bluuebunny/crossref_metadata_2025_split huggingface dataset:
A self‐organizing algorithm for molecular alignment and pharmacophore development
Authors: Bandyopadhyay Deepak , Agrafiotis Dimitris K. 
Published: November 2007

AbstractWe present a method for simultaneous three‐dimensional (3D) structure generation and pharmacophore‐based alignment using a self‐organizing algorithm called Stochastic Proximity Embedding (SPE). Current flexible molecular alignment methods either start from a single low‐energy structure for each molecule and tweak bonds or torsion angles, or choose from multiple conformations of each molecule. Methods that generate structures and align them iteratively (e.g., genetic algorithms) are often slow. In earlier work, we used SPE to generate good‐quality 3D conformations by iteratively adjusting pairwise distances between atoms based on a set of geometric rules, and showed that it samples conformational space better and runs faster than earlier programs. In this work, we run SPE on the entire ensemble of molecules to be aligned. Additional information about which atoms or groups of atoms in each molecule correspond to points in the pharmacophore can come from an automatically generated hypothesis or be specified manually. We add distance terms to SPE to bring pharmacophore points from different molecules closer in space, and also to line up normal/direction vectors associated with these points. We also permit pharmacophore points to be constrained to lie near external coordinates from a binding site. The aligned 3D molecular structures are nearly correct if the pharmacophore hypothesis is chemically feasible; postprocessing by minimization of suitable distance and energy functions further improves the structures and weeds out infeasible hypotheses. The method can be used to test 3D pharmacophores for a diverse set of active ligands, starting from only a hypothesis about corresponding atoms or groups. © 2007 Wiley Periodicals, Inc. J Comput Chem 2008
On the applicability of multireference second‐order perturbation theory to study weak magnetic coupling in molecular complexes
Authors: Queralt Núria , Taratiel David , de Graaf Coen , Caballol Rosa , Cimiraglia Renzo , Angeli Celestino 
Published: November 2007

AbstractThe performance of multiconfigurational second‐order perturbation techniques is established for the calculation of small magnetic couplings in heterobinuclear complexes. Whereas CASPT2 gives satisfactory results for relatively strong magnetic couplings, the method shows important deviations from the expected Heisenberg spectrum for couplings smaller than 15–20 cm−1. The standard choice of the zeroth‐order CASPT2 Hamiltonian is compared to alternative definitions published in the literature and the stability of the results is tested against increasing level shifts. Furthermore, we compare CASPT2 with an alternative implementation of multiconfigurational perturbation theory, namely NEVPT2 and with variational calculations based on the difference dedicated CI technique. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Linear‐scaling Cholesky decomposition
Authors: Schweizer Sabine , Kussmann Jörg , Doser Bernd , Ochsenfeld Christian 
Published: November 2007

AbstractWe present linear‐scaling routines for the calculation of the Cholesky decomposition of a symmetric positive‐definite matrix and its inverse. As an example, we consider the inversion of the overlap matrix of DNA and amylose fragments as well as of linear alkanes, where the largest system corresponds to a 21,442 × 21,442 matrix. The efficiency and the scaling behavior are discussed and compared to standard LAPACK routines. Our Cholesky routines are publicly available on the web. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Chondrogenesis and ossification of the lissamphibian pectoral girdle
Authors: Shearman Rebecca M. 
Published: November 2007

AbstractKnowledge of amphibian shoulder development is requisite for further understanding of gnathostome pectoral girdle evolution. Fish and amniotes share few pectoral girdle elements, but modern amphibians exhibit a unique combination of traits that bridge the morphological gap between these two groups. I analyzed patterns of chondrogenesis, ossification, and bone histology of the pectoral girdles of two anuran species (Xenopus laevis and Bombina orientalis) and two urodele species (Ambystoma mexicanum and Desmognathus aeneus) to provide new insight into the evolution of the tetrapod pectoral girdle. Comparisons reveal the following: 1) variation in the pattern of chondrogenesis among the anuran species analyzed correlates to variation in adult pectoral girdle morphology; 2) morphologically similar pectoral skeletons do not necessarily have similar patterns of bone histology; and 3) the urodele and anuran pectoral girdles included herein share a common morphology despite differences in patterns of chondrogenesis. J. Morphol., 2008. © 2007 Wiley‐Liss, Inc.
Renal sexual segment of the Cottonmouth snake, Agkistrodon piscivorous (Reptilia, Squamata, Viperidae)
Authors: Sever David M. , Siegel Dustin S. , Bagwill April , Eckstut Mallory E. , Alexander Laura , Camus Angelle , Morgan Colby 
Published: November 2007

AbstractThe seasonal variation of the renal sexual segment (RSS) of males of the Cottonmouth snake, Agkistrodon piscivorous, is described using light and electron microscopy. This study is the first to describe the ultrastructure of the RSS of a viper (Viperidae) and only the fourth on a snake. Renal sexual segments from males collected February to May and from August to November are similar in appearance. The cells are eosinophilic and react with periodic acid/Schiff procedure (PAS) for neutral carbohydrates and bromphenol blue (BB) for proteins. At the ultrastructure level, the cells contain large (2 μm diameter), electron‐dense secretory granules and smaller vesicles with a diffuse material, and these structures abut against the luminal border and upon clear vacuoles continuous with intercellular canaliculi. Evidence was found for both apocrine and merocrine processes of product release. In June and July, the RSS are significantly smaller in diameter, largely basophilic, and have only scattered granules that are PAS+ and BB+. Cytologically, the RSS from June to July lack electron‐dense secretory granules and the smaller vesicles with diffuse material. Numerous condensing vacuoles and abundant rough endoplasmic reticulum, however, indicate that active product synthesis is occurring. This is the first report of significant seasonal variation in the histology and ultrastructure of the RSS of a snake, although such reports exist for lizards. The seasons when the RSS is most highly hypertrophied correspond to the fall and spring mating seasons of A. piscivorous, as determined by other studies. J. Morphol., 2008. © 2007 Wiley‐Liss, Inc.
Organic and inorganic selenium speciation in environmental and biological samples by nanometer‐sized materials packed dual‐column separation/preconcentration on‐line coupled with ICP‐MS
Authors: Huang Chaozhang , Hu Bin , He Man , Duan Jiankun 
Published: November 2007

AbstractA novel, fast, and cheap nonchromatographic method for direct speciation of dissolved inorganic and organic selenium species in environmental and biological samples was developed by flow injection (FI) dual‐column preconcentration/separation on‐line coupled with ICP‐MS determination. In the developed technique, the first column packed with nanometer‐sized Al2O3 could selectively adsorb the inorganic selenium [Se(IV), Se(VI)], and the retained inorganic selenium could be eluted by 0.2 mol l−1 NaOH, while the organic Se [selenocystine (SeCys2) and selenomethionine (Se–Met)] was not retained. On the other hand, the second column packed with mesoporous TiO2 chemically modified by dimercaptosuccinic acid (DMSA) could selectively adsorb Se(IV) and SeCys2 and barely adsorb Se(VI) and Se–Met. When the sample solution was passed through the column 1, separation of inorganic selenium and organic selenium could be achieved first. Then, the effluent from column 1 was successively introduced into the column 2 and the speciation of organic selenium could be attained due to the different adsorption behaviors of Se–Met and SeCys2 on DMSA modified TiO2. After that, the eluent from column 1 contained Se(IV), and Se(VI) was adjusted to desired pH and injected into column 2, and the speciation of Se(IV) and Se(VI) could also be realized thanks to their different retention on column 2. The parameters affecting the separation were investigated systematically and the optimal separation conditions were established. The detection limits obtained for Se(IV), Se(VI), Se–Met and SeCys2 were 45–210 ng l−1 with precisions of 3.6–9.7%. The proposed method has been successfully applied for the speciation of dissolved inorganic and organic selenium in environmental and biological samples. In order to validate the methodology, the developed method was also applied to the speciation of selenium in certified reference material of SELM‐1 yeast, and the determined values were in good agreement with the certified values. Copyright © 2007 John Wiley & Sons, Ltd.
The sodium ion affinities of cytosine and its methylated derivatives
Authors: Wang Ping , Polce Michael J. , Ohanessian Gilles , Wesdemiotis Chrys 
Published: November 2007

AbstractThe sodium ion affinities of cytosine (Cyt), 5‐methylcytosine (5MeCyt) and 1‐methylcytosine (1MeCyt) have been determined by experimental and quantum chemical methods. Na+‐bound heterodimers were produced carrying one cytosine or methylated cytosine ligand (designated as C) and one peptide or amino acid reference base (designated as Pep); the Pep molecules included the peptides GlyLeu, GlyPhe, SerGly, and PheGly, and the amino acid His. The dissociation kinetics of these CNa+Pep ions were determined by collisionally activated dissociation (CAD) and converted to relative and absolute Na+ affinities via kinetic method approaches. Relative Na+ affinities increase in the order (kJ/mol): GlyLeu (0) < Cyt (3) < GlyPhe (4) < SerGly (6) < 5MeCyt (8) < PheGly (11) < 1MeCyt (13) < His (17). Anchoring the relative values of the nucleobases to the absolute affinities of the reference bases leads to absolute Na+ affinities of 214 ± 8, 219 ± 8, and 224 ± 8 kJ/mol for Cyt, 5MeCyt, and 1MeCyt, respectively. Ab initio calculations were used to confirm these results. The computed affinities of Cyt (213 kJ/mol) and 1MeCyt (217 kJ/mol) are in very good agreement with the experiments. These values unambiguously correspond to Na+ complexes with the keto form of cytosine and its methyl derivatives. Ab initio calculations on tautomerization mechanisms in the gas versus condensed phase are used to discuss why the sodiated keto isomers were formed in the present electrospray ionization (ESI) experiments, but the enol isomers in previous fast atom bombardment (FAB) experiments. Copyright © 2007 John Wiley & Sons, Ltd.
Links between circulation weather types and teleconnection patterns and their influence on precipitation patterns in Galicia (NW Spain)
Authors: Lorenzo M. N. , Taboada J. J. , Gimeno L. 
Published: November 2007

AbstractAn automated version of the Lamb weather type classification scheme was used to study the relationship between atmospheric circulation patterns and rainfall in the northwestern part of the Iberian Peninsula, which is an important area of crossing influences of the different teleconnection patterns of the Northern Hemisphere. We calculated the correlation between the most important teleconnection patterns that affect this area and the different types of weather circulation. In this area, anticyclone weather types are the most frequent in any part of the year. The frequency of occurrence of W and SW situations is also significant in autumn and winter. The correlation between weather types (WT) and teleconnection patterns showed that the North Atlantic Oscillation (NAO) index has significant correlations only in winter, while other patterns, such as the Eastern Atlantic (EA), have significant correlations in the other seasons. As a result of these correlations, the EA is a more relevant pattern than the NAO for describing the Galician climate throughout the year. We also calculated correlations between the North Hemisphere Annular Mode (NAM) and the different types of weather types. The NAM shows significant correlations throughout the year. Hence, the NAM is more relevant than the NAO, which is its local manifestation. Copyright © 2007 Royal Meteorological Society
Pharmacokinetics of isolated lung perfusion with melphalan for resectable pulmonary metastases, a phase I and extension trial
Authors: Grootenboers Marco JJ H. , Hendriks Jeroen M.H. , van Boven Wim J. , Knibbe Catherijne A.J. , van Putte Bart , Stockman Bernard , De Bruijn Ernst , Vermorken Jan B. , Van Schil Paul E.Y. , Schramel Franz MNH 
Published: November 2007

AbstractBackgroundIsolated lung perfusion (ILuP) with melphalan was performed under normo‐ and hyperthermic conditions combined with pulmonary metastasectomy for patients with resectable lung metastases. We present the results of pharmacokinetic analysis of a phase I and extension trial.MethodsTwenty‐one procedures of ILuP with melphalan were performed in the phase I trial according to a dose‐escalation schedule under normothermic and hyperthermic conditions followed by surgical resection of pulmonary metastases. In an extension trial 8 additional procedures with 15 and 45 mg melphalan were performed under hyperthermic conditions. Samples of serum, perfusate, lung, and tumor tissue were obtained.ResultsHigh perfusate concentrations of melphalan were recorded in contrast to low systemic concentrations. Marked interindividual variability was observed in melphalan concentrations in perfusate, tumor, and lung tissue. Statistically significant correlation between melphalan dose, and perfusate area under the concentration–time curve (R2 = 0.578, P = 0.001) and lung tissue concentrations (R2 = 0.459, P = 0.028) were noted. No significant correlation between melphalan dose and tumor tissue concentrations could be established.ConclusionIsolated lung perfusion effectively delivers high doses of melphalan to the lung and tumor tissues with minimal systemic levels. Significant correlation between perfused melphalan dose, perfusate area under the concentration–time curve and lung tissue melphalan concentrations were observed. J. Surg. Oncol. 2007;96:583–589. © 2007 Wiley‐Liss, Inc.
Vacuum‐assisted closure for radiation‐associated wound complications
Authors: Siegel Herrick J. , Long James L. , Watson Kevin M. , Fiveash John B. 
Published: November 2007

AbstractBackground and ObjectivesVacuum‐assisted closure (VAC) technology has proven to be effective in the management of soft tissue loss from infections, vascular insufficiency, and traumatic disorders and may have a similar benefit in the musculoskeletal oncology patient. This study reports a single institution's experience with VAC technology in the management of radiation‐associated wound complications in patients with soft tissue sarcomas.MaterialsTwenty‐two patients treated with both surgical intervention and radiation therapy developed either superficial or deep wound complications that were managed with the VAC device. This study group was compared to a retrospectively identified comparison group of 19 patients, in which the VAC device was not used.ResultsHospital stay (P < 0.025), length of overall treatment (P < 0.025), number of operative debridements (P < 0.05) and success of wound closure without the need for soft tissue transposition (P < 0.01) was found to be significantly less in the study groups as compared to those not treated with the VAC device.ConclusionVAC technology appears to be safe and effective in the treatment of radiation‐associated wound complications. J. Surg. Oncol. 2007;96:575–582. © 2007 Wiley‐Liss, Inc.
Actively Q-switched all-fiber lasers
Authors: Andrés M V , Cruz J L , Díez A , Pérez-Millán P , Delgado-Pinar M 
Published: November 2007

Q-switching of fiber lasers using bulk elements has important drawbacks as reduced mechanical stability and high insertion losses. The development of efficient all-fiber modulation techniques is the key to obtain robust, compact and efficient Q-switched all-fiber lasers.
Certainly, the development of fiber Bragg gratings (FBG) has been crucial to make progress on fiber lasers. FBGs permit a simple way to assemble all-fiber laser cavities and can be written in the active fiber itself. The Q-factor of this type of cavities is determined by the reflectivity of the FBGs and the losses of the fiber. Here, we focus on the use of magnetostrictive materials and the acousto-optic interaction to develop efficient Q-factor modulators. Most of these modulators include an FBG and take advantage of the specific interaction of the magnetostrictive materials or the acoustic wave with the FBG itself.
Fiber optic technologies permit the development of a rather unique type of fiber lasers, i.e., actively Q-switched distributed feedback (DFB) fiber lasers. In this case, both the use of magnetostrictive materials and the acousto-optic interaction permit the generation of dynamic defects in an FBG that has been previously written in a highly Er-doped fiber.
Understanding and assessing land degradation—comments on research in Chuquisaca, Bolivia
Authors: Preston D. A. 
Published: November 2007

AbstractA recent paper in this journal offers observations and research findings on apparent land degradation in three areas of the Andean valleys in the Department of Chuquisaca, Bolivia. It is suggested that the evidence of an increase in degradation during the past 40 years is unconvincing and a possible link with population increase is inconclusive. The landscape is naturally one where land degradation is frequently visible, sometimes catastrophic, and widespread, whatever the use of natural resources by humans. The paper is potentially valuable for its use of data based on farmer consultation but fails to recognise that farming is only one of many activities for rural households. Copyright © 2007 John Wiley & Sons, Ltd.
p53 regulates FAK expression in human tumor cells
Authors: Golubovskaya Vita M. , Finch Richard , Kweh Frederick , Massoll Nicole A. , Campbell‐Thompson Martha , Wallace Margaret R. , Cance William G. 
Published: November 2007

AbstractAttenuation of the p53 protein is one of the most common abnormalities in human tumors. Another important marker of tumorigenesis is focal adhesion kinase (FAK), a 125‐kDa tyrosine kinase that is overexpressed at the mRNA and protein levels in a variety of human tumors. FAK is a critical regulator of adhesion, motility, metastasis, and survival signaling. We have characterized the FAK promoter and demonstrated that p53 can inhibit the FAK promoter activity in vitro. In the present study, we showed that p53 can bind the FAK promoter‐chromatin region in vivo by chromatin immunoprecipitation (ChIP) assay. Furthermore, we demonstrated down‐regulation of FAK mRNA and protein levels by adenoviral overexpression of p53. We introduced plasmids with different mutations in the DNA‐binding domain of p53 (R175H, p53 R248W and R273H) into HCTp53−/− cells and showed that these mutations of p53 did not bind FAK promoter and did not inhibit FAK promoter activity, unlike wild type p53. We analyzed primary breast and colon cancers for p53 mutations and FAK expression, and showed that FAK expression was increased in tumors containing mutations of p53 compared to tumors with wild type p53. In addition, tumor‐derived missense mutations in the DNA‐binding domain (R282, R249, and V173) also led to increased FAK promoter activity. Thus, the present data show that p53 can regulate FAK expression during tumorigenesis. © 2007 Wiley‐Liss, Inc.
Global existence for a contact problem with adhesion
Authors: Bonetti Elena , Bonfanti Giovanna , Rossi Riccarda 
Published: November 2007

AbstractIn this paper, we analyze a contact problem with irreversible adhesion between a viscoelastic body and a rigid support. On the basis of Frémond's theory, we detail the derivation of the model and of the resulting partial differential equation system. Hence, we prove the existence of global in time solutions (to a suitable variational formulation) of the related Cauchy problem by means of an approximation procedure, combined with monotonicity and compactness tools, and with a prolongation argument. In fact the approximate problem (for which we prove a local well‐posedness result) models a contact phenomenon in which the occurrence of repulsive dynamics is allowed for. We also show local uniqueness of the solutions, and a continuous dependence result under some additional assumptions. Copyright © 2007 John Wiley & Sons, Ltd.
Human mitochondrial transfer RNAs: Role of pathogenic mutation in disease
Authors: Scaglia Fernando , Wong Lee‐Jun C. 
Published: November 2007

AbstractThe human mitochondrial genome encodes 13 proteins. All are subunits of the respiratory chain complexes involved in energy metabolism. These proteins are translated by a set of 22 mitochondrial transfer RNAs (tRNAs) that are required for codon reading. Human mitochondrial tRNA genes are hotspots for pathogenic mutations and have attracted interest over the last two decades with the rapid discovery of point mutations associated with a vast array of neuromuscular disorders and diverse clinical phenotypes. In this review, we use a scoring system to determine the pathogenicity of the mutations and summarize the current knowledge of structure–function relationships of these mutant tRNAs. We also provide readers with an overview of a large variety of mechanisms by which mutations may affect the mitochondrial translation machinery and cause disease. Muscle Nerve, 2007
Bottomhole assembly analysis by finite difference differential method
Authors: Yang Dongquan , Rahman M. K. , Chen Yibai 
Published: November 2007

AbstractThis paper presents a three‐dimensional finite difference differential method for bottomhole assembly (BHA) analysis under static loads. The analysis is required to optimize the BHA configurations for drilling directional boreholes in the petroleum industry. The optimization of BHA configurations ensures the controlled cruising of the drill bit to drill the hole along a planned trajectory. The model incorporates the contact response between drillstring and wellbore wall, the upper tangent point problem, stabilizer configurations, bent sub model and other considerations for numerical solutions. The overall formulations are presented in a matrix format within convenient coordinate systems developing a transformation matrix. Key solution algorithms for computer programming are then described in detail. One analytical solution for beams under weight and torque is used to verify the method. Also the analytical solutions of three other simple BHA configurations are used for verification. The verified method is then applied in a series of parametric investigations to characterize the responses of typical BHAs. The BHA responses studied include the side force at bit and lateral deformation of the assembly along its length with varying weights on bit and hole inclination angles for typical building, dropping and holding assemblies. BHAs with bent sub are analyzed with various tool face angles and bent angles. The effect of wellbore curvature on side forces is also demonstrated. Copyright © 2007 John Wiley & Sons, Ltd.