bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of osteopontin on functional activity of late endothelial progenitor cells
Authors: Yu Min , Liu Qian , Yi Kaihong , Wu Libiao , Tan Xuerui 
Published: February 2011

AbstractThe aim of this study is to investigate the effect of osteopontin (OPN) on functional activity of late endothelial progenitor cells (EPCs). Total mononuclear cells (MNCs) were isolated from human umbilical cord blood by Ficoll density gradient centrifugation, and then the cells were plated on fibronectin‐coated culture plates. Late EPCs were positive for both 1,1‐dioctadecyl‐3,3,3,3‐tetramethylindocarbocyanine‐labeled acetylated low‐density lipoprotein (DiI‐acLDL) and fluorescein‐isothiocyanate‐conjugated Ulex europaeus agglutinin lectin (UEA‐1). Expression of von Willbrand factor (vWF) and kinase insert domain receptor (KDR) were detected by indirect immunofluorescence staining. Late EPCs of 3–5 passages were treated for 24 h with OPN (to make a series of final concentration: 0.005 µg/ml, 0.01 µg/ml, 0.05 µg/ml, 0.5 µg/ml, 2.5 µg/ml), or vehicle control. The proliferation, migration, and in vitro vasculogenesis activity of late EPCs were assayed by 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide (MTT) assay, modified Boyden chamber assay and an in vitro angiogenesis assay, respectively. Late EPCs adhesion assay was performed by replating cells on fibronectin‐coated plates, and then adherent cells were counted. Incubation with OPN dose‐dependently inhibited the proliferative, adhesive, and in vitro vasculogenesis capacity and increased migratory activity of late EPCs. J. Cell. Biochem. 112: 1730–1736, 2011. © 2011 Wiley‐Liss, Inc.
Molecular cytogenetic characterization of telomere‐specific repetitive DNA sequences in Rana rugosa
Authors: Suda Mari , Uno Yoshinobu , Mori Yumiko , Matsuda Yoichi , Nakamura Masahisa 
Published: February 2011

AbstractWe performed a molecular cloning of the glutamic oxaloacetic transaminase (GOT1) gene from R. rugosa, and determined its chromosomal location. This gene was reportedly localized near the sex‐determining region of the ZW sex chromosomes in the frog Buergeria buergeri; however, the GOT1 gene was mapped to the distal end of chromosome 9 in R. rugosa using a GOT1 cDNA FISH probe. This was also the case when a 46.3 kb genomic clone containing exon 8 and 9 and the 3′‐neighboring region of the GOT1 gene, designated clone B, was used as probe. However, weak signals were also detected at the telomeric ends of other autosomes and the Z sex chromosome, and near the centromeric region of the W sex chromosome. To intensify the signals, we used eight internal fragments in clone B and applied them to chromosome mapping. Consequently, only two fragments containing repeated sequence blocks produced hybridization signals; those signals were observed on autosomes and ZW sex chromosomes. The 3′‐neighboring region contained two types of repeated sequence elements: a 41 bp element, designated 41‐REL, localized to telomeric ends of autosomes and a 31 bp element, designated 31‐REL, localized to telomeric ends of all autosomes and the ZW sex chromosomes, and also near the centromere on the W long arm. The results collectively suggest that the two repeated sequence elements were independently amplified around the chromosomal telomeres in R. rugosa, indicating that they will be useful cytogenetic markers for studying karyotypic evolution—especially the W chromosome differentiation—in this species. J. Exp. Zool. 315A:222–231, 2011. © 2011 Wiley‐Liss, Inc.
Oxidation of small unsaturated methyl and ethyl esters
Authors: Bennadji Hayet , Coniglio Lucie , Billaud Francis , Bounaceur Roda , Warth Valerie , Glaude Pierre‐Alexandre , Battin‐Leclerc Frédérique 
Published: February 2011

AbstractThe ignition delay times were measured behind reflected shock waves for temperatures from 1280 to 1930 K, pressures from of 7–9.65 atm, fuel concentrations of 0.4, 0.5, and 1%, and equivalence ratios equal to 0.25, 1.0, and 2.0 in the cases of four unsaturated esters: methyl crotonate, methyl acrylate, ethyl crotonate, and ethyl acrylate. Ignition delay times were measured using chemiluminescence emission from OH at 306 nm and piezoelectric pressure measurements made at the shock tube sidewall. No important difference of reactivity was observed between methyl and ethyl unsaturated esters, methyl and ethyl crotonate having the same reactivity as methyl butanoate. The reactivity of acrylates is greater than that of crotonates especially at the lowest investigated temperatures. Detailed mechanisms for the combustion of the four studied unsaturated esters have been automatically generated using the version of EXGAS software recently improved to take into account this class of oxygenated reactants. These mechanisms have been validated through satisfactory comparison of simulated and experimental results. The main reaction pathways have been derived from flow rate and sensitivity analyses. © 2011 Wiley Periodicals, Inc. Int J Chem Kinet 43: 204–218, 2011
Autoignition of methanol: Experiments and computations
Authors: Kumar Kamal , Sung Chih‐Jen 
Published: February 2011

AbstractAn experimental and computational investigation into the autoignition of methanol under high‐pressure and low‐to‐intermediate temperature conditions is conducted. The ignition delay results have been obtained using a heated rapid compression machine, over a pressure range of 7–30 bar, a temperature range of 850–1100 K, and an equivalence ratio range of 0.25–2.0. Using kinetic schemes recently reported in the literature for the combustion of methanol, the experimental results are compared to computationally obtained values. The kinetic schemes studied are found to significantly underpredict ignition delays for the conditions investigated. A sensitivity analysis of the computed results to reaction rate constants is also conducted. It is shown that the reaction of methanol with HO2 radical is critical to the predicted values of ignition delays under the current experimental conditions. © 2011 Wiley Periodicals, Inc. Int J Chem Kinet 43: 175–184, 2011
Improved facial nerve identification with novel fluorescently labeled probe
Authors: Wu Amy P. , Whitney Michael A. , Crisp Jessica L. , Friedman Beth , Tsien Roger Y. , Nguyen Quyen T. 
Published: February 2011

AbstractObjectives/Hypothesis:By phage display, we have developed a novel peptide (NP41) that binds selectively to nerves following systemic administration. We evaluated the pattern of facial nerve labeling with fluorescently‐labeled NP41 (F‐NP41). We also tested whether F‐NP41 highlights facial nerves well enough to identify nerve stumps accurately several weeks after nerve transection.Study Design:Forty‐seven wild‐type mice were studied prospectively. One surgeon performed the nerve transection, reanastomoses, and monitoring of functional recovery.Methods:Fluorescent labeling: F‐NP41 was administered intravenously (20 mice). Nerve labeling was studied with fluorescence microscopy. Transection and reanastomosis: the right facial nerve was transected (25 mice). Three weeks after transection, F‐NP41 was administered intravenously and fluorescence microscopy was used to identify the nerve stumps and reanastomosis in one group. Nerve identification and renastomosis was performed with white light in another group without F‐NP41. The control group underwent sham surgery. Time to nerve identification was recorded. Functional recovery was monitored for at least 8 weeks.Results:We found excellent labeling of intact and transected facial nerves following F‐NP41 administration. Several weeks following nerve transection, F‐NP41 provided accurate identification of the proximal and distal nerve stumps. Following reanastomosis, time to recovery and level of functional recovery was similar in the absence and presence of F‐NP41.Conclusions:We show improved visualization of facial nerves with a novel systemically applied fluorescently labeled probe. Use of F‐NP41 resulted in accurate identification of facial nerve stumps several weeks following transection. Functional recovery was similar with and without the use of F‐NP41. Laryngoscope, 2011
Increased serum interleukin‐17 levels in patients with myasthenia gravis
Authors: Roche Jose C. , Capablo Jose L. , Larrad Luis , Gervas‐Arruga Javier , Ara Jose R. , SáNCHEZ Alejandro , Alarcia Raquel 
Published: February 2011

AbstractIt has been suggested that interleukin‐17 (IL‐17) plays a crucial role in the development of several autoimmune diseases. However, there are no data about the relationship between myasthenia gravis and IL‐17. The aim of this study was to measure the concentration of IL‐17 and determine whether levels depend on the severity of MG. Serum IL‐17 concentrations were measured in 25 patients. IL‐17 concentrations were higher in generalized MG compared with controls and correlated with anti‐acetylcholinesterase receptor antibody titers. Muscle Nerve, 2011
Fetal ventriculomegaly secondary to isolated large choroid plexus cysts: prenatal findings and postnatal outcome
Authors: Fong Katherine , Chong Karen , Toi Ants , Uster Tami , Blaser Susan , Chitayat David 
Published: February 2011

AbstractObjectiveTo report the prenatal findings and postnatal outcome of fetal ventriculomegaly associated with isolated large choroid plexus cysts (CPCs).MethodCases of isolated fetal ventriculomegaly and large CPCs (>10 mm) were identified through a search of patient records from 2003 to 2006. Ultrasound (US) findings were reviewed: unilateral or bilateral ventriculomegaly, ventricular size, size of CPCs, and changes on serial scans. Correlation was made with fetal magnetic resonance imaging (MRI), pregnancy outcome, and long‐term follow‐up.ResultsSix cases of isolated large CPCs (12–30 mm) with ventriculomegaly (11–17 mm) were detected on US at 18 to 26 weeks of gestation. Serial prenatal US showed the CPCs resolved (one case) or decreased in size (five cases). Ventricular size became normal during pregnancy in five cases and decreased in size in one case. Fetal MRI performed in three cases showed no additional findings. Five patients had amniocentesis which showed normal karyotype. There was one termination of pregnancy (the fetus showed no abnormality on external examination). There were five healthy newborns, with follow‐up to 4.5 years of age (one), 5.5 years (one), and 6 years (three). All had normal physical and developmental outcome.ConclusionLarge isolated CPCs may transiently dilate the fetal cerebral ventricles. Follow‐up to 6 years has shown normal growth and development. Copyright © 2011 John Wiley & Sons, Ltd.
Effect of fenofibrate treatment on the low molecular weight urinary proteome of healthy volunteers
Authors: Foucher Christelle , Schiffer Eric , Mischak Harald , Ansquer Jean‐Claude , Wilbraham Darren 
Published: February 2011

AbstractPurpose: Urinary peptidome changes and discrimination for potential renal glomerular and tubular damage after 6 wk of fenofibrate treatment were evaluated in 26 healthy subjects.Experimental design: Peptide profiling was performed in urine samples before and after treatment using high‐resolution capillary electrophoresis coupled with electrospray ionization mass spectrometry.Results: A panel of 88 fenofibrate‐sensitive peptides was detected with a frequency of ≥50% before and after treatment. This was reduced to 36 peptides by repeating the comparison ten times by randomly excluding samples at each time‐point. Nineteen peptides were consistent and reliable biomarkers after an additional comparison with an age and sex‐matched subject control group. Levels of peptides identified as fragments of Collagen α‐1 (I), Collagen α‐1 (XVII), Collagen α‐2 (VIII) or sodium/potassium‐transporting ATPase subunit gamma were reduced after fenofibrate treatment. Classification scores for renal tubular and glomerular damages determined by support vector machine based biomarker models increased after treatment but remained below pathological score cutoff values.Conclusions and clinical relevance: Fenofibrate treatment led to minor modifications of the urinary proteomic profile in a way that does not create safety issues affecting glomerular and tubular functions. Urinary peptide profiling proved to be appropriate to monitor drug pharmacological effects in a clinical setting.
Oxidative stress occurs early in Down syndrome pregnancy: A redox proteomics analysis of amniotic fluid
Authors: Perluigi Marzia , di Domenico Fabio , Fiorini Ada , Cocciolo Annalisa , Giorgi Alessandra , Foppoli Cesira , Butterfield D. Allan , Giorlandino Maurizio , Giorlandino Claudio , Eugenia Schininà M. , Coccia Raffaella 
Published: February 2011

AbstractPurpose: The present study aims to evaluate a set of oxidative stress biomarkers in the amniotic fluid (AF) of women carrying Down syndrome (DS) fetuses that could prove in vivo the early occurrence of oxidative damage in DS.Experimental design: To assess the extent of protein oxidation in DS AF, we measured protein carbonylation and protein‐bound HNE by slot‐blot analysis, total and oxidized GSH levels by enzymatic assay and heat shock proteins (HSPs) thioredoxin (Trx) induction by Western blot. Further, by a redox proteomics approach specific targets of protein carbonylation were identified.Results: We found increased levels of oxidative stress, as indexed by increased protein oxidation, lipid peroxidation, reduction of GSH and Trx levels and induction of the HSP response. By a redox proteomics approach, we identified selective proteins which showed increased oxidation in DS fetuses compared with healthy controls. The identified proteins are involved in iron homeostasis (ceruloplasmin and transferin), lipid metabolism (zinc‐α2‐glycoprotein, retinol‐binding protein 4 and apolipoprotein A1) and inflammation (complement C9, α‐1B‐glycoprotein, collagen α‐1V chain) with critical relevance in the clinical outcome of DS.Conclusions and clinical relevance: Our results indicate that oxidative damage is an early event in the DS pathogenesis and might contribute to the development of deleterious DS phenotypes, including abnormal development and AD‐like neuropathology.
Development of a sandwich ELISA for the 5.9‐kDa fibrinogen alpha C chain fragment detected by serum proteome analysis
Authors: Noda Kenta , Sogawa Kazuyuki , Kikuchi Wataru , Kiyokawa Iwao , Miura Toshihide , Kojima Ryo , Katayama Katsuhiro , Kodera Yoshio , Nomura Fumio 
Published: February 2011

AbstractPurpose: We previously identified novel biomarker candidates in heavy consumers of alcohol using serum proteome analysis. Among several candidates, a 5.9 kDa peptide identified as a fragment of the fibrinogen alpha C chain (FIC5.9) was the most promising. To move FIC5.9 toward potential diagnostic use, we developed an enzyme immunoassay that enables measurement of serum FIC5.9 levels.Experimental design: Two monoclonal antibodies specific to the N and C‐termini of the 5.9‐kDa peptide were used to develop a FIC5.9 sandwich ELISA. The assay was evaluated by comparing the results with those obtained by the stable isotope‐labeled dilution mass spectrometry (SID‐MS) using the ClinProt™ system.Results: The ELISA results correlated with the SID‐MS findings (slope=0.795, intercept=−0.011, r2=0.908) and the performance of the ELISA was satisfactory in terms of recovery (98.5–103.0%) and within‐run (1.4–4.7%) and between‐day (2.8–8.4%) reproducibility. The assay was capable of detecting changes in FIC5.9 during abstinence from drinking in patients with alcohol dependency (p<0.0001).Conclusions and clinical relevance: The sandwich ELISA developed in this study will be useful for validation of the diagnostic significance of serum FIC5.9 levels in various pathological conditions, including alcoholism.
Predicted structures of agonist and antagonist bound complexes of adenosine A3 receptor
Authors: Kim Soo‐Kyung , Riley Lindsay , Abrol Ravinder , Jacobson Kenneth A. , Goddard William A. 
Published: February 2011

AbstractWe used the GEnSeMBLE Monte Carlo method to predict ensemble of the 20 best packings (helix rotations and tilts) based on the neutral total energy (E) from a vast number (10 trillion) of potential packings for each of the four subtypes of the adenosine G protein‐coupled receptors (GPCRs), which are involved in many cytoprotective functions. We then used the DarwinDock Monte Carlo methods to predict the binding pose for the human A3 adenosine receptor (hAA3R) for subtype selective agonists and antagonists. We found that all four A3 agonists stabilize the 15th lowest conformation of apo‐hAA3R while also binding strongly to the 1st and 3rd. In contrast the four A3 antagonists stabilize the 2nd or 3rd lowest conformation. These results show that different ligands can stabilize different GPCR conformations, which will likely affect function, complicating the design of functionally unique ligands. Interestingly all agonists lead to a trans χ1 angle for W6.48 that experiments on other GPCRs associate with G‐protein activation while all 20 apo‐AA3R conformations have a W6.48 gauche+ χ1 angle associated experimentally with inactive GPCRs for other systems. Thus docking calculations have identified critical ligand‐GPCR structures involved with activation. We found that the predicted binding site for selective agonist Cl‐IB‐MECA to the predicted structure of hAA3R shows favorable interactions to three subtype variable residues, I2536.58, V169EL2, and Q167EL2, while the predicted structure for hAA2AR shows weakened to the corresponding amino acids: T2566.58, E169EL2, and L167EL2, explaining the observed subtype selectivity. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Structure‐guided forcefield optimization
Authors: Song Yifan , Tyka Michael , Leaver‐Fay Andrew , Thompson James , Baker David 
Published: February 2011

AbstractAccurate modeling of biomolecular systems requires accurate forcefields. Widely used molecular mechanics (MM) forcefields obtain parameters from experimental data and quantum chemistry calculations on small molecules but do not have a clear way to take advantage of the information in high‐resolution macromolecular structures. In contrast, knowledge‐based methods largely ignore the physical chemistry of interatomic interactions, and instead derive parameters almost exclusively from macromolecular structures. This can involve considerable double counting of the same physical interactions. Here, we describe a method for forcefield improvement that combines the strengths of the two approaches. We use this method to improve the Rosetta all‐atom forcefield, in which the total energy is expressed as the sum of terms representing different physical interactions as in MM forcefields and the parameters are tuned to reproduce the properties of macromolecular structures. To resolve inaccuracies resulting from possible double counting of interactions, we compare distribution functions from low‐energy modeled structures to those from crystal structures. The structural and physical bases of the deviations between the modeled and reference structures are identified and used to guide forcefield improvements. We describe improvements resolving double counting between backbone hydrogen bond interactions and Lennard‐Jones interactions in helices; between sidechain‐backbone hydrogen bonds and the backbone torsion potential; and between the sidechain torsion potential and Lennard‐Jones interactions. Discrepancies between computed and observed distributions are also used to guide the incorporation of an explicit Cα‐hydrogen bond in β sheets. The method can be used generally to integrate different sources of information for forcefield improvement. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Multibody coarse‐grained potentials for native structure recognition and quality assessment of protein models
Authors: Gniewek Pawel , Leelananda Sumudu P. , Kolinski Andrzej , Jernigan Robert L. , Kloczkowski Andrzej 
Published: February 2011

AbstractMultibody potentials have been of much interest recently because they take into account three dimensional interactions related to residue packing and capture the cooperativity of these interactions in protein structures. Our goal was to combine long range multibody potentials and short range potentials to improve recognition of native structure among misfolded decoys. We optimized the weights for four‐body nonsequential, four‐body sequential, and short range potentials to obtain optimal model ranking results for threading and have compared these data against results obtained with other potentials (26 different coarse‐grained potentials from the Potentials ‘R’Us web server have been used). Our optimized multibody potentials outperform all other contact potentials in the recognition of the native structure among decoys, both for models from homology template‐based modeling and from template‐free modeling in CASP8 decoy sets. We have compared the results obtained for this optimized coarse‐grained potentials, where each residue is represented by a single point, with results obtained by using the DFIRE potential, which takes into account atomic level information of proteins. We found that for all proteins larger than 80 amino acids our optimized coarse‐grained potentials yield results comparable to those obtained with the atomic DFIRE potential. Proteins 2011; © 2011 Wiley‐Liss, Inc.
A multiple‐template approach to protein threading
Authors: Peng Jian , Xu Jinbo 
Published: February 2011

AbstractMost threading methods predict the structure of a protein using only a single template. Due to the increasing number of solved structures, a protein without solved structure is very likely to have more than one similar template structures. Therefore, a natural question to ask is if we can improve modeling accuracy using multiple templates. This article describes a new multiple‐template threading method to answer this question. At the heart of this multiple‐template threading method is a novel probabilistic‐consistency algorithm that can accurately align a single protein sequence simultaneously to multiple templates. Experimental results indicate that our multiple‐template method can improve pairwise sequence‐template alignment accuracy and generate models with better quality than single‐template models even if they are built from the best single templates (P‐value <10−6) while many popular multiple sequence/structure alignment tools fail to do so. The underlying reason is that our probabilistic‐consistency algorithm can generate accurate multiple sequence/template alignments. In another word, without an accurate multiple sequence/template alignment, the modeling accuracy cannot be improved by simply using multiple templates to increase alignment coverage. Blindly tested on the CASP9 targets with more than one good template structures, our method outperforms all other CASP9 servers except two (Zhang‐Server and QUARK of the same group). Our probabilistic‐consistency algorithm can possibly be extended to align multiple protein/RNA sequences and structures. Proteins 2011; © 2011 Wiley‐Liss, Inc.
A computational study on the ring stretching modes of halogen‐substituted pyridine involved in H‐bonding
Authors: Cao Li Juan , Li An Yong , Xu Li , Zhang Ying 
Published: February 2011

AbstractDensity functional method B3LYP plus the AUG‐cc‐pVDZ and AUG‐cc‐pVTZ basis sets is used to investigate ring normal modes of halogen‐substituted pyridines involved in the N···HX H‐bonds with HX (X = F, Cl). The results demonstrated that the formation of hydrogen bond leads to an increase in the frequencies of the ring breathing modev1, the N‐para‐C stretching modev6aand the meta‐CC stretching modev8a, whereas there is no change in the triangle modev12for free pyridine and a smaller blue shift for substituted pyridines. There is a strong coupling between the CY stretching vibration and the triangle mode (ortho‐ and para‐substituted) or the breathing mode (meta‐substituted) in substituted pyridines, which leads to the frequency decrease in the triangle or breathing modes. The natural bond orbital analysis suggests that electrostatic interaction and charge transfer caused by the intermolecular and intramolecular hyperconjugations are the origin of the frequency blue shift in the ring stretching modes. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012