bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and meta‐analysis of a small gene expression signature for the diagnosis of estrogen receptor status in invasive ductal breast cancer
Authors: Schneider Jörg , Ruschhaupt Markus , Buneß Andreas , Asslaber Martin , Regitnig Peter , Zatloukal Kurt , Schippinger Walter , Ploner Ferdinand , Poustka Annemarie , Sültmann Holger 
Published: October 2006

AbstractIn breast cancer, the determination of estrogen receptor (ER) expression is crucial for the decision on therapeutic strategies. Current ER expression analysis is based on immunohistochemical (IHC) staining of ER on formalin fixed tissue sections. However, low levels of ER expression frequently escape detection because of varying sensitivities of routine histopathological laboratories. Moreover, in estimating ER by IHC the receptor protein only is tested instead of the complex underlying ER pathway, which reflects its biological activity. To overcome this limitation, we have used the microarray technology to study 56 samples of invasive ductal carcinoma. We infer a robust and reliable signature of 10 genes, which is associated with ER expression and presumably therapeutically relevant biological processes. In a meta‐analysis, the signature was tested on 3 further independent microarray gene expression data sets, covering different laboratories, array platforms, and clinics. The classification based on the signature showed a very low misclassification rate. In summary, the expression of few genes is sufficient to determine ER status. Future decisions on antiestrogen based therapy in breast cancer could be based on this signature rather than on immunostaining alone. © 2006 Wiley‐Liss, Inc.
Surface modification of polymeric biomaterials: Utilization of cyclodextrins for blood compatibility improvement
Authors: Zhao Xiaobin , Courtney James M. 
Published: October 2006

AbstractA novel modified polymeric biomaterial surface using cyclodextrins (CDs) for improved blood compatibility was studied. Plasticized poly(vinyl chloride) (PVC‐P) was selected for modification and polyethylene was used as a reference material. The modification was achieved by polymer blending. Fibrinogen and albumin adsorption were utilized as indices for the assessment of the blood compatibility. Surface characterization confirmed that CDs were able to accumulate at the PVC surface and alter the surface properties. The combination of other hydrophilic polymers such as poly(ethylene oxide) (PEO) and PEO/poly(propylene oxide) (PPO) copolymers, such as Pluronic F68 (F68), with CDs were also investigated. These modified materials have a remarkable protein‐resistant surface. The combination of B‐cyclodextrin (B‐CD)/PEO and B‐CD/F68 in certain feeding ratio are synergistic in producing enhanced blood compatibility. © 2006 Wiley Periodicals, Inc. J Biomed Mater Res, 2007
Electron microscopic study of novel threadlike structures on the surfaces of mammalian organs
Authors: Lee Byung‐Cheon , Yoo Jung Sun , Ogay Vyacheslav , Kim Ki Woo , Dobberstein Harald , Soh Kwang‐Sup , Chang Byung‐Soo 
Published: October 2006

AbstractThe ultrastructures of novel threadlike structures (NTSs) and corpuscles on the surfaces of internal organs of rats were investigated using electron microscopy. The samples were studied in situ by using a stereomicroscope and were taken for further morphological analysis. Scanning electron microscope (SEM) images revealed a bundle structure of threadlike tissue, which was composed of several 10‐μm‐thick subducts. The surfaces of the corpuscles were rather coarse and fenestrated. The corpuscles had cucumber‐like shapes with an average length of about 2 mm and a thickness of about 400 μm. Transmission electron microscope (TEM) images disclosed disordered collagen fibers, which formed the extracellular matrix of the threadlike tissue, and immune‐function cells, like macrophages, mast cells, and eosinophils. Sinuses of various diameters, which were thought to be cross‐sections of the lumens of the subducts, were observed in the TEM, cryo‐SEM and focused‐ion‐beam SEM images. These SEM images were obtained for the first time to reveal the detailed structure of the NTSs that were only recently discovered. Microsc. Res. Tech., 2006. © 2006 Wiley‐Liss, Inc.
Effect of estradiol and progesterone on thyroid gland in pigs: A histochemical, stereological, and ultrastructural study
Authors: Sekulić Milka , Šošić‐Jurjević Branka , Filipović Branko , Nestorović Nataša , Negić Nataša , Stojanoski Milica Manojlović , Milošević Verica 
Published: October 2006

AbstractThe cellular and subcellular organization of thyroid follicular cells in peripubertal (6‐month‐old) male pigs treated with estradiol‐dipropionate (Oe) plus progesterone (Pr) in combination on the first postnatal day was studied. A stereological method was used for morphometric determinations of the relative volume densities of the follicular epithelium, colloid and interstitium, and for establishing the epithelial height and index of activation rate. Statisticaly significant differences of the examined parameters between the control and Oe+Pr‐treated groups were determined by Student's t‐test. The subcellular organization of thyroid follicular cells was studied using transmission electron microscopy (TEM). When compared with the control group, in the Oe+Pr‐treated pigs, thyroid follicles possessed a noticeably higher follicular epithelium when compared with the control animals. The observed changes were quantified and comparison between the experimental groups showed that the height, volume density of follicular epithelium, and index of activation rate were significantly (P < 0.05) increased, whereas the relative volume density of the colloid was significantly (P < 0.05) decreased. At the subcellular level the thyroid follicular cells of Oe+Pr‐treated pigs were characterized by increased number of polysomes and dense bodies and extensive endoplasmatic reticulum. It was concluded that a single neonatal treatment with female gonadal steroids exerted a prolonged effect on the pig's thyroid, characterized by increased biosynthesis and reabsorption of the colloid by the follicular cells. Microsc. Res. Tech., 2006. © 2006 Wiley‐Liss, Inc.
Development of a biodegradable alginate carrier system for antibiotics and bone cells
Authors: Ueng Steve W.N. , Lee Mel S. , Lin Song–Shu , Chan Err‐Cheng , Liu Shih‐Jung 
Published: October 2006

AbstractThis study presents a novel biodegradable alginate delivery system for antibiotics and bone cells to treat infected bone defects. About 2 × 107 New Zealand rabbit mesenchymal stem cells (MSCs) and 5 mL vancomycin solution (50 mg/mL) were added to 5 mL of 2.5% (w/v) sodium alginate solution to form biodegradable antibiotic and MSCs alginate beads 3 mm in diameter. The alginate beads were then cultured in an osteogenic medium for 14 days. The profiles of antibiotics released from the alginate beads were evaluated using the method of high performance liquid chromatography (HPLC). The expression of osteogenic genes, including Cbfa1 and osteopontin, in the alginate beads was determined by reverse transcription‐polymerase chain reaction (RT‐PCR) analysis. The alkaline phosphatase activity, calcium level, and mineral deposition of the cultured cells within the alginate beads were assessed. Analytical results demonstrated that the concentrations of vancomycin eluted from the alginate beads were, for 14 days, well above the minimal inhibitory concentration of Staphylococcus aureus. Osteopontin and mRNA of Cbfa1 were detected and increased alkaline phosphatase activity and calcium levels were noted, as was a substantial mineral deposition in cultured MSCs. The PKH 26‐labeled MSCs and vancomycin alginate beads were implanted in rabbit bony cavities for in vivo analysis. Implanted PKH 26‐labeled MSCs were identified in the newly formed bony trabeculae in all specimens at 2 and 4 months after implantation and there was abundant mineral deposition. The results of in vitro study demonstrated sustained elution of vancomycin from the alginate carrier for 14 days and good osteogenic differentiation of cultured MSCs in the alginate carrier matrix. The results of in vivo study demonstrated the implanted MSCs participating in new bone formation. Based on experimental evidence, development of a biodegradable alginate carrier system for antibiotics and bone cells is possible, providing a potential treatment procedure for infected bone defects. © 2006 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 25:62–72, 2007
Potential opportunity in the development of new therapeutic agents based on endogenous and exogenous inhibitors of the proprotein convertases
Authors: Bontemps Yannick , Scamuffa Nathalie , Calvo Fabien , Khatib Abdel‐Majid 
Published: October 2006

AbstractThe proprotein convertases (PCs) are responsible for the endoproteolytic processing of various protein precursors (e.g., growth factors, receptors, adhesion molecules, and matrix metalloproteinases) implicated in several diseases such as obesity, diabetes, atherosclerosis, cancer, and Alzheimer disease. The potential clinical and pharmacological role of the PCs has fostered the development of various PC‐inhibitors. In this review we summarized the recent findings on PCs inhibitors, their mode of actions and potential use in the therapy of various diseases. © 2006 Wiley Periodicals, Inc. Med Res Rev, 27, No. 5, 631–648, 2007
Structure and processing relationship for olefin copolymers
Authors: Halász L. , Belina K. , Vorster O. 
Published: October 2006

AbstractThe fractional free volume values were calculated from the group‐contributed equation of state in the case of poly(propylene) and 1‐pentene‐propylene copolymers. The calculated values were compared to those, which were determined from the zero shear viscosity. The fractional free volume is an excellent parameter to convert pressure‐volume‐temperature (PVT) data to viscosity and vica versa. Copyright © 2006 John Wiley & Sons, Ltd.
Data mining for signals in spontaneous reporting databases: proceed with caution
Authors: Stephenson Wendy P. , Hauben Manfred 
Published: October 2006

AbstractPurposeTo provide commentary and points of caution to consider before incorporating data mining as a routine component of any Pharmacovigilance program, and to stimulate further research aimed at better defining the predictive value of these new tools as well as their incremental value as an adjunct to traditional methods of post‐marketing surveillance.Methods/ResultsCommentary includes review of current data mining methodologies employed and their limitations, caveats to consider in the use of spontaneous reporting databases and caution against over‐confidence in the results of data mining.ConclusionsFuture research should focus on more clearly delineating the limitations of the various quantitative approaches as well as the incremental value that they bring to traditional methods of pharmacovigilance. Copyright © 2006 John Wiley & Sons, Ltd.
New insights into DHFR interactions: Analysis of Pneumocystis carinii and mouse DHFR complexes with NADPH and two highly potent 5‐(ω‐carboxy(alkyloxy) trimethoprim derivatives reveals conformational correlations with activity and novel parallel ring stacking interactions
Authors: Cody Vivian , Pace Jim , Chisum Kim , Rosowsky Andre 
Published: October 2006

AbstractStructural data are reported for two highly potent antifolates, 2,4‐diamino‐5‐[3′,4′‐dimethoxy‐5′‐(5‐carboxy‐1‐pentynyl)]benzylpyrimidine (PY1011), with 5000‐fold selectivity for Pneumocystis carinii dihydrofolate reductase (pcDHFR), relative to rat liver DHFR, and 2,4‐diamino‐5‐[2‐methoxy‐5‐(4‐carboxybutyloxy)benzyl]pyrimidine (PY957), that has 80‐fold selectivity for pcDHFR. Crystal structures are reported for NADPH ternary complexes with PY957 and pcDHFR, refined to 2.2 Å resolution; with PY1011 and pcDHFR, refined to 2.0 Å resolution; and with PY1011 and mouse DHFR (mDHFR), refined to 2.2 Å resolution. These results reveal that the carboxylate of the ω‐carboxyalkyloxy side chain of these inhibitors form ionic interactions with the conserved Arg in the substrate binding pocket of DHFR. These data suggest that the enhanced inhibitory activity of PY1011 compared with PY957 is, in part, due to the favorable contacts with Phe69 of pcDHFR by the methylene carbons of the inhibitor side chain that are oriented by the triple bond of the 1‐pentynyl side chain. These contacts are not present in the PY957 pcDHFR complex, or in the PY1011 mDHFR complex. In the structure of mDHFR the site of Phe69 in pcDHFR is occupied by Asn64. These data also revealed a preference for an unusual parallel ring stacking interaction between Tyr35 of the active site helix and Phe199 of the C‐terminal β sheet in pcDHFR and by Tyr33 and Phe179 in mDHFR that is independent of bound ligand. A unique His174–His187 parallel ring stacking interaction was also observed only in the structure of pcDHFR. These ring stacking interactions are rarely found in any other protein families and may serve to enhance protein stability. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Aggregating the amyloid Aβ11–25 peptide into a four‐stranded β‐sheet structure
Authors: Boucher Geneviève , Mousseau Normand , Derreumaux Philippe 
Published: October 2006

AbstractWe present a detailed analysis of the structural properties of one monomer of Aβ11–25 as well as of the aggregation mechanisms for four chains of Aβ11–25 using the activation–relaxation technique coupled with a generic energy potential. Starting from a random distribution of these four chains, we find that the system assembles rapidly into a random globular state that evolves into three‐ and four‐stranded antiparallel β‐sheets. The aggregation process is considerably accelerated by the presence of preformed dimers. We also find that the reptation mechanism already identified in shorter peptides plays a significant role here in allowing the structure to reorganize without having to fully dissociate. Proteins 2006. © 2006 Wiley‐Liss, Inc.
DFT and TD‐DFT investigation of IR and UV spectra of solvated molecules: Comparison of two SCRF continuum models
Authors: Preat Julien , Loos Pierre‐François , Assfeld Xavier , Jacquemin Denis , Perpète Eric A. 
Published: October 2006

AbstractWe report the calculation of liquid‐phase infrared (IR) and ultraviolet (UV) spectra in the framework of the solute's response to the reaction field of several solvents. In particular, we compare these two properties for the multipolar expansion model developed in the Nancy continuum model (NCM) and the polarized continuum model (PCM) scheme developed in Pise and Naples. All calculations are carried out at the (TD‐)DFT/6–311G(2d,2p) level of theory. The cavity size used for modeling the solute effects on the IR and UV spectra are examined. To calibrate the solute cavity size, we have investigated the IR spectra of coumarin and of a set of 14 additional solutes of different size and polarity in several dielectrical surroundings. It turns out that: (i) PCM and NCM present an identical behavior when a common cavity is used to calibrate the models; and (ii) for both NCM and PCM models, the IR spectra are highly sensitive to the solute and solvent polarity. The UV/VIS investigation of coumarin derivatives demonstrates that both models provide close estimates of λmax independent of the solute cavity size. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
From anisole to 1,2,4,5‐tetramethoxybenzene: Theoretical study of the factors that determine the conformation of methoxy groups on a benzene ring
Authors: Velde Christophe Vande , Bultinck Evi , Tersago Karla , Alsenoy Christian Van , Blockhuys Frank 
Published: October 2006

AbstractUnhindered ortho‐dimethoxy‐substituted phenyl rings often display a coplanar conformation. A theoretical study of a series of methoxybenzenes consisting of methoxybenzene (anisole), the three dimethoxybenzenes, and 1,2,4,5‐tetramethoxybenzene, at the DFT/B3LYP/6‐311++G** level of theory, allows us to identify the factors influencing the conformational preference and attribute the coplanarity of such methoxy groups to mesomeric effects. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Comment on “The electron‐pair origin of anti‐aromaticity: Spectroscopic manifestations”
Authors: Dufey Florian 
Published: October 2006

AbstractIn the article by Zilberg and Haas, “The Electron‐Pair Origin of Anti‐aromaticity: Spectroscopic Manifestations,” the relative sign of the two Kekulé valence bond functions, R and L, in conjugated cyclic hydrocarbons was discussed. It was proposed that in the ground‐state wave function of aromatic compounds, the two functions contribute with like sign, while in the ground state of anti‐aromatic compounds, the two functions contribute with opposite sign. In this Comment, it is shown that the two functions enter with like sign also into the ground‐state wave function of anti‐aromatic compounds. Furthermore, it was argued that resonance tends to (de)stabilize a symmetric ground‐state geometry in case of the (anti‐)aromatic compounds. The expression derived by Zilberg and Haas for the stabilization energy shows an unusual dependence on the ring size and distortion coordinate. An alternative formula is derived for the stabilization energy, in which the energy depends quadratically on the distortion coordinate. Without further numerical calculations, it is not possible to predict whether this term will (de)stabilize a symmetric geometry of the ground state of (anti‐)aromatic molecules. Rather, we are led to believe that the influence of term in question on the geometric stability may be small, thus not providing the main reason for the geometric distortion of anti‐aromatic compounds. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
DFT and local MP2 study of switching process in a pH controllable molecular “shuttle”
Authors: Fomine Serguei , Guadarrama Patricia , Zolotukhin Mikhail 
Published: October 2006

AbstractA pH controllable molecular “shuttle,” comprising of dibenzo24crown‐8 (DB24C8) macroring bound to a “finger” molecule possessing two different recognition sites has been studied at the density functional theory (DFT) and Møller‐Plesset second‐order (MP2) levels of theory. The calculation confirmed experimental results that translational conformer with DB24C8 located around NH station has the lowest energy, while the conformer with DB24C8 located around NH station shows the highest energy. It has been found that Bpym2+ unit consists of two “substations” separated by an energy barrier of 3–17 kcal/mol depending on the state of the NH–NH station. The translational conformers are stabilized by NH…O, +NH…O, +NCH…OH‐bonds, and π–π stacking with different contributions, depending on the conformer type. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem 2007
Guanidination chemistry for qualitative and quantitative proteomics
Authors: Warwood Stacey , Mohammed Shabaz , Cristea Ileana M. , Evans Caroline , Whetton Anthony D. , Gaskell Simon J. 
Published: October 2006

AbstractThe application of guanidination chemistry, the conversion of lysine into homoarginine residues, is used to illustrate several important general considerations relating to the use of differential isotope labelling for relative quantification in proteomics. The derivatisation procedure has been optimised for automation using a liquid handling station designed for proteomics. Automated application of the procedure to the analysis of in‐gel tryptic digests of multiple spots from the two‐dimensional gel electrophoretic (2DE) analysis of proteins from the FDCP‐mix cell line shows near‐universal improvement in protein identification as a result of derivatisation. This chemistry has been extended for relative quantification, applicable to matrix‐assisted laser desorption/ionisation mass spectrometry (MALDI‐MS) and also tandem mass spectrometry (MS/MS). It provides a robust method for the quantitative comparison of two samples that have been separated by 2DE. A peptide pair may display poor detection during MS analysis, causing their reliable relative quantification to be difficult. In such circumstances, the additional selectivity of detection provided by MS/MS can substantiate identification and allow relative quantification of these species via product ion signal ratios. Copyright © 2006 John Wiley & Sons, Ltd.
Effect of thermal processing on the flavonols rutin and quercetin
Authors: Buchner Nadja , Krumbein Angelika , Rohn Sascha , Kroh Lothar W. 
Published: October 2006

AbstractThe current research involves the study of the thermal treatment of quercetin and rutin in an aqueous model system (cooking). These substances were heated and their degradation was followed by high‐performance liquid chromatography/diode‐array detection (HPLC/DAD). The influence of pH and the involvement of oxygen in the degradation were studied. HPLC/electrospray ionization multi‐stage mass spectrometry (ESI‐MSn) was used for the structural characterization of the compounds produced. The influence of the degradation of the phenolic compounds on their antioxidant properties was elucidated by a electron spin resonance (ESR) spectrometry study of the reaction samples mixed with the stabilized radical, Fremy's salt. Strong degradation of the model substances took place under weak basic and oxidative conditions. Quercetin showed the most intense degradation. Protocatechuic acid could be identified as a cleavage reaction product by analyzing its retention time and molar mass during the degradation of quercetin. The structure of a second cleavage product could be identified on the basis of ESI‐MSn fragmentation data. Also, several structures for reaction products of oxidized quercetin are suggested. The ESR analysis showed a decrease in the antioxidant activity of the reaction samples after heat treatment in aqueous solution. Copyright © 2006 John Wiley & Sons, Ltd.
Coaxial multi‐electrode cell (‘O‐trap’) for high‐sensitivity detection at a multiple frequency in Fourier transform ion cyclotron resonance mass spectrometry: main design and modeling results
Authors: Misharin Alexander S. , Zubarev Roman A. 
Published: October 2006

AbstractSeparation of the functions of ion excitation and detection between different cell compartments allows for implementation of excitation and detection techniques unattainable in a single compartment of the conventional ion cyclotron resonance (ICR) cell. In particular, multi‐electrode detection at a multiple of the main cyclotron frequency can be utilized without the loss of sensitivity and other negative effects. The new O‐trap designed exclusively for ion detection adds an additional, internal coaxial cylinder around which ions with excited cyclotron orbits rotate. Comparison of simulated performance characteristics of the new O‐trap with those of the same‐size conventional cylindrical cell shows that the O‐trap can provide higher sensitivity and ion capacity. Multiplexing of the O‐traps can further increase the analysis speed. Future efforts will be aimed at building and testing experimentally the coaxial O‐trap, including optimization of the method of ion transfer between the compartments of the cell. Copyright © 2006 John Wiley & Sons, Ltd.