bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational populations of ligand‐sized molecules by replica exchange molecular dynamics and temperature reweighting
Authors: Okumura Hisashi , Gallicchio Emilio , Levy Ronald M. 
Published: October 2009

AbstractThe use of the replica exchange (RE) molecular dynamics (MD) method for the efficient estimation of conformational populations of ligand‐sized molecules in solution is investigated. We compare the computational efficiency of the traditional constant temperature MD technique with that of the parallel RE molecular dynamics method for a series of alkanes and rilpivirine (TMC278), an inhibitor against HIV‐1 reverse transcriptase, with implicit solvation. We show that conformational populations are accurately estimated by both methods; however, replica exchange estimates converge at a faster rate, especially for rilpivirine, which is characterized by multiple stable states separated by high‐free energy barriers. Furthermore, convergence is enhanced when the weighted histogram analysis method (WHAM) is used to estimate populations from the data collected from multiple RE temperature replicas. For small drug‐like molecules with energetic barriers separating the stable states, the use of RE with WHAM is an efficient computational approach for estimating the contribution of ligand conformational reorganization to binding affinities. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010
Density functional theory study of calix[4]arene‐N‐azacrown‐5, calix[4]arene‐N‐phenyl‐azacrown‐5, and their complexes with alkali‐metal cations: Na+, K+, and Rb+
Authors: Zheng Xiaoyan , Wang Xueye , Yi Shanfeng , Wang Nuanqing , Peng Yueming 
Published: October 2009

AbstractTheoretical studies of 1,3‐alternate‐25,27‐bis(1‐methoxyethyl)calix[4]arene‐azacrown‐5 (L1), 1,3‐alternate‐25,27‐bis(1‐methoxyethyl)calix[4]arene‐N‐phenyl‐azacrown‐5 (L2), and the corresponding complexes M+/ L of L1 and L2 with the alkali‐metal cations: Na+, K+, and Rb+ have been performed using density functional theory (DFT) at B3LYP/6‐31G* level. The optimized geometric structures obtained from DFT calculations are used to perform natural bond orbital (NBO) analysis. The two main types of driving force metal–ligand and cation–π interactions are investigated. The results indicate that intermolecular electrostatic interactions are dominant and the electron‐donating oxygen offer lone pair electrons to the contacting RY* (1‐center Rydberg) or LP* (1‐center valence antibond lone pair) orbitals of M+ (Na+, K+, and Rb+). What's more, the cation–π interactions between the metal ion and π‐orbitals of the two rotated benzene rings play a minor role. For all the structures, the most pronounced changes in geometric parameters upon interaction are observed in the calix[4]arene molecule. In addition, an extra pendant phenyl group attached to nitrogen can promote metal complexation by 3D encapsulation greatly. In addition, the enthalpies of complexation reaction and hydrated cation exchange reaction had been studied by the calculated thermodynamic data. The calculated results of hydrated cation exchange reaction are in a good agreement with the experimental data for the complexes. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010
Generation and characterization of low‐energy structures in atomic clusters
Authors: Marques J. M. C. , Pais A. A. C. C. , Abreu P. E. 
Published: October 2009

AbstractFactors relevant for controlling the structures determined in the local optimization of argon clusters are investigated. In particular, the role of volume and shape for the box where initial structures are generated is assessed. A thorough characterization of the optimization is also presented, based on a nearest‐neighbor analysis, in clusters ranging from 30 to 55 atoms. This includes the assessment of the degree of preservation of aspects of the initial randomly generated structure in the final optimized counterpart, and the correlation between optimized energy and the number of nearest neighbors and average departure from the diatomic reference distance. The usefulness of this analysis to explore the energy landscape of atomic clusters is also highlighted. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010
Including receptor flexibility and induced fit effects into the design of MMP‐2 inhibitors
Authors: Durrant Jacob D. , de Oliveira César Augusto F. , McCammon J. Andrew 
Published: October 2009

AbstractMatrix metalloproteinases (MMPs) comprise a class of flexible proteins required for normal tissue remodeling. Overexpression of MMPs is associated with a wide range of pathophysiological processes, including vascular disease, multiple sclerosis, Alzheimer's disease, and cancer. Nearly all MMP inhibitors have failed in clinical trials, in part due to lack of specificity. Due to the highly dynamic molecular motions of the MMP‐2 binding pockets, the rational drug design of MMP inhibitors has been very challenging. To address these challenges, in the current study we combine computer docking with molecular dynamics (MD) simulations in order to incorporate receptor‐flexibility and induced‐fit effects into the drug‐design process. Our strategy identifies molecular fragments predicted to target multiple MMP‐2 binding pockets. Copyright © 2009 John Wiley & Sons, Ltd.
Generation of gas‐phase sodiated arenes such as [(Na3(C6H4)+] from benzene dicarboxylate salts
Authors: Attygalle Athula B. , Chan Chang‐Ching , Axe Frank U. , Bolgar Mark 
Published: October 2009

AbstractUpon collision‐induced activation, gaseous sodium adducts generated by electrospray ionization of disodium salts of 1,2‐ 1,3‐, and 1,4‐benzene dicarboxylic acids (m/z 233) undergo an unprecedented expulsion of CO2 by a rearrangement process to produce an ion of m/z 189 in which all three sodium atoms are retained. When isolated in a collision cell of a tandem‐in‐space mass spectrometer, and subjected to collision‐induced dissociation (CID), only the m/z 189 ions derived from the meta and para isomers underwent a further CO2 loss to produce a peak at m/z 145 for a sodiated arene of formula (Na3C6H4)+. This previously unreported m/z 145 ion, which is useful to differentiate meta and para benzene dicarboxylates from their ortho isomer, is in fact the sodium adduct of phenelenedisodium. Moreover, the m/z 189 ion from all three isomers readily expelled a sodium radical to produce a peak at m/z 166 for a radical cation [(•C6H4CO2Na2)+], which then eliminated CO2 to produce a peak at m/z 122 for the distonic cation (•C6H4Na2)+. Copyright © 2009 John Wiley & Sons, Ltd.
Enhanced extraction yields and mobile phase separations by solvent mixtures for the analysis of metabolites in Annona muricata L. leaves
Authors: Ribeiro de Souza Eloana Benassi , da Silva Renata Reis , Afonso Sabrina , Scarminio Ieda Spacino 
Published: October 2009

AbstractThe effects of five extraction solvents and their mixtures on the yield of metabolites in crude and fractionated extracts of Annona muricata L. leaves were investigated by direct comparison. Extraction media were prepared using simplex centroid mixtures of ethanol, ethyl acetate, dichloromethane, acetone, and chloroform. The effects of the mobile phase solvent strength and the analysis wavelength on the chromatographic separation were also investigated. Solvent mixtures rather than pure solvents were found to be the most efficient extractors for the different fractions. The results indicated that the mobile phase composed of methanol/acetonitrile/water (26:27:47 v/v/v) was most suitable for the basic fraction analysis at 254 nm, whereas the mobile phase composed of methanol/acetonitrile/water (35:35:30 v/v/v) was the most adequate for the organic fraction analysis at 254 nm. The results indicated that the chromatographic profiles and number of peaks were affected by the mobile phase strength and analysis wavelength.
An automatic peak finding method for LC‐MS data using Gaussian second derivative filtering
Authors: Fredriksson Mattias J. , Petersson Patrik , Axelsson Bengt‐Olof , Bylund Dan 
Published: October 2009

AbstractA highly automated procedure for localising and characterising peaks in the chromatographic time domain of LC‐MS data has been developed. The work was initiated by an identified need to facilitate the detection and tracking of chromatographic peaks during method development for the analysis of impurities in pharmaceutical products. The algorithm is mainly based on a digital filter for which the settings are automatically adapted to the data set under study. The procedure was evaluated for synthetic data sets with various S/N levels, peak widths and baseline properties. It was found that even for the worst case tested with S/N=10 and a high variability in the baseline, 94% of the simulated analytical peaks could be detected without producing any false‐positive identifications. Furthermore, the number of correctly estimated peak heights and peak widths falling within a 10% error of the true values were 94 and 91%, respectively. For experimental data sets, peak height, and width estimations were more difficult, but the processed reconstructions showed an excellent agreement with the analytical signals of the raw data, and also a clearly improved visualisation in total ion‐ and base‐peak chromatograms.
Quantitative structure–retention relationships for mycotoxins and fungal metabolites in LC‐MS/MS
Authors: Ji Caihong , Li Yanwei , Su Li , Zhang Xiaoyun , Chen Xingguo 
Published: October 2009

AbstractQuantitative structure–retention relationship (QSRR) models were used to predict the retention time (tR) of mycotoxins and fungal metabolites. Heuristic method and radial basis function neural networks (RBFNN) were utilized to construct the linear and non‐linear QSRR models, respectively. The optimal QSRR model was developed based on a 5‐21‐1 RBFNN architecture using molecular descriptors calculated from molecular structure alone. The RBFNN model gave a square of correlation coefficient (R2) of 0.8709 and root mean square error of 1.2892 for the test set. This article provided a useful tool for predicting the tR of other mycotoxins when experiment data are unknown.
Phenyl‐type and C1 stationary phases for environmentally friendlier chromatography
Authors: Stevenson Paul G. , Soliven Arianne , Dennis Gary R. , Shalliker Ross A. 
Published: October 2009

AbstractC1 and phenyl‐type stationary phases were assessed in terms of their environmental impact on separations using as test solutes polycyclic aromatic hydrocarbons. Methanol (MeOH) and acetonitrile (ACN) mobile‐phase gradients were employed. These stationary phases were examined to determine if different physical and chemical properties possessed by these surfaces decreased the organic solvent consumption, and yet maintained peak capacity. The cumulative energy demand (CED) was used to gauge the environmental impact of the separations. The separation of the polycyclic aromatic hydrocarbon test mixture using current methodologies (i.e. a C18/ACN combination) had a CED of 1.13 MJ‐eq, and a peak capacity of 27 peaks (resolving 7 of 12 peak pairs with Rs>1). In comparison, a butyl phenyl stationary phase with a methanol mobile phase had a peak capacity of 26, but with a CED of 0.670 MJ‐eq. Monolithic columns containing C18 and C1 phases were also tested. A monolithic C18 column with MeOH had the lowest CED at 0.675 MJ‐eq, a peak capacity of 28 peaks and good resolving power (resolving ten peak pairs with Rs>1), suggesting that this is a viable option with respect to reducing environmental impact for these types of analyses.
Solid‐phase extraction of liquiritin and glycyrrhizic acid from licorice using ionic liquid‐based silica sorbent
Authors: Tian Minglei , Bi Wentao , Row Kyung Ho 
Published: October 2009

AbstractA new ionic liquid‐based silica sorbent was developed by a process involving surface chemical modification of commercial silica using a synthesized ionic liquid. The obtained particles were successfully used as a special sorbent in a solid‐phase extraction process to isolate liquiritin and glycyrrhizic acid from licorice. Different washing and elution solvents, such as water, methanol/water (v/v), and pure methanol were evaluated. Ionic liquid‐based silica sorbent was compared with traditional C18 sorbent and it exhibited higher selectivity. Quantitative analysis was carried out by using a C18 column. Good linearities of two compounds were obtained from 5×10−4 to 0.2 mg/mL (r2>0.99) with the relative standard deviations <1.0%. The target compounds in commercial herbal medicines containing licorice were determined, and the bound rates between the target compounds and protein were obtained by this sorbent.
Evaluation of sulfobetaine‐type polymer resin as an SPE adsorbent in the analysis of trace tetracycline antibiotics in honey
Authors: Tsukamoto Tomoyasu , Yasuma Mari , Yamamoto Atsushi , Hirayama Kayo , Kihou Takafumi , Kodama Shuji , Inoue Yoshinori 
Published: October 2009

AbstractA new sulfobetaine polymer resin SPE method combined with HPLC‐MS/MS for the determination of tetracycline (TC) antibiotics residues from honey samples is presented. The sulfobetaine resin was synthesized and was packed into a syringe‐type tube, which served as the SPE cartridge for selective adsorption of TCs. TCs were quantitatively adsorbed on the sulfobetaine cartridge, when the loading solvent was 95% v/v acetonitrile solution, and TCs adsorbed were not eluted by aqueous acetonitrile washing solution. TFA aqueous solution was used for eluting the adsorbed TCs. The proposed SPE method has been applied to the determination of TCs in honey samples. The recoveries of TCs spiked in honey samples ranged from 70 to 80%. Reduction of the recoveries might be derived from low solubility of TCs in acetonitrile. Compared with other SPE resins, this resin was superior in terms of selectivity with simple pretreatment.
Nash problem for stable toric varieties
Authors: Petrov Peter 
Published: October 2009

AbstractThe main result of this paper is the proof of the Nash conjecture for stable toric varieties. We also introduce the Nash problem for pairs and prove it in the case of pairs (X, Y) of a toric variety X and a proper closed T ‐invariant subset Y containing Sing(X) (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Carathéodory–Julia type conditions and symmetries of boundary asymptotics for analytic functions on the unit disk
Authors: Bolotnikov Vladimir , Kheifets Alexander 
Published: October 2009

AbstractIt is shown that the following conditions are equivalent for the generalized Schur class functions at a boundary point t0 ∈ 𝕋: 1) Carathéodory–Julia type condition of order n; 2) agreeing of asymptotics of the original function from inside and of its continuation by reflection from outside of the unit disk 𝔻 up to order 2n + 1; 3) t0‐isometry of the coefficients ofthe boundary asymptotics; 4) a certain structured matrix ℙ constructed from these coefficients being Hermitian. It is also shown that for an arbitrary analytic function, properties 2), 3), 4) are still equivalent to each other and imply 1) (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Osculating properties of decomposable scrolls
Authors: Lanteri Antonio , Mallavibarrena Raquel 
Published: October 2009

AbstractOsculating spaces of decomposable scrolls (of any genus and not necessarily normal) are studied and their inflectional loci are related to those of their generating curves by using systematically an idea introduced by Piene and Sacchiero in the setting of rational normal scrolls. In this broader setting the extra components of the second discriminant locus – deriving from flexes – are investigated and a new class of uninflected surface scrolls is presented and characterized. Further properties related to osculation are discussed for (not necessarily decomposable) scrolls (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A variational characterization of rate‐independent evolution
Authors: Stefanelli Ulisse 
Published: October 2009

AbstractRate‐independent evolution driven by non‐convex potentials is by nature non‐smooth and some weak solvability notions have been recently advanced. This note is intended to contribute to this discussion by proposing a variational characterization of rate‐independent evolution based on a variational principle and a maximal dissipation criterion. The resulting novel solution notion is assessed in an elementary yet critical scalar case (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
HIV lumbosacral radiculoplexus neuropathy mimicking lymphoma: Diffuse infiltrative lymphocytosis syndrome (DILS) restricted to nerve?
Authors: Chahin Nizar , Temesgen Zelalem , Kurtin Paul J. , Spinner Robert J. , Dyck P. James B. 
Published: October 2009

AbstractDiffuse infiltrative lymphocytosis syndrome (DILS) is a hyperimmune reaction against HIV. It leads to MHC‐restricted clonal expansion of CD8 T cells characterized by circulating CD8 hyperlymphocytosis and CD8 T‐cell infiltration in organs. Our patient presented with painful lumbosacral radiculoplexus neuropathy and tested positive for HIV. Nerve biopsy showed large collections of CD8 lymphocytes suspicious for lymphoma. Symptoms, signs, and repeat biopsy improved with antiretroviral treatment. The presentation and treatment response suggest that this case is localized DILS. Muscle Nerve, 2010
Martin–Gruber anastomosis with anomalous superficial radial innervation to ulnar dorsum of hand: A pitfall when common variants coexist
Authors: Leis A. Arturo , Stetkarova Ivana , Wells Keionna J. 
Published: October 2009

AbstractThe Martin–Gruber anastomosis (MGA) is the most common anatomic variation in the upper extremity. Anomalous superficial radial innervation to the ulnar dorsum of the hand is the most common cause of an absent dorsal ulnar cutaneous (DUC) response. The coexistence of these variants introduces a relatively common yet underrecognized potential pitfall in nerve conduction studies (NCS). We performed confirmatory NCS in two cases referred for ulnar neuropathy in the forearm (case 1) and at the elbow (UNE, case 2). Initial NCS in both cases suggested ulnar nerve injury at the forearm and elbow, respectively, based on an apparent conduction block in ulnar motor fibers in the forearm (case 1) and elbow (case 2), and absent DUC responses. Additional NCS documented an MGA in the mid‐forearm (case 1) and high proximal forearm (case 2) with anomalous superficial radial innervation to the ulnar dorsum of the hand (both cases). Failure to recognize the coexistence of these two common variants may lead to misdiagnosis of ulnar neuropathy and inappropriate treatment. Muscle Nerve, 2009
Driving with polyneuropathy
Authors: Cho S. Charles , Katzberg Hans D. , Rama Anil , Kim Byung‐Jo , Roh Hakjae , Park Jongsoo , Katz Jonathan , So Yuen T. 
Published: October 2009

AbstractPolyneuropathy may result in pain, numbness, and weakness, which may in turn affect driving ability. Medications used to treat neuropathic pain may alter cognition, which may further affect driving. Although such impairments have engendered questions about the driving safety in this group of patients, the rate of motor vehicle accidents (MVAs) in patients with neuropathy has not been studied rigorously. We surveyed patients with neuropathy from three medical centers for reported accident rate, and we analyzed variables related to increased risk for accidents compared to National Highway Traffic Safety Administration data. Surveys from 260 subjects demonstrated that 40.6% were involved in traffic accidents (0.11 accidents/year). Their accident rate was 10.8 MVAs per million vehicle miles traveled (MVA/MVMT), compared to 3.71 MVA/MVMT in 55–59‐year‐old drivers and 3.72 in 60–64‐year‐olds (National Highway Traffic Safety Administration data). In all, 72.4% cited their neuropathy and 55.2% cited their medications as playing a role in their accidents, and 51.6% changed their driving habits after developing neuropathy. Independently, elevated levels of pain, motor weakness, and ambulation difficulty met statistical significance for increased MVA frequency. We conclude that accident frequency and discomfort with driving are higher in neuropathy patients compared to age‐matched national statistics. However, most patients seem to change habits according to their ability to drive; as such, driving issues should be addressed with caution and on a case‐by‐case basis. Muscle Nerve, 2009
Homozygosity for dominant mutations increases severity of muscle channelopathies
Authors: Arzel‐hézode Marianne , Sternberg Damien , Tabti Nacira , Vicart Savine , Goizet Cyril , Eymard Bruno , Fontaine Bertrand , Fournier Emmanuel 
Published: October 2009

AbstractMuscle channelopathies caused by mutations in the SCN4A gene that encodes the muscle sodium channel are transmitted by autosomal‐dominant inheritance. We report herein the first cases of homozygous patients for sodium channel mutations responsible for paramyotonia congenita (I1393T) or hypokalemic periodic paralysis (R1132Q). A parallel was drawn between this unprecedented situation and that of myotonia congenita by including patients homozygous or heterozygous for the CLCN1 I556N channel mutation, which is known for incomplete dominance and penetrance. Standardized electromyographic (EMG) protocols combining exercise and cold served as provocative tests to compare homozygotes with heterozygotes for each of the three mutations. Surface‐recorded compound muscle action potentials (CMAPs) were used to monitor muscle electrical activity, and myotonic discharges were evaluated by needle EMG. In heterozygous patients, exercise tests disclosed abnormal patterns of CMAP changes, which matched those previously described for similar dominant sodium and chloride channel mutations. Homozygotes showed much more severe clinical features and CMAP changes. We hypothesized that the presence of 100% defective ion channels in the homozygotes could account for the most severe phenotype. This suggests that the severity of muscle channelopathies depends both on the degree of channel impairment caused by the mutation and on the number of mutant channels engaged in the pathophysiological process. Overall, this study has practical consequences for the diagnosis of muscle channelopathies and raises new questions about their pathophysiology. Muscle Nerve, 2010
Unusual Charcot–Marie–Tooth phenotype due to a mutation within the intracellular domain of myelin protein zero
Authors: Schneider‐Gold Christiane , Kötting Judith , Epplen Jörg T. , Gold Ralf , Gerding Wanda M. 
Published: October 2009

AbstractMyelin protein zero (MPZ/P0) constitutes a major component of compact peripheral myelin. We report a family with a missense mutation, c.700G>T p.Asp234Tyr (deviant nomenclature: c.670G>T, p.Asp224Tyr), within the intracellular domain of myelin protein zero, who has distal sensorimotor symptoms, cramps, restless legs syndrome, neuropathic pain, and carpal tunnel syndrome. The index patient responded to intravenous immunoglobulin and immunosuppression, so there may be a possible secondary autoimmune process, probably triggered by altered antigen presentation due to mutated MPZ protein. Muscle Nerve, 2010