bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methylglyoxal and high glucose co‐treatment induces apoptosis or necrosis in human umbilical vein endothelial cells
Authors: Chan Wen‐Hsiung , Wu Hsin‐Jung 
Published: August 2007

AbstractHyperglycemia and elevation of methylglyoxal (MG) are symptoms of diabetes mellitus (DM). We previously showed that high glucose (HG; 30 mM) or MG (50–400 µM) could induce apoptosis in mammalian cells, but these doses are higher than the physiological concentrations of glucose and MG in the plasma of DM patients. The physiological concentration of MG and glucose in the normal blood circulation is about 1 µM and 5 mM, respectively. Here, we show that co‐treatment with concentrations of MG and glucose comparable to those seen in the blood circulation of DM patients (5 µM and 15–30 mM, respectively) could cause cell apoptosis or necrosis in human umbilical vein endothelial cells (HUVECs) in vitro. HG/MG co‐treatment directly increased the reactive oxygen species (ROS) content in HUVECs, leading to increases in intracellular ATP levels, which can control cell death through apoptosis or necrosis. Co‐treatment of HUVECs with 5 µM MG and 20 mM glucose significantly increased cytoplasmic free calcium levels, activation of nitric oxide synthase (NOS), caspase‐3 and ‐9, cytochrome c release, and apoptotic cell death. In contrast, these apoptotic biochemical changes were not detected in HUVECs treated with 5 µM MG and 30 mM glucose, which appeared to undergo necrosis. Pretreatment with nitric oxide (NO) scavengers could inhibit 5 µM MG/20 mM glucose‐induced cytochrome c release, decrease activation of caspase‐9 and caspase‐3, and increase the gene expression and protein levels of p53 and p21, which are known to be involved in apoptotic signaling. Inhibition of p53 protein expression using small interfering RNA (siRNA) blocked the activation of p21 and the cell apoptosis induced by 5 µM MG/20 mM glucose. In contrast, inhibition of p21 protein expression by siRNA prevented apoptosis in HUVECs but had no effect on p53 expression. These results collectively suggest that the treatment dosage of MG and glucose could determine the mode of cell death (apoptosis vs. necrosis) in HUVECs, and both ROS and NO played important roles in MG/HG‐induced apoptosis of these cells. J. Cell. Biochem. 103: 1144–1157, 2008. © 2007 Wiley‐Liss, Inc.
S100A6 (calcyclin) enhances the sensitivity to apoptosis via the upregulation of caspase‐3 activity in Hep3B cells
Authors: Joo Joung Hyuck , Yoon Sun Young , Kim Joo Heon , Paik Sang‐Gi , Min Sung Ran , Lim Jong‐Seok , Choe In Seong , Choi Inpyo , Kim Jae Wha 
Published: August 2007

AbstractS100A6 (calcyclin) is a small calcium‐binding protein which has been implicated in several cellular processes such as cell cycle progression, cytoskeleton rearrangement, and exocytosis. Also the upregulation of S100A6 has been reported in a variety of tumors and linked to metastasis. However, exact intracellular roles of S100A6 related with apoptosis have not been clarified yet. Here we demonstrated that the upregulation of S100A6 enhances the cell death rate compared to the control under the apoptotic conditions. In exogenously S100A6 induced Hep3B cells, cell viability was significantly decreased compared with mock and S100A6‐knockdown cells under calcium ionophore A23187 treatment. The exogenously introduced S100A6 significantly affected the caspase‐3‐like activity in programmed cell death through the enhanced caspase‐3 expression, which was verified by promoter assay in wild or mutant S100A6‐transfected Hep3B cells. Next, the promoter activity of caspase‐3 was increased by 2.5‐folds in wild‐type S100A6‐transfected cells compared to mutant 2 (E67K, mutant of EF‐hand motif) or control. Our results suggest that S100A6 might be involved in the processing of apoptosis by modulating the transcriptional regulation of caspase‐3. J. Cell. Biochem. 103: 1183–1197, 2008. © 2007 Wiley‐Liss, Inc.
Purα as a cellular co‐factor of Rev/RRE‐mediated expression of HIV‐1 intron‐containing mRNA
Authors: Kaminski Rafal , Darbinian Nune , Sawaya Bassel E. , Slonina Dorota , Amini Shohreh , Johnson Edward M. , Rappaport Jay , Khalili Kamel , Darbinyan Armine 
Published: August 2007

AbstractTo ensure successful replication, HIV‐1 has developed a Rev‐mediated RNA transport system that promotes the export of unspliced genomic RNA from nuclei to cytoplasm. This process requires the Rev responsive element (RRE) that is positioned in the viral transcript encoding Env protein, as well as in unspliced and singly spliced viral transcripts. We identified Purα, a single‐stranded nucleic acid binding protein as a cellular partner for Rev that augments the appearance of unspliced viral RNAs in the cytoplasm. A decrease in the level of Purα expression by siRNA diminishes the level of Rev‐dependent expression of viral RNA. Through its nucleic acid binding domain, Purα exhibits the ability to interact with the multimerization and RBD domains of Rev. Similar to Rev, Purα associates with RRE and in the presence of Rev forms a complex with slower electrophoretic mobility than those from Rev:RRE and Purα:RRE. The interaction of Purα with RRE occurs in the cytoplasm where enhanced association of Rev with RRE is observed. Our data indicate that the partnership of Purα with Rev is beneficial for Rev‐mediated expression of the HIV‐1 genome. J. Cell. Biochem. 103: 1231–1245, 2008. © 2007 Wiley‐Liss, Inc.
All in the family: Using inherited cancer syndromes to understand de‐regulated cell signaling in brain tumors
Authors: Houshmandi S. Sean , Gutmann David H. 
Published: August 2007

AbstractThe cell signaling pathways that are tightly regulated during development are often co‐opted by cancer cells to allow them to escape from the constraints that normally limit cell growth and cell movement. In this regard, de‐regulated signaling in cancer cells confers a number of key tumor‐associated properties, including increased cell proliferation, decreased cell death, and increased cell motility. The identification of some of these critical signaling pathways in the nervous system has come from studies of inherited cancer syndromes in which affected individuals develop brain tumors. The study of brain tumors arising in patients with neurofibromatosis 1 (NF1), neurofibromatosis 2 (NF2), and tuberous sclerosis complex (TSC) has already uncovered several key intracellular signaling pathways important for modulating brain tumor growth. An in‐depth analysis of these intracellular signaling pathways will not only lead to an improved understanding of the process of brain tumorigenesis, but may also provide important molecular targets for future therapeutic drug design. J. Cell. Biochem. 102: 811–819, 2007. © 2007 Wiley‐Liss, Inc.
Osteopontin overexpression in breast cancer: Knowledge gained and possible implications for clinical management
Authors: Tuck Alan B. , Chambers Ann F. , Allan Alison L. 
Published: August 2007

AbstractOsteopontin (OPN) is a secreted protein that is overexpressed in a number of human cancers, and has been associated with increased metastatic burden and poor prognosis in breast cancer patients. The OPN protein contains several conserved structural elements including heparin‐ and calcium‐binding domains, a thrombin‐cleavage site, a CD44 binding site, and two integrin‐binding sites. Experimental studies have shown that the ability of OPN to interact with a diverse range of factors, including cell surface receptors (integrins, CD44), secreted proteases (matrix metalloproteinases, urokinase plasminogen activator), and growth factor/receptor pathways (TGFα/EGFR, HGF/Met) is central to its role in malignancy. These complex signaling interactions can result in changes in gene expression, which ultimately lead to alterations in cell properties involved in malignancy such as adhesion, migration, invasion, enhanced tumor cell survival, tumor angiogenesis, and metastasis. Therefore, OPN is not merely associated with cancer, but rather it plays a multi‐faceted functional role via complex molecular cross‐talk with other factors. This review will focus on the role of OPN in breast cancer, in particular on the malignancy‐promoting aspects of OPN that may reveal opportunities for new approaches to the clinical management of breast cancer. J. Cell. Biochem. 102: 859–868, 2007. © 2007 Wiley‐Liss, Inc.
Overexpression of Akt1 upregulates glycogen synthase activity and phosphorylation of mTOR in IRS‐1 knockdown HepG2 cells
Authors: Varma Shailly , Khandelwal Ramji L. 
Published: August 2007

AbstractInsulin receptor substrate (IRS) proteins are important docking proteins in mediating the insulin signaling cascade. We have investigated the effect of short interfering RNA (siRNA) mediated knockdown of IRS‐1 on insulin signaling cascade in primary human hepatocellular carcinoma HepG2 cell line and HepG2 cells overexpressing Akt1/PKB‐α (HepG2‐CA‐Akt/PKB). IRS‐1 knockdown in both cell lines resulted in reduction of insulin stimulated Akt1 phosphorylation at Ser 473. In parental HepG2 cells, IRS‐1 knockdown resulted in reduction (ca. 50%) in the basal level of phosphorylated mTOR (Ser 2448) irrespective of insulin treatment. In contrast, HepG2‐CA‐Akt/PKB cells showed an upregulation in the basal level of phosphorylated mTOR (Ser 2448) (ca. 40%). Insulin mediated phosphorylation of mTOR was reduced. IRS‐1 knockdown also reduced the cell proliferation of parental HepG2 cells by ca. 30% in the presence/absence of insulin, whereas in HepG2‐CA‐Akt/PKB the cell proliferation was reduced by 15% and treatment of insulin further reduced it to ca. 50% (vs. control). IRS‐1 knockdown also reduced the glycogen synthase (GS) activity in parental HepG2 cells, however, it was upregulated in HepG2‐CA‐Akt/PKB cells.These results suggest that knockdown of IRS‐1 abolished basal as well as insulin mediated phosphorylation/activity of proteins involved in cell proliferation or glycogen metabolism in the parental Hep2 cells. IRS‐1 knockdown in cells overexpressing constitutively active Akt1/PKB‐α either did not change or upregulated the basal levels of phosphorylated/active proteins. However, insulin mediated response was either not altered or downregulated in these cells. J. Cell. Biochem. 103: 1424–1437, 2008. © 2007 Wiley‐Liss, Inc.
Systematic studies on the computation of nuclear magnetic resonance shielding constants and chemical shifts: The density functional models
Authors: Wu Anan , Zhang Ying , Xu Xin , Yan Yijing 
Published: August 2007

AbstractWe present a systematic density functional investigation on the prediction of the 13C, 15N, 17O, and 19F NMR properties of 23 molecules with 21 density functionals. Extensive comparisons are made for both 13C magnetic shieldings and chemical shifts with respect to the gas phase experimental data and the best CCSD(T) results. We find that the OPBE and OPW91 exchange‐correlation functionals perform significantly better than some popular functionals such as B3LYP and PBE1PBE, even surpassing, in many cases, the standard wavefunction‐based method MP2. Further analysis has been performed to explore the individual role played by various exchange and correlation functionals. We find that the B88 and PBE exchange functionals have a too strong tendency of deshielding, leading to too deshielded magnetic shielding constants; whereas the OPTX exchange functional performs remarkably well. We claim that the main source of error arises from the exchange functional, but correlation functional also makes important contribution. We find that the correlation functionals may be grouped into two classes. class A, such as LYP and B98, leads to deshielded NMR values, deteriorating the overall performance; whereas class B, such as PW91 and PBE, generally increases the absolute shieldings, which complements the exchange functionals, leading to improved results in the calculation of NMR data. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Excited states of GFP chromophore and active site studied by the SAC‐CI method: Effect of protein‐environment and mutations
Authors: Hasegawa Jun‐Ya , Fujimoto Kazuhiro , Swerts Ben , Miyahara Tomoo , Nakatsuji Hiroshi 
Published: August 2007

AbstractExcited states of fluorescent proteins were studied using symmetry‐adapted cluster‐configuration interaction (SAC‐CI) method. Protein‐environmental effect on the excitation and fluorescence energies was investigated. In green fluorescent protein (GFP), the overall protein‐environmental effect on the first excitation energy is not significant. However, glutamine (Glu) 94 and arginine (Arg96) have the red‐shift contribution as reported in a previous study (Laino et al., Chem Phys 2004, 298, 17). The excited states of GFP active site (GFP‐W22‐Ser205‐Glu222‐Ser65) were also calculated. Such large‐scale SAC‐CI calculations were performed with an improved code containing a new algorithm for the perturbation selection. The SAC‐CI results indicate that a charge‐transfer state locates at 4.19 eV, which could be related to the channel of the photochemistry as indicated in a previous experimental study. We also studied the excitation and fluorescence energies of blue fluorescent protein, cyan fluorescent protein, and Y66F. The SAC‐CI results are very close to the experimental ones. The protonation state of blue fluorescent protein was determined. Conformation of cyan fluorescent protein indicated by the present calculation agrees to the experimentally observed structure. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Theoretical investigation on the protonation reactions and products of the stable [N,C,C,S] isomers
Authors: Kan Wei , Yu Hai‐Tao , Fu Hong‐Gang , Wu Yi‐Qun 
Published: August 2007

AbstractA theoretical study on the protonation system of [N,C,C,S], [H,N,C,C,S]+, was performed at the B3LYP/6‐311++G(d,p) and CCSD(T)/6‐311++G(2df,2p) (single point) levels of theory. On the doublet [H,N,C,C,S]+ surface, 24 species were located as energy minima and 10 of them were considered as kinetically stable species. The species HNCCS+ with 2A′ state and a shallow W‐shaped skeleton was predicted to be the global minimum and kinetically the most stable species, being in good agreement with previous experimental findings. Furthermore, the protonation reactions of the stable [N,C,C,S] isomers were investigated in detail. The calculation results indicated that the [N,C,C,S] isomers may be significantly stabilized upon protonation. Finally, the possible covalent structures of the [H,N,C,C,S]+ isomers with considerable stability were briefly discussed. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
IDEA: Interface dynamics and energetics algorithm
Authors: Duca D. , Barone G. , Giuffrida S. , Varga Zs. 
Published: August 2007

AbstractIDEA, interface dynamics and energetics algorithm, was implemented, in FORTRAN, under different operating systems to mimic dynamics and energetics of elementary events involved in interfacial processes. The code included a parallel elaboration scheme in which both the stochastic and the deterministic components, involved in the developed physical model, worked simultaneously. IDEA also embodied an optionally running VISUAL subroutine, showing the dynamic energy changes caused by the surface events, e.g., occurring at the gas‐solid interface. Monte Carlo and ordinary differential equation system subroutines were employed in a synergistic way to drive the occurrence of the elementary events and to manage the implied energy flows, respectively. Biphase processes, namely isothermal and isobaric adsorption of carbon monoxide on nickel, palladium, and platinum surfaces, were first studied to test the capability of the code in modeling real frames. On the whole, the simulated results showed that IDEA could reproduce the inner characteristics of the studied systems and predict properties not yet experimentally investigated. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water
Authors: Gao Jiali , Wong Kin‐Yiu , Major Dan T. 
Published: August 2007

AbstractAn integrated Feynman path integral‐free energy perturbation and umbrella sampling (PI‐FEP/UM) method has been used to investigate the kinetic isotope effects (KIEs) in the proton transfer reaction between nitroethane and acetate ion in water. In the present study, both nuclear and electronic quantum effects are explicitly treated for the reacting system. The nuclear quantum effects are represented by bisection sampling centroid path integral simulations, while the potential energy surface is described by a combined quantum mechanical and molecular mechanical (QM/MM) potential. The accuracy essential for computing KIEs is achieved by a FEP technique that transforms the mass of a light isotope into a heavy one, which is equivalent to the perturbation of the coordinates for the path integral quasiparticle in the bisection sampling scheme. The PI‐FEP/UM method is applied to the proton abstraction of nitroethane by acetate ion in water through molecular dynamics simulations. The rule of the geometric mean and the Swain–Schaad exponents for various isotopic substitutions at the primary and secondary sites have been examined. The computed total deuterium KIEs are in accord with experiments. It is found that the mixed isotopic Swain–Schaad exponents are very close to the semiclassical limits, suggesting that tunneling effects do not significantly affect this property for the reaction between nitroethane and acetate ion in aqueous solution. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Full configuration interaction calculation of the low lying valence and Rydberg states of BeH
Authors: Pitarch‐Ruiz J. , Sánchez‐Marín J. , Velasco A. M. 
Published: August 2007

AbstractThe all‐electron full configuration interaction (FCI) vertical excitation energies for some low lying valence and Rydberg excited states of BeH are presented in this article. A basis set of valence atomic natural orbitals has been augmented with a series of Rydberg orbitals that have been generated as centered onto the Be atom. The resulting basis set can be described as 4s2p1d/2s1p (Be/H) + 4s4p3d. It allows to calculate Rydberg states up to n= {3,4,5} of the s, p, and d series of Rydberg states. The FCI vertical ionization potential for the same basis set and geometry amounts to 8.298 eV. Other properties such as FCI electric dipole and quadrupole moments and FCI transition dipole and quadrupole moments have also been calculated. The results provide a set of benchmark values for energies, wave functions, properties, and transition properties for the five electron BeH molecule. Most of the states have large multiconfigurational character in spite of their essentially single excited nature and a number of them present an important Rydberg‐valence mixing that is achieved through the mixed nature of the particle MO of the single excitations. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Components for integral evaluation in quantum chemistry
Authors: Kenny Joseph P. , Janssen Curtis L. , Valeev Edward F. , Windus Theresa L. 
Published: August 2007

AbstractSharing low‐level functionality between software packages enables more rapid development of new capabilities and reduces the duplication of work among development groups. Using the component approach advocated by the Common Component Architecture Forum, we have designed a flexible interface for sharing integrals between quantum chemistry codes. Implementation of these interfaces has been undertaken within the Massively Parallel Quantum Chemistry package, exposing both the IntV3 and Cints/Libint integrals packages to component applications. Benchmark timings for Hartree‐Fock calculations demonstrate that the overhead due to the added interface code varies significantly, from less than 1% for small molecules with large basis sets to nearly 10% for larger molecules with smaller basis sets. Correlated calculations and density functional approaches encounter less severe performance overheads of less than 5%. While these overheads are acceptable, additional performance losses occur when arbitrary implementation details, such as integral ordering within buffers, must be handled. Integral reordering is observed to add an additional overhead as large as 12%; hence, a common standard for such implementation details is desired for optimal performance. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Understanding topological symmetry: A heuristic approach to its determination
Authors: Contreras M. L. , Alvarez J. , Guajardo D. , Rozas R. 
Published: August 2007

AbstractAn algorithm based on heuristic rules for topological symmetry perception of organic structures having heteroatoms, multiple bonds, and any kind of cycle, and configuration, is presented. This algorithm identifies topological symmetry planes and sets of equivalent atoms in the structure, named symmetry atom groups (SAGs). This approach avoids both the need to explore the entire graph automorphism groups, and to encompass cycle determination, resulting in a very effective computer processing. Applications to several structures, some of them highly symmetrical such as dendrimers, are presented. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Excitation and circular dichroism spectra of (−)‐(3aS, 7aS)‐2‐chalcogena‐trans‐hydrindans(Ch = S, Se, Te): SAC and SAC‐CI calculations
Authors: Honda Yasushi , Kurihara Atsushi , Hada Masahiko , Nakatsuji Hiroshi 
Published: August 2007

AbstractThe ground and several electronic excited states of (3aS,7aS)‐2‐chalcogena‐trans‐hydrindans were calculated by the symmetry adapted cluster (SAC) and SAC‐configuration interaction (SAC‐CI) methods. Theoretical electronic excitation spectra and natural circular dichroism (CD) spectra were obtained for these compounds, and the calculated spectra showed good agreement with the experimental ones reported by Laur (Proceedings of the Third International Symposium on Organic Selenium and Tellurium compounds, Metz, France, 1979, pp. 219–299). For all the chalcogen compounds, the first singlet excited states are assigned to n‐σ* and the other states are assigned to n‐Rydberg in our calculations. It indicates that the spectra for the sulfide, selenide, and telluride are almost regarded as the analogues except for the red shifts of the band positions from the sulfide to the telluride. For the telluride, however, the experimental spectra have shapes that cannot be interpreted by the singlet excitations solely. Our calculations predict the triplet states that account for the spectral shapes, indicating importance of the spin‐orbit interaction effects for the accurate reproduction of the experimental spectra of the telluride. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Uterine artery pseudoaneurysm: Unusual cause of delayed postpartum hemorrhage
Authors: Gürses Cemil , Yılmaz Saim , Bıyıklı Sabiha , Yıldız İ. Okan , Sindel Timur 
Published: August 2007

AbstractWe describe a case of uterine artery pseudoaneurysm in a 21‐year‐old woman with postpartum hemorrhage. This condition is easily diagnosed with duplex Doppler sonography and can be treated with embolization, but only if delayed postpartum hemorrhage is considered in the differential diagnosis. © 2007 Wiley Periodicals, Inc. J Clin Ultrasound, 2008