bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational exploration of the activated pathways associated with DNA damage response in breast cancer
Authors: Wen Liting , Li Wei , Sobel Marc , Feng Jin‐an 
Published: July 2006

AbstractMolecular signaling events regulate cellular activity. Cancer stimulating signals trigger cellular responses that evade the regulatory control of cell development. To understand the mechanism of signaling regulation in cancer, it is necessary to identify the activated pathways in cancer. We have developed RepairPATH, a computational algorithm that explores the activated signaling pathways in cancer. The RepairPATH integrates RepairNET, an assembled protein interaction network associated with DNA damage response, with the gene expression profiles derived from the microarray data. Based on the observation that cofunctional proteins often exhibit correlated gene expression profiles, it identifies the activated signaling pathways in cancer by systematically searching the RepairNET for proteins with significantly correlated gene expression profiles. Analyzing the gene expression profiles of breast cancer, we found distinct similarities and differences in the activated signaling pathways between the samples from the patients who developed metastases and the samples from the patients who were disease free within 5 years. The cellular pathways associated with the various DNA repair mechanisms and the cell‐cycle checkpoint controls are found to be activated in both sample groups. One of the most intriguing findings is that the pathways associated with different cellular processes are functionally coordinated through BRCA1 in the disease‐free sample group, whereas such functional coordination is absent in the samples from patients who developed metastases. Our analysis revealed the potential cellular pathways that regulate the signaling events in breast cancer. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Evolutionary identification of a subtype specific functional site in the ligand binding domain of steroid receptors
Authors: Raviscioni Michele , He Qiang , Salicru Eleni M. , Smith Carolyn L. , Lichtarge Olivier 
Published: July 2006

AbstractNuclear receptors are ubiquitous eukaryotic ligand‐activated transcription factors that modulate gene expression through varied interactions. However, the highly conserved functional sites known today seem insufficient to explain receptor specific recruitment of different coactivator and corepressor proteins and regulation of transcription. To search for new receptor‐subtype specific functional sites, we applied difference evolutionary trace (difference ET) analysis to the ligand binding domain of steroid receptors, a subgroup of the nuclear receptor (NR) family. This computational approach identified a new functional site located on a surface opposite to currently known protein–protein interaction sites and distinct from the ligand binding pocket. Strikingly, the literature shows that in vivo variations at residues in the new site are linked to androgen resistance and leukemia, and our own targeted mutations to this site lower but do not eradicate transcriptional activation by estrogen receptor α (ERα), with reduced ligand binding affinity and SRC‐1 interaction. Thus, these data demonstrate that this evolutionary important surface can function as an allosteric site that modulates some but not all receptor binding interactions. Evolutionary analysis further shows that this allosteric regulatory site is shared among all NRs from groups 2 (HNF4‐like) and 4 (NGFIB‐like), suggesting a role among many nuclear receptors. Its concave structure, hydrophobic composition, and residue variability among nuclear receptors further suggest that it would be amenable for specific drug design. This highlights the power of evolutionary information for the identification of new functional sites even in a protein family as well studied as NRs. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Juvenile hormone III, hydroprene and a juvenogen as soldier caste differentiation regulators in three Reticulitermes species: potential of juvenile hormone analogues in termite control
Authors: Hrdý Ivan , Kuldová Jelena , Hanus Robert , Wimmer Zdeněk 
Published: July 2006

AbstractThe efficacy of juvenile hormone III (JH III) and two JH‐mimicking compounds was compared in laboratory experiments with Reticulitermes lucifugus (Rossi), R. santonensis Feytaud and R. virginicus (Banks). Induction of presoldier, soldier and/or soldier‐worker intercaste differentiation was taken as positive response to the treatment. The novel juvenogen, a fatty acid ester of a juvenoid alcohol, induced greatest soldier differentiation in all species tested, followed by hydroprene. JH III was less effective. Representatives of three Reticulitermes species showed similar trends in soldier induction rates. Differences in mortality in treatments of termites of the same species from different colonies with the same compound were observed and evidently were caused by differences in the conditions of respective colonies. Copyright © 2006 Society of Chemical Industry
Reduction in an almond moth Ephestia cautella (Lepidoptera: Pyralidae) population by means of mating disruption
Authors: Ryne Camilla , Ekeberg Mats , Jonzén Niclas , Oehlschlager Cam , Löfstedt Christer , Anderbrant Olle 
Published: July 2006

AbstractPheromone‐based mating disruption of the almond moth (Ephestia cautella) (Walk.) (Lepidoptera: Pyralidae) was carried out in a chocolate factory in Sweden. Population monitoring was conducted with pheromone‐baited traps and water traps. Pheromone traps showed a 94% catch reduction, and monitoring with water traps showed a significant decrease in total catch (5.0 and 1.6 individuals per trap per week before and during treatment respectively). The significance of the results was tested by fitting the observed data to a first‐order autoregressive model. This made it possible to test the data with a 95% confidence interval, comparing trap catches before mating disruption treatment with trapping data during the experiment. It is suggested that this statistical approach may be used more frequently in mating disruption experiments where it is extremely difficult to control external factors and therefore equally difficult to use a comparable control plot to evaluate the treatment. Copyright © 2006 Society of Chemical Industry
Light pulse delay in semiconductor quantum well Bragg structures
Authors: Binder R. , Yang Z. S. , Kwong N. H. , Nguyen D. T. , Smirl Arthur L. 
Published: July 2006

AbstractWe discuss a scheme for controlled stopping, storing, and releasing of light pulses in one‐dimensional resonant photonic band gap structures (RPBG's) made of Bragg spaced quantum wells. Our scheme is based on parametric manipulation of the RPBG's bandstructure in real time. We extend earlier studies on the limitations of presently existing quantum well Bragg structures to the regime of small detunings of the exciton resonance from the Bragg frequency. We also set the stage for exploring mechanisms of bandstructure control by studying the nonlinear response of the quantum well RPBG. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Inhibition of respiratory burst in human neutrophils and lipoxygenase enzyme by compounds fromHaloxylon griffithii
Authors: Choudhary Muhammad Iqbal , Azizuddin  , Jalil Saima , Israr Muddasir , Attar‐ur‐Rahman  
Published: July 2006

AbstractSecondary metabolites, ferulic acid (1), 2,6‐dimethoxy‐4‐hydroxy acetophenone (2), herniarin (3),p‐hydroxy acetophenone (4), methyl 3,4‐dihydroxycinnamate (5), and methyl 4‐hydroxy‐3‐methoxycinnamate (6) were isolated fromHaloxylon griffithii, a member of the family Chenopodiaceae. The structures of compounds 1–6 were identified with the help of spectroscopic techniques. These compounds were isolated for the first time from this plant. The lipoxygenase and respiratory burst inhibitory activities were determined. Compound 5 was found to be the most potent inhibitory activity against respiratory burst in human neutrophils among all the compounds as well as exhibited moderate lipoxygenase inhibitory activity from this plant. Copyright © 2006 John Wiley & Sons, Ltd.
Tulbaghia alliacea phytotherapy: a potential anti‐infective remedy for candidiasis
Authors: Thamburan S. , Klaasen J. , Mabusela W. T. , Cannon J. F. , Folk W. , Johnson Q. 
Published: July 2006

AbstractThe reproductive health of individuals is severely compromised by HIV infection, with candidiasis being the most prevalent oral complication in patients. Although not usually associated with severe morbidity, oropharyngeal candidiasis can be clinically significant, as it can interfere with the administration of medications and adequate nutritional intake, and may spread to the esophagus. Azole antifungal agents are commonly prescribed for the treatment and prophylaxis of candidal infections, however, the emergence of drug resistant strains and dose limiting toxic effects has complicated the treatment of candidiasis. Consequently, safe and effective and affordable medicine is required to combat this fungus. Commercial garlic (Allium sativum) has been used since time immemorial as a natural antibiotic, however, very little is known about the antifungal properties of two indigenous South African species of garlic, namely Tulbaghia alliacea and Tulbaghia violacea, used as folk medicines for a variety of infections. This study compares the in vitro anticandidal activity of Tulbaghia alliacea, Tulbaghia violacea and Allium sativum extracts. It was found that the greatest concentrations of inhibitory components were extracted by chloroform or water. The IC50 concentrations of Tulbaghia alliacea were 0.007–0.038% (w/v). Assays using S. cerevisiae revealed that the T. alliacea extract was fungicidal, with a killing half‐life of approximately 2 h. This inhibitory effect of the T. alliacea extracts was observed via TLC, and may be due to an active compound called marasmicin, that was identified using NMR. This investigation confirms that extracts of T. alliacea exhibit anti‐infective activity against candida species in vitro. Copyright © 2006 John Wiley & Sons, Ltd.
Fluorous 2,4‐Dichloro‐1,3,5‐triazines (F‐DCTs) as Nucleophile Scavengers
Authors: Lu Yimin , Zhang Wei 
Published: July 2006

Abstract1H,1H,2H,2H,3H,3H‐perfluoroundecanol‐ and 1H,1H,2H,2H‐perfluorodecanethiol‐displaced 2,4‐dichloro‐1,3,5‐triazines 1 and 2 are synthesized and used as nucleophile scavengers to remove thiols and amines from solution‐phase reactions. Two active sites on the triazine ring are able to remove two equivalents of nucleophiles. The purification of reaction mixtures is accomplished by plate‐to‐plate fluorous solid‐phase extraction or automated solid‐phase extraction on the RapidTrace system.
Recent Applications of Fluorous Separation Methods in Organic and Bioorganic Chemistry
Authors: Dandapani Sivaraman 
Published: July 2006

AbstractInitially introduced as a niche technique to recover and recycle catalysts, fluorous chemistry has rapidly expanded into organic synthesis and combinatorial chemistry over the past 12 years. Recently, fluorous methods are also enabling purification of biomolecules such as peptides, oligosaccharides, and oligonucleotides assembled by traditional solid‐phase synthesis. Apart from synthetic applications, fluorous chemistry is also providing solutions for critical problems in proteomics and microarray chip technology. This review highlights selected recent advances that underscore the impact of fluorous separation methods in organic and bioorganic chemistry.
Synthesis of Bistratamide H Using a New Fluorous Protecting Group
Authors: Nakamura Yutaka , Takeuchi Seiji 
Published: July 2006

AbstractBistratamide H was expeditiously synthesized using a new fluorous protecting group, 2‐(tris(perfluorodecyl)silyl)ethoxycarbonyl (FTeoc) via a preparation of thiazole amino acid by a modified Hantzsch's method. The intermediates of the synthesis were easily isolated by fluorous liquid–liquid extraction. The fluorous protecting group was removed from the precursor of bistratamide H with TBAF and the recovered fluorous fragment, tris(perfluorodecyl)silylfluoride, was reacted with vinyl magnesium chloride to give an intermediate in the synthesis of FTeoc reagent.
Fluorous Phosphine‐Assisted Recycling of Gold Catalysts for Hydrosilylation of Aldehydes
Authors: Lantos Diána , Contel María , Larrea Angel , Szabó Dénes , Horváth István T. 
Published: July 2006

AbstractThe facile recycling of gold hydrosilylation catalyst was achieved by using fluorous phosphine‐modified gold complexes and/or nanoparticles.
Pyridyl Tags as Phase Labels in Organic Synthesis: Fluorous and Non‐Fluorous Approaches
Authors: El Bakkari Mounir , Vincent Jean‐Marc 
Published: July 2006

AbstractPyridyl tags represent very attractive phase labels for reactants and reagents. Pyridyl tags are the prototypical example of “masked phase tags” which require an activation step to modify the natural phase affinity of the tagged compound. The activation is carried out by either protonation or coordination to a metal ion, whereas deactivation is achieved by basification or addition of competitive ligands. By such simple operations the tagged compounds can be reversibly switched between a liquid‐organic phase and other liquid phases (aqueous or fluorous) or between a liquid‐organic phase and a solid phase. The purification of reaction products can thus be achieved by straightforward liquid/liquid or solid/liquid separation procedures. Additionally, the pyridyl tags may function both as a phase label and directing tags by accelerating reactions and/or increasing their selectivity.
First Fluorous Synthesis of Fluorinated Uracils
Authors: Fustero Santos , Catalán Silvia , Flores Sonia , Jiménez Diego , del Pozo Carlos , Luis Aceña José , Sanz‐Cervera Juan F. , Mérida Salvador 
Published: July 2006

AbstractThis paper describes a novel fluorous synthesis of fluorinated uracils 4. In this new protocol, fluorous alcohols 1, which are used as fluorous tags, are acetylated to yield acetates 2, which in turn are treated with a base to form their enolates. These are then reacted with fluorinated nitriles to furnish tagged β‐enamino esters 3. Although this condensation step had been performed easily in previous solution and solid‐phase syntheses, it proved to be very elusive in the fluorous version. Meticulous control of the reaction conditions was thus essential in order to achieve satisfactory yields of β‐enamino esters 3. The final treatment of compounds 3 with isocyanates or isothiocyanates efficiently afforded uracils 4 with concomitant elimination of the fluorous tag, thereby facilitating the preparation of a small library of these derivatives.
Ab initio study of the unimolecular decomposition of 2‐butenenitrile: Molecular elimination channels
Authors: Oh Chang Young , Choi Heechol , Kim Hong Lae 
Published: July 2006

AbstractAb initio molecular orbital calculations have been performed for the unimolecular decomposition of 2‐butenenitrile (CH3CHCHCN), especially for HCN and H2 molecular elimination channels. Structures and energies of the reactants, products, and relevant species in the individual reaction pathways were determined by MP2 gradient optimization and MP4 CCSD(T) single‐point energy calculations. Direct 1,1 and 1,2 molecular eliminations and H or CN migration followed by elimination channels were identified. Dissociation rates for the individual reaction pathways were calculated from vibrational frequencies at the ab initio transition state geometries by employing Rice–Ramsperger–Kassel–Marcus theory, from which channel branching ratios were determined. It was concluded that the most important reaction channel should be the direct 1,1 three‐center molecular elimination of HCN. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Quantum chemical study of the mechanism of action of vitamin K epoxide reductase (VKOR)
Authors: Deerfield David , Davis Charles H. , Wymore Troy , Stafford Darrel W. , Pedersen Lee G. 
Published: July 2006

AbstractPossible model, but simplistic, mechanisms for the action of vitamin K epoxide reductase (VKOR) are investigated with quantum mechanical methods (B3LYP/6‐311G**). The geometries of proposed model intermediates in the mechanisms are energy optimized. Finally, the energetics of the proposed (pseudo‐enzymatic) pathways are compared. We find that the several pathways are all energetically feasible. These results will be useful for designing quantum mechanical/molecular mechanical method (QM/MM) studies of the enzymatic pathway once three‐dimensional structural data are determined and available for VKOR. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
‘Rationalizing sustainable development’ – a critical treatise
Authors: Kallio Tomi J. , Nordberg Piia , Ahonen Ari 
Published: July 2006

AbstractThis paper analyses the themes of rationality and legitimation in the discourse of sustainable development. We start by constructing ideal types of interpretation of sustainable development (weak and strong) and rationality (value rationality and instrumental rationality) as conceptual and theoretical ‘tools’ for our further analysis. We then discuss the role of and analyze the construction of rationality and legitimation in the sustainable development discourse. We explore the ways in which rationality and legitimation are constructed to support one's own interpretation, and, on the other hand, how the rationality and legitimacy of the opposing interpretations are nullified. We then discuss the basis of prudent decision‐making, and the possibilities and problems that are bound up in the concept of sustainable development. The paper concludes by stating that when it comes to sustainable development neither societal decision‐making nor the actions based on it is currently prudent. Copyright © 2006 John Wiley & Sons, Ltd and ERP Environment.
Dimensions of environmentally sustainable innovation: the structure of eco‐innovation concepts
Authors: Hellström Tomas 
Published: July 2006

AbstractThe present study analyses environmentally sustainable innovation, or eco‐innovation for short, from the perspective of extant theories of innovation, in order to establish dominant structures of such innovations and current weaknesses, as well as fruitful ways forward. 105 venture concepts were sampled from the winning contributions of a national environmental innovation competition, and analysed in terms of Schumpeterian innovation type and innovation mode (radical–incremental and component–architectural). The resulting distribution confirms a bias towards incremental process innovations, but points towards interesting characteristics in radical–architectural modes of eco‐innovation, e.g. the tendency to combine ‘hardware’ and ‘software’, or technology and social arrangements, the combination of generically diverse technologies and finally the ‘eco‐enabling’ of old technologies by the application of new ones. Copyright © 2006 John Wiley & Sons, Ltd and ERP Environment.
Classical galactosaemia revisited
Authors: Bosch Annet M. 
Published: July 2006

SummaryClassical galactosaemia (McKusick 230400) is an: autosomal recessive disorder of galactose metabolism, caused by a deficiency of the enzyme galactose‐1‐phosphate uridyltransferase (GALT; EC 2.7.712). Most patients present in the neonatal period, after ingestion of galactose, with jaundice, hepatosplenomegaly, hepatocellular insufficiency, food intolerance, hypoglycaemia, renal tubular dysfunction, muscle hypotonia, sepsis and cataract. The gold standard for diagnosis of classical galactosaemia is measurement of GALT activity in erythrocytes. Gas‐chromatographic determination of urinary sugars and sugar alcohols demonstrates elevated concentrations of galactose and galactitol. The only therapy for patients with classical galactosaemia is a galactose‐restricted diet, and initially all galactose must be removed from the diet as soon as the diagnosis is suspected. After the neonatal period, a lactose‐free diet is advised in most countries, without restriction of galactose‐containing fruit and vegetables. In spite of the strict diet, long‐term complications such as retarded mental development, verbal dyspraxia, motor abnormalities and hypergonadotrophic hypogonadism are frequently seen in patients with classical galactosaemia. It has been suggested that these complications may result from endogenous galactose synthesis or from abnormal galactosylation. Novel therapeutic strategies, aiming at the prevention of galactose 1‐phosphate production, should be developed. In the meantime, the follow‐up protocol for patients with GALT deficiency should focus on early detection, evaluation and, if possible, early intervention in problems of motor, speech and cognitive development.
On the motion of a rigid body immersed in a bidimensional incompressible perfect fluid
Authors: Ortega Jaime , Rosier Lionel , Takahashi Takéo 
Published: July 2006

We consider the motion of a rigid body immersed in a bidimensional incompressible perfect fluid. The motion of the fluid is governed by the Euler equations and the conservation laws of linear and angular momentum rule the dynamics of the rigid body. We prove the existence and uniqueness of a global classical solution for this fluid–structure interaction problem. The proof relies mainly on weighted estimates for the vorticity associated with the strong solution of a fluid–structure interaction problem obtained by incorporating some viscosity.

Résumé
Nous étudions le mouvement d'un corps rigide immergé dans un fluide parfait incompressible bidimensionnel. Le mouvement du fluide est modélisé par les équations d'Euler, et la dynamique du corps rigide est régie par les lois de conservation des moments linéaires et angulaires. Nous prouvons l'existence et l'unicité d'une solution globale classique pour ce problème d'interaction fluide–structure. La preuve repose essentiellement sur des estimées à poids pour la vorticité associée à la solution forte d'un problème d'interaction fluide–structure obtenu en incorporant de la viscosité.
The effects of intravenous sildenafil on hemodynamics and cardiac sympathetic activity in chronic human heart failure
Authors: Al‐Hesayen Abdul , Floras John S. , Parker John D. 
Published: July 2006

AbstractBackgroundErectile dysfunction is common in patients with chronic heart failure and sildenafil is an effective treatment option in this population. Sildenafil has been reported to increase sympathetic outflow in normal volunteers. To date, experience with sildenafil in patients with congestive heart failure is limited and the impact of phosphodiesterase‐5 inhibition on sympathetic activity in this population has not been evaluated.Methods and results10 patients with heart failure (ejection fraction 23±3%) were studied. Generalized and cardiac sympathetic activity responses to an intravenous infusion of sildenafil were measured by the norepinephrine spillover method. In response to sildenafil, there was a significant reduction in mean pulmonary artery (− 26±5%, P<0.01) and mean arterial pressures (−8±1%, P<0.01). These hemodynamic responses were accompanied by a 22±5% reduction in cardiac norepinephrine spillover (P<0.02) but no change in total body norepinephrine spillover.ConclusionsThe acute administration of sildenafil is associated with a modest reduction in systemic arterial blood pressure and a more substantial reduction in pulmonary arterial pressure. These hemodynamic changes are observed in the absence of systemic sympathetic activation and are associated with a reduction in cardiac norepinephrine spillover in patients with chronic heart failure. These observations are relevant given the high prevalence of erectile dysfunction in this patient population.