bluuebunny/crossref_metadata_2025_split huggingface dataset:
GnRH actions on rat preovulatory follicles are mediated by paracrine EGF‐like factors
Authors: Motola Shmulik , Cao Xiumei , Ashkenazi Helena , Popliker Malka , Tsafriri Alex 
Published: July 2006

AbstractGonadotropin releasing hormone (GnRH) has been shown to mimic the actions of LH/hCG on oocyte maturation and ovulation. Recent studies demonstrated that induction of ovulation by LH/hCG is mediated, at least in part, by transactivation of epidermal growth factor receptors (EGFR) by autocrine/paracrine EGF‐like factors activated by metalloproteases. Here we have examined whether the action of GnRH on the preovulatory follicles is exerted through similar mechanisms involving activation of EGFR. The EGFR kinase inhibitor, AG1478, inhibited GnRH‐induced oocyte maturation in explanted follicles in vitro. Its inactive analog, AG43, did not affect GnRH‐stimulated resumption of meiosis. GnRH, like LH, stimulated transient follicular expression of EGF‐like agents, as well as rat cycloxygenase‐2 (rCOX‐2), rat hyaluronan synthase‐2 (rHAS‐2), and rat tumor necrosis factor‐α‐stimulated gene 6 (rTSG‐6) mRNAs, known ovulatory enzymes. Likewise, GnRH stimulated follicular progesterone synthesis. Conversely AG1478 inhibited all these actions of GnRH. Furthermore, Galardin, a broad‐spectrum metalloprotease inhibitor, blocked GnRH‐induced oocyte maturation and follicular progesterone synthesis. In conclusion, we have demonstrated that follicular EGF‐like factors mediate also the GnRH‐stimulation of ovulatory changes, like these of LH/hCG. Mol. Reprod. Dev. © 2006 Wiley‐Liss, Inc.
Parotid acinic cell carcinoma in a long‐term survivor of childhood acute lymphoblastic leukemia
Authors: Cheuk Daniel Ka Leung , Shek Tony Wai Hung , Chan Godfrey Chi Fung , Lau Yu Lung , Ha Shau Yin , Chiang Alan Kwok Shing 
Published: July 2006

AbstractSecondary malignancies are an important cause of morbidity and mortality in childhood cancer survivors. Salivary gland tumors account for about 6% of the second cancers. The majority of these are mucoepidermoid carcinomas (MEC) of the parotid gland. We report the clinical and pathological features of a rarer histological type, acinic cell carcinoma (ACC), in a childhood acute lymphoblastic leukemia (ALL) survivor. The behavior of secondary ACC appears similar to primary tumor and similar treatment may be adopted. Early recognition and complete resection is important for achieving a good outcome. Careful monitoring for recurrence or a third malignancy is needed. Pediatr Blood Cancer 2008;50:636–639. © 2006 Wiley‐Liss, Inc.
Predicting G‐protein coupled receptors–G‐protein coupling specificity based on autocross‐covariance transform
Authors: Guo Yanzhi , Li Menglong , Lu Minchun , Wen Zhining , Huang Zhongtian 
Published: July 2006

AbstractDetermining G‐protein coupled receptors (GPCRs) coupling specificity is very important for further understanding the functions of receptors. A successful method in this area will benefit both basic research and drug discovery practice. Previously published methods rely on the transmembrane topology prediction at training step, even at prediction step. However, the transmembrane topology predicted by even the best algorithm is not of high accuracy. In this study, we developed a new method, autocross‐covariance (ACC) transform based support vector machine (SVM), to predict coupling specificity between GPCRs and G‐proteins. The primary amino acid sequences are translated into vectors based on the principal physicochemical properties of the amino acids and the data are transformed into a uniform matrix by applying ACC transform. SVMs for nonpromiscuous coupled GPCRs and promiscuous coupled GPCRs were trained and validated by jackknife test and the results thus obtained are very promising. All classifiers were also evaluated by the test datasets with good performance. Besides the high prediction accuracy, the most important feature of this method is that it does not require any transmembrane topology prediction at either training or prediction step but only the primary sequences of proteins. The results indicate that this relatively simple method is applicable. Academic users can freely download the prediction program at http://www.scucic.net/group/database/Service.asp. © 2006 Wiley‐Liss, Inc.
Analysis of wood‐composite laminated frames under dynamic loads—analytical models and model validation. Part I: connection model
Authors: Heiduschke A , Kasal B , Haller P 
Published: July 2006

AbstractThis paper describes the analytical models of timber connections that were used to simulate the full time‐history response of moment‐resisting frames subjected to dynamic loads. Special attention was paid to connection modeling to capture the hysteretic damping that significantly affected the performance of the system subjected to dynamic forces. To model the hysteretic properties of the dowel‐type connections a combination of bilinear springs and gaps was used. This approach allows the modeling of various hysteretic shapes including pinching, asymmetric behavior, contact phenomena, and an initial slip of the fasteners. Load–deformation curves obtained from the cyclic experiments of small‐ and full‐scale joints were used to extract the model parameters. The hysteretic models were verified by comparing the simulation with the experimental data obtained from cyclic tests. The comparison reveals that the presented approach can be successfully used to simulate the load‐history‐dependent behavior of timber joints, provided that strength degradation is negligible and a brittle failure does not occur. The predictive ability of a 3D frame model will be demonstrated in Part II by comparing the simulation with the results of shake table experiments.
Analysis of wood‐composite laminated frames under dynamic loads ‐ analytical models and model validation. Part II: frame model
Authors: Heiduschke A , Kasal B , Haller P 
Published: July 2006

AbstractThis paper describes the analytical models that were used to simulate the full time‐history response of timber frames subjected to dynamic loads. Three‐dimensional models of two‐story timber frames were developed and verified via small‐ and full‐scale shake table experiments. The modeling of the hysteretic properties of the connections was presented in Part I. Verification of the frame model was done using the time‐history response and the dissipated energy as a measure of accuracy. The comparison reveals that the presented approach can be successfully used to simulate the load‐history‐dependent behavior of inelastic systems. The developed model reliably predicted the frame response in the nonlinear range and is capable of simulating initial slippage in the joints due to previous loading. The proposed model is applicable to design and analyze timber frames of arbitrary geometry and configuration under arbitrary loads.
3D‐QSAR CoMFA Study on Aminothiazole Derivatives as Cyclin‐Dependent Kinase 2 Inhibitors
Authors: Dessalew Nigus , Bharatam Prasad V. , Singh Sanjeev Kumar 
Published: July 2006

AbstractCyclin Dependent Kinases (CDKs) have come out as attractive targets in drug discovery programs over the years with lots of therapeutic potentials for inhibitors of these enzymes. With the intention of designing new ligands with enhanced inhibitory potencies against CDK2, the 3D‐QSAR CoMFA study carried out on 47 aminothiazole derivatives as inhibitors of this protein kinase is reported here. The developed model shows a good correlative and predictive capability having a cross‐validated correlation coefficient of 0.592. The conventional and predictive correlation coefficients were found respectively to be 0.984 and 0.522. The models could be usefully employed to design selective CDK2 inhibitors and to find novel scaffolds through screening of chemical databases.
Polarizabilities of hydrated and free ions derived from DFT calculations
Authors: Serr Andreas , Netz Roland R. 
Published: July 2006

AbstractGeometries, static dipole polarizabilities, ionization energies, and dipole moments of small ionic and a few uncharged species have been derived from density functional theory (DFT) (aug‐cc‐pV5Z) zero‐temperature calculations. Both cases of hydrated and gas phase species are reviewed. For the two test cases, Na+ and Cl−, different methods for including solvent effects [polarizable continuum model (PCM), supermolecule, charge distribution, semi‐continuum] are reviewed, showing pronounced differences in the results for the polarizabilities. While pure PCM calculations tend almost always to increase the polarizabilities with respect to the gas phase values, methods mimicking the surrounding solvent by point charge distributions usually give smaller values. Semi‐continuum calculations include both polarization effects of the medium as well as electronic confinement due to electrostatic repulsion. It remains a challenge to incorporate such polarizabilities into either classical molecular mechanics simulations or analytical theories of ionic solutions in an unambiguous and accurate fashion. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Magnetic anisotropy energies of metal–benzene sandwiches
Authors: Mokrousov Yuriy , Atodiresei Nicolae , Bihlmayer Gustav , Blügel Stefan 
Published: July 2006

AbstractWe report on ab initio calculations of the electronic and magnetic properties of metal–benzene sandwiches Mn(C6H6)m (M = V, Nb, Ta) and infinite wires, obtained by an infinite repetition of metal–benzene half‐sandwiches, based on the density functional theory (DFT) in the generalized gradient approximation (GGA). Because of the increasing influence of the spin‐orbit interaction on the magnetic properties, as going from V to Ta, a significant increase of the magnetic anisotropy energy (MAE) in the molecules is observed. In particular, an infinite Nb–benzene wire is predicted to change its ballistic conductance upon changing of magnetization direction (ballistic anisotropic magnetoresistance). The origin of the peculiar magnetic properties of the molecules is analyzed, and new possible technological applications are proposed. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
The Planck–Benzinger thermal work function in the condensation of water vapor
Authors: Chun Paul W. 
Published: July 2006

AbstractBased on the Planck–Benzinger thermal work function using Chun's method, the innate temperature‐invariant enthalpy at 0 K, ΔH0(T0), for the condensation of water vapor as well as the dimer, trimer, tetramer, and pentamer form in the vapor phase, was determined to be 0.447 kcal mol−1 for vapor, 1.127 for the dimer, 0.555 for the trimer, 0.236 for the tetramer, and 0.079 kcal mol−1 for the pentamer using ΔG(T) data reported by Kell et al. in 1968 and Kell and McLaurin in 1969. These results suggest that the predominant dimeric form is the most stable of these n‐mers. Using Nemethy and Scheraga's 1962 data for the Helmholtz free energy of liquid water, the value of ΔH0(T0) was determined to be 1.21 kcal mol−1. This is very close to the value for the energy of the hydrogen bond EH of 1.32 kcal mol−1 reported by Nemethy and Scheraga, using statistical thermodynamics. It seems clear that very little energy is required for interconversion between the hypothetical supercooled water vapor and glassy water at 0 K. A hypothetical supercooled water vapor at 0 K is apparently almost as highly associated as glassy water at that temperature, suggesting a dynamic equilibrium between vapor and liquid. This water vapor condensation is highly similar in its thermodynamic behavior to that of sequence‐specific pairwise (dipeptide) hydrophobic interaction, except that the negative Gibbs free energy change minimum at 〈Ts〉, the thermal setpoint for vapor condensation, where TΔS = 0, occurs at a considerably lower temperature, 270 K (below 0°C) compared with ∼350 K. The temperature of condensation 〈Tcond〉 at which ΔG(T) = 0, where water vapor begins to condense, was found to be 383 K. In the case of a sequence‐specific pairwise hydrophobic interaction, the melting temperature, 〈Tm〉, where ΔG(Tm) = 0 was found to be 460 K. Only between two temperature limits, 〈Th〉 = 99 K and 〈Tcond〉 = 383 K, where ΔG(Tcond) = 0, is the net chemical driving force favorable for polymorphism of glassy water and hypothetical supercooled water vapor. Analysis of the water vapor condensation process based on the Planck–Benzinger thermal work function confirms that a thermodynamic molecular switch occurs at 10 K, wherein a change of sign in [ΔCp(T)]cond leads to a true negative minimum in the Gibbs free energy of vapor condensation, and hence a maximum in the related equilibrium constant, Kcond. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Rapid test by liquid chromatography/tandem mass spectrometry to evaluate equine urine reactivity towards 17β‐OH steroids
Authors: Fidani Marco , Casagni Eleonora , Montana Marco , Pasello Emanuela , Pecoraro Chiara , Gambaro Veniero 
Published: July 2006

AbstractBacteria frequently found in equine urine samples may cause degradation of 17β‐OH steroids. A simple liquid chromatography/tandem mass spectrometry (LC/MS/MS) method has been developed to evaluate the microbiological contamination of equine urine as a marker of poor storage conditions. Norethandrolone was used as the internal standard, and the linearity, sensitivity, precision and accuracy of the method were evaluated. 17β‐OH oxidation was demonstrated for testosterone, nandrolone, trenbolone and boldenone, but did not occur in α‐epimers such as α‐boldenone and epitestosterone, demonstrating the stereoselectivity of the reaction. A rapid test was performed by spiking one of the four 17β‐OH steroids in samples of diluted equine urine. The steroids were transformed into their respective ketones in the presence of bacterial activity. The test allows direct injection of diluted samples into the LC/MS system, without the need for prior extraction. Results show that the best method of storage is freezing at −18°C. Urine specimens should be analyzed as soon as possible after thawing. This allows bacterial degradation of equine urine to be arrested temporarily, so that the urine can be used for qualitative or quantitative analysis of 17β‐OH steroids. Copyright © 2006 John Wiley & Sons, Ltd.
Direct combination of immersed single‐drop microextraction with atmospheric pressure matrix‐assisted laser desorption/ionization tandem mass spectrometry for rapid analysis of a hydrophilic drug via hydrogen‐bonding interaction and comparison with liquid‐liquid extraction and liquid‐phase microextraction using a dual gauge microsyringe with a hollow fiber
Authors: Wu Hui‐Fen , Lin Chi‐Hsien 
Published: July 2006

AbstractThis study presents the feasibility of direct coupling of the immersed single‐drop microextraction (SDME) technique with atmospheric pressure matrix‐assisted laser desorption/ionization mass spectrometry (AP‐MALDI‐MS) for the rapid analysis of a hydrophilic drug (dopamine) from aqueous solution and human urine in an ion trap tandem mass spectrometer through hydrogen‐bonding interaction of dopamine with the extraction solvent (octanol). The optimum conditions for the SDME experiments coupled to AP‐MALDI/MS were: stirring rate, 240 rpm; extraction time, 5 min; sample pH value, 8; and matrix concentration, 2000 ppm, using α‐cyano‐4‐hydroxycinnamic acid (α‐CHCA) as matrix. The limits of detection (LODs) for the SDME/AP‐MALDI‐MS experiments were 25 and 40 ppm in water and human urine, respectively. In a comparison of this method with the traditional liquid‐liquid extraction (LLE), the SDME method shows better LODs than the LLE (40 ppm) and the same LODs (25 ppm) as the liquid‐phase microextraction using a dual gauge microsyringe with a hollow fiber (LPME/DGM‐HF). However, the SDME method is more convenient than the LPME/DGM‐HF method. Copyright © 2006 John Wiley & Sons, Ltd.
Resolving stoichiometries and oligomeric states of glutamate synthase protein complexes with curve fitting and simulation of electrospray mass spectra
Authors: van Breukelen Bas , Barendregt Arjan , Heck Albert J. R. , van den Heuvel Robert H. H. 
Published: July 2006

AbstractA complicating factor in analyzing electrospray ionization mass spectra of intact macromolecular heterogeneous protein complexes is the potential overlap of ions from different species present in solution. Therefore, it is often not possible to assign all ion signals. With the aim of allowing the more efficient and comprehensive analysis of very complex mass spectra of intact heterogeneous protein complexes we developed a software program: SOMMS. The program uses simple user input parameters together with Gaussian curve fitting to simulate putative mass spectra of protein (sub)complexes within a specified charge state window. In addition, the program can simulate spectra for heterogeneous protein complexes using bi‐ and multinomial distributions and it can calculate zero‐charge spectra and relatively quantify the abundance of each component in a mixture. As a proof of concept we analyzed the complex mass spectra of α‐glutamate synthase and αβ‐glutamate synthase from Azosprillum brasilense. Using our program we could determine that α‐glutamate synthase is in equilibrium between its dimeric, tetrameric, hexameric and dodecameric conformation, whereas αβ‐glutamate synthase forms up to 15 different heterooligomeric assemblies composed of α‐ and β‐subunits. Thus, SOMMS allows resolving stoichiometries and oligomeric states of protein complexes even from very complicated mass spectra. These complexes could not be assigned by using maximum entropy calculations. We compared our mass spectrometry data on glutamate synthases with available X‐ray, small‐angle X‐ray scattering and size‐exclusion chromatography data. Copyright © 2006 John Wiley & Sons, Ltd.
A situational method engineering approach to requirements elicitation workshops in the software development process
Authors: Coulin Chad , Zowghi Didar , Sahraoui Abd‐El‐Kader 
Published: July 2006

AbstractThe elicitation of requirements for software systems is one of the most critical and complex activities within the development lifecycle. Although the subject has received some degree of attention in the research literature, there remains a need for situational methods and processes that can be easily utilized by the majority of practitioners in typical projects. In this paper we present a flexible yet systematic approach to the early stages of requirements elicitation in software development, based on collaborative workshops and the construction of a lightweight situational method, within a general process framework. The research provides practitioners with an approach to requirements elicitation that can be readily applied to real‐world projects in order to improve both the process and the results. The work also offers researchers an example of how lightweight situational method engineering can be applied to very practical activities and situations in the software process. Copyright © 2006 John Wiley & Sons, Ltd.
A vector for double epitope tagging with a recyclable marker
Authors: Germino Mary , Sohail Honeah , Germino Elizabeth , Germino Joseph 
Published: July 2006

AbstractMultimeric protein complexes play diverse and vital roles in the cell, but following the composition of these complexes under varying growth conditions can be challenging. Toward that goal, we have designed a vector that permits the double epitope tagging of a protein at its carboxy terminus. One ‘universal’ tag, a triple repeat of the HA1 epitope, is fused with every protein to be studied, allowing the composition and stoichiometry of the proteins in a complex to be detected with a single antibody. Each protein also can be tagged with a second epitope specific for that protein. This ‘specific’ tag can be used to immunoprecipitate complexes containing that protein of interest. Any epitope to which a specific antibody is available can be used for this second tag. Because there are a limited number of selection markers for cloning in yeast, the kanamycin cassette, flanked by loxP sites, was incorporated into the vector to permit marker recycling using Cre‐lox recombinase. This vector was used to tag 4 proteins involved in ribosome biogenesis—Ytm1, Cic1, Brx1 and Drs1. An anti‐HA1 antibody could detect all four proteins in crude lysates and yielded the relative abundance of these four proteins, of which Drs1 is reproducibly less abundant than any of the others, which may have implications for the control of ribosome biogenesis. The Ytm1 protein was also tagged with the VSV epitope and can be specifically detected using an anti‐VSV antibody. This vector may prove useful for exploring other protein complexes. Copyright © 2006 John Wiley & Sons, Ltd.
Transabdominal Modified Devascularization Procedure with or without Esophageal Stapler Transection—An Operation Adequate for Effective Control of a Variceal Bleed. Is Esophageal Stapler Transection Necessary?
Authors: Johnson M. , Rajendran S. , Kannan T.G. Balachandar D. , Jeswanth S. , Ravichandran P. , Surendran R. 
Published: July 2006

AbstractBackgroundIn Japan, the original Sugiura procedure reported favorable results in non‐cirrhotic patients but in the West, the modified Sugiura procedure is not widely accepted because of high rebleeding, morbidity, and mortality in cirrhotics. We retrospectively analyzed the efficacy of our modified Sugiura procedure i.e., devascularization with/without esophageal transection combined with salvage endotherapy and pharmacotherapy for control of a variceal bleed.Materials and MethodsBetween January 1999 and December 2004, 912 patients with variceal bleeding were treated. Of these, 66 (7.2%) patients were subjected to surgery after failed endotherapy/propranolol. Among these 66 patients, 52 had transabdominal devascularization (16 emergency, 36 elective); 14 patients underwent devascularization with esophageal stapler transection (group I), and 38 patients had devascularization without esophageal stapler transection (group II). Another 14 patients underwent elective end‐to‐side proximal splenorenal shunt surgery.ResultsPostoperative mortality was 7.1% in group I, 10.5% in group II (P > 0.05). Mortality for emergency surgery was 31.2% (5/16) but there were no deaths in the elective surgery group. Overall morbidity was 57.1% in group I and 21.0% in group II (P < 0.05). The rates of variceal rebleeding were 7.1% and 7.8%; residual varices were 30.7% and 32.3%; recurrent varices were 7.6% and 5.8% following the group I and group II procedures, respectively, over a mean follow‐up period of 39.9 (7–2) months. Esophageal transection–related morbidity (leak, stricture, and bleeding) was 21.4% (3/14) in group I.ConclusionsDevascularization without esophageal stapler transection is a safe and effective procedure for adequate (urgent and long‐term) control of variceal bleeding with similar results and less morbidity when compared to devascularization with esophageal transection in cirrhotic patients, as well as non‐cirrhotic patients.
Carnitine transporter defect: Diagnosis in asymptomatic adult women following analysis of acylcarnitines in their newborn infants
Authors: Vijay S. , Patterson A. , Olpin S. , Henderson M. J. , Clark S. , Day C. , Savill G. , Walter J. H. 
Published: July 2006

SummaryCarnitine transporter defect (CTD) is an autosomal recessive disorder characterized by episodes of non‐ketotic hypoglycaemia, hyperammonaemia and liver disease, or by the development of cardiomyopathy, both of which occur in infancy and childhood. Blood carnitine concentrations are extremely low. The diagnosis can be confirmed by finding abnormal fat oxidation and carnitine uptake in skin fibroblasts. The condition has not previously been thought to present later in life or to be benign. We report the identification of four women discovered to have CTD as a consequence of finding low carnitine concentrations in the cord blood or newborn samples from their infants. All four mothers had been asymptomatic and none had a cardiomyopathy.