bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hypercalcemia and osteoblastic lesions induced by 13‐Cis‐retinoic acid mimicking relapsed neuroblastoma
Authors: Cross Siobhan F. , Pozza Luciano Dalla , Munns Craig F. 
Published: June 2009

AbstractA 6‐year‐old male diagnosed with extensive neuroblastoma was treated with chemotherapy, surgery, autotransplantation, and radiotherapy. He was then enrolled on a study to assess the monoclonal antibody Ch14.18 (anti‐GD2) with 13 cis‐retinoic acid. 13‐cis‐retinoic acid therapy caused severe bone pain and hypercalcemia. Bone scans showed multiple osteoblastic lesions suggesting recurrent disease however MIBG scans were negative. Serum markers of bone turnover were increased and the patient required pamidronate therapy to treat persistent hypercalcemia. Retinoic acid toxicity needs to be considered in the differential of painful osteoblastic lesions and/or hypercalcemia. MIBG scans can assist in differentiating from recurrent disease. Pediatr Blood Cancer 2009;53:666–668. © 2009 Wiley‐Liss, Inc.
Health care utilization and expenditures for privately and publicly insured children with sickle cell disease in the United States
Authors: Mvundura Mercy , Amendah Djesika , Kavanagh Patricia L. , Sprinz Philippa G. , Grosse Scott D. 
Published: June 2009

AbstractBackgroundThere are no current national estimates on health care utilization and expenditures for US children with sickle cell disease (SCD).ProcedureWe used the MarketScan® Medicaid Database and the MarketScan® Commercial Claims and Encounters Database for 2005 to estimate health services use and expenditures. The final samples consisted of 2,428 Medicaid‐enrolled and 621 privately insured children with SCD.ResultsThe percentage of children with SCD enrolled in Medicaid with an inpatient admission was higher compared to those privately insured (43% vs. 38%), yet mean expenditures per admission were 35% lower ($6,469 vs. $10,013). The mean number of emergency department (ED) visits was 49% higher for Medicaid‐enrolled children compared to those with private insurance (1.36 vs. 0.91), but mean expenditures per ED visit were 28% lower. The mean number of non‐ED outpatient visits was similar (12.6 vs. 11.5) but mean expenditures were 40% lower for the Medicaid‐enrolled children ($3,557 vs. $5,908). The mean expenditures on drug claims were higher among those with Medicaid than private insurance ($1,049 vs. $531). Mean total expenditures for children with SCD enrolled in Medicaid were 25% lower than for privately insured children ($11,075 vs. $14,722). The samples were comparable with respect to SCD‐related inpatient discharge diagnoses and use of outpatient blood transfusions.ConclusionsChildren with SCD enrolled in Medicaid had lower expenditures than privately insured children, despite higher utilization of medical care, which indicates lower average reimbursements. Research is needed to assess the quality of care delivered to Medicaid‐enrolled children with SCD and its relation to health outcomes. Pediatr Blood Cancer 2009;53:642–646. Published 2009 Wiley‐Liss, Inc.
Protein–protein interactions at an enzyme–substrate interface: Characterization of transient reaction intermediates throughout a full catalytic cycle of Escherichia coli thioredoxin reductase
Authors: Negri Ana , Rodríguez‐Larrea David , Marco Esther , Jiménez‐Ruiz Antonio , Sánchez‐Ruiz José M. , Gago Federico 
Published: June 2009

AbstractA large collection of structural snapshots along a full catalytic cycle of Escherichia coli thioredoxin reductase (TrxR) has been generated and characterized using a combination of theoretical methods. Molecular models were built starting from the available X‐ray crystallographic structures of dimeric wild‐type TrxR in the flavin‐oxidizing conformation and a C135S TrxR mutant enzyme in a flavin‐reducing conformation “trapped” by a cross‐link between Cys138 of TrxR and Cys32 of C35S mutant thioredoxin (Trx). The transition between these two extreme states, which is shown to be reproduced in a normal mode analysis, as well as natural cofactor binding and dissociation, were simulated for the wild‐type species using unrestrained and targeted molecular dynamics following docking of oxidized Trx to reduced TrxR. The whole set of simulations provides a comprehensive structural framework for understanding the mechanism of disulfide reduction in atomic detail and identifying the most likely intermediates that facilitate entry of NADPH and exit of NADP+. The crucial role assigned to Arg73 and Lys36 of Trx in substrate binding and complex stabilization was ascertained when R73G, R73D, and K36A site‐directed mutants of Trx were shown to be impaired to different extents in their ability to be reduced by TrxR. On the basis of previous findings and the results reported herein, E. coli TrxR appears as a beautifully engineered molecular machine that is capable of synchronizing cofactor capture and ejection with substrate binding and redox activity through an interdomain twisting motion. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Prediction of global and local model quality in CASP8 using the ModFOLD server
Authors: McGuffin Liam J. 
Published: June 2009

AbstractThe development of effective methods for predicting the quality of three‐dimensional (3D) models is fundamentally important for the success of tertiary structure (TS) prediction strategies. Since CASP7, the Quality Assessment (QA) category has existed to gauge the ability of various model quality assessment programs (MQAPs) at predicting the relative quality of individual 3D models. For the CASP8 experiment, automated predictions were submitted in the QA category using two methods from the ModFOLD server–ModFOLD version 1.1 and ModFOLDclust. ModFOLD version 1.1 is a single‐model machine learning based method, which was used for automated predictions of global model quality (QMODE1). ModFOLDclust is a simple clustering based method, which was used for automated predictions of both global and local quality (QMODE2). In addition, manual predictions of model quality were made using ModFOLD version 2.0—an experimental method that combines the scores from ModFOLDclust and ModFOLD v1.1. Predictions from the ModFOLDclust method were the most successful of the three in terms of the global model quality, whilst the ModFOLD v1.1 method was comparable in performance to other single‐model based methods. In addition, the ModFOLDclust method performed well at predicting the per‐residue, or local, model quality scores. Predictions of the per‐residue errors in our own 3D models, selected using the ModFOLD v2.0 method, were also the most accurate compared with those from other methods. All of the MQAPs described are publicly accessible via the ModFOLD server at: http://www.reading.ac.uk/bioinf/ModFOLD/. The methods are also freely available to download from: http://www.reading.ac.uk/bioinf/downloads/. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior
Authors: Gerek Z. Nevin , Keskin Ozlem , Ozkan S. Banu 
Published: June 2009

AbstractPDZ domains (PDZs), the most common interaction domain proteins, play critical roles in many cellular processes. PDZs perform their job by binding specific protein partners. However, they are very promiscuous, binding to more than one protein, yet selective at the same time. We examined the binding related dynamics of various PDZs to have insight about their specificity and promiscuity. We used full atomic normal mode analysis and a modified coarse‐grained elastic network model to compute the binding related dynamics. In the latter model, we introduced specificity for each single parameter constant and included the solvation effect implicitly. The modified model, referred to as specific‐Gaussian Network Model (s‐GNM), highlights some interesting differences in the conformational changes of PDZs upon binding to Class I or Class II type peptides. By clustering the residue fluctuation profiles of PDZs, we have shown: (i) binding selectivities can be discriminated from their dynamics, and (ii) the dynamics of different structural regions play critical roles for Class I and Class II specificity. s‐GNM is further tested on a dual‐specific PDZ which showed only Class I specificity when a point mutation exists on the βA‐βB loop. We observe that the binding dynamics change consistently in the mutated and wild type structures. In addition, we found that the binding induced fluctuation profiles can be used to discriminate the binding selectivity of homolog structures. These results indicate that s‐GNM can be a powerful method to study the changes in binding selectivities for mutant or homolog PDZs. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Two modes of electroluminescence from single‐walled carbon nanotubes
Authors: Lefebvre Jacques , Austing D. Guy , Finnie Paul 
Published: June 2009

AbstractThe electroluminescence from single‐walled carbon nanotube field effect transistors is spectrally resolved, and shows two distinct modes of light emission. The vast majority of nanotubes have spectrally broad emission consistent with the spectrum of blackbody radiation. Much more rarely, superposed on the broad emission is a single narrow (<50 meV) peak which is consistent with expectation for electron–hole recombination. The narrow emission is strong even at lower biases and in general has greater peak intensity than the broadband emission. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Simplification of the CBS‐QB3 method for predicting gas‐phase deprotonation free energies
Authors: Casasnovas Rodrigo , Frau Juan , Ortega‐Castro Joaquín , Salvà Antoni , Donoso Josefa , Muñoz Francisco 
Published: June 2009

AbstractSimplified versions of CBS‐QB3 model chemistry were used to calculate the free energies of 36 deprotonation reactions in the gas phase. The best such version, S9, excluded coupled cluster calculation [CCSD(T)], and empirical (ΔEemp) and spin‐orbit (ΔEint) correction terms. The mean absolute deviation and root mean square thus obtained (viz. 1.24 and 1.56 kcal/mol, respectively) were very‐close to those provided by the original CBS‐QB3 method (1.19 and 1.52 kcal/mol, respectively). The high‐accuracy of the proposed simplification and its computational expeditiousness make it an excellent choice for energy calculations on gas‐phase deprotonation reactions in complex systems. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
First‐principles calculation of magnetic circular dichroism of transition‐metal L2,3‐edge X‐ray absorption near‐edge structures
Authors: Ogasawara K. , Chaya A. , Watanabe S. , Yoshida H. 
Published: June 2009

AbstractWe performed first‐principles calculations for the magnetic circular dichroism of transition‐metal (TM) L2,3‐edge X‐ray absorption near‐edge structures of some rock‐salt type TM oxides using the relativistic discrete‐variational multielectron method. We also investigated the validity of the sum rules quantitatively by comparing the magnetic moments calculated from the theoretical spectra using the sum rules and those calculated directly from the explicit many‐electron wave functions. It was found that discrepancy is significant in the case of the spin moment. The configuration analysis of the many‐electron wave function indicated that the magnitude of the mixing between L2 and L3 edges could be the major cause of this discrepancy. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Interpretation of the emission fluorescence spectra of two fluoroionophores: DMABN‐Crown4 and DMABN‐Crown5
Authors: Carlotto Silvia , Ferrante Camilla , Polimeno Antonino , Benzi Caterina , Barone Vincenzo 
Published: June 2009

AbstractWe discuss an interpretation of the emission signal of a class of dimethylaminobenzonitrile (DMABN) derivatives, based on a stochastic model approach. This study is prompted by the interest in building relatively simple theoretical tools for understanding the static and dynamic properties of metal chelation‐controlled fluorescent molecular systems with internal flexibility and solvation effects, which can be used as fluorescent sensors of metal ions. We proceed by extending a stochastic modeling approach, previously used for DMABN, in which internal degrees of freedom are coupled to an effective solvent relaxation variable. The model is based on an integrated approach that combines stochastic methods and QM calculations. The static and dynamic properties of the molecule are obtained by a combination of a continuum treatment and a detailed solute dynamics. Simple computational approximations lead to a semianalytical treatment of the resulting equations, which reproduce correctly the static spectra at room temperature of 4‐(1‐aza‐4,7,10‐trioxacyclododecyl) benzonitrile (DMABN‐Crown4) and 4‐(1‐aza‐4,7,10,13‐tetraoxacyclododecyl) benzonitrile (DMABN‐Crown5) in solvents with different polarity. A qualitative analysis of the dynamic spectra of the DMABN‐Crown4 is also presented. A discussion is finally provided on how combined quantum and classical methods can be used to define a general robust and reliable computational approach for predicting fluorescence properties of organic molecules in solution. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Magnetic vortex dynamics induced by an electrical current
Authors: Gaididei Yuri , Kravchuk Volodymyr P. , Sheka Denis D. 
Published: June 2009

AbstractA magnetic nanoparticle in a vortex state is a promising candidate for the information storage. One bit of information corresponds to the upward or downward magnetization of the vortex core (vortex polarity). The dynamics of the magnetic vortex driven by a spin current is studied theoretically. Using a simple analytical model and numerical simulations, we show that a nondecaying vortex motion can be excited by a dc spin–polarized current, whose intensity exceeds a first threshold value as a result of the balance between a spin‐torque pumping and damping forces. The irreversible switching of the vortex polarity takes place for a current above a second threshold. The mechanism of the switching, which involves the process of creation and annihilation of a vortex–antivortex pair is described analytically, using a rigid model, and confirmed by detailed spin–lattice simulations. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Models for the adsorption and self‐assembly of ethanol and 1‐decanethiol on Au(111) surfaces. A comparative study by computer simulation
Authors: Fartaria Rui P. S. , Freitas Filomena F. M. , Silva Fernandes Fernando M. S. 
Published: June 2009

AbstractResults from computer simulations, based on different models to study theadsorption and self‐assembly of the ethanol and 1‐decanethiol on gold surfaces, Au(111), are presented. Canonical ensemble Monte Carlo simulations were performed at 298 K using two different force fields. One from DFT calculations, where the gold electrode has an explicit structure (corrugated electrode), and the other representing an electrode, in which the structure is taken into account on an average way (flat electrode). The behavior of the ethanol adsorption on gold surfaces, with and without the 1‐decanethiol presence, is analyzed. The introduction of molecular flexibility is also discussed. The relative surface density for the ethanol oxygen, adsorbed on gold, and the density profiles, in different conditions, show that the structure of the surface has a fundamental role on the way the adsorption takes place, not only on the preferential adsorption sites of the surface but also on the ethanol distribution over the electrodes. Potentials of mean force have also been calculated for the two surface models, giving the free energy barriers to the 1‐decanethiol crossing of the solvent adsorption layers. The average tilt angle, obtained with a single thiol molecule in the simulation box, presents the values: ∼26° for the rigid molecule model and 74° ± 18° for the flexible one. These differences are analyzed. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Three computational mise‐en‐scènes of red‐ and blue‐shifted hydrogen bonding motifs: Concept of negative intramolecular coupling—What else?
Authors: Kryachko Eugene S. 
Published: June 2009

AbstractThis work is a kind of attempt to rethink some problems which are related to the blue‐shifted “hydrogen bonds” and which have been left in the past decade as not yet fully resolved. The impetus for such rethink is originated from the three computational mise‐en‐scènes on red‐ and blue‐shifted hydrogen bonding motifs, which are aimed to be thoroughly studied in this work, thus resolving the above problems. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Conditions on the Kohn–Sham kinetic energy and associated density
Authors: Trickey S. B. , Karasiev V. V. , Jones R. S. 
Published: June 2009

AbstractEffective, explicitly density‐dependent (i.e., orbital‐free) approximations to the Kohn–Sham kinetic energy functional Ts remain elusive. In the course of developing such functionals in collaboration with Frank Harris, various issues have arisen that have gone unaddressed. We consider four of them here: positivity of the KS kinetic energy density, supposed requirements on its functional dependence, the use of cutoffs to insure positivity, and the role of the Coulomb virial theorem in the asymptotic analysis of Ts. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Gas‐phase fragmentation study of biotin reagents using electrospray ionization tandem mass spectrometry on a quadrupole orthogonal time‐of‐flight hybrid instrument
Authors: Sioud Salim , Genestie Benoit , Jahouh Farid , Martin Patrick , Banoub Joseph 
Published: June 2009

AbstractIn this study, we evaluated, by electrospray ionization mass spectrometry (ESI‐MS) and collision‐induced dissociation tandem mass spectrometry (CID‐MS/MS) using a quadrupole orthogonal time‐of‐flight (QqToF)‐MS/MS hybrid instrument, the gas‐phase fragmentations of some commercially available biotinyl reagents. The biotin reagents used were: psoralen‐BPE 1, p‐diazobenzoyl biocytin (DBB) 2, photoreactive biotin 3, biotinyl‐hexaethyleneglycol dimer 4, and the sulfo‐SBED 5. The results showed that, during ESI‐MS and CID‐MS/MS analyses, the biotin reagents followed a similar gas‐phase fragmentation pattern and the cleavages usually occurred at either end of the spacer arm of the biotin reagents. In general we have observed that the CID‐MS/MS fragmentation routes of the five precursor protonated molecules obtained from the biotin linkers 1–5 afforded a series of product ions formed essentially by similar routes. The genesis and the structural identities of all the product ions obtained from the biotin linkers 1–5 have been assigned. All the exact mass assignments of the protonated molecules and the product ions were verified by conducting separate CID‐MS/MS analysis of the deuterium‐labelled precursor ions. Copyright © 2009 John Wiley & Sons, Ltd.
Fuzzy pole placement based on piecewise Lyapunov functions
Authors: Tognetti Eduardo S. , Oliveira Vilma A. 
Published: June 2009

AbstractThis paper presents a controller design method for fuzzy dynamic systems based on piecewise Lyapunov functions with constraints on the closed‐loop pole location. The main idea is to use switched controllers to locate the poles of the system to obtain a satisfactory transient response. It is shown that the global fuzzy system satisfies the requirements for the design and that the control law can be obtained by solving a set of linear matrix inequalities, which can be efficiently solved with commercially available softwares. An example is given to illustrate the application of the proposed method. Copyright © 2009 John Wiley & Sons, Ltd.
Site‐specific dual ink dip pen nanolithography™
Authors: Nafday Omkar A. , Haaheim Jason R. , Villagran Fredy 
Published: June 2009

AbstractThe ability to deposit different materials with nanoscale precision at user‐specified locations is a very important attribute of dip pen nanolithography (DPN®). However, the potential of DPN goes beyond simple deposition since DPN used in conjunction with lateral force microscopy (LFM) allows site‐specific investigations of nanoscale properties. In this work, we use two different inks, 16‐mercaptohexadecanoic acid (MHA) and 1‐octadecanethiol (ODT) to show site‐specific dual ink DPN enabled exclusively by our proprietary software. A diamond‐dot pattern was created by using a layer‐to‐layer alignment (LLA) algorithm, which enables a MHA pattern (diamond) to be written concentric with another ODT (central dot) pattern. This simple demonstration of multi‐ink DPN is not specific to alkanethiol ink systems, but is also applicable to other multi‐material patterning, interaction, and exchange studies. SCANNING 31: 122–126, 2009. © 2009 Wiley Periodicals, Inc.
M X‐ray production cross sections for heavy elements by proton impact
Authors: Deghfel B. , Nekkab M. , Kahoul A. 
Published: June 2009

AbstractWe present in this paper, M‐shell ionization cross sections and M X‐ray production cross sections calculated within the Energy loss, Coulomb deflection, Perturbed Stationary State and Relativistic effects (ECPSSR) theory for elements with 72 ≤ Z ≤ 90 for protons with 0.1–4.0 MeV energy. Our results are compared to the plane wave Born approximation (PWBA) predictions, the relativistic plane‐wave Born approximation including corrections for binding and Coulomb deflection effect (RPWBA‐BC) results and the ECPSSR calculations from earlier works. On the other hand, semiempirical and empirical M X‐ray production cross sections are deduced from the polynomial fitting of the available experimental data collected from different sources. A comparison is made between the different sets of results. The differences between the above calculations and the experimental results are pointed out and discussed. Copyright © 2009 John Wiley & Sons, Ltd.
Dietary polyunsaturated fatty acids and adaptation to chronic hypoxia alter acyl composition of serum and heart lipids
Authors: Balková Patricie , Ježková Jana , Hlaváčková Markéta , Neckář Jan , Staňková Barbora , Kolář František , Novák František , Nováková Olga 
Published: June 2009

The effects of dietary supplementation with fat of different fatty acid profile and chronic intermittent hypoxia (CIH) on the fatty acid composition of serum and heart lipids were analysed. Adult male Wistar rats were fed a standard non-fat diet enriched with 10 % of lard, fish oil (n-3 PUFA) or maize oil (n-6 PUFA) for 10 weeks. After 4 weeks on the diets, each group was divided in two subgroups, either exposed to CIH in a barochamber (7000 m, twenty-five exposures) or kept at normoxia. In normoxic rats, the fish oil diet increased the level of conjugated dienes. Then-6:n-3 PUFA ratio in serum TAG, phospholipids (PL), cholesteryl esters (CE) and heart TAG, PL and diacylglycerols (DAG) followed the ratio in the fed diet (in the sequence maize oil>lard>fish oil). In heart TAG, PL and DAG, 20 : 4n-6 and 18 : 2n-6 were replaced by 22 : 6n-3 in the fish oil group. The main fatty acid in CE was 20 : 4n-6 in the lard and maize oil groups whereas in the fish oil group, half of 20 : 4n-6 was replaced by 20 : 5n-3. CIH further increased 20 : 5n-3 in CE in the fish oil group. CIH decreased then-6:n-3 PUFA ratio in serum CE, heart TAG, PL and DAG in all dietary groups and stimulated the activity of catalase in the maize and fish oil groups. In conclusion, PUFA diets and CIH, both interventions considered to be cardioprotective, distinctly modified the fatty acid profile in serum and heart lipids with specific effects on conjugated diene production and catalase activity.