bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aerobic glycolysis in cancers: Implications for the usability of oxygen‐responsive genes and fluorodeoxyglucose‐PET as markers of tissue hypoxia
Authors: Busk Morten , Horsman Michael R. , Kristjansen Paul E.G. , van der Kogel Albert J. , Bussink Johan , Overgaard Jens 
Published: March 2008

AbstractThe hypoxia‐responsiveness of the glycolytic machinery may allow pretreatment identification of hypoxic tumors from HIF‐1 targets (e.g., Glut‐1) or [18F]‐fluorodeoxyglucose positron emission tomography but results have been mixed. We hypothesized that this discrepancy is an inevitable consequence of elevated aerobic glycolysis in tumors (Warburg effect) as energetics in predominantly glycolytic cells is little affected by hypoxia. Accordingly, we characterized glycolytic and mitochondrial ATP generation in normoxic and anoxic cell lines. Measurements demonstrated that most cancer cells rely largely on aerobic glycolysis as it accounts for 56–63% of their ATP budget, but in the cervical carcinoma SiHa, ATP synthesis was mainly mitochondrial. Moreover, the stimulatory effect of anoxia on glycolytic flux was inversely correlated to the relative reliance on aerobic glycolysis. Next, tumor cells representing a Warburg or a nonglycolytic phenotype were grown in mice and spatial patterns of hypoxia (pimonidazole‐stained), Glut‐1 expression and 18F‐FDG uptake were analysed on sectioned tumors. Only in SiHa tumors did foci of elevated glucose metabolism consistently colocalize with regions of hypoxia and elevated Glut‐1 expression. In contrast, spatial patterns of Glut‐1 and pimonidazole staining correlated reasonably well in all tumors. In conclusion, Glut‐1's value as a hypoxia marker is not severely restricted by aerobic glycolysis. In contrast, the specificity of 18F‐FDG uptake and Glut‐1 expression as markers of regional hypoxia and glucose metabolism, respectively, scales inversely with the intensity of the Warburg effect. This linkage suggests that multi‐tracer imaging combining FDG and hypoxia‐specific markers may provide therapeutically relevant information on tumor energetic phenotypes. © 2008 Wiley‐Liss, Inc.
Gain of 1q21 and distinct adverse cytogenetic abnormalities correlate with increased microcirculation in multiple myeloma
Authors: Hillengass Jens , Zechmann Christian M. , Nadler Andreas , Hose Dirk , Cremer Friedrich W. , Jauch Anna , Heiss Christiane , Benner Axel , Ho Anthony D. , Bartram Claus R. , Kauczor Hans‐Ulrich , Delorme Stefan , Goldschmidt Hartmut , Moehler Thomas M. 
Published: March 2008

AbstractTo identify genetic mechanisms controlling bone marrow microcirculation and angiogenesis in patients with plasma cell disease we simultaneously performed bone marrow dynamic contrast‐enhanced magnetic resonance imaging (DCE‐MRI) and cytogenetics (iFISH) on CD138 purified plasma cells of MGUS (n=31) and untreated multiple myeloma (MM) (n = 87) patients. The adverse cytogenetic abnormalities gain of 1q21, deletion 17p13 and deletion 13q14 significantly correlated with at least one DCE‐MRI finding (aberrant “focal” microcirculation pattern, increase in median microcirculation parameter Amplitude A or exchange rate constant kep). We conclude that gain of 1q21, deletion 13q14 and deletion 17p13 trigger the angiogenic cascade in MM. Our findings will have important implications for the design, analysis and stratification for clinical studies of patients with MM in particular if compounds with antiangiogenic activity are used. © 2008 Wiley‐Liss, Inc.
Selected class I and class II HLA alleles and haplotypes and risk of high‐grade cervical intraepithelial neoplasia
Authors: Ades Steven , Koushik Anita , Duarte‐Franco Eliane , Mansour Nabil , Arseneau Jocelyne , Provencher Diane , Gilbert Lucy , Gotlieb Walter , Ferenczy Alex , Coutlée François , Roger Michel , Franco Eduardo L. ,   for the Biomarkers of Cervical Cancer Risk (BCCR) Study Team
Published: March 2008

AbstractHuman leukocyte antigens (HLAs) present foreign antigens to the immune system and may be important determinants of cervical neoplasia. Previously published associations between HLA and cervical neoplasia exhibit considerable variation in findings. The biomarkers of cervical cancer risk (BCCR) case‐control study addressed the role of specific HLA alleles as cofactors in the development of high‐grade cervical intraepithelial neoplasia (HG‐CIN) based on the most consistent evidence from published literature. Cases (N = 381) were women with histologically‐confirmed HG‐CIN attending colposcopy clinics and controls (N = 884) were women from outpatient clinics with normal cytological screening smears. Subjects were mainly of French‐Canadian descent. Cervical specimens were tested for human papillomavirus (HPV) DNA and HLA genotypes by PGMY L1 consensus primer PCR and a PCR sequence‐specific primer method, respectively. Unlike other studies, the DQB1*03 and DRB1*13 allele groups were not associated with risk of HG‐CIN. The B7‐DRB1*1501‐DQB1*0602 haplotype was associated with a 41% overall reduction in HG‐CIN risk (odds ratio [OR] = 0.59; 95% confidence interval [CI]: 0.36–0.96), and an 83% reduction in risk of HG‐CIN among HPV 16 or HPV 18‐positive subjects (OR = 0.17; 95%CI: 0.05–0.54). Paradoxically, however, the same haplotype was associated with HPV 16/18 infection risk among controls (OR = 8.44, 95%CI: 1.12–63.73). In conclusion, the B7‐DRB1*1501‐DQB1*0602 haplotype was protective against HG‐CIN, especially in individuals infected with oncogenic HPV, but the mechanism of the association seems to involve multiple steps in the natural history of HPV and CIN. © 2008 Wiley‐Liss, Inc.
Two‐dimensional differential gel electrophoresis/analysis of diethylnitrosamine induced rat hepatocellular carcinoma
Authors: Qi Yanting , Chen Xiaona , Chan Chu‐yan , Li Dan , Yuan Chonggang , Yu Fei , Lin Marie C. , Yew David T. , Kung Hsiang‐Fu , Lai Lihui 
Published: March 2008

AbstractDiethylnitrosamine (DEN) is a known carcinogen that can alkylate DNA molecules. In rats, DEN‐induced hepatocellular carcinoma (HCC) model is well established. In this study, we used a two‐dimensional differential gel electrophoresis (2D‐DIGE) system and liquid chromatography/mass spectrometry/mass spectrometry to identify the differential expression protein profiles between the DEN‐induced HCC and healthy liver cells. Western blotting and semiquantitative RT‐PCR were used to further confirm the results. Seventeen differentially expressed spots were identified in DEN‐induced HCC cells. Among all, the most prominent upregulated proteins include the members of the glutathione S‐transferase super family, aldo‐keto reductase superfamily and proteins involved in the response to oxidative stress. Downregulation was observed in 2 proteins that were known to contribute to hepatic dysfunction. This study provides the first comprehensive protein profiling of the DEN‐induced HCC in rats. This model simulates the differential protein expression of human HCC and may be useful for further understanding the mechanism of HCC tumorigenesis. © 2008 Wiley‐Liss, Inc.
Nonadditive effects in ternary H2–cation–PAH systems
Authors: Donchev Alexander G. 
Published: March 2008

AbstractThis article reports state‐of‐the‐art ab initio calculations at the second order of Møller‐Plesset perturbation theory of molecular hydrogen binding in its ternary complexes with lightweight alkali cations (M = Li or Na) and polycyclic aromatic hydrocarbons (PAHs) up to coronene. The study revealed a substantial nonadditive contribution to the H2 stabilization energy. In the most stable conformation, the nonadditive contribution weakens the H2 binding by a factor of nearly 1.5 and 1.3 for Li and Na cations, respectively, as compared with the pairwise sum of direct H2–M+ and H2–PAH contributions. In the Li case, the presence of PAH not only does not promote H2 binding but has a large (∼20%) weakening effect in comparison with the initial H2–Li+ interaction. In the Na case, the presence of PAH has the usual stabilizing influence on the hydrogen binding. A careful analysis of the physical components of the nonadditive effect on the example of H2–M+–benzene complexes revealed the dominating role of the induction nonadditivity. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Combining a polarizable force‐field and a coarse‐grained polarizable solvent model: Application to long dynamics simulations of bovine pancreatic trypsin inhibitor
Authors: Masella Michel , Borgis Daniel , Cuniasse Philippe 
Published: March 2008

AbstractThe dynamic coupling between a polarizable protein force field and a particle‐based implicit solvent model is described. The polarizable force field, TCPEp, developed recently to simulate protein systems, is characterized by a reduced number of polarizable sites, with a substantial gain in efficiency for an equal chemical accuracy. The Polarizable Pseudo‐Particle (PPP) solvent model represents the macroscopic solvent polarization by induced dipoles placed on mobile Lennard‐Jones pseudo‐particles. The solvent‐induced dipoles are sensitive to the solute electric field, but not to each other, so that the computational cost of solvent–solvent interactions is basically negligible. The solute and solvent induced dipoles are determined self‐consistently and the equations of motion are solved using an efficient iterative multiple time step procedure. The solvation cost with respect to vacuum simulations is shown to decrease with solute size: the estimated multiplicative factor is 2.5 for a protein containing about 1000 atoms, and as low as 1.15 for 8000 atoms. The model is tested for six 20 ns molecular dynamics trajectories of a traditional benchmark system: the hydrated Bovine Pancreatic Trypsin Inhibitor (BPTI). Even though the TCPEp parameters have not been refined to be used with the solvent PPP model, we observe a good conservation of the BPTI structure along the trajectories. Moreover, our approach is able to provide a description of the protein solvation thermodynamic at the same accuracy as the standard Poisson‐Boltzman continuum methods. It provides in addition a good description of the microscopic structural aspects concerning the solute/solvent interaction. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Empirical entropic contributions in computational docking: Evaluation in APS reductase complexes
Authors: Chang Max W. , Belew Richard K. , Carroll Kate S. , Olson Arthur J. , Goodsell David S. 
Published: March 2008

AbstractThe results from reiterated docking experiments may be used to evaluate an empirical vibrational entropy of binding in ligand–protein complexes. We have tested several methods for evaluating the vibrational contribution to binding of 22 nucleotide analogues to the enzyme APS reductase. These include two cluster size methods that measure the probability of finding a particular conformation, a method that estimates the extent of the local energetic well by looking at the scatter of conformations within clustered results, and an RMSD‐based method that uses the overall scatter and clustering of all conformations. We have also directly characterized the local energy landscape by randomly sampling around docked conformations. The simple cluster size method shows the best performance, improving the identification of correct conformations in multiple docking experiments. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Systematic investigation on the geometric dependence of the calculated nuclear magnetic shielding constants
Authors: Zhang Ying , Xu Xin , Yan Yijing 
Published: March 2008

AbstractWe perform a systematic examination on the dependence of the calculated nuclear magnetic shielding constants on the chosen geometry for a selective set of density functional methods of B3LYP, PBE0, and OPBE. We find that the OPBE exchange‐correlation functional performs remarkably well when either the optimized geometries or the experimental geometries are used. The popular B3LYP and PBE0 functionals have a clear tendency of deshielding, giving shieldings that are usually too low and shifts that are usually too high, at the experimental geometries. Combined with the Hartree‐Fock geometries, however, much improved magnetic constants are obtained for B3LYP and PBE0, due to the compensation effect from the systematic underestimation of bond lengths by the Hartree‐Fock method. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Novel H‐bonded base dimers as repeat units for information‐bearing self‐associative duplexes: A B3LYP/6‐31G* search
Authors: Neihsial Siamkhanthang , Lyngdoh Richard H. Duncan 
Published: March 2008

AbstractDensity functional theory at the B3LYP/6‐31G* level with counterpoise correction has been employed to study six sets of nitrogenous bases for the capacity of each to form H‐bonded dimers restricted to a chosen pairing configuration. These results are augmented by MP2/6‐311++G(d,p) single point calculations on the B3LYP/6‐31G* optimized geometries. Each set has two bases, including substituted azoles, imidazoles, pyrimidines, and fused ring systems. This study aims to determine the suitability of each set to furnish H‐bonded base pairs which may serve as repeat units for self‐associative H‐bonded macromolecular duplexes with the capacity to store and replicate information at the molecular level. Out of the various possibilities tested here, a set of two substituted pyrimidines best satisfies the prescribed criteria and may be put forward as a good candidate to yield isomorphic repeat units for designing such synthetic information‐bearing macromolecular duplexes. The optimized configurations of these chosen base pairs as calculated at the B3LYP/6‐31G* level compare well with those calculated at the B3LYP/6‐31++G(d,p) and MP2/6‐31G(d,p) levels, and indicate that isomorphism of the two base pairs is independent of method used. Assuming a one‐to‐one correspondence for encoding information in the macromolecule, such a set of two bases can allow the macromolecule to encode up to 8 types of encrypted species. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Density functional study on the reaction mechanism of palladium‐catalyzed addition of cyanoboranes to alkynes
Authors: Wang M. Y. , Cheng L. , Wu Z. J. 
Published: March 2008

AbstractThe B3LYP hybrid density functional method has been carried out to study theoretically the mechanism of Pd(0)‐catalyzed alkyne cyanoboration reaction. Both the intermolecular and intramolecular alkyne cyanoboration reactions were studied. For each reaction, three paths were proposed. In path A of each reaction, the first step is BCN bond oxidative addition to bisphosphine complex Pd(PH3)2, in path B of each reaction, the first step is alkyne coordination to bisphosphine complex Pd(PH3)2, and in path C of each reaction, the first step is the PH3 dissociation from Pd(PH3)2 to form monophosphine complex Pd(PH3). For both reactions, path B is favored. The dissociation and recoordination of phosphine ligand are found to be very important for the entire reaction, in agreement with the experiment. In both intermolecular and intramolecular cyanoboration reactions, cyano migration is preferred to take place compared with alkenylboryl migration for the formation of the final cis products. The rate‐determining step for both intermolecular and intramolecular cyanoboration reactions is found to be the insertion of carbon‐carbon triple bond into PdB bond with the activation energy of 38.4 and 34.3 kcal/mol relative to the initial reactants, respectively. These values suggest that intramolecular reaction is relatively easy to occur. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
The intensity, location and structure of the tropical rainbelt over west Africa as factors in interannual variability
Authors: Nicholson Sharon E. 
Published: March 2008

AbstractThis study examines the nature of the tropical rainbelt over west Africa in 4 years corresponding to the four most common patterns of rainfall anomalies in the region. These include 2 years that were anomalously wet in the Sahel, 1955 and 1950, and 2 years, 1983 and 1984, that were anomalously dry. The year 1955 is ubiquitously wet, while a rainfall dipole prevails in 1950, with abnormally high rainfall in the Sahelian latitudes but drought conditions in the Guinea Coast latitudes to the south. The year 1983 is ubiquitously dry and 1984 is a year with a rainfall dipole but opposite in phase (i.e. Sahel dry, Guinea Coast wet). The main results of the study are that the contrast between wet and dry years is associated with a weakening and contraction of the tropical rainbelt. In addition, a north/south displacement of the rainbelt is associated with the dipole patterns, with a northward/southward shift bringing good rains to the Sahel/Guinea Coast. These shifts are associated with north/south shifts in the latitude of the African Easterly Jet (AEJ) over west Africa. The latitudinal position and extent of the rainbelt correspond to the latitudinal position and extent of an immense ‘tongue’ of strong ascending motion. The core of the ascending motion is bound by the axes of the AEJ on the north and the Tropical Easterly Jet (TEJ) in the south. This importance of these two jets in determining the character of the summer rainy season implies that the Sahelian region provides the link between the Sahel and global scale phenomena. Copyright © 2008 Royal Meteorological Society
Muscle satellite cell and atypical myogenic progenitor response following exercise
Authors: Parise Gianni , McKinnell Iain W. , Rudnicki Michael A. 
Published: March 2008

AbstractSkeletal muscle satellite cells play an essential role in muscle regeneration and exercise adaptation. In recent years atypical myogenic progenitors (non–satellite‐cell muscle stem cells) have been identified in skeletal muscle and have been hypothesized to play an important role in the process of muscle regeneration. It remains unknown, however, whether any populations other than satellite cells play a significant role in repair and adaptation following exercise‐induced damage. We assessed the response of the satellite cell population and the CD45+:Sca‐1+ cell population, previously shown to support muscle regeneration following cardiotoxin‐induced injury, after acute eccentrically biased exercise in wild‐type mice. We observed evidence of focal muscle damage and repair following the exercise protocol using electron microscopy, hematoxylin–eosin staining, and single‐fiber analysis. In addition, we observed an approximately sixfold increase in the number of Myf5‐expressing cells by 48 h, which remained elevated until at least 96 h following exercise. We did not, however, observe any significant expansion of the CD45+:Sca‐1+ cell population or commitment of resident CD45+:Sca‐1+ cells to the myogenic lineage. Furthermore, expression of Wnt gene family members, previously associated with myogenic specification of CD45+:Sca‐1+ cells, did not differ following exercise. Therefore, we conclude that muscle satellite cells are the primary responders to exercise‐induced stress and that the CD45+:Sca‐1+ myogenic progenitors do not contribute to muscle repair/adaptation following exercise. Muscle Nerve, 2008
Cross‐sectional area reference values for nerve ultrasonography
Authors: Cartwright Michael S. , Passmore Leah V. , Yoon Joon‐Shik , Brown Martin E. , Caress James B. , Walker Francis O. 
Published: March 2008

AbstractUltrasound allows for a non‐invasive structural assessment of nerves, muscles, and surrounding tissues, and therefore it is increasingly being used as a supplement to traditional electrodiagnostic studies. As investigators have begun to use ultrasound to explore peripheral nerves, it has become clear that conditions such as entrapment, hereditary neuropathies, acquired neuropathies, trauma, and nerve tumors result in an increase in nerve cross‐sectional area. Reference values have not been published for the cross‐sectional area of many nerves commonly studied in diseases of the peripheral nervous system, so our goal was to obtain reference values for the nerve cross‐sectional area at the following sites: radial at antecubital fossa; radial at distal spiral groove; musculocutaneous in upper arm; trunks of the brachial plexus; vagus at carotid bifurcation; sciatic in distal thigh; tibial in popliteal fossa; tibial in proximal calf; tibial at ankle; peroneal in popliteal fossa; peroneal at fibular head; and sural in distal calf. Mean cross‐sectional area, as well as side‐to‐side differences, are reported for each site, and qualitative data are provided to guide imaging at each site. The information provided in this study should serve as the starting point for quantitatively evaluating these nerve sites with ultrasound. Muscle Nerve, 2008
Implementation of the finite element method in the three‐dimensional discontinuous deformation analysis (3D‐DDA)
Authors: Grayeli Roozbeh , Hatami Kianoosh 
Published: March 2008

AbstractA modified three‐dimensional discontinuous deformation analysis (3D‐DDA) method is derived using four‐noded tetrahedral elements to improve the accuracy of current 3D‐DDA algorithm in practical applications. The analysis program for the modified 3D‐DDA method is developed in a C++ environment and its accuracy is illustrated through comparisons with several analytical solutions that are available for selected problems. The predicted solutions for these problems using the modified 3D‐DDA approach all show satisfactory agreement with the corresponding analytical results. Results presented in this paper demonstrate that the modified 3D‐DDA method with discontinuous modeling capabilities offers a useful computational tool to determine stresses and deformations in practical problems involving fissured elastic media with reasonable accuracy. Copyright © 2008 John Wiley & Sons, Ltd.
External urethral sphincter activity in diabetic rats
Authors: Liu Guiming , Lin Yi‐Hao , Yamada Yasuhiro , Daneshgari Firouz 
Published: March 2008

AbstractAimTo examine the temporal effects of diabetes on the bladder and the external urethral sphincter (EUS) activity in rats.MethodsFemale Sprague‐Dawley rats (n = 24) were divided into two groups: streptozotocin‐induced diabetic rats and age‐matched controls. Cystometrograms (CMGs) were taken under urethane anesthesia and electromyograms (EMG) of the EUS were evaluated in all rats at 6 and 20 weeks after diabetes induction. After EMG assessment, the tissues of the urethra were harvested for morphological examination.ResultsDiabetes caused reduction of body weight, but an increase in bladder weight. CMG measurements showed diabetes increased threshold volume, contraction duration, high‐frequency oscillations (HFO), and residual volume. Peak contraction amplitude increased in 6‐week but not 20‐week diabetic rats. EUS‐EMG measurements showed increased frequency of EUS‐EMG bursting discharge during voiding in 6‐week diabetic rats (8.1 ± 0.2 vs. 6.9 ± 0.6/sec) but not in 20‐week (5.8 ± 0.3 vs. 6.0 ± 0.2/sec) diabetic rats compared with controls. EUS‐EMG bursting periods were also increased in both 6‐week and 20‐week diabetic rats compared with controls. EUS‐EMG silent periods were reduced in 6‐week diabetic rats, but were not changed in 20‐week diabetic rats compared with controls. Active periods did not change in 20‐week diabetic rats, but increased in 6‐week diabetic rats compared with controls. Morphometric analysis showed atrophy of the EUS after 20 week but not 6 weeks of DM induction.ConclusionsOur data indicates diabetes causes functional and anatomical abnormalities of the EUS. These abnormalities may contribute to the time‐dependent bladder dysfunction in diabetic rats. Neurourol. Urodynam. 27:429–434, 2008. © 2008 Wiley‐Liss, Inc.