bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toward an alternative notion of information systems ontologies: Information engineering as a hermeneutic enterprise
Authors: Fonseca Frederico T. , Martin James E. 
Published: December 2004

AbstractIn this paper we discuss the construction of information systems ontologies. We summarize and discuss Barry Smith's review (2003a) of the field in the paper, “Ontology.” In that essay Smith concludes with a plea for ontologies that reflect the categories of current scientific theories because they represent our best knowledge of the world. In this context, we develop an argument for a hermeneutic approach to ontologies—one compatible with the orientation introduced into information science by Winograd and Flores (1986) and later developed by many others. To do this, we argue that the literature in the philosophy and history of science supports a hermeneutic interpretation of the nature and growth of science. This, given Smith's argument, shows the relevance of hermeneutics to the creation of information system ontologies. The problems associated with understanding and creating information systems ontologies are addressed fruitfully only if one begins by acknowledging that databases are mechanisms for communication involving judgments and interpretations by intelligent and knowledgeable users. The main contributions of this paper are our conclusions that (a) information system ontologies should take into consideration a perspective of the philosophy and history of science, and (b) hermeneutics as construed by Gadamer (1975, 1979) constitutes a place from which we can understand the tasks of information ontologists and database users.
Article impact calculated over arbitrary periods
Authors: Frandsen Tove Faber , Rousseau Ronald 
Published: December 2004

AbstractIn this paper we address the various formulations of impact of articles, usually groups of articles as gauged by citations that these articles receive over a certain period of time. The journal impact factor, as published by ISI (Philadelphia, PA), is the best‐known example of a formulation of impact of journals (considered as a set of articles) but many others have been defined in the literature. Impact factors have varying publication and citation periods and the chosen length of these periods enables, e.g., a distinction between synchronous and diachronous impact factors. It is shown how an impact factor for the general case can be defined. Two alternatives for a general impact factor are proposed, depending on whether different publication years are seen as a whole, and hence treating each one of them differently, or by operating with citation periods of identical length but allowing each publication period different starting points.
A Density Functional Study on a Biomimetic Non‐Heme Iron Catalyst: Insights into Alkane Hydroxylation by a Formally HOFeVO Oxidant
Authors: Bassan Arianna , Blomberg Margareta R. A. , Siegbahn Per E. M. , Que Lawrence 
Published: December 2004

AbstractThe reactivity of [HO(tpa)FeVO] (TPA=tris(2‐pyridylmethyl)amine), derived from OO bond heterolysis of its [H2O(tpa)FeIIIOOH] precursor, was explored by means of hybrid density functional theory. The mechanism for alkane hydroxylation by the high‐valent iron–oxo species invoked as an intermediate in Fe(tpa)/H2O2 catalysis was investigated. Hydroxylation of methane and propane by HOFeVO was studied by following the rebound mechanism associated with the heme center of cytochrome P450, and it is demonstrated that this species is capable of stereospecific alkane hydroxylation. The mechanism proposed for alkane hydroxylation by HOFeVO accounts for the experimentally observed incorporation of solvent water into the products. An investigation of the possible hydroxylation of acetonitrile (i.e., the solvent used in the experiments) shows that the activation energy for hydrogen‐atom abstraction by HOFeVO is rather high and, in fact, rather similar to that of methane, despite the similarity of the HCH2CN bond strength to that of the secondary CH bond in propane. This result indicates that the kinetics of hydrogen‐atom abstraction are strongly affected by the cyano group and rationalizes the lack of experimental evidence for solvent hydroxylation in competition with that of substrates such as cyclohexane.
Efficient Synthesis of Thioesters and Amides from Aldehydes by Using an Intermolecular Radical Reaction in Water
Authors: Nambu Hisanori , Hata Kayoko , Matsugi Masato , Kita Yasuyuki 
Published: December 2004

AbstractThe combination of the water‐soluble radical initiator, 2,2′‐azobis[2‐(2‐imidazolin‐2‐yl)propane] dihydrochloride (VA‐044) and the surfactant, cetyltrimethyl‐ammonium bromide (CTAB), was found to be the most suitable condition for the effective and direct synthesis of useful active thioesters (pentafluorophenyl thioesters) in water. In addition, the direct amidation of aldehydes was achieved by the addition of the amines to the thioesterification reaction mixture in water.
Erstes technisches Verfahren mit ionischen Flüssigkeiten
Authors: Maase Matthias 
Published: December 2004

AbstractIonische Flüssigkeiten sind neuartige Materialien mit einem Eigenschaftsprofil, das bislang nicht zur Verfügung stand [1]. Das BASIL™‐Verfahren der BASF, das seit 2002 routinemäßig in der Produktion von Alkoxyphenylphosphinen eingesetzt wird, ist das erste Beispiel, bei dem ionische Flüssigkeiten gezielt in einem technischen Prozess genutzt werden.
Ephrin signaling in vivo: Look both ways
Authors: Davy Alice , Soriano Philippe 
Published: December 2004

AbstractEph receptors and ephrins have captured the interest of the developmental biology community in recent years for their pleiotropic functions during embryogenesis. Loss‐of‐function studies using various animal models have demonstrated the involvement of Ephs and ephrins in many aspects of embryogenesis including segmentation, neural crest cells migration, angiogenesis, and axon guidance. An essential property of this signaling pathway is the ability of both Ephs and ephrins to behave as receptors or ligands and their consequent cell autonomous and nonautonomous mode of action. While many reports did not discriminate between Eph autonomous signaling (forward) and ephrin autonomous signaling (reverse), recent genetic and in vivo studies have shown that both forward and reverse signaling play important roles during embryogenesis. Developmental Dynamics 232:1–10, 2005. © 2004 Wiley‐Liss, Inc.
T‐box genes and heart development: Putting the “T” in heart
Authors: Plageman Timothy F. , Yutzey Katherine E. 
Published: December 2004

AbstractMembers of the T‐box gene family (Tbx) are essential for normal heart development, and mutations in human TBX genes cause congenital cardiovascular malformations. T‐box genes have been implicated in early cardiac lineage determination, chamber specification, valvuloseptal development, and diversification of the specialized conduction system in vertebrate embryos. These genes include Tbx1, Tbx2, Tbx3, Tbx5, Tbx18, and Tbx20, all of which exhibit complex temporal spatial regulation in developing cardiac structures. Less is known about T‐box genes in invertebrate heart development, but multiple T‐box genes are expressed in Drosophila cardiac lineages. The molecular hierarchies and developmental processes controlled by T‐box genes in the heart are the focus of this review. Developmental Dynamics 232:11–20, 2005. © 2004 Wiley‐Liss, Inc.
Quantitative evaluation of morpholino‐mediated protein knockdown of GFP, MSX1, and PAX7 during tail regeneration in Ambystoma mexicanum
Authors: Schnapp Esther , Tamaka Elly M. 
Published: December 2004

AbstractVertebrate regeneration is a fascinating but poorly understood biological phenomena. Urodele amphibians such as Ambystoma mexicanum (the axolotl) can functionally regenerate complex body structures such as the limb and tail, including the spinal cord, throughout life. So far, molecular studies on regeneration have been limited due to the paucity of tools for knocking‐down gene and protein function. In this article, we quantitatively assessed the ability of morpholinos to specifically down‐regulate protein expression in both cultured urodele cells and in vivo. We focused on the down‐regulation of green fluorescent protein and two axolotl proteins, MSX1 and PAX7. Our data show that the expression of these proteins can be efficiently reduced by morpholinos. MSX1 has been hypothesized to be involved in muscle dedifferentiation based on experiments using cultured myotubes. Our studies in in vivo muscle fibers so far have shown no influence of overexpressing or down‐regulating MSX1 on the dedifferentiation process. Developmental Dynamics 232:162–170, 2005. © 2004 Wiley‐Liss, Inc.
Clearance of apoptotic cells is not impaired in mouse embryos deficient in class A scavenger receptor types I and II (CD204)
Authors: Komohara Yoshihiro , Terasaki Yasuhiro , Kaikita Koichi , Suzuki Hiroshi , Kodama Tatsuhiko , Takeya Motohiro 
Published: December 2004

AbstractElimination of apoptotic cells is an important mechanism to maintain proper embryonal morphogenesis. The class A scavenger receptor type I, II (CD204), one of the major receptors expressed on macrophages, is a receptor actively involved in recognition and ingestion of apoptotic cells. To clarify the role of CD204 in embryonic morphogenesis, we performed immunohistochemical and immunoelectron microscopic studies using CD204‐deficient mouse embryos. In control mice, almost all macrophages expressed CD204 from embryonic day 9.5 (E9.5). Phagocytes engulfing dead cells in the E13.5 interdigit region showed strong expression of CD204, indicating that CD204 was actively involved in apoptotic cell clearance. However, CD204 is not essential for the embryonic clearance of apoptotic cells, because CD204‐deficient embryos developed normally without any retardation in footplate remodeling. Up‐regulation of CD36 in CD204‐deficient fetal macrophages suggested that CD36 substitutes for CD204 function. We also found that mesenchymal cells frequently engulfed apoptotic cells especially in early embryonal stages. These data suggest that CD204 is partially but not essentially involved in apoptotic cell clearance in embryogenesis. During early embryonal development, mesenchymal cells, rather than macrophages, play a major role in apoptotic cell clearance. Developmental Dynamics 232:64–74, 2005. © 2004 Wiley‐Liss, Inc.
Repression of fibroblast growth factor receptor 1 gene expression by E2F4 in skeletal muscle cells
Authors: Parakati Rajini , DiMario Joseph X. 
Published: December 2004

AbstractFibroblast growth factor receptor 1 (FGFR1) gene expression is positively and negatively regulated during muscle differentiation. We recently reported that FGFR1 gene expression was up‐regulated by Sp transcription factors in proliferating myoblasts. However, the mechanism of down‐regulation of this gene during differentiation is unknown. We have identified the transcription factor E2F4 as a negative regulator of FGFR1 gene expression. Immunodetection studies revealed that endogenous E2F1 and E2F2 proteins were cytoplasmic in myoblasts and myotubes, whereas E2F4 was abundant in the nuclei of both. Upon overexpression, E2F4 repressed FGFR1 promoter activity in a dose‐dependent manner in myoblasts and Drosophila SL2 cells, and mutation of the E2F4 binding site increased FGFR1 promoter activity and reduced E2F4‐mediated repression. Gel shift assays detected E2F4 binding to a synthetic FGFR1 E2F4 binding site and chromatin immunoprecipitation assays detected E2F4 binding to the endogenous FGFR1 promoter in proliferating myoblasts and myotubes. The results indicate that FGFR1 promoter activity in skeletal muscle cells is repressed by E2F4. Developmental Dynamics 232:119–130, 2005. © 2004 Wiley‐Liss, Inc.
Telomerase activity and differential expression of telomerase genes and c‐myc in chicken cells in vitro
Authors: Swanberg Susan E. , Payne William S. , Hunt Henry D. , Dodgson Jerry B. , Delany Mary E. 
Published: December 2004

AbstractThe original article to which this Erratum refers was published in Developmental Dynamics 231:14–21Developmental Dynamics (2004) 231(1) 14–21
Matrix metalloproteinase genes in Xenopus development
Authors: Harrison Michael , Abu‐Elmagd Muhammad , Grocott Timothy , Yates Clara , Gavrilovic Jelena , Wheeler Grant N. 
Published: December 2004

AbstractThe original article to which this Erratum refers was published in Developmental Dynamics 231:214–220 Developmental Dynamics(2004) 231(1) 214–220
Adenosine and cAMP are potent inhibitors of the NF‐κB pathway downstream of immunoreceptors
Authors: Minguet Susana , Huber Michael , Rosenkranz Lisa , Schamel Wolfgang W. A. , Reth Michael , Brummer Tilman 
Published: December 2004

AbstractAnergic B lymphocytes exert compromised signal transduction towards the activation of NF‐κB in response to B cell antigen receptor (BCR) triggering, whereas activation of the ERK pathway appears normal. How this differential down‐regulation of the NF‐κB pathway is regulated remains still elusive. Here, we demonstrate that stimuli known to enhance 3′,5′‐cyclic adenosine monophosphate (cAMP) are capable of selectively suppressing the activation both of NF‐κB downstream of the BCR and Toll‐like receptor 4 in splenic B lymphocytes and of the high‐affinity receptor for IgE in BM‐derived mast cells. This suppression is accomplished by blocking phosphorylation and subsequent degradation of the inhibitor of NF‐κB. A cAMP‐dependent protein kinase (PKA) inhibitor reverses this suppressive effect, indicating that PKA is a downstream effector of cAMP in this process. Importantly, not only drugs that artificially elevate intracellular cAMP levels, but also the nucleoside adenosine, which is known to be a mediator of cellular distress, inhibit the NF‐κB pathway. This suggests that adenosine‐mediated signals represent an important step in the molecular decision process controlling inflammation versus anergic immune responses.See accompanying Commentary: http://dx.doi.org/10.1002/eji.200425738
New insights into adenosine‐receptor‐mediated immunosuppression and the role of adenosine in causing the immunodeficiency associated with adenosine deaminase deficiency
Authors: Hershfield Michael S. 
Published: December 2004

AbstractThere is growing interest in manipulating adenosine (Ado) signal transduction to control inflammation and autoimmunity. This concept probably originated with the discovery of severe combined immunodeficiency disease (SCID) in infants with inherited deficiency of adenosine deaminase (ADA). However, the basis for immunosuppression by Ado has not been well defined, and effects of 2′‐deoxyadenosine (dAdo), which does not activate Ado receptors, have also been implicated in causing SCID. Here I discuss recent evidence that Ado, acting through its A2A receptor, interferes with NF‐κB activation in antigen‐receptor‐stimulated B and T lymphocytes. I also assess the relative contributions of Ado and dAdo to the pathogenesis of ADA‐deficient SCID.See accompanying article: http://dx.doi.org/10.1002/eji.200425524
CD8+ T cells from most HIV‐1‐infected patients, even when challenged with mature dendritic cells, lack functional recall memory to HIV gag but not other viruses
Authors: Arrode Geraldine , Finke Jennifer S. , Zebroski Henry , Siegal Frederick P. , Steinman Ralph M. 
Published: December 2004

AbstractChronically HIV‐1‐infected patients fail to contain their viremia despite high frequencies of HIV‐1‐specific, IFN‐γ‐producing CD8+ T cells. However, these cells are known to exhibit both phenotypic and functional defects. We tested if mature dendritic cells (DC) could correct defective HIV‐1 gag‐specific T cell responses and if responses to other viral antigens were comparably affected. The circulating gag‐specific CD8+ T cells in fresh blood reliably produced IFN‐γ but lacked IL‐2 and high perforin levels and failed to expand significantly during culture with mature DC presenting HIV‐1 gag peptides. In contrast, CD8+ T cells from long‐term nonprogressors contained gag‐specific IFN‐γ and IL‐2 double producers, and the numbers of IFN‐γ producers expanded ∼15‐fold during culture with DC. DC from chronically infected patients could expand IFN‐γ‐ and IL‐2‐producing cells specific for influenza, cytomegalovirus and Epstein Barr virus, and the expansions were comparable to those in healthy donors. When the proliferative capacity of CD8+ T cells from progressor patients was assessed by CFSE dilution, proliferation to other viral antigens was more vigorous than to HIV‐1 gag. Therefore, monocyte‐derived DC from HIV patients present viral antigens effectively, but there is a selective inability to expand CD8+ IFN‐γ‐producing and IFN‐γ and IL‐2 double‐producing T cells when challenged with HIV‐1 gag.
Titanium Dioxide Nanoparticles Functionalized with Pd and W Complexes of a Catecholphosphane Ligand
Authors: Lucas Nigel T. , Hook James M. , McDonagh Andrew M. , Colbran Stephen B. 
Published: December 2004

AbstractPalladium and tungsten complexes containing the bifunctional ligand 4‐diphenylphosphanylcatechol (L1) have been synthesized. The catecholate functionality strongly binds to titanium dioxide nanoparticles, effectively anchoring the complexes to the TiO2 surface. Solid‐state 31P NMR spectroscopy was used to probe the surface‐bound compounds. Diffuse reflectance infrared spectroscopy also provided data on surface‐bound tungsten carbonyl complexes. Preliminary experiments show that the palladium phosphane complex [PdBr2(L1)2] supported on TiO2 catalyzes the Sonogashira coupling of phenylacetylene with 4‐iodonitrobenzene. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)
Anionic Phosphane − A New Ligand with a Phosphane and a Weakly Coordinating Heteroborate Moiety
Authors: Ronig Benno , Schulze Herbert , Pantenburg Ingo , Wesemann Lars 
Published: December 2004

AbstractReaction of chloropropyl‐substituted stanna‐closo‐dodecaborate [Cl(CH2)3SnB11H11]− with the nucleophile Li[CH2PPh2] provided a straightforward synthesis of an anionic phosphane [Ph2PCH2SnB11H11]−. Derivatization of the phosphane was carried out in reaction with sulfur and hydrochloric acid to give [Bu3MeN][Ph2P(S)CH2SnB11H11] and the zwitterion [Ph2P(H)CH2SnB11H11]. In reaction with various transition metal electrophiles, complexation reactions were accomplished resulting in the isolation of trans‐substituted palladium and platinum complexes [Bu3MeN]2[trans‐(Ph2PCH2SnB11H11)2MCl2] (M = Pd, Pt), a neutral silver adduct [(acetone)Ag(Ph2PCH2SnB11H11)], and a linearly coordinated bisphosphane of gold [Bu3MeN][Au(Ph2PCH2SnB11H11)2]. The solid state structures of the ligand salt, the palladium and gold coordination compounds were determined and discussed. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)
Low Reynolds number k–ε model for near‐wall flow
Authors: Rahman M. M. , Siikonen T. 
Published: December 2004

AbstractA wall‐distance free k–ε turbulence model is developed that accounts for the near‐wall and low Reynolds number effects emanating from the physical requirements. The model coefficients/functions depend non‐linearly on both the strain rate and vorticity invariants. Included diffusion terms and modified Cε(1,2) coefficients amplify the level of dissipation in non‐equilibrium flow regions, thus reducing the kinetic energy and length scale magnitudes to improve prediction of adverse pressure gradient flows, involving flow separation and reattachment. The model is validated against a few flow cases, yielding predictions in good agreement with the direct numerical simulation (DNS) and experimental data. Copyright © 2005 John Wiley & Sons, Ltd.
Microextraction in packed syringe (MEPS) for liquid and gas chromatographic applications. Part II—Determination of ropivacaine and its metabolites in human plasma samples using MEPS with liquid chromatography/tandem mass spectrometry
Authors: Abdel‐Rehim Mohamed , Altun Zeki , Blomberg Lars 
Published: December 2004

AbstractA new technique for sample preparation on‐line with liquid chromatographic/tandem mass spectrometric (LC/MS/MS) assay was developed. Microextraction in a packed syringe (MEPS) is a new miniaturized, solid‐phase extraction technique that can be connected on‐line to gas or liquid chromatography without any modifications. In MEPS ∼1 mg of the solid packing material is inserted into a syringe (100–250 µl) as a plug. Sample preparation takes place on the packed bed. The bed can be coated to provide selective and suitable sampling conditions. The new method is very promising, very easy to use, fully automated, of low cost and rapid in comparison with previously used methods. This paper presents the development and validation of a method for MEPS on‐line with LC/MS/MS. Ropivacaine and its metabolites (PPX and 3‐OH‐ropivacaine) in human plasma samples were used as model substances. The method was validated and the calibration curves were evaluated by means of quadratic regression and weighted by the inverse of the concentration, 1/x, for the calibration range 2–2000 nM. The applied polymer could be used more than 100 times before the syringe was discarded. The extraction recovery was between 40 and 60%. The results showed high correlation coefficients (R2 > 0.999) for all analytes in the calibration range studied. The accuracy, expressed as a percentage variation from the nominal concentration values, ranged from 0 to 6%. The precision, expressed as the relative standard deviation, at three different concentrations (quality control samples) was consistently about 2–10%. The limit of quantification was 2 nM. Copyright © 2004 John Wiley & Sons, Ltd.
A simple and sensitive assay for the quantitative analysis of paclitaxel in human and mouse plasma and brain tumor tissue using coupled liquid chromatography and tandem mass spectrometry
Authors: Stokvis E. , Ouwehand M. , Nan L. G. A. H. , Kemper E. M. , van Tellingen O. , Rosing H. , Beijnen J. H. 
Published: December 2004

AbstractThe development and validation of an assay for the determination of paclitaxel in human plasma, human brain tumor tissue, mouse plasma and mouse brain tumor tissue is described. Paclitaxel was extracted from the matrices using liquid–liquid extraction with tert‐butyl methyl ether, followed by chromatographic analysis using an alkaline eluent. Positive ionization electrospray tandem mass spectrometry was performed for selective and sensitive detection. The method was validated according to the FDA guidelines on bioanalytical method validation. Validation results indicate that calibration standards in human plasma can be used to quantify paclitaxel in all tested matrices. In human samples, the validated range for paclitaxel was from 0.25–1000 ng ml−1 using 200 µl plasma aliquots and from 5 to 5000 ng g−1 using 50 µl tumor homogenate aliquots (0.2 g tissue ml−1 control human plasma). In mice, the ranges were 1–1000 ng ml−1 and 5–5000 ng g−1 using 50 µl of mouse plasma and 50 µl of tumor homogenate aliquots (0.2 g tissue ml−1 control human plasma), respectively. The method can be applied to studies generating only small sample volumes (e.g. mouse plasma and tumor tissue), but also to studies in human plasma requiring a lower limit of quantitation. The assay was applied successfully to several studies with both human and mouse samples. Copyright © 2004 John Wiley & Sons, Ltd.