bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards inference of a biochemical ontology from a metabolic database
Authors: McShan D. C. 
Published: February 2006

AbstractIn order to predict the metabolic fate of an arbitrary compound based solely on structure, it is useful to be able to identify substructural ‘functional groups’ that are biochemically reactive. These functional groups are the substructural elements that can be removed and replaced to transform one compound into another. This problem of identifying functional groups is related to the problem of classifying compounds. The research presented here discusses the state of the art in biochemical databases and how these sources may be applied to the problem of classifying compounds based solely on structure. We describe a biochemical informatics system for processing molecular data and describe how 100 255 compositional (hasA) relationships are inferred between 835 abstractions and 9500 metabolites from the KEGG Ligand database. Specifically, we focus on the identification of amino acids and consider ways in which the inference of biochemical ontologies for metabolites will be improved in the future. Copyright © 2006 John Wiley & Sons, Ltd.
From Diphosphane to Diphosphodiide Gold(III) Derivatives of 1,2‐Diphosphinobenzene
Authors: Blanco M. Carmen , Fernández Eduardo J. , Olmos M. Elena , Pérez Javier , Laguna Antonio 
Published: February 2006

AbstractTreatment of 1,2‐diphosphinobenzene with [Au(C6F5)3(tht)] leads to the diphosphane derivative [{Au(C6F5)3}(1,2‐PH2C6H4PH2)] (1), which further reacts with other pentafluorophenylgold(III) reagents in the presence of acetylacetonate as deprotonating agent to afford phosphane–phosphide complexes. The noncyclic PPN[{Au(C6F5)3}2(1,2‐PHC6H4PH2)] (2; PPN=bis(triphenylphosphine)iminium) has been shown to be a useful starting material for the synthesis of higher nuclearity cyclic or noncyclic diphosphide or even diphosphodiide derivatives through similar reactions. The crystal structures of the trinuclear anionic NBu4[{Au(C6F5)3}(1,2‐PHC6H4PH){Au(C6F5)2Cl}{μ‐Au(C6F5)2}] (3) and the hexanuclear [{Au(C6F5)3}(1,2‐PC6H4P){Au(C6F5)3}{μ‐M(dppe)M}2] (M=Au (12), Ag (13)) have been established by X‐ray diffraction methods, the last complexes having a bicyclic ring containing three intramolecular interactions between the MI centres.
Electrochromic Films Composed of MnO2 Nanosheets with Controlled Optical Density and High Coloration Efficiency.
Authors: Sakai Nobuyuki , Ebina Yasuo , Takada Kazunori , Sasaki Takayoshi 
Published: February 2006

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Regioselective One‐Pot Synthesis of 3,5‐Diarylpyrazoles.
Authors: Lokhande P. D. , Waghamare B. Y. , Sakate S. S. 
Published: February 2006

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Thienopyrimidines as Hetryl Moiety in 2‐Azetidinones: Synthesis of 4‐Hetryl‐2‐azetidinones.
Authors: Kanwar Seema , Sharma S. D. 
Published: February 2006

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Clinical outcomes of single‐fraction stereotactic radiation therapy of lung tumors
Authors: Hara Ryusuke , Itami Jun , Kondo Tatsuya , Aruga Takashi , Uno Takashi , Sasano Nakashi , Ohnishi Kayoko , Kiyozuka Makoto , Fuse Masashi , Ito Masashi , Naoi Kuniji , Kohno Yuzuru 
Published: February 2006

AbstractBACKGROUNDThe objective of the current study was to investigate the effects and the morbidities of single‐fraction stereotactic radiation therapy (SRT) for lung tumors.METHODSA Microtron device was modified to deliver stereotactic irradiation under respiratory gating. Between August 1998 and December 2004, 59 malignant lung tumors (11 primary tumors, 48 metastases) that measured < 40 mm in greatest dimension were treated by single‐fraction SRT. Nine tumors received a minimal dose of < 30 grays (Gy), and 50 tumors received a minimal dose of ≥ 30 Gy. The macroscopic target volume ranged from 1 cc to 19 cc (mean, 5 cc).RESULTSThe 1‐year and 2‐year local progression‐free rates (LPFRs) were 93% and 78%, respectively. The overall survival rate was 76.5% at 1 year and 41% at 2 years. Local regrowth of the irradiated tumor was a direct cause of death in two patients. Only the minimal radiation dose to the reference target volume tended to have an influence on the LPFR (P = 0.068). The 2‐year LPFRs for patients who received irradiation doses of ≥ 30 Gy and < 30 Gy were 83% and 52%, respectively. With regard to morbidities, Grade 3 respiratory symptoms (according to the Radiation Therapy Oncology Group/European Organization for Research and Treatment of Cancer late radiation morbidity scoring scheme) were noted in one patient.CONCLUSIONSThe results from the current study suggested that single‐fraction SRT was tolerable and was capable of attaining excellent local control in patients who had malignant lung tumors that measured < 4 cm in greatest dimension. Cancer 2006. © 2006 American Cancer Society.
Iterative restaining as a pivotal tool for n‐color immunophenotyping by slide‐based cytometry
Authors: Laffers Wiebke , Mittag Anja , Lenz Dominik , Tárnok Attila , Gerstner Andreas O. H. 
Published: February 2006

AbstractAimSlide‐based cytometry (SBC) allows to “ask a cell a second time.” We used this tool for detailed immunophenotyping of peripheral blood leukocytes (PBLs).MethodsPBLs primarily stained for CD‐markers and DNA were immobilized on a glass slide and analyzed by laser scanning cytometry. Then, iterative restaining was applied for a second and a third analysis. Based on the cells' fixed location, analyses were merged on a single‐cell level.ResultsWe analyzed six virtual immunostainings by “recycling” the PE‐channel for four CD‐markers.ConclusionIterative restaining might prove to be a pivotal tool for n‐color immunophenotyping exclusive to SBC concepts. © 2006 International Society for Analytical Cytology
A new method to quantify phagocytosis and intracellular degradation using green fluorescent protein‐labeled Escherichia coli: Comparison of cord blood macrophages and peripheral blood macrophages of healthy adults
Authors: Gille Christian , Spring Baerbel , Tewes Lena , Poets Christian F. , Orlikowsky Thorsten 
Published: February 2006

AbstractInteractions between innate and adaptive immune functions in neonatal macrophages (MΦ) are still unclear. We therefore established a method to quantify bacterial phagocytosis and intracellular degradation, using green fluorescent protein (GFP)‐labeled Escherichia coli in combination with phenotypic analysis. The kinetics of the proportion of phagocyting MΦ, phagocytosed bacteria per MΦ, and bacterial degradation were comparable for cord blood MΦ of term neonates and MΦ of healthy adults. Phenotyping revealed CD14 and CD16 to be down‐modulated within minutes. GFP‐labeled E. coli may be useful tools to further study MΦ subpopulations and determinants of phagocytosis in cord blood MΦ. © 2006 International Society for Analytical Cytology
Proteasome inhibitor‐induced apoptosis in human monocyte‐derived dendritic cells
Authors: Nencioni Alessio , Garuti Anna , Schwarzenberg Karin , Cirmena Gabriella , Dal Bello Giovanna , Rocco Ilaria , Barbieri Eleonora , Brossart Peter , Patrone Franco , Ballestrero Alberto 
Published: February 2006

AbstractProteasome inhibitors possess potent antitumor activity against a broad spectrum of human malignancies. However, the effects of these compounds on the immune system still have to be clearly determined. In the present study, we have investigated the effects of proteasome inhibitors on dendritic cells (DC), antigen‐presenting cells playing a key role in the initiation of immune responses. Exposure to the proteasome inhibitors bortezomib, MG132 or epoxomicin was found to promote apoptosis of human monocyte‐derived DC and to reduce the yield of viable DC when given to monocytes early during differentiation to DC. DC apoptosis via proteasome inhibition was accompanied by mitochondria disruption and subsequent activation of the caspase cascade. Up‐regulation and intracellular redistribution of Bcl‐2‐associated X protein (Bax), a pro‐apoptotic Bcl‐2 family protein, were observed in DC treated with these compounds and represent a suitable mechanism leading to activation of the intrinsic apoptotic pathway. Finally, active protein synthesis was found to represent an upstream prerequisite for DC apoptosis induced by proteasome inhibitors, since the translation inhibitor cycloheximide blocked all of the steps of the observed apoptotic response. In conclusion, induction of apoptosis in DC may represent a novel mechanism by which proteasome inhibitors affect the immune response at the antigen‐presenting cell level.
Pertussis toxin as an adjuvant suppresses the number and function of CD4+CD25+ T regulatory cells
Authors: Chen Xin , Winkler‐Pickett Robin T. , Carbonetti Nicholas H. , Ortaldo John R. , Oppenheim Joost J. , Howard O. M. Zack 
Published: February 2006

AbstractWe observed a remarkable reduction in the frequency and immunosuppressive activity of splenic CD4+CD25+ T cells in C57BL/6 mice with MOG33–55‐induced experimental autoimmune encephalomyelitis (EAE). Our study revealed that pertussis toxin (PTx), one component of the immunogen used to induce murine EAE, was responsible for down‐regulating splenic CD4+CD25+ cells. Treatment of normal BALB/c mice with PTx in vivo reduced the frequency, suppressive activity and FoxP3 expression by splenic CD4+CD25+ T cells. However, PTx treatment did not alter the expression of characteristic phenotypic markers (CD45RB, CD103, GITR and CTLA‐4) and did not increase the expression of CD44 and CD69 by the residual splenic and lymph node CD4+CD25+ T cells. This property of PTx was attributable to its ADP‐ribosyltransferase activity. PTx did not inhibit suppressive activity of purified CD4+CD25+ T regulatory (Treg) cells in vitro, but did so in vivo, presumably due to an indirect effect. Although the exact molecular target of PTx that reduces Treg activity remains to be defined, our data suggests that alteration of both distribution and function of splenic immunocytes should play a role. This study concludes that an underlying cause for the immunological adjuvanticity of PTx is down‐regulation of Treg cell number and function.
Alternative activation deprives macrophages of a coordinated defense program to Mycobacterium tuberculosis
Authors: Kahnert Antje , Seiler Peter , Stein Maik , Bandermann Silke , Hahnke Karin , Mollenkopf Hans , Kaufmann Stefan H. E. 
Published: February 2006

AbstractA potent Th1 immune response is critical to the control of tuberculosis. The impact of an additive Th2 response on the course of disease has so far been insufficiently characterized, despite increased morbidity after co‐infection with Mycobacterium tuberculosis and Th2‐eliciting helminths and possible involvement of Th2 polarization in reactivation of latent tuberculosis. Here, we describe the gene expression profile of murine bone marrow‐derived macrophages alternatively activated by IL‐4 in response to infection with M. tuberculosis. Comparison of transcriptional profiles of infected IL‐4‐ and IFN‐γ‐activated macrophages revealed delayed and partially diminished responses to intracellular bacteria in alternatively activated macrophages, characterized by reduced exposure to nitrosative stress and increased iron availability, respectively. Alternative activation of host macrophages correlated with elevated expression of the M. tuberculosis iron storage protein bacterioferritin as well as reduced expression of the mycobactin synthesis genes mbtI and mbtJ. The extracellular matrix‐remodeling enzyme matrix metalloproteinase (MMP)‐12 was induced in alternatively activated macrophages in vitro, and MMP‐12‐expressing macrophages were abundant at late, but not early, stages of tuberculosis in murine lungs. Our findings emphasize that alternative activation deprives macrophages of control mechanisms that limit mycobacterial growth in vivo, thus supporting intracellular persistence of M. tuberculosis.
Measurement of specific radioactivity in proteins separated by two‐dimensional gel electrophoresis
Authors: Zhou Shaobo , Mann Christopher J. , Dunn Michael J. , Preedy Victor R. , Emery Peter W. 
Published: February 2006

AbstractWe report a method to quantify the specific radioactivity of proteins that have been separated by 2‐DE. Gels are stained with SyproRuby, and protein spots are excised. The SyproRuby dye is extracted from each spot using DMSO, and the fluorescence is quantified automatically using a plate reader. The extracted gel piece is then dissolved in hydrogen peroxide and radioactivity is quantified by liquid scintillation counting. Gentle agitation with DMSO for 24 h was found to extract all the SyproRuby dye from gel fragments. The fluorescence of the extract was linearly related to the amount of BSA loaded onto a series of 1‐D gels. When rat muscle samples were run on 2‐DE gels, the fluorescence extracted from 54 protein spots showed a good correlation (r = 0.79, p < 0.001) with the corresponding spot intensity measured by conventional scanning and image analysis. DMSO extraction was found not to affect the amount of radioactive protein left in the gel. When a series of BSA solutions of known specific radioactivity were run on 2‐DE gels, the specific radioactivity measured by the new method showed a good correlation (r = 0.98, p < 0.01, n = 5) with the specific radioactivity measured directly before loading. Reproducibility of the method was measured in a series of 2‐DE gels containing proteins from the livers of rats and mice that had been injected with [35S]methionine. Variability tended to increase when the amount of radioactivity in the protein spot was low, but for samples containing at least 10 dpm above background the CV was around 30%, which is comparable to that obtained when measuring protein expression by conventional image analysis of SyproRuby‐stained 2‐DE gels. Similar results were obtained whether spots were excised manually or using a spot excision robot. This method offers a high‐throughput, cost‐effective and reliable method of quantifying the specific radioactivity of proteins from metabolic labelling experiments carried out in vivo, so long as sufficient quantities of radioactive tracer are used.
Theoretical and empirical approaches to express the mobility of small ions in capillary electrophoresis
Authors: Jouyban Abolghasem , Kenndler Ernst 
Published: February 2006

AbstractA discussion is given about the concepts of the ion mobility, the analyte property which governs migration and thus separation selectivity in CE. It deals with small organic and inorganic ions, not with charged polymers or large particles like colloids. The discussion is directed to two main concepts. (i) The first is based on physico‐chemistry of ion conductance in solution, and distinguishes three types of mobility. The absolute mobility is the limiting mobility at zero ionic strength; it depends on the solvent and the temperature. It is obtained by extrapolation of the actual mobilities, those of the fully charged particles at finite ion concentration. The observed reduction of the absolute mobility with ionic concentration is related to an ion cloud, and is formulated by the established theories of ion conductance. It explains the actual mobility as function of (beside other factors) the ionic strength, the viscosity and relative permittivity of the solvent, the temperature, the relaxation time of solvent polarisation and the distance of closest approach between ion and counterion. The effective mobility, finally, is the mobility when association and dissociation equilibria play a role. Most important are acid–base reactions, but complexation, ion pairing and homo‐ and heteroconjugation were considered as well. (ii) The second approach treats mobility data with different mathematical methods, and formulates their dependence on variables like solvent composition with appropriate algorithms. These empirical methods mainly include least squares and neural network‐based methods. The least square methods ranges from the simplest model, which uses only the molecular weight of the analyte, to more complicated model requiring three‐dimensional structural descriptors of the solutes. Neural networks have been applied to model the mobility using different input variables and various architectures. Work comparing the accuracy of least squares and neural network methods was discussed; the results showed that the neural network method leads to a more accurate mobility calculation. However, the least squares methods could give some information to the factors affecting the mobility of the analytes. The resulting methods allow the prediction of mobilities under different experimental conditions with certain accuracy. It has been shown that using such models, it is possible to predict mobility of analytes after training the models by a minimum number of data to speed up the method development stage.
Analytic study of 2D and 3D grid motion using modified Laplacian
Authors: Burg Clarence 
Published: February 2006

AbstractThe modified Laplacian has been used to move unstructured grids in response to changes in the surface grid for a variety of grid movement applications including store separation, aero‐elastic wing deformation and free surface flow simulations. However, the use of the modified Laplacian can result in elements with negative areas/volumes, because it has no inherent mechanism to prevent inversion of elements. In this paper, the use of a modified Laplacian is studied analytically for a two‐dimensional problem of deforming the inner circle of two concentric circles and for a three‐dimensional problem of deforming the inner sphere of two concentric spheres. By analysing the exact solution for this problem, the amount of translation and deformation of the inner circle that maintains a valid mesh is determined. A general grid movement theorem is presented which determines analytically the maximum allowable deformation before an invalid mesh results. Under certain circumstances, the inner circle and sphere can be expanded until it reaches the outer circle or sphere, while remaining a valid grid, and the inner circle and sphere can be rotated by an extreme amount before failure of the mesh occurs. By choosing the exponent to the modified Laplacian appropriately, extreme deformations for single frequency deformations is possible, although for practical applications where the grid movement has multiple frequencies, choosing the optimal exponent for the modified Laplacian may not be practical or provide much improvement. For grid movement simulations involving rigid body translation and rotation or uniform expansion, the modified Laplacian can yield excellent results, and the optimum choice of the modified Laplacian can be analytically determined for these types of motions, but when there are multiple frequencies in the deformation, the modified Laplacian does not allow much deformation before an invalid grid results. Copyright © 2006 John Wiley & Sons, Ltd.
Adaptive mesh refinement for high‐resolution finite element schemes
Authors: Möller M. , Kuzmin D. 
Published: February 2006

AbstractNew a posteriori error indicators based on edgewise slope‐limiting are presented. The L2‐norm is employed to measure the error of the solution gradient in both global and element sense. A second‐order Newton–Cotes formula is utilized in order to decompose the local gradient error from a 𝒫1 finite element solution into a sum of edge contributions. The slope values at edge midpoints are interpolated from the two adjacent vertices. Traditional techniques to recover (superconvergent) nodal gradient values from consistent finite element slopes are reviewed. The deficiencies of standard smoothing procedures—L2‐projection and the Zienkiewicz–Zhu patch recovery—as applied to nonsmooth solutions are illustrated for simple academic configurations. The recovered gradient values are corrected by applying a slope limiter edge‐by‐edge so as to satisfy geometric constraints. The direct computation of slopes at edge midpoints by means of limited averaging of adjacent gradient values is proposed as an inexpensive alternative. Numerical tests for various solution profiles in one and two space dimensions are presented to demonstrate the potential of this postprocessing procedure as an error indicator. Finally, it is used to perform adaptive mesh refinement for compressible inviscid flow simulations. Copyright © 2006 John Wiley & Sons, Ltd.
Genomic analysis of early adenocarcinoma of the esophagus or gastroesophageal junction: Tumor progression is associated with alteration of 1q and 8p sequences
Authors: van Dekken Herman , Wink Josiane C. , Vissers Kees J. , van Marion Ronald , Koppert Linetta B. , Tilanus Hugo W. , Siersema Peter D. , Tanke Hans J. , Szuhai Karoly , Hop Wim C. J. 
Published: February 2006

AbstractEarly (T1 stage) adenocarcinoma of the esophagus or gastroesophageal junction is a potentially curable disease. We analyzed the genomic spectra of 33 early neoplastic lesions after subdividing the tumors into six depths of invasion (T1–mucosal, m1–m3; T1–submucosal, sm1–sm3). Two subgroups were defined, T1m1–sm1 (n = 18) and T1sm2–sm3 (n = 15). The latter group is associated with frequent lymphatic spread and a high percentage of local and/or distant recurrence. Comparative genomic hybridization with a genomewide 3,500‐element BAC‐PAC array revealed a characteristic gastroesophageal adenocarcinoma pattern of changes, with losses on chromosome arms 4pq, 5q, 8p, 9p, 17p, and 18q and gains on 1q, 6p, 7pq, 11q, 15q, 17q, and 20pq. However, when the two groups were compared, the following BAC clones showed significantly more alterations in the T1sm2–sm3 group: RP11‐534L20 (1q32.1) and RP11‐175A4 (6p21.32), showing gains, and RP11‐356F24, RP11‐433L7, and RP11‐241P12 (all at 8p), showing losses. Gain of RP11‐534L20 (1q32.1) and loss of RP11‐433L7 (8p22) were associated not only with a recurrence‐free period (P = 0.0007 and 0.007, respectively), but also with regional lymphatic dissemination (P = 0.005 and 0.003, respectively). These DNA clones can be considered genomic markers for the aggressive behavior of early esophageal and gastroesophageal junction adenocarcinoma. © 2006 Wiley‐Liss, Inc.