bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combined deficiency of MSH2 and Sμ region abolishes class switch recombination
Authors: Leduc Claire , Haddad Dania , Laviolette‐Malirat Nathalie , Nguyen Huu Ngoc‐Sa , Khamlichi Ahmed Amine 
Published: July 2010

AbstractClass switch recombination (CSR) is mediated by G‐rich tandem repeated sequences termed switch regions. Transcription of switch regions generates single‐stranded R loops that provide substrates for activation‐induced cytidine deaminase. Mice deficient in MSH2 have a mild defect in CSR and analysis of their switch junctions has led to a model in which MSH2 is more critical for switch recombination events outside than within the tandem repeats. It is also known that deletion of the whole Sμ region severely impairs but does not abrogate CSR despite the lack of detectable R loops. Here, we demonstrate that deficiency of both MSH2 and the Sμ region completely abolishes CSR and that the abrogation occurs at the genomic level. This finding further supports the crucial role of MSH2 outside the tandem repeats. It also indicates that during CSR, MSH2 has access to activation‐induced cytidine deaminase targets in R‐loop‐deficient Iμ‐Cμ sequences rarely used in CSR, suggesting an MSH2‐dependent DNA processing activity at the Iμ exon that may decrease with transcription elongation across the Sμ region.
Systematic Hydrothermal Investigation of Metal Phosphonatobenzenesulfonates by High‐Throughput Methods
Authors: Maniam Palanikumar , Näther Christian , Stock Norbert 
Published: July 2010

AbstractA high‐throughput (HT) investigation using the rigid bifunctional ligand 4‐phosphonobenzenesulfonic acid, H2O3P‐C6H4‐SO3H (H3L), generated five new phosphonatobenzenesulfonates with copper(II) or lead(II) ions. A comprehensive HT study comprising the screenings of different metal ions, metal salt types and the synthesis optimization were conducted whereby the influence of pH and molar ratios M2+/H3L were investigated. The HT‐study led to five new compounds Pb2[(O3P‐C6H4‐SO3)(OH)] (1), Cu1.5[(O3P‐C6H4‐SO3)(H2O)] (2), NaCu(O3P‐C6H4‐SO3)(H2O)3 (3), Cu2[(O3P‐C6H4‐SO3)(OH)(H2O)] (4) and Cu3[(O3P‐C6H4‐SO3)2(H2O)2] (5). Metal ion screening showed lead(II) and copper(II) to be suitable metal ions. The utilization of discovery and focused arrays allowed to determine the optimal formation fields of the respective compounds. The crystal structures were determined from single‐crystal X‐ray diffraction and revealed the presence of various MOx polyhedra that form clusters, chains or layers which are connected through the organic linker. IR spectra, thermogravimetric studies, magnetic susceptibility measurements and elemental analyses were conducted to further characterize the compounds 1, 3, 4 and 5.
Porous Porphyrin Nanoarchitectures on Surfaces
Authors: Makiura Rie , Kitagawa Hiroshi 
Published: July 2010

AbstractControlling the size and the growth direction of porous hybrid objects – metal–organic frameworks (MOFs) or porous coordination polymers (PCPs) – at the nanoscale is a critical issue for enabling their use in a number of potential applications that have arisen from the current remarkable activity in studying such porous materials. This microreview describes the recent progress in the design, growth, and characterization of multidimensional nanoarchitectures by employing porphyrin‐based components. The versatility of the sequential bottom‐up fabrication process, which uses multitopic molecular building units assembled by appropriately chosen linkers, is suitable to be extended to the formation of a rich variety of nanostructures endowed with pores on surfaces.
Effect of carnitine on serum cholesterol of alcoholic cardiomyopathy dogs
Authors: Yuan Lin , Li Wei‐Min , Jing Ling , Zhou Li‐Jun 
Published: July 2010

AbstractCarnitine is known to be essential for metabolism regulation in some heart diseases such as coronary heart disease. We evaluated the effect of carnitine and valsartan on alcoholic cardiomyopathy (ACM); surprisingly, it was found that carnitine leads to variations in serum lipids. The results of our study, supported by cardiac function assessment, LVW/BW ratio, hematoxylin and eosin staining, and electron microscopic morphology, not only demonstrated the validity of our ACM model but also addressed the therapeutic benefits of carnitine and valsartan in antagonizing ACM development. The alcohol group displayed a high LVEDd and low EF and FS, indicating both heart failure and cardiac remodeling. Compared with the alcohol and alcohol/valsartan groups, the concentration of serum cholesterol in the alcohol/carnitine group was significantly increased between baseline and 6 months. The body weights of dogs from the alcohol group slowly increased between baseline and 6 months, although the LV weight increased quickly. The results suggest that both carnitine and valsartan have a favorable effect on ACM. However, the fact that carnitine could increase the serum cholesterol level should lead to caution in the treatment of ACM patients who are suffering from coronary disease in the meantime.
Analysis of triacylglycerols in refined edible oils by isocratic HPLC‐ESI‐MS
Authors: Zeb Alam , Murkovic Michael 
Published: July 2010

AbstractA simple, fast and reproducible reversed‐phase high performance liquid chromatography (HPLC) method coupled to electrospray ionization mass spectrometry (ESI‐MS) for the analysis of triacylglycerols (TAGs) species in the commercial edible oils has been developed. The TAGs species were separated using isocratic 18% isopropanol in methanol and a Phenomenex C18 column. The ESI‐MS conditions were optimized using flow injection analysis of standard TAG. Fifteen, fourteen, and sixteen TAGs were separated and identified in corn oil, rapeseed oil, and sunflower oil, respectively. The presence of intense protonated molecular (M + H+), ammonium (M + ${\rm NH}_{4}^{ + } $), and sodium (M + Na+) adducts ions and their respective diacylglycerols ions in the ESI‐MS spectra showed correct identification of TAGs. Some minor potassium adducts (M + K+) were also found. In addition, the identity of the fatty acid, position of each fatty acid, and the location of the double bond in the fatty acid moiety were explained. It was found that this isocratic method is useful for fast screening and identification of triacylglycerols in lipids.
Self‐Assembling Depsipeptide Dendrimers and Dendritic Fullerenes with New cis‐ and trans‐Symmetric Hamilton Receptor Functionalized Zn–Porphyrins: Synthesis, Photophysical Properties and Cooperativity Phenomena
Authors: Maurer Katja , Grimm Bruno , Wessendorf Florian , Hartnagel Kristine , Guldi Dirk M. , Hirsch Andreas 
Published: July 2010

AbstractTwo novel supramolecular building blocks, namely cis‐ and trans‐symmetric zinc–porphyrins bearing Hamilton receptors as their focal points (10 and 15), were self‐assembled with (i) first‐, second‐ and third‐generation depsipeptide cyanurates (21–23); (ii) second‐generation dendrofullerene (24), and (iii) cyanuric acid substituted fullerene (20), and probed in a series of photophysical investigations. Importantly, an overall 1:2 stoichiometry was confirmed with binding constants Kn, and Hill coefficients nH that indicate remarkable cooperativities. As a general feature, stronger binding evolves from the trans‐symmetric porphyrin isomer, although the increased steric demand of the depsipeptide ligandsmeans that the binding constants decrease with each generation. The self‐assembly of 10 or 15 with 20 affords novel electron donor–acceptor hybrids that reveal, upon excitation,intra‐hybrid charge‐transfer events.
Stereochemical Analysis of the Enzymic Reduction of the Double Bond of α‐ and β‐Substituted Nitrostyrenes and α‐Ethoxycinnamaldehyde through Deuterium Labelling Experiments
Authors: Brenna Elisabetta , Fronza Giovanni , Fuganti Claudio , Gatti Francesco G. 
Published: July 2010

Abstract2H NMR studies and comparison with authentic labelled reference compounds prepared from the (Z)‐acetamido‐cinnamic acid 10 and from (Z)‐2‐ethoxy‐3‐(4‐methoxyphenyl)prop‐2‐en‐1‐ol (14), respectively, by catalytic syn reduction with deuterium gas show that the baker's yeast‐mediated saturation in the presence of deuterated water of the double bond of (E)‐α‐(hydroxymethyl)nitrostyrene (2) and of the (Z)‐α‐ethoxycinnamaldehyde (3) leads to (2R,3R)‐[2,3‐2H2]‐3‐(4‐methoxyphenyl)‐2‐nitropropan‐1‐ol (5) and to(1R,2S,3R)‐[1,2,3‐3H2]‐2‐ethoxy‐3‐(4‐methoxyphenyl)propan‐1‐ol (6), respectively, thus supporting an anti mode of hydrogen addition across the activated double bond, with hydride delivery in β‐position respect to the activating group from the upper side of the molecule.
Quantitative assessment of multi‐laboratory reproducibility of SDS‐PAGE assays: Digestion pattern of β‐casein and β‐lactoglobulin under simulated conditions
Authors: Defernez Marianne , Mandalari Giuseppina , Mills Elizabeth Noami Clare 
Published: July 2010

AbstractA digestion protocol was applied in triplicate by ten laboratories, simulating in vivo gastric and duodenal conditions. The intra‐ and inter‐laboratory variability in the kinetics of protein degradation was quantified, focussing on the digestion of β‐casein under gastric conditions, and of β‐lactoglobulin (β‐Lg) under duodenal conditions. The addition of surfactants such as phosphatidylcholine (PC) in the digestion mix was also evaluated. Identification and quantification of peptide bands on SDS‐PAGE gels formed the basis for analysis. An average intensity loss of 69% (SD=13.5) at 5 min (89% at 10 min, with SD=5.5) was observed for β‐casein, whereas the β‐Lg duodenal digestion showed an 82% loss at 30 min (SD=14.2). Constant rates of first‐order reactions showed that for fast reactions, inaccuracies in the time of first sampling contributed to the variability, which were also affected by image quality, saturation, and the splitting of time courses across gels. Breakdown products for β‐casein included ten other polypeptides, with four detected in all and two in most gels, and for β‐Lg ten polypeptides, with five detected in most, and two in two‐third of the cases. Addition of PC in the gastric phase led to β‐Lg intensity loss only a quarter as large as without PC and altered β‐Lg proteolysis in the duodenal compartment.
Epigenetic regulation of miR‐196b expression in gastric cancer
Authors: Tsai Kuo‐Wang , Hu Ling‐Yueh , Wu Chew‐Wun , Li Sung‐Chou , Lai Chun‐Hung , Kao Hsiao‐Wei , Fang Wen‐Liang , Lin Wen‐chang 
Published: July 2010

AbstractMicroRNAs (miRNAs) are short noncoding RNAs that play important roles in cellular processes and disease pathogenesis via the control of specific targeted gene expression. The miR‐196s miRNA is encoded at three paralogous loci in three HOX clusters and acts as an oncogenic miRNA in cancer progression. Recent studies have demonstrated that the expression of miR‐196b increases cell proliferation and survival in leukemic cells. Here, we used a sequential methylation analysis to reveal that the methylation status correlated well with miR‐196b expression in different cell lines. Treatment with the demethylating drug 5‐Aza‐dC reactivated miR‐196b transcription in methylation‐silenced cells. Using in vitro methylation approach, we further provide evidences that promoter hypermethylation represses miR‐196b transcriptional activation tightly in human cancer cell lines. We also demonstrate that the expression of miR‐196b is significantly elevated in gastric cancer and that hypomethylation status of miR‐196b CpG islands frequently is observed in primary gastric tumors. Our results provide important information on miR‐196s regulation and demonstrate that abnormal DNA hypomethylation induces overexpression of miR‐196b in gastric cancer. © 2010 Wiley‐Liss, Inc.
Interphase fluorescence in situ hybridization on selected plasma cells is superior in the detection of cytogenetic aberrations in plasma cell dyscrasia
Authors: Put Natalie , Lemmens Heidi , Wlodarska Iwona , Konings Peter , Moreau Yves , Hagemeijer Anne , Vandenberghe Peter , Michaux Lucienne 
Published: July 2010

AbstractInterphase fluorescence in situ hybridization (FISH) detects nonrandom cytogenetic abnormalities in plasma cell (PC) dyscrasia according to PC burden. However, when performed on cultured whole bone marrow (BM), it often fails to detect these aberrations. We have compared this interphase FISH technique with FISH after PC purification or identification to detect recurrent aberrations. In this study, 235 BM samples were collected from patients with multiple myeloma (MM) or related PC disorders regardless of disease status. All samples were analyzed in parallel. Clonal abnormalities were detected in 34.9% of cultured samples compared with 71.0% PC selected samples (P < 0.001). Moreover, FISH on PCs allowed to detect more abnormalities per case (P < 0.001) and identified higher percentages of abnormal nuclei (P < 0.001). This study indicates that FISH on PCs is the preferred technique for routine cytogenetic investigation of MM. © 2010 Wiley‐Liss, Inc.
The alcohol use disorders identification test (AUDIT) and its derivatives in screening for heavy drinking among the elderly
Authors: Aalto Mauri , Alho Hannu , Halme Jukka T. , Seppä Kaija 
Published: July 2010

AbstractObjectiveThe performance of the Alcohol Use Disorders Identification Test (AUDIT) in screening for heavy drinking among the elderly has been unsatisfactory. The aim of the present study was to determine whether tailoring the cut point improves the performance of the AUDIT and its derivatives in this age group.MethodsFrom a stratified random sample of 804 Finns aged 65–74 years, 517 subjects (64.3%) completed the AUDIT and the Timeline Follow‐back (TLFB) interview regarding alcohol consumption. A subject was defined as a heavy drinker if consumption of ≥8 drinks (approx. 12 g) on average in a week or ≥4 drinks at least in 1 day during the prior 28 days was reported. Combinations in which both sensitivity and specificity are ≥0.8 were defined as optimal. The elderly specific AUDIT‐3 is a modification in which the binge drinking threshold is ≥4 drinks.ResultsBased on the TLFB, 118 subjects (22.8%) were heavy drinkers. The areas under receiving operating characteristics curves (AUROCs) were equivalent (≥0.898) for all questionnaires. When using the standard cut point of ≥8 for the AUDIT, the sensitivity was 0.48. Lowering the cut point to ≥5 led to both a sensitivity and specificity over 0.85. The optimal cut point of the AUDIT‐C was ≥4. The AUDIT‐QF, AUDIT‐3 and elderly specific AUDIT‐3 did not provide optimal combinations of sensitivity and specificity with any cut point.ConclusionsThe AUDIT and AUDIT‐C are accurate in screening for heavy drinking among the elderly if the cut points are tailored to this age group. Copyright © 2010 John Wiley & Sons, Ltd.
The flexible alignment of molecular structures using simulated annealing with weighted Lagrangian multipliers
Authors: Raymond John W. , Holsworth Daniel D. , Jalaie Mehran 
Published: July 2010

AbstractA framework for superimposing small molecules is presented. The proposed method consists of a simple atom‐based, flexible alignment. The optimization procedure used in the alignment is based on a recently published variant of the simulated annealing whereby nonlinear constraints are accommodated using Lagrangian multipliers. It differs from other published superposition algorithms in that any number of nonlinear constraints can be readily imposed on the structural alignment directly through the objective function without assuming an a priori trade‐off between competing conditions. These can include equality and equality constraints on distances, angles, and energy states. Examples illustrating the use of the proposed approach are also provided. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011
Understanding of bonding and mechanical characteristics of cementitious mineral tobermorite from first principles
Authors: Tunega Daniel , Zaoui Ali 
Published: July 2010

AbstractThis paper reports density functional theory study of the structural and mechanical properties of tobermorite mineral (9 Å phase) as one of the main component of cementitious materials in a concrete chemistry. Calculated bulk modulus and elastic constants reflect a relatively high resistance of the tobermorite structure with respect to external isostatic compression. Moreover, the elastic constants proved the anisotropic character of the tobermorite structure. The directions parallel to the axb plane are more resistant to the compression than the perpendicular direction. The largest contribution to this resistance comes from the “dreierketten” silicate chains. The bonding analysis linked macroscopic mechanical properties and the atomic structure of the tobermorite. It was found that polar covalent SiO bonds are stiffer than iono‐covalent CaO bonds. The SiO4 tetrahedra are resistant with respect to the compression and the effect of external pressure is reflected by the large mutual tilting of these tetrahedra as it is shown by changes of the SiOSi bridging angles. Polyhedra with the seven‐fold coordinated Ca2+ cations undergo large structural changes. Especially, axial CaO bonds perpendicular to the axb plane are significantly shortened. Besides, it was shown that structural parameters, more or less in parallel orientation to the axb plane, are mainly responsible for the high resistance of the tobermorite structure to external pressure. The main mechanism of a dissipation of energy entered to the structure through the compression is proceeded by the tilting of the tetrahedra of the silicate chains and by large shortening of the axial CaO distances. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011
An estimation method of binding free energy in terms of ABEEMσπ/MM and continuum electrostatics fused into LIE method
Authors: Chen Shu‐Ling , Zhao Dong‐Xia , Yang Zhong‐Zhi 
Published: July 2010

AbstractA method is proposed for the estimation of absolute binding free energy of interaction between proteins and ligands. The linear interaction energy method is combined with atom‐bond electronegativity equalization method at σπ level Force field (fused into molecular mechanics) and generalized Born continuum model calculation of electrostatic solvation for the estimation of the absolute free energy of binding. The parameters of this method are calibrated by using a training set of 24 HIV‐1 protease–inhibitor complexes (PDB entry 1AAQ). A correlation coefficient of 0.93 was obtained with a root mean square deviation of 0.70 kcal mol−1. This approach is further tested on seven inhibitor and protease complexes, and it provides small root mean square deviation between the calculated binding free energy and experimental binding free energy without reparametrization. By comparing the radii of gyration and the hydrogen bond distances between ligand and protein of three training model molecules, the consistent comparison result of binding free energy is obtained. It proves that this method of calculating the binding free energy with appropriate structural analysis can be applied to quickly assess new inhibitors of HIV‐1 proteases. To test whether the parameters of this method can apply to other drug targets, we have validated this method for the drug target cyclooxygenase‐2. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011
Density functional theory study of a molecular allosteric switch for 2,2′‐bipyridyl‐3,3′‐15‐crown‐5
Authors: Miao Yuan , Wang Xueye , Jin Xin , Yi Ling , Ren Cuihuan 
Published: July 2010

AbstractA classical model of “molecular machine,” which acts as an ON–OFF switch for 2,2′‐bipyridyl‐3,3′‐15‐crown‐5 (L), has been theoretically studied. It is highly important to understand the mechanism of this switch. The alkali‐metal cations (Na+ and K+) and W(CO)4 fragment are introduced to coordinate with the different active sites of L, respectively. The density functional theory (DFT) method is used for understanding the stereochemical structural natures and thermodynamic properties of all the target molecules at B3LYP/6‐31G(d) and SDD (Stuttgart–Dresden) level, together with the corresponding effective core potential (ECP) for tungsten (W). The fully optimized geometries have been performed with real frequencies, which indicate the minima states. The nucleophilicity of L has been investigated by the Fukui functions. The natural bond orbital analysis is used to study the intermolecular charge‐transfer interactions and explore the origin of the internal forces of the molecular switch. In addition, the binding energies, enthalpies, Gibbs free energies, and the cation exchange energies have been studied for L, W(CO)4L, and their corresponding complexes. The properties of the complexes displayed by in presence or absence of the W(CO)4 fragment are also analyzed. The calculated results of allosterism displayed by L are in a good agreement with the experimental results. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011
Promising antimicrobial agents: Synthetic approaches to novel tricyclic and tetracyclic pyrimidinones with antimicrobial properties
Authors: Gaber Hatem M. , Bagley Mark C. , Sherif Sherif M. , Abdul‐Raouf Usama M. 
Published: July 2010

Abstract
magnified image New tricyclic pyrimidinone derivatives were obtained from the corresponding thiazolopyrimidinone or hydrazino systems. The annelation of tricyclic hydrazino compound with 1,2,4‐triazole and tetrazole moieties gave novel tetracyclic condensed pyrimidinones. The investigation of the antimicrobial properties of tricyclic and tetracyclic pyrimidinones, by agar‐well diffusion assay, was carried out against six pathogenic bacteria (Bacillus cereus, Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, Klebsiella spp, and Salmonella typhyrium) and four pathogenic fungi (Aspergillus flavus, Aspergillus niger, Aspergillus fumigatus, and Trichderma horozianum). Most of the compounds tested exhibited some degree of antimicrobial activity against microorganisms. Among these compounds, 4‐benzylidenhydrazino‐8‐cyano‐7‐(furan‐2‐yl)thiazolo[3,2‐a:4,5‐d′]dipyrimidin‐9‐one (12) showed the most favorable antibacterial activity, while compound 17 showed the highest effect on fungi. Interestingly, tetrazole derivative 19 displayed a remarkable effect on fungi much more than the corresponding 3‐substituted triazole derivatives on the one hand, whereas the lowest effect on bacteria on the other. J. Heterocyclic Chem., (2010).
Ester‐ and ketone‐substituted (±)‐1‐alkyl‐6‐nitro‐1,2,3,4‐tetrahydroquinolines by a tandem SNAr‐Michael reaction
Authors: Bunce Richard A. , Lee Eric J. 
Published: July 2010

Abstract
magnified image A synthesis of ester‐ and ketone‐substituted (±)‐1‐alkyl‐6‐nitro‐1,2,3,4‐tetrahydroquinolines has been developed from 2‐pentenoates and 2‐penten‐1‐ones substituted at C5 by a 2‐fluoro‐5‐nitrophenyl group. The cyclization involves an SNAr reaction followed by a Michael addition that occurs exo to the final ring. A previously reported version of this annulation proceeded by an initial endo Michael addition (acceptor became part of the final ring) followed by an SNAr ring closure. The current reactions proceed in 82–97% yields in DMSO using primary amines that are unbranched at the α carbon. The synthesis of the reaction substrates as well as process optimization, mechanistic studies to elucidate the reaction chronology and comparisons with the endo Michael variant are presented. J. Heterocyclic Chem., (2010).
Synthesis of new sulfur‐linked 1,2,4‐triazolothienopyrimidine and 1,2,4‐triazolopyrazolopyrimidine derivatives containing fused heterocyclic pyrimidines
Authors: Song Yang‐Heon , Son Hoon Young 
Published: July 2010

Abstract
magnified image A series of novel bis‐heterocyclic compounds 12, 13, 14, 15, 16, 17, 18, 19, 20 were synthesized by integrating fused heterocyclic pyrimidines, such as thienopyrimidine and pyrazolopyrimidine into the scaffold of thienotriazolo‐ pyrimidines, and pyrazolotriazolopyrimidines through a sulfur‐linkage. J. Heterocyclic Chem., (2010).