), 0.090 ± 0.012 (n = 2), and 0.038 ± 0.009 (n = 6), respectively. Magn Reson Med, 2013. © 2012 Wiley Periodicals, Inc.
A new method for detecting exchanging amide protons using chemical exchange rotation transfer
Authors: Zu Zhongliang , Janve Vaibhav A. , Xu Junzhong , Does Mark D. , Gore John C. , Gochberg Daniel F. 
Published: April 2012

AbstractIn this study, we introduce a new method for amide proton transfer imaging based on chemical exchange rotation transfer. It avoids several artifacts that plague conventional chemical exchange saturation transfer approaches by creating label and reference scans based on varying the irradiation pulse rotation angle (π and 2π radians) instead of the frequency offset (3.5 and −3.5 ppm). Specifically, conventional analysis is sensitive to confounding contributions from magnetic field (B0) inhomogeneities and, more problematically, inherently asymmetric macromolecular resonances. In addition, the lipid resonance at −3.5 ppm complicates the interpretation of the reference scan and decreases the resulting contrast. Finally, partial overlap of the amide signal by nearby amines and hydroxyls obscure the results. By avoiding these issues, our new method is a promising approach for imaging endogenous protein and peptide content and mapping pH. Magn Reson Med, 2013. © 2012 Wiley Periodicals, Inc.
PEO‐like Plasma Polymers Prepared by Atmospheric Pressure Surface Dielectric Barrier Discharge
Authors: Gordeev Ivan , Choukourov Andrei , Šimek Milan , Prukner Václav , Biederman Hynek 
Published: April 2012

AbstractThis work investigates the properties of poly(ethylene oxide)‐like plasma polymers prepared by amplitude‐modulated AC surface dielectric barrier discharge at atmospheric pressure. The discharge was driven in argon with admixtures of di(ethylene glycol) vinyl ether and special attention was paid to optimization of the experimental parameters for fabrication of thin films with enhanced retention of ether structure. Chemical composition of the plasma polymers was studied by XPS and FTIR whereas their non‐fouling properties were tested in terms of adsorption of fibrinogen. Under investigated range of discharge conditions, plasma polymers with up to 70% retention of the poly(ethylene oxide) character and with non‐fouling properties were obtained.magnified image
Mutagenesis of the bovSERPINA3‐3 demonstrates the requirement of aspartate‐371 for intermolecular interaction and formation of dimers
Authors: Blanchet X. , Péré‐Brissaud A. , Duprat N. , Pinault E. , Delourme D. , Ouali A. , Combet C. , Maftah A. , Pélissier P. , Brémaud L. 
Published: April 2012

AbstractThe family of serpins is known to fold into a metastable state that is required for the proteinase inhibition mechanism. One of the consequences of this conformational flexibility is the tendency of some mutated serpins to form polymers, which occur through the insertion of the reactive center loop of one serpin molecule into the A‐sheet of another. This “A‐sheet polymerization” has remained an attractive explanation for the molecular mechanism of serpinopathies. Polymerization of serpins can also take place in vitro under certain conditions (e.g., pH or temperature). Surprisingly, on sodium dodecyl sulfate/polyacrylamide gel electrophoresis, bovSERPINA3‐3 extracted from skeletal muscle or expressed in Escherichia coli was mainly observed as a homodimer. Here, in this report, by site‐directed mutagenesis of recombinant bovSERPINA3‐3, with substitution D371A, we demonstrate the importance of D371 for the intermolecular linkage observed in denaturing and reducing conditions. This residue influences the electrophoretic and conformational properties of bovSERPINA3‐3. By structural modeling of mature bovSERPINA3‐3, we propose a new “non‐A‐sheet swap” model of serpin homodimer in which D371 is involved at the molecular interface.
Graphene coupling to circularly polarized photons
Authors: Kibis O. V. 
Published: April 2012

AbstractWe have demonstrated theoretically that the Dirac electron spectrum of graphene leads to the strong electron in‐teraction with circularly polarized photons for low light intensities. This results in bound electron‐photon states (charged quasiparticles) which should be considered as a substantially new kind of light‐matter coupling.The energy spectrum of the quasiparticles is of dielectric type, that leads to the photon‐induced metal‐insulator transition in graphene. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Crystallization of hydrogenated amorphous‐nanocrystalline silicon films under high‐pressure annealing
Authors: Tyschenko Ida , Volodin Vladimir , Misiuk Andrzej 
Published: April 2012

AbstractCrystallization of the hydrogen ion implanted silicon‐on‐insulator (SOI) layers under conditions of high‐pressure (10.5 kbar) annealing at the temperature Ta = 450‐1000 °C was investigated by Raman spectroscopy. The as‐implanted films had composite structure consisted of the Si nanocrystals surrounded by the hydrogenated amorphous silicon. The retardation of hydrogenated Si crystallization was obtained under high‐pressure annealing at the temperature higher than 600 °C. The SOI layers remained to be nanocrystalline up to the annealing temperature of 1000 °C. The average size of the nanocrystals and the crystalline volume fraction were estimated from the Raman spectra as a function of the annealing temperature. The origin of the pressure effect on the crystallization of hydrogenated silicon is discussed. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Aqueous bromine etching of InP: a specific surface chemistry
Authors: Causier A. , Bouttemy M. , Gérard I. , Aureau D. , Vigneron J. , Etcheberry A. 
Published: April 2012

AbstractThe n ‐InP behaviour in HBr (0.1‐1.0 M)/Br2 (1.25 × 10‐2M) aqueous solutions is studied by AAS, XPS and SEM‐FEG. Indium AAS‐titrations of the HBr/Br2 solutions demonstrate that InP undergoes an etching mechanism whatever the HBr/Br2 formulation. The etching process is always linear with time but its rate depends on the HBr concentration. XPS analyses permit to link the apparent slow‐down of the dissolution process when decreasing the HBr molarity from 1.0 M to 0.1 M to the presence of a mixed (In,P)ox oxide layer on the surface. Therefore, the dissolution process of InP in HBr/Br2 solution appears to be ruled by the surface chemical state (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Confinement of electrons in a geometrically patterned non‐circular two‐dimensional semiconductor quantum dot
Authors: Ciftja Orion , Rasco Torrance , Vargas Guillermo , Dunn Stevonnise 
Published: April 2012

AbstractSemiconductor quantum dots are artificial nanoscale systems in which charge carriers, such as electrons, are usually confined in a small two‐dimensional (2D) region of space. In many occasions the confinement potential of the electrons is considered to be circularly symmetric with the parabolic form as the most commonly used one. Despite the variety of other confinement potentials with both infinite and finite range, all these choices share the property that the potential is circular in space. While these confinement models can be very good in many circumstances, there are situations in which the experimental setup in a semiconductor quantum dot involves application of several gate potentials which have very sharp geometric features. In these experimental instances, the area depleted of electrons, that represents the confining region is not circular and many times is better approximated as square or rectangular in shape. In this work we introduce a confinement potential that describes the confinement of electrons in a non‐circular2D semiconductor quantum dot in which the domain where the electrons are confined has a square or rectangular geometric shape. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Balancing the atomic waistline: Isodensity‐based scrf radii for main‐group elements and transition metals
Authors: Tao Jia‐Yuan , Mu Wei‐Hua , Chass Gregory Adam , Tang Ting‐Hua , Fang De‐Cai 
Published: April 2012

AbstractToward cracking the problem of understanding, characterizing, and predicting “solvent‐effect” while the world awaits an effective explicit solvent model, we introduce and justify herein a novel set of atomic radii to be used within the most commonly used continuum reaction field, the polarizable continuum model (PCM). The radial values emerge from a quantitative description of the elemental electronic density distribution and are shown to be accurate in such a self‐consistent reaction field (SCRF); labeled accordingly as isodensity‐based SCRF (IDSCRF) radii. Transition row elements with dynamic oxidation states are addressed through an averaging of the electronic properties from all states in the determination of their effective radii. All results for nonmetal elements have been verified with Guthrie's SAMPLE1 test set and are in quantitative agreement with experimental values from the literature and self‐consistent isodensity polarizable continuum model (SCIPCM) calculations. For the compounds with transition metal elements, our IDSCRF results have been verified with SCIPCM results as there are rarely experimental results available. Finally, explicit solvent particles “solvating” Pd‐ and Ni‐containing homogeneous catalysts are also shown to be in close agreement with the IDSCRF radii calculations. © 2012 Wiley Periodicals, Inc.
Quantum chemical study on molecular‐level affinity of DJ‐1 binding compounds
Authors: Shigemitsu Yasuhiro 
Published: April 2012

AbstractThe computationally evaluated binding free energies of DJ‐1, a clue protein to Parkinson's disease, with three potential curative agents are presented and discussed. The simple docking analysis offered fair absolute agreements of the calculated and the experimental binding energies while it failed to predict the binding affinity rank among the candidates. Computationally demanding analysis based on molecular dynamics and quantum chemical calculations unexpectedly worsen the gap between theory and experiment. The failure presumably comes from the inaccurate enthalpy terms owing to the basis set quality limitation and dispersion energy uncertainties, as well as from the inaccuracies of the entropy terms. The interfragment interaction analysis elucidated the driving force of the receptor–ligand affinity, which is not driven by Cys106 (the active site) but by the surrounding residues. © 2012 Wiley Periodicals, Inc.
Isotope effects associated with the preparation and methylation of fatty acids by boron trifluoride in methanol for compound‐specific stable hydrogen isotope analysis via gas chromatography/thermal conversion/isotope ratio mass spectrometry
Authors: Chivall David , Berstan Robert , Bull Ian D. , Evershed Richard P. 
Published: April 2012

RATIONALECompound‐specific stable hydrogen isotope analysis of fatty acids is being used increasingly as a means of deriving information from a diverse range of materials of archaeological, geological and environmental interest. Preparative steps required prior to isotope ratio mass spectrometry (IRMS) analysis have the potential to alter determined δD values and hence must be accounted for if accurate δD values for target compounds are to be obtained.METHODSMyristic, palmitic, stearic, arachidic and behenic saturated fatty acids were derivatised to their respective fatty acid methyl esters (FAMEs), using 14% (w/v) boron trifluoride in methanol then analysed by gas chromatography/thermal conversion/IRMS (GC/TC/IRMS). FAMEs generated from fatty acid sodium salts of unknown δD values were then used to test a correction factor determined for this method of derivatisation.RESULTSDerivatisation was found to alter the hydrogen isotopic composition of FAMEs although this effect was reproducible and can be accounted for. The difference between the mean corrected and mean bulk δD values was always less than 6.7 ‰. Extraction of saturated fatty acids and acyl lipids from samples, subsequent hydrolysis, then separation on a solid‐phase extraction cartridge, was found to alter the determined δD values by less than one standard deviation.CONCLUSIONSOverall, it has been shown that for natural abundance hydrogen isotope determinations, the isolation and derivatisation of extracted fatty acids alters the determined δD values only by a numerical increment comparable with the experimental error. This supports the use of the described analytical protocol as an effective means of determining fatty acid δD values by GC/TC/IRMS. Copyright © 2012 John Wiley & Sons, Ltd.
Determination of isotopic labeling of proteins by precursor ion scanning liquid chromatography/tandem mass spectrometry of derivatized amino acids applied to nuclear magnetic resonance studies
Authors: LeBlanc André , Arnold Alexandre A. , Genard Bertrand , Nadalini Jean‐Bruno , Heine Marc‐Olivier Séguin , Marcotte Isabelle , Tremblay Réjean , Sleno Lekha 
Published: April 2012

RATIONALEA method has been developed for the quantitation of isotopic labeling of proteins using liquid chromatography/tandem mass spectrometry (LC/MS/MS) for the application of protein nuclear magnetic resonance (NMR) studies. NMR relies on specific isotopic nuclei, such as 13C and 15N, for detection and, therefore, isotopic labeling is an important sample preparation step prior to in‐depth structural characterization of proteins. The goal of this study was to develop a robust quantitative assay for assessing isotopic labeling in proteins while retaining information on the extent of labeling for individual amino acids.METHODSComplete digestion of proteins by acid hydrolysis was followed by derivatization of free amino acids with 6‐aminoquinolyl N‐hydroxysuccinimidyl carbamate (AQC) forming derivatives having identical MS/MS fragmentation behavior. Precursor ion scanning on a hybrid quadrupole‐linear ion trap platform was used for amino acid analysis and determining isotopic labeling of proteins.RESULTSUsing a set of isotope‐labeled amino acid standards mixed with their unlabeled counterparts, the method was validated for accurately measuring % isotopic contribution. We then applied the method for determining the 13C isotopic content of algal proteins during a feeding study using 13C6‐glucose‐ or 13C‐bicarbonate‐supplemented culture media as well as the level of labeling in mussel byssal threads obtained after feeding with labeled algae.CONCLUSIONSThis method is ideally suited for assessing the extent of protein labeling prior to NMR studies, where the isotopic labeling is a determining factor in the quality of resulting protein spectra, and can be applied to a multitude of different biological samples. Copyright © 2012 John Wiley & Sons, Ltd.