bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast Prediction of Cytochrome P450 Mediated Drug Metabolism
Authors: Rydberg Patrik , Vasanthanathan Poongavanam , Oostenbrink Chris , Olsen Lars 
Published: October 2009

AbstractCytochrome P450 mediated metabolism of drugs is one of the major determinants of their kinetic profile, and prediction of this metabolism is therefore highly relevant during the drug discovery and development process. A new rule‐based method, based on results from density functional theory calculations, for predicting activation energies for aliphatic and aromatic oxidations by cytochromes P450 is developed and compared with several other methods. Although the applicability of the method is currently limited to a subset of P450 reactions, these reactions describe more than 90 % of the metabolites. The rules employed are relatively few and general, and when combined with solvent‐accessible surface area calculations to account for steric accessibility, the method gives a major P450 metabolite as first‐ranked position for 75 % of the substrates, and ranked in the top three for 90 % of substrates for a set of 20 substrates. In combination with docking, it can predict isoform‐specific metabolism, and we apply this on CYP1A2 with very good results on 81 substrates, for which we find a major metabolite ranked in the top three for 90 % of the substrates (100 % in the training set and 87 % in the larger test set).
Inflammatory myofibroblastic tumors in childhood
Authors: Alaggio Rita , Cecchetto Giovanni , Bisogno Gianni , Gambini Claudio , Calabrò Maria Luisa , Inserra Alessandro , Boldrini Renata , De Salvo Gian Luca , G. d'Amore Emanuele S. , Dall'Igna Patrizia 
Published: October 2009

AbstractBACKGROUND:Inflammatory myofibroblastic tumors (IMTs) are myofibroblastic lesions with unpredictable biologic behavior that occur at a young age. For this report, the authors investigated clinicopathologic features in a series of pediatric IMTs. The objective of the study was to identify morphologic or immunohistochemical prognostic markers and the possible pathogenic role of human herpes virus 8 (HHV‐8).METHODS:Twenty‐six patients were observed over a period of 18 years. Clinical/histologic data were reviewed, and immunohistochemical/molecular studies were performed.RESULTS:Patients ages 8‒216 months (median age, 60 months) presented with tumors of the lung‐bronchus (8 patients), abdomen (17 patients), and thoracic wall (1 patient). Twenty‐one patients underwent complete excision, and microscopic or macroscopic residual disease was present in 5 of those patients. Chemotherapy was received by 5 patients. After a median follow‐up of 6.6 years, 24 patients were in complete remission, and 2 patients had died of disease. Local recurrences were observed in 6 patients (including 4 recurrences that occurred after a complete excision). Cytologic atypia, low inflammatory infiltrate, and a rich myxoid pattern were detected in patients who had recurrent disease or a poor prognosis. Anaplastic lymphoma kinase (ALK) was positive in 7 patients (including 2 patients with recurrent disease). No correlation between clusterin expression and prognosis was demonstrated. HHV‐8 was identified in 1 pulmonary IMT.CONCLUSIONS:IMTs are locally aggressive lesions. In this series, the local recurrence rate was 23%, and the 5‐year and 10‐year event‐free survival rates were 87.4% and 72.8%, respectively. The results indicated that the treatment of choice is a complete, nonmutilating excision; chemotherapy may be given to patients who have microscopic or macroscopic residual disease, although the results are controversial; cytologic atypia and positive ALK status are more frequent in aggressive tumors, whereas metastatic tumors are negative for ALK; and HHV8 is not involved in the pathogenesis of IMT. Cancer 2010. © 2010 American Cancer Society.
Mesh dependence and slip complexity in earthquake fault models
Authors: Olsen‐Kettle L. M. , Mühlhaus H. B. 
Published: October 2009

AbstractWe study the origins of mesh dependence in earthquake dynamics and show that mesh sensitivity in numerical models of earthquake rupture can unearth new, exciting physical phenomena, and provide hidden clues to discovering the physics underlying earthquake complexity. We show (in agreement with previous numerical studies of dynamic rupture at faults) that coarse meshes or discrete models produce more interesting physics because these numerical simulations produce richer spatio‐temporal complexity at faults over multiple earthquake cycles. These discrete models are desirable as they reproduce the observed Gutenberg–Richter power‐law frequency magnitude distribution of earthquakes more accurately. However, this complexity is lost as the mesh size is refined, which is undersirable from a physical point of view. We investigate this mesh sensitivity by analysing the higher‐order perturbative terms introduced into numerical models with coarse meshes. The introduction of these higher‐order, nonlinear terms into standard continuum models generally used to describe earthquake dynamics may provide a key to reproducing earthquake complexity while partially removing the associated mesh dependence without the need to modify the underlying mesh. This is a first step towards deriving a physical law capable of reproducing the scale‐invariant behaviour in earthquake sizes and reconciling continuum and discrete models of earthquake rupture. Copyright © 2009 John Wiley & Sons, Ltd.
Stromal vascular progenitors in adult human adipose tissue
Authors: Zimmerlin Ludovic , Donnenberg Vera S. , Pfeifer Melanie E. , Meyer E. Michael , Péault Bruno , Rubin J. Peter , Donnenberg Albert D. 
Published: October 2009

AbstractThe in vivo progenitor of culture‐expanded mesenchymal‐like adipose‐derived stem cells (ADSC) remains elusive, owing in part to the complex organization of stromal cells surrounding the small vessels, and the rapidity with which adipose stromal vascular cells adopt a mesenchymal phenotype in vitro. Immunohistostaining of intact adipose tissue was used to identify three markers (CD31, CD34, and CD146), which together unambiguously discriminate histologically distinct inner and outer rings of vessel‐associated stromal cells, as well as capillary and small vessel endothelial cells. These markers were used in multiparameter flow cytometry in conjunction with stem/progenitor markers (CD90 and CD117) to further characterize stromal vascular fraction (SVF) subpopulations. Two mesenchymal and two endothelial populations were isolated by high speed flow cytometric sorting, expanded in short term culture, and tested for adipogenesis. The inner layer of stromal cells in contact with small vessel endothelium (pericytes) was CD146+/α‐SMA+/CD90±/CD34−/CD31−; the outer adventitial stromal ring (designated supra adventitial‐adipose stromal cells, SA‐ASC) was CD146−/α‐SMA−/CD90+/CD34+/CD31−. Capillary endothelial cells were CD31+/CD34+/CD90+ (endothelial progenitor), whereas small vessel endothelium was CD31+/CD34−/CD90− (endothelial mature). Flow cytometry confirmed these expression patterns and revealed a CD146+/CD90+/CD34+/CD31− pericyte subset that may be transitional between pericytes and SA‐ASC. Pericytes had the most potent adipogenic potential, followed by the more numerous SA‐ASC. Endothelial populations had significantly reduced adipogenic potential compared with unsorted expanded SVF cells. In adipose tissue, perivascular stromal cells are organized in two discrete layers, the innermost consisting of CD146+/CD34− pericytes, and the outermost of CD146−/CD34+ SA‐ASC, both of which have adipogenic potential in culture. A CD146+/CD34+ subset detected by flow cytometry at low frequency suggests a population transitional between pericytes and SA‐ASC. © 2009 International Society for Advancement of Cytometry
Development of small and inexpensive digital data acquisition systems using a microcontroller‐based approach
Authors: Naivar Mark A. , Wilder Mark E. , Habbersett Robert C. , Woods Travis A. , Sebba David S. , Nolan John P. , Graves Steven W. 
Published: October 2009

AbstractFully digital data acquisition systems for use in flow cytometry provide excellent flexibility and precision. Here, we demonstrate the development of a low cost, small, and low power digital flow cytometry data acquisition system using a single microcontroller chip with an integrated analog to digital converter (ADC). Our demonstration system uses a commercially available evaluation board making the system simple to integrate into a flow cytometer. We have evaluated this system using calibration microspheres analyzed on commercial, slow‐flow, and CCD‐based flow cytometers. In our evaluations, our demonstration data system clearly resolves all eight peaks of a Rainbow microsphere set on both a slow‐flow flow cytometer and a retrofitted BD FACScalibur, which indicates it has the sensitivity and resolution required for most flow cytometry applications. It is also capable of millisecond time resolution, full waveform collection, and selective triggering of data collection from a CCD camera. The capability of our demonstration system suggests that the use of microcontrollers for flow cytometry digital data‐acquisition will be increasingly valuable for extending the life of older cytometers and provides a compelling data‐system design approach for low‐cost, portable flow cytometers. © 2009 International Society for Advancement of Cytometry.
Structural Elucidation of tmeda‐Solvated Alkali Metal Diphenylamide Complexes
Authors: Kennedy Alan R. , Klett Jan , O'Hara Charles T. , Mulvey Robert E. , Robertson Gemma M. 
Published: October 2009

AbstractLithium, sodium and potassium salts of diphenylamine have been prepared by using a deprotonative route and characterised in both, solid state (by X‐ray crystallography) and solution (by NMR spectroscopic studies). In each case the metal atom's coordination sphere is completed by coordination to the synthetically important co‐ligand N,N,N′,N′‐tetramethylethylenediamine (tmeda). Complexes 1 and 2 [{(tmeda)M(NPh2)}2] (M = Li for 1, Na for 2) can be prepared by treating 1 mol.‐equiv. of the parent amine with an equimolar quantity of nBuM and tmeda in hexane solution. In the solid state, 1 and 2 are essentially isostructural, being dimeric with a four‐atom M–N–M–N framework. The coordination sphere of each M atom is completed by a bidentate tmeda molecule. Complex 3 [{(tmeda)3/2K(NPh2)}2] has been prepared in a similar way to 1 and 2 except that benzylpotassium has been utilised as the metallating agent. In addition, 4 mol‐equiv. of tmeda is required to fully solubilise the heavy alkali metal amide mixture. In the solid state, 3 exists as a polymeric array of dinuclear K–N–K–N rings. Akin to 1 and 2, the K atom is coordinated to a bidentate tmeda molecule; however, each K atom is also bound to another tmeda molecule that acts as a monodentate bridge, thus producing the coordination polymer. Crystalline 1 and 2 are soluble in C6D6; hence, NMR spectroscopic studies could be performed. These show that the solid‐state structure appears to stay intact in arene solution. On the other hand, 3 is not soluble in C6D6; so solution studies have been performed in [D8]thf. These studies reveal that 3 readily looses tmeda during in‐vacuo isolation. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)
Bis(oxazolinylmethyl) Derivatives of C4H4E Heterocycles (E = NH, O, S) as C2‐Chiral Meridionally Coordinating Ligands for Nickel and Chromium
Authors: Konrad Felix , Lloret Fillol Julio , Rettenmeier Christoph , Wadepohl Hubert , Gade Lutz H. 
Published: October 2009

AbstractThe synthesis of the three ligands employed in this study is based on the condensation of two molar equivalents of (S)‐valinol with the diester precursors pyrrole‐2,5‐bis(ethyl)acetate (2a), furan‐2,5‐bis(ethyl)acetate (2b) and thiophene‐2,5‐bis(ethyl)acetate (2c). This gave the corresponding bis(oxazolinylmethyl)pyrrole (iPrLNH, 4a), bis(oxazolinylmethyl)furan (iPrLO, 4b) and bis(oxazolinylmethyl)thiophene (iPrLS, 4c) ligands. Stirring 4a in MeOD at ambient temperature in the presence of a catalytic amount of acetic acid (1 mol‐%) led to complete hydrogen/deuterium exchange in the two bridging methylene groups of the ligand. This behaviour is explained by an acetate‐mediated reversible proton transfer between the oxazoline N atom and the methylene bridge, a conjecture which was supported by a DFT study of the process. Deprotonation of iPrLNH (4a) with tBuLi at –78 °C and subsequent stirring with NiCl2 yielded the square planar nickel(II) complex [Ni(iPrLN)Cl] (5). However, on stirring iPrLNH (4a) with nickel acetate in methanol, a deep red nickel acetato complex [Ni(iso‐iPrLN)(OAc)] (6) bearing the isomerized tridentate pincer ligand was obtained. Reaction of acetato complex 6 with Me3SiCl in dichloromethane cleanly gave the corresponding chlorido complex [Ni(iso‐iPrLN)Cl] (7), which is the isomer of compound 5. The intraligand rearrangement was explained by acetate‐mediated proton transfer between the methylene bridges and the 3/4‐positions of the pyrrole ring, the computed thermodynamic driving force being ΔG = –9.8 kcal mol–1. Neither thiophene derivative 4c nor furan‐derived ligand 4b gave robust, isolable complexes with nickel(II). However, reaction of iPrLO (4b) with [CrCl3(thf)3] in thf yielded the yellow‐green complex [CrCl3(iPrLO)] (8), whereas no complexation occurred with the analogous thiophene‐derived bisoxazoline 4c. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)
What's in a name? Classifying ‘the dropout’ from treatment for anorexia nervosa
Authors: Sly Richard 
Published: October 2009

AbstractTreatment drop‐out rates for anorexia nervosa (AN) are notoriously high, and have remained so over the course of time, and across different treatment settings and modalities. The outcome for such patients is frequently poor. Despite the prevalence of this problem, there is little quality evidence as to why this is the case, and what the predictors of drop‐out are. Methodological uniformity has been called for in order to develop a cohesive literature in this field, and this paper argues that we must also reflect upon how our labelling of ‘the dropout’ has shaped what we have examined to date, and how that has in turn led to a weak evidence base. A new, less pejorative term for those who do not complete treatment is needed to reflect the direction research in this area needs to take. Copyright © 2009 John Wiley & Sons, Ltd and Eating Disorders Association.
Wide‐area time‐delay robust damping control for power system
Authors: Qi Jun , Jiang Quanyuan , Wang Guangzeng , Cao Yijia 
Published: October 2009

AbstractThis paper presents time‐delay robust damping control for inter‐area oscillation in power system by using remote signals from wide‐area measurement system (WAMS). To ensure satisfactory performance, variations of operating condition and time delay are considered. Design of damping controller is formulated as time‐delay output‐feedback control problem. Time‐delay power system model is constructed by system identification and Pade approximation. Based on the time‐delay system model, robust damping controller is designed employing mixed‐sensitivity H∞ control theory and pole placement approach in the linear matrix inequality (LMI) framework. This method is applied to design damping controller for prototype power system reinforced with static var compensator (SVC). Damping performance of the controller is examined in the frequency and time domains for various operating scenarios. The controller is found to be effective in damping inter‐area oscillation and robust to variations of operating condition and time delay. Copyright © 2008 John Wiley & Sons, Ltd.
Large eddy simulation of bluff body wake in planar shear flow
Authors: Lankadasu A. , Vengadesan S. 
Published: October 2009

AbstractLarge eddy simulation of planar shear flow past a square cylinder has been investigated. Dynamic Smagorinsky model has been used to model subgrid scale stress. The shear parameter, K, namely the nondimensional streamwise velocity gradient in the lateral direction, is 0.0, 0.1 and 0.2. Reynolds number based on the centerline velocity is fixed at Re=21400. The time and span‐averaged velocity components, pressure coefficient, Reynolds stresses for uniform are in good agreement with the literature. In shear flow the calculated flow structure and mean velocity components are shown to be markedly different from those of the uniform flow. With increasing shear parameter, the cylinder wake is dominated by clockwise vortices. Both the velocity components in shear flow are compared with respective components in uniform flow. Comparison of normal and shear stresses between shear and no shear case have also been presented. Copyright © 2009 John Wiley & Sons, Ltd.
Regional impact of field strength on voxel‐based morphometry results
Authors: Tardif Christine L. , Collins D. Louis , Pike G. Bruce 
Published: October 2009

AbstractThe objective of this study was to characterize the sensitivity of voxel‐based morphometry (VBM) results to choice field strength. We chose to investigate the two most widespread acquisition sequences for VBM, FLASH and MP‐RAGE, at 1.5 and 3 T. We first evaluated image quality of the four acquisition protocols in terms of SNR and image uniformity. We then performed a VBM study on eight subjects scanned twice using the four protocols to evaluate differences in grey matter (GM) density and corresponding scan‐rescan variability, and a power analysis for each protocol in the context a longitudinal and cross‐sectional VBM study. As expected, the SNR increased significantly at 3 T for both FLASH and MP‐RAGE. Image non‐uniformity increased as well, in particular for MP‐RAGE. The differences in CNR and contrast non‐uniformity cause regional biases between protocols in the VBM results, in particular between sequences at 3 T. The power analysis results show an overall decrease in the number of subjects required in a longitudinal study to detect a difference in GM density at 3 T for MP‐RAGE, but an increase for FLASH. The number of subjects required in a cross‐sectional VBM study is higher at 3 T for both sequences. Our results show that each protocol has a distinct regional sensitivity pattern to morphometric change, which goes against the classical view of VBM as an unbiased whole brain analysis technique, complicates the combination of data within a VBM study and the direct comparison of VBM studies based on different protocols. Hum Brain Mapp, 2010. © 2009 Wiley‐Liss, Inc.
Bulk and supported tungstophosphoric acid as friendly, efficient, recyclable catalysts for the synthesis of bis‐indolylmethanes under solvent‐free conditions
Authors: Aliyan Hamid , Fazaeli Razieh , Naghash Hamid Javaherian , Massah Ahmad Reza , Momeni Ahmad Reza , Iravani Zohreh 
Published: October 2009

AbstractThe treatment of indole with structurally diverse aldehydes in the presence of catalytic amount of inorganic‐supported polyoxometalates, heterogeneous, reusable and efficient catalysts at room temperature gave the corresponding bis‐indolylmethanes in excellent yields and shorter reaction times under solvent‐free conditions. The catalyst can be reused for several times, but it will be less active. © 2009 Wiley Periodicals, Inc. Heteroatom Chem 20:325–331, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.20554
New tin(IV) complexes with sterically hindered o‐iminobenzoquinone ligand: Synthesis and structure
Authors: Piskunov Alexandr V. , Mescheryakova Irina N. , Fukin Georgii K. , Bogomyakov Artyem S. , Romanenko Galina V. , Cherkasov Vladimir K. , Abakumov Gleb A. 
Published: October 2009

AbstractThe reduction of 4,6‐di‐tert‐butyl‐N‐(2, 6‐di‐iso‐propylphenyl)‐o‐iminobenzoquinone (imQ) by tin amalgam in hexane solution leads to new six‐coordinated o‐iminoquinonato tin(IV) complex (iSQ)2SnAP (1) (where iSQ and AP are o‐iminosemiquinolate and dianion o‐amidophenolate, respectively). Variable temperature magnetic susceptibility measurements of 1 have shown that this complex possesses a weak ferromagnetic exchange between o‐iminosemiquinonate ligands. The oxidation of 1 with air oxygen produces new o‐iminoquinonolate tin(IV) derivatives [(iSQ)Sn(AP)]2O (2) and (iSQ)2Sn(OH)2 (3) containing μ‐oxo‐ and hydroxo‐ligands, respectively. The electronic structure of 1 was examined by DFT analysis. Complexes 1–3 have been investigated using single‐crystal X‐ray diffraction. © 2009 Wiley Periodicals, Inc. Heteroatom Chem 20:332–340, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.20555
Microwave‐mediated pyrazole fluorinations using selectfluor®
Authors: Sloop Joseph C. , Jackson James L. , Schmidt Robert D. 
Published: October 2009

AbstractMicrowave‐mediated electrophilic fluorinations and a new single‐pot condensation en route to ring‐fluorinated pyrazoles were examined:
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The monofluorination by these methods was successful for a variety of pyrazoles, with yields ranging from 13% to 75%. While electrophilic aromatic fluorination of 3‐CF3 pyrazoles proved largely ineffective, development of a single‐pot process overcame this limitation. The microwave‐mediated reaction is regioselective; ring fluorination of the heterocycle occurs preferentially over phenyl and alkyl substituents. Alkyl side chain fluorination, when desired, can be modulated by reactant ratios. The single‐pot method, which involves acid catalysis by H‐TEDA, produces 4‐fluoropyrazoles products. © 2009 Wiley Periodicals, Inc. Heteroatom Chem 20:341–345, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.20556
Empirical and policy performance of a forward‐looking monetary model
Authors: Onatski Alexei , Williams Noah 
Published: October 2009

AbstractIn this paper we consider the implications of a fully specified dynamic general equilibrium model, developed by Smets and Wouters (2003). This is a relatively large‐scale forward‐looking model, which was shown to provide a good fit to the data. We show that systematically accounting for prior uncertainty may lead to substantially different parameter estimates. However many of the qualitative features of the model remain similar under the alternative estimates that we find. We then formulate and analyze optimal policy rules in the model, focusing on a simple loss function which is commonly used and is independent of the estimates. We determine the optimal equilibrium dynamics for our estimates as well as those of Smets and Wouters, and find that they imply largely similar behavior. We then analyze simple policy rules, finding that these rules perform relatively well and are robust to our different sets of parameter estimates. Overall, our results suggest that the model may be relatively robust in its ability to capture certain aspects of the data. However some caution should be exercised in basing inference on the structural estimates, as these seem to be only weakly identified. Copyright © 2009 John Wiley & Sons, Ltd.