bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adrenalectomy‐induced granule cell degeneration in the hippocampus causes spatial memory deficits that are not reversed by chronic treatment with corticosterone or fluoxetine
Authors: Spanswick Simon C. , Epp Jonathan R. , Keith Julian R. , Sutherland Robert J. 
Published: December 2006

AbstractLong‐term adrenalectomy (ADX) causes a nearly complete and selective loss of granule cells in the dentate gyrus (DG) of the hippocampus. Previously, learning and memory deficits have been observed following ADX‐induced granule cell degeneration for tasks that require the hippocampus. Our objective here was to determine whether corticosterone (CORT) replacement and treatment with the neurogenic compound fluoxetine could reverse behavioral deficits after ADX. We trained ADX and control rats in a moving, hidden platform version of the Morris water task before chronic administration (6 weeks) of CORT and either fluoxetine or vehicle. After treatment, all rats were retested in the Morris water task. Brains were labeled for the endogenous neurogenic markers Ki67 and doublecortin. Here we provide evidence that neurogenesis persists at a normal rate in the hippocampus after long‐term ADX. After 8 weeks of CORT and fluoxetine administration, ADX‐fluoxetine rats did not differ significantly compared to ADX‐vehicle rats receiving CORT or compared to control rats in the number of Ki67 or doublecortin labeled cells. ADX‐fluoxetine rats also did not significantly differ from ADX‐vehicle rats in regards to granule cell layer thickness. Our results indicate that long‐term ADX is associated with impaired spatial ability in the Morris water task and that neither chronic treatment with CORT, nor with CORT and fluoxetine are capable of altering the Morris water task deficit. © 2006 Wiley‐Liss, Inc.
Comparison of drying methods in the fabrication of collagen scaffold via indirect rapid prototyping
Authors: Yeong Wai‐Yee , Chua Chee‐Kai , Leong Kah‐Fai , Chandrasekaran Margam , Lee Mun‐Wai 
Published: December 2006

AbstractPorous collagen scaffolds with predefined 3‐dimesional (3‐D) networks of internal channels are fabricated via an indirect rapid prototyping technique. To obtain the scaffolds, two drying methods, namely critical point drying and freeze‐drying were investigated. The latter was found to be a more suitable process as it induced less shrinkage and reproduced the design morphology accurately. The resulting scaffold contained internal hollow channels with porous foam‐like structure occupying the surrounding volume. The mean diameter of the pores was 180 ± 60 μm and the channels diameter obtained was measured as 437 ± 100 μm. The channels were defined and strengthened by a layer of skin due to the process of freeze‐drying. These networks of internal channels serve to enhance the mass transport rate through the scaffold and help to increase the depth of cells penetration in the scaffold. © 2006 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 2006.
Effects of airborne‐particle abrasion, sodium hydroxide anodization, and electrical discharge machining on porcelain adherence to cast commercially pure titanium
Authors: Acar Aslı , İnan Özgür , Halkacı Selçuk 
Published: December 2006

AbstractThe aim of this study was to determine the effect of airborne‐particle abrasion (APA), sodium hydroxide anodization (SHA), and electrical discharge machining (EDM) on cast titanium surfaces and titanium–porcelain adhesion. Ninety titanium specimens were cast with pure titanium and the alpha‐case layer was removed. Specimens were randomly divided into three groups. Ten specimens from each group were subjected to APA. SHA was applied to the second subgroups, and the remaining specimens were subjected to the EDM. For the control group, 10 specimens were cast using NiCr alloy and subjected to only APA. Surfaces were examined by using scanning electron microscope and a surface profilometer. Three titanium porcelains were fused on the titanium surfaces, whereas NiCr specimens were covered with conventional porcelain. Titanium–porcelain adhesion was characterized by a 3‐point bending test. Statistical analysis showed that the porcelain–metal bond strength of the control group was higher than that of the titanium–porcelain system (p < 0.05). There were no significant differences between the bond strengths of titanium groups (p 0.05), except the bond strengths of Noritake Super Porcelain TI‐22 groups on which APA and SHA were applied (p < 0.05). SHA and EDM as surface treatment did not improve titanium–porcelain adhesion when compared to APA. © 2006 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 2006.
CHARMM force field parameters for simulation of reactive intermediates in native and thio‐substituted ribozymes
Authors: Mayaan Evelyn , Moser Adam , MacKerell Alexander D. , York Darrin M. 
Published: December 2006

AbstractForce field parameters specifically optimized for residues important in the study of RNA catalysis are derived from density‐functional calculations, in a fashion consistent with the CHARMM27 all‐atom empirical force field. Parameters are presented for residues that model reactive RNA intermediates and transition state analogs, thio‐substituted phosphates and phosphoranes, and bound Mg2+and di‐metal bridge complexes. Target data was generated via density‐functional calculations at the B3LYP/6–311++G(3df,2p)// B3LYP/6–31++G(d,p) level. Partial atomic charges were initially derived from CHelpG electrostatic potential fitting and subsequently adjusted to be consistent with the CHARMM27 charges. Lennard‐Jones parameters were determined to reproduce interaction energies with water molecules. Bond, angle, and torsion parameters were derived from the density‐functional calculations and renormalized to maintain compatibility with the existing CHARMM27 parameters for standard residues. The extension of the CHARMM27 force field parameters for the nonstandard biological residues presented here will have considerable use in simulations of ribozymes, including the study of freeze‐trapped catalytic intermediates, metal ion binding and occupation, and thio effects. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 495–507, 2007
SODOCK: Swarm optimization for highly flexible protein–ligand docking
Authors: Chen Hung‐Ming , Liu Bo‐Fu , Huang Hui‐Ling , Hwang Shiow‐Fen , Ho Shinn‐Ying 
Published: December 2006

AbstractProtein–ligand docking can be formulated as a parameter optimization problem associated with an accurate scoring function, which aims to identify the translation, orientation, and conformation of a docked ligand with the lowest energy. The parameter optimization problem for highly flexible ligands with many rotatable bonds is more difficult than that for less flexible ligands using genetic algorithm (GA)‐based approaches, due to the large numbers of parameters and high correlations among these parameters. This investigation presents a novel optimization algorithm SODOCK based on particle swarm optimization (PSO) for solving flexible protein–ligand docking problems. To improve efficiency and robustness of PSO, an efficient local search strategy is incorporated into SODOCK. The implementation of SODOCK adopts the environment and energy function of AutoDock 3.05. Computer simulation results reveal that SODOCK is superior to the Lamarckian genetic algorithm (LGA) of AutoDock, in terms of convergence performance, robustness, and obtained energy, especially for highly flexible ligands. The results also reveal that PSO is more suitable than the conventional GA in dealing with flexible docking problems with high correlations among parameters. This investigation also compared SODOCK with four state‐of‐the‐art docking methods, namely GOLD 1.2, DOCK 4.0, FlexX 1.8, and LGA of AutoDock 3.05. SODOCK obtained the smallest RMSD in 19 of 37 cases. The average 2.29 Å of the 37 RMSD values of SODOCK was better than those of other docking programs, which were all above 3.0 Å. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 612–623, 2007
Convergence of third order correlation energy in atoms and molecules
Authors: Kahn Kalju , Granovsky Alex A. , Noga Jozef 
Published: December 2006

AbstractWe have investigated the convergence of third order correlation energy within the hierarchies of correlation consistent basis sets for helium, neon, and water, and for three stationary points of hydrogen peroxide. This analysis confirms that singlet pair energies converge much slower than triplet pair energies. In addition, singlet pair energies with (aug)‐cc‐pVDZ and (aug)‐cc‐pVTZ basis sets do not follow a converging trend and energies with three basis sets larger than aug‐cc‐pVTZ are generally required for reliable extrapolations of third order correlation energies, making so the explicitly correlated R12 calculations preferable. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 547–554, 2007
A simple algorithm to accelerate the computation of non‐bonded interactions in cell‐based molecular dynamics simulations
Authors: Gonnet Pedro 
Published: December 2006

AbstractCell lists are ubiquitous in molecular dynamics simulations—be it for the direct computation of short‐range inter‐atomic potentials, the short‐range direct part of a long‐range interaction or for the periodic construction of Verlet lists. The conventional approach to computing pairwise interactions using cell lists leads to a large number of unnecessary interparticle distance calculations. In this paper, an algorithm is presented which reduces the number of spurious distance calculations by first sorting the particles along the cell pair axis and then only interacting two particles if their distance along the axis is smaller than the cutoff distance of the interaction. This approach is shown to be more efficient than the conventional approach and similar approaches using smaller cells. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 570–573, 2007
Blue‐shifting hydrogen bond in the benzene–benzene and benzene–naphthalene complexes
Authors: Hermida‐Ramón Jose M. , Graña Ana M. 
Published: December 2006

AbstractAb initiocomplete optimizations at MP2/6‐31++G** level have been performed in the T‐shaped geometry of the benzene–benzene and benzene–naphthalene complexes. To check the effect of the basis set superposition error (BSSE), optimizations have been done in the BSSE corrected and BSSE uncorrected potential energy surfaces. The BSSE effect in the calculation of the Hessian has also been evaluated to check its influence in the frequency values. Quantum theory atoms in molecules (QTAIM) calculations have also been performed on both dimers. Intermolecular energies differ around a 25% when the optimization is performed with or without counterpoise corrected gradients. The influence of BSSE is also noticeable in the distances. Frequency shifts show big changes because of the BSSE. Thus, uncorrected values are up 350% larger than corrected ones. The hypotheses given in the literature to explain the origin of the blue‐shifting hydrogen bond do not seem to give a suitable explanation for all characteristics of the behavior found in the studied systems. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 540–546, 2007
Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations
Authors: Jurečka Petr , Černý Jiří , Hobza Pavel , Salahub Dennis R. 
Published: December 2006

AbstractStandard density functional theory (DFT) is augmented with a damped empirical dispersion term. The damping function is optimized on a small, well balanced set of 22 van der Waals (vdW) complexes and verified on a validation set of 58 vdW complexes. Both sets contain biologically relevant molecules such as nucleic acid bases. Results are in remarkable agreement with reference high‐level wave function data based on the CCSD(T) method. The geometries obtained by full gradient optimization are in very good agreement with the best available theoretical reference. In terms of the standard deviation and average errors, results including the empirical dispersion term are clearly superior to all pure density functionals investigated—B‐LYP, B3‐LYP, PBE, TPSS, TPSSh, and BH‐LYP—and even surpass the MP2/cc‐pVTZ method. The combination of empirical dispersion with the TPSS functional performs remarkably well. The most critical part of the empirical dispersion approach is the damping function. The damping parameters should be optimized for each density functional/basis set combination separately. To keep the method simple, we optimized mainly a single factor, sR, scaling globally the vdW radii. For good results, a basis set of at least triple‐ζ quality is required and diffuse functions are recommended, since the basis set superposition error seriously deteriorates the results. On average, the dispersion contribution to the interaction energy missing in the DFT functionals examined here is about 15 and 100% for the hydrogen‐bonded and stacked complexes considered, respectively. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 555–569, 2007
Obestatin‐mediated proliferation of human retinal pigment epithelial cells: Regulatory mechanisms
Authors: Camiña Jesus P. , Campos Jacobo F. , Caminos J. Eduardo , Dieguez Carlos , Casanueva Felipe F. 
Published: December 2006

AbstractIn this work, we have evaluated the effect of the new discovered peptide obestatin on cell proliferation in primary cultures of human retinal epithelial cells (hRPE cells). The results showed that this peptide induced, in a dose‐dependent manner, cell proliferation by MEK/ERK 1/2 phosphorylation. A sequential analysis of the obestatin transmembrane signaling pathway showed that the ERK 1/2 activity is partially blocked after preincubation of the cells with pertussis toxin (PTX), as well as by wortmannin (an inhibitor of PI3K), claphostin C (an inhibitor of PKC), and PP2 (which inhibits the non receptor tyrosine kinase Src). Upon administration of obestatin, the intracellular levels of phospho‐PKCε‐, θ‐, and µ‐isoenzymes rise with different time courses, from which PKCε might be responsible for ERK 1/2 response. Based on the experimental data, a signaling pathway involving the consecutive activation of Gi, PI3K, novel PKC (probably PKCε), and Src for ERK 1/2 activation is proposed. These results incorporate a new mitogenic factor to the group of factors that regulate proliferation of hRPE cells. J. Cell. Physiol. 211: 1–9, 2007. © 2006 Wiley‐Liss, Inc.
Impaired activity of volume‐sensitive Cl− channel is involved in cisplatin resistance of cancer cells
Authors: Lee Elbert L. , Shimizu Takahiro , Ise Tomoko , Numata Tomohiro , Kohno Kimitoshi , Okada Yasunobu 
Published: December 2006

AbstractThe platinum‐based drug cisplatin is a widely used anticancer drug which acts by causing the induction of apoptosis. However, resistance to the drug is a major problem. In this study we show that the KCP‐4 human epidermoid cancer cell line, which serves as a model of acquired resistance to cisplatin, has virtually no volume‐sensitive, outwardly rectifying (VSOR) chloride channel activity. The VSOR chloride channel's molecular identity has not yet been determined, and semi‐quantitative RT‐PCR experiments in this study suggested that the channel corresponds to none of three candidate genes. However, because it is known that the channel current plays an essential role in apoptosis, we hypothesized that lack of the current contributes to cisplatin resistance in these cells and that its restoration would reduce resistance. To test this hypothesis, we attempted to restore VSOR chloride current in KCP‐4 cells. It was found that treatment with trichostatin A (TSA), a histone deacetylase inhibitor, caused VSOR chloride channel function to be partially restored. Treatment of the cells with both TSA and cisplatin resulted in an increase in caspase‐3 activity at 24 h and a decrease in cell viability at 48 h. These effects were blocked by simultaneous treatment of the cells with a VSOR chloride channel blocker. These results indicate that restoration of the channel's functional expression by TSA treatment leads to a decrease in the cisplatin resistance of KCP‐4 cells. We thus conclude that impaired activity of the VSOR chloride channel is involved in the cisplatin resistance of KCP‐4 cancer cells. J. Cell. Physiol. 211: 513–521, 2007. © 2006 Wiley‐Liss, Inc.
Community‐acquired pneumonia: Defining quality care
Authors: Seymann Gregory B. 
Published: December 2006

AbstractBACKGROUNDCommunity‐acquired pneumonia (CAP) is one of 3 initial conditions for which the Joint Commission for Accreditation of Healthcare Organizations and the Centers for Medicare & Medicaid Services have defined quality measures. Eight “core measures” of pneumonia care have been targeted for reporting by U.S. hospitals to facilitate performance monitoring.METHODSA review of the literature supporting the core measures was performed.RESULTSIndicators encouraging influenza vaccination and appropriate antibiotic selection had the most robust evidence. Rapid delivery of antibiotics also showed significant reduction in mortality, though the actual timing (4 versus 8 hours) varied between studies. Other measures, such as performance of blood cultures, pneumococcal vaccination, smoking cessation, and oxygenation assessment, demonstrated less obvious clinical benefit.CONCLUSIONSThere is inherent value in setting standards of care for high‐impact conditions such as CAP, but these standards should be chosen on the basis of high‐quality research. Public reporting of the current measures is problematic, as it implies they represent best practices for CAP despite relatively weak evidence. Journal of Hospital Medicine 2006;1:344–353. © 2006 Society of Hospital Medicine.
What effect does an educational intervention have on interns' confidence and knowledge regarding acute dyspnea management?. A randomized controlled trial
Authors: Reittinger Tracy M. , Kaufman Samuel R. , Saint Sanjay 
Published: December 2006

AbstractBACKGROUNDThough acute dyspnea is commonly encountered in hospitalized patients, interns often receive only informal instruction in managing such patients. We hypothesized that formal instruction would improve interns' knowledge and confidence in managing patients with acute dyspnea.METHODSTwenty‐six internal medicine interns were randomized to receive either standard education or standard education plus the educational intervention. The educational intervention included two small‐group, case‐based discussions on acute dyspnea management. All participants completed pre‐ and post‐intervention surveys over four months that assessed their knowledge and confidence in managing patients with acute dyspnea.RESULTSOf the 16 interns in the intervention group, 14 attended one of the two small‐group sessions while seven attended both sessions. Mean confidence increased by 21.2% in the intervention group and 14.4% in the control group. The trend over time for both groups was significant (P < .001); the effect of the intervention was not (P = .19). Mean knowledge scores increased 7.6% in the intervention group and 5.5% in the control group. Again, the trend over time for both groups was significant (P < .01), but the effect of the intervention was not (P = .65). A per‐protocol analysis revealed a trend toward significance with mean scores increasing 15.6% (P = .067).CONCLUSIONSOur trial found that intern confidence and knowledge about acute dyspnea management increased significantly over time; however, no significant differences between the intervention and control groups were seen. The complete intervention was not administered to the majority of the intervention group, thereby skewing results to the null. The per‐protocol analysis suggests attendance at educational sessions may improve knowledge. Future interventions should use a more sensitive testing instrument, a larger sample, and a more powerful intervention. Journal of Hospital Medicine 2006;1:339–343. © 2006 Society of Hospital Medicine.
Improved use of thromboprophylaxis for deep vein thrombosis following an educational intervention
Authors: Cohn Steven L. , Adekile Ayoola , Mahabir Vishal 
Published: December 2006

AbstractBACKGROUNDWe evaluated venous thromboembolism (VTE) prophylaxis rates in hospitalized medical patients in a teaching hospital, the State University of New York–Downstate Medical Center–University Hospital of Brooklyn, before and after implementation of a multifaceted VTE prophylaxis quality improvement intervention that combined regular education, dissemination of a decision support tool, and regular audit‐and‐feedback to resident physicians.METHODSThe charts of 312 hospitalized medical patients were retrospectively reviewed to assess baseline rates of appropriate VTE prophylaxis. Rates of appropriate VTE prophylaxis were then determined 12 and 18 months after implementation of the quality improvement intervention. Data collected included risk factors for VTE, contraindications to anticoagulant prophylaxis, type of VTE prophylaxis prescribed, and whether the prophylaxis was appropriate.RESULTSMost of the hospitalized medically ill patients had 3 or more risk factors for VTE. At baseline, the proportion of patients receiving any form of VTE prophylaxis, primarily unfractionated heparin, was 47%. The proportion of patients for whom a physician provided appropriate prophylaxis was 43%. After the intervention, the proportion of patients receiving prophylaxis significantly increased, to 86% at 12 months, and this level was maintained at 18 months. The rate of appropriate prophylaxis increased to 68% and 85% after 12 and 18 months, respectively.CONCLUSIONSThe proportion of hospitalized medical patients receiving appropriate VTE prophylaxis as recommended by evidence‐based guidelines can be increased significantly by combining regular education, a decision support tool, and regular audit‐and‐feedback. Journal of Hospital Medicine 2006;1:331–338. © 2006 Society of Hospital Medicine.
Antiapoptotic mechanism of cannabinoid receptor 2 agonist on cisplatin‐induced apoptosis in the HEI‐OC1 auditory cell line
Authors: Jeong Hyun‐Ja , Kim Su‐Jin , Moon Phil‐Dong , Kim Na‐Hyun , Kim Jung‐Sun , Park Rae‐Kil , Kim Min‐Sun , Park Byung‐Rim , Jeong Sejin , Um Jae‐Young , Kim Hyung‐Min , Hong Seung‐Heon 
Published: December 2006

AbstractCisplatin is a highly effective chemotherapeutic agent but with significant ototoxic side effects. Apoptosis is an important mechanism of cochlear hair cell loss following exposure to an ototoxic level of cisplatin. The present study investigated the effects of the cannabinoid receptor 2 (CB2) ligand JWH‐015 on cisplatin‐induced apoptosis. CB2 mRNA was constitutively expressed in the auditory cell line HEI‐OC1. By using MTT assay, DNA fragmentation, and FACS analysis, we demonstrated that apoptosis induced by cisplatin was inhibited by treatment with JWH‐015 in a dose‐dependent manner. Activation of caspase‐3, caspase‐8, and caspase‐9 was detected after treatment with cisplatin, and the cleavage of poly‐(ADP)‐ribose polymerase (PARP) was observed within cisplatin‐treated HEI‐OC1 cells. JWH‐015 inhibited the activation of caspase‐3, caspase‐8, and caspase‐9; cleavage of PARP; and release of cytochrome c. JWH‐015 also inhibited the apoptosis through activation of the extracellular signal‐regulated kinase pathway. Finally, JWH‐015 inhibited cisplatin‐induced reactive oxygen species and tumor necrosis factor‐α production. Collectively, these findings show that blocking a critical step in apoptosis by using JWH‐015 may be a useful strategy to prevent harmful side effects of cisplatin ototoxicity in patients having to undergo chemotherapy. © 2006 Wiley‐Liss, Inc.