bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Modeling and Receptor‐Dependent (RD) 3D‐QSAR Approach to a Set of Antituberculosis Derivatives
Authors: Pasqualoto Kerly Fernanda Mesquita , Ferreira Márcia Miguel Castro 
Published: December 2009

AbstractIn this study, receptor‐dependent (RD) 3D‐QSAR models were built for a set of thirty‐seven isoniazid derivatives bound to the enoyl‐acp reductase from M. tuberculosis, called InhA (PDB entry code 1zid). Ligand‐receptor (L‐R) molecular dynamics (MD) simulations [500 000 steps; the step size was 0.001 ps (1 fs)] were carried out at 310 K (biological assay temperature). The hypothesized active conformations resulting from a previously reported receptor‐independent (IR) 4D‐QSAR analysis were used as the molecular geometries of each ligand in this structure‐based L‐R binding research. The dependent variable is the reported MIC values against M. tuberculosis var. bovis. The independent variables (descriptors) are energy terms of a modified first‐generation AMBER force field combined with a hydration shell aqueous solvation model. Genetic function approximation (GFA) formalism and partial least squares (PLS) regression were employed as the fitting functions to develop 3D‐QSAR models. The bound ligand solvation energy, the sum of electrostatic and hydrogen bonding energies of the unbound ligand, the bending energy of the unbound ligand, the electrostatic intermolecular L‐R energy, and the change in hydrogen bonding energy upon binding were found as important energy contributions to the binding process. The 3D‐QSAR model at 310 K has good internal and external predictability and may be regarded as representative of the binding process of ligands to InhA.
Selection of Appropriate Training Set of Chemicals for Modeling Dermal Permeability Using Uniform Coverage Design
Authors: Vijay Vikrant , Baynes Ronald E. , Young S. Stanley , Riviere Jim E. 
Published: December 2009

AbstractIn silico approaches to model dermal permeability require a training set of chemicals. Selection of an appropriate set of chemicals is the key factor in the precision of a model. The objective is to develop a training set of chemicals representing a wider chemical space relevant to biological activity such as dermal permeability and compare it with the currently used training set of chemicals by our laboratory, which was based on a subjective selection process. Wider chemical space refers to structurally diverse chemicals with a wide range of all the descriptor values. A parent dataset of 4098 chemicals with 5 solvatochromic descriptors obtained from ADME boxes database was used for this study. The approach for diverse chemical selection was performed using ‘uniform coverage design’ (UCD) run by SpaceFill program and compared with a cluster analysis using SAS. Five sets of 25 chemicals were obtained from the design and evaluated based on gas chromatographic assay amenability and representation of structurally diverse group. A final set of 25 chemicals to be used for modeling dermal permeability was selected, based on aforementioned criteria. Graphical plot of the principal components demonstrated that currently used training set of chemicals have narrow representation of parent dataset whereas the selected training set have appropriate representation in terms of chemical space. QSAR models were built from both training set of chemicals. The model based on the 25 selected chemicals (R2=0.83) performed equally if not slightly better then the model based on currently used training set of 32 chemicals (R2=0.82).
Nonlinear optical properties of the M @ C60 endohedrals (M = Cs, Li, and Na)
Authors: Yaghobi M. , Koohi A. 
Published: December 2009

AbstractThe Hartree–Fock (HF) approximation and the Single‐excitation configuration interaction (single‐CI) method are used, with sum‐over‐state (SOS) approach, in order to determine the static (ω = 0) and frequency dependent linear and non linear optical (NLO) properties of the M @ C60 endohedrals (M = Cs, Li, and Na). We discuss the effects of displacement, movement direction, and type of atom on the (hyper) polarizability of the M at C60 endohedrals. A HF‐single‐CI model yields the (hyper) polarizability magnitudes and spectra, which are in agreement with experiment. Our results indicate that the movement of the atom (M) effect on the NLO spectra of M @ C60 endohedrals is dramatic. These results may provide new means to design some new types of NLO materials. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
DFT performance for the hole transfer parameters in DNA π stacks
Authors: Félix Martín , Voityuk Alexander A. 
Published: December 2009

AbstractRecently, we showed that unoccupied Kohn‐Sham (KS) orbitals stemming from DFT calculations of a neutral system can be used to derive accurate estimates of the free energy and electronic couplings for excess electron transfer in DNA (Félix and Voityuk, J Phys Chem A 2008, 112, 9043). In this article, we consider the propagation of radical cation states (hole transfer) through DNA π‐stacks and compare the performance of different exchange‐correlation functionals to estimate the hole transfer (HT) parameters. Two different approaches are used: (1) calculations that use occupied KS orbitals of neutral π stacks of nucleobases, and (2) the time‐dependent DFT method which is applied to the radical cation states of these stacks. Comparison of the calculated parameters with the reference data suggests that the best results are provided by the KS scheme with hybrid functionals (B3LYP, PBE0, and BH&HLYP). The TD DFT approach gives significantly less accurate values of the HT parameters. In agreement with high‐level ab initio results, the KS scheme predicts that the hole in π stacks is confined to a single nucleobase; in contrast, the spin‐unrestricted DFT method considerably overestimates the hole delocalization in the radical cations. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Many‐body effects on structures of small Ca2+Arn clusters
Authors: Gaied W. , Ben El Hadj Rhouma M. 
Published: December 2009

AbstractThe structure and stabilities of Ca2+Arn (n = 1–24) clusters are investigated using analytical potential functions. The energy of the systems, in its ground state, is described using additive potentials with V(Ca2+‐Ar) and V(Ar‐Ar) representing the pair potential interactions, and many‐body effects are described using the interaction between dipoles induced by the calcium ion. To find the geometry of the lowest energy isomers of Ca2+Arn clusters, we use the so‐called basin‐hopping method of Wales et al. We show that in the equilibrium structures of Ca2+Arn clusters, the Ca2+ cation is always solvated by argon clusters. For n = 2, we have found a strong competition between the symmetric linear shape (D∞) and the bent isomer (C2v). The relative importance of the three‐body interactions due to the presence of the induced dipoles on the Ar atoms can be inferred from the magnitude of the known Ar2 interaction, and lead to a more stabilized linear structure. The global minimum of Ca2+Ar3 is planar (D3h), but a second three‐dimensional isomer with a pyramidal C3v symmetry exists. The absolute minimum of Ca2+Ar4 is a regular tetrahedron, and that of Ca2+Ar6, is a regular octahedron. The particularly stable sizes with respect to their immediate neighbors were studied by calculating the second energy difference between size n and its immediate neighbors. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Ab initio study of the potential energy surface and product branching ratios for the reaction of O(1D) with CH3CH2Br
Authors: Tian Zhimei , Song Chongfu , Li Quanxin 
Published: December 2009

AbstractThe potential energy surface of O(1D) + CH3CH2Br reaction has been studied using QCISD(T)/6‐311++G(d,p)//MP2/6‐311G(d,p) method. The calculations reveal an insertion‐elimination reaction mechanism of the title reaction. The insertion process has two possibilities: one is the O(1D) inserting into CBr bond of CH3CH2Br producing one energy‐rich intermediate CH3CH2OBr and another is the O(1D) inserting into one of the CH bonds of CH3CH2Br producing two energy‐rich intermediates, IM1 and IM2. The three intermediates subsequently decompose to various products. The calculations of the branching ratios of various products formed though the three intermediates have been carried out using RRKM theory at the collision energies of 0, 5, 10, 15, 20, 25, and 30 kcal/mol. CH3CH2O + Br are the main decomposition products of CH3CH2OBr. CH3COH + HBr and CH2CHOH + HBr are the main decomposition products for IM1; CH2CHOH + HBr are the main decomposition products for IM2. As IM1 is more stable and more likely to form than CH3CH2OBr and IM2, CH3COH + HBr and CH2CHOH + HBr are probably the main products of the O(1D) + CH3CH2Br reaction. Our computational results can give insight into reaction mechanism and provide probable explanations for future experiments. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
A biplanar robot navigation system for the distal locking of intramedullary nails
Authors: Lei Hu , Sheng Luan , Manyi Wang , Junqiang Wang , Wenyong Liu 
Published: December 2009

AbstractBackgroundDistal locking is the key procedure of the intramedullary nailing operation. It is difficult to precisely locate the locking path, and intraoperative radiation exposure is also a serious problem. The advantages and disadvantages of different approaches applied in this operation are summarized.MethodA biplanar robot navigation system for the distal locking of intramedullary nails is presented. The novel mechanical structure and the surgical process are introduced. Then the positioning accuracy of the robot is experimented and validated.ResultsThe positioning precision of the biplanar robot is tested, and the average error is 0.24 mm. The tibia sawbone is used for distal locking to test the accuracy of the robot navigation system. The maximal deviation between the drilling centre and the nail hole centre is 0.44 mm.ConclusionThe biplanar robot has the advantages of high positioning accuracy, operational stability and safety. It can be used not only for the distal locking of intramedullary nails but also for other orthopaedic surgeries that demand precise positioning. Copyright © 2009 John Wiley & Sons, Ltd.
Three‐dimensional A‐mode ultrasound calibration and registration for robotic orthopaedic knee surgery
Authors: Mozes Alon , Chang Ta‐Cheng , Arata Louis , Zhao Weizhao 
Published: December 2009

AbstractBackgroundRegistration is a key step for computer‐navigated robot‐assisted surgery. Registration links the live patient anatomical location to the prescanned CT or MRI images, so that predesigned procedures can be performed accurately. Fiducial markers or mechanical probes are usually used to identify anatomical features or collect data points for registration. This conventional invasive approach is common; however, using ultrasound probes may provide a non‐invasive alternative.MethodsThis report presents investigations of selecting an A‐mode ultrasound transducer, calibrating it, analysing the ultrasound signal and using it to register phantom‐sawbones of tibia and femur as well as cadaveric specimens. To ensure accurate registration, the A‐mode ultrasound probe is calibrated by a designed calibration system. Detailed mathematical derivation and procedures for the calibration are provided in the Appendix. The calibration and registration experiments were performed in conjunction with MAKO Surgical Corporation's Tactile Guidance System™ (TGS™) at their headquarters and at the South Florida Spine Clinic for cadaveric experiments.ResultsCalibration results show that an A‐mode ultrasound probe can reach the same accuracy level as a mechanical probe. By using the A‐mode ultrasound probe, averaged root mean square errors (RMSE) are <0.5 mm for calibration, <1.0 mm for phantom‐sawbones and <2.0 mm for cadaveric specimens.ConclusionThe registration results from phantom and cadaveric experiments are suitable for clinical applications. A‐mode ultrasound registration is a viable option for registration of the bones in orthopaedic knee surgery but with reduced incision size. Copyright © 2009 John Wiley & Sons, Ltd.
Differentiated security in wireless mesh networks
Authors: Gamer Thomas , Völker Lars , Zitterbart Martina 
Published: December 2009

AbstractThe upcoming IEEE 802.11s standard enables easy establishment and maintenance of wireless mesh networks in residential and enterprise scenarios. They, however, need special attention with respect to security. Due to multi‐hop communication and routing on layer 2 in mesh networks, attacks on the routing, selective forwarding, and eavesdropping on confidential data become relatively easy. To avoid such attacks, we introducedifferentiated securitywhich is based on protection levels associated with nodes in the network. Participation in the MAC layer routing is facilitated according to the respective protection level of a node. Using additional cryptographic protection our approach can also avoid unintentional disclosure of confidential data. Copyright © 2009 John Wiley & Sons, Ltd.
Performance of Al alloys following excimer LSM—anodising approaches
Authors: Viejo F. , Aburas Z. , Coy A. E. , Garcia‐Garcia F. J. , Liu Z. , Skeldon P. , Thompson G. E. 
Published: December 2009

AbstractThe potential application of laser surface melting (LSM) as a pre‐treatment prior to conventional anodising in sulfuric acid electrolyte has been evaluated. For this purpose, AA2050‐T8 (AlCuLi) and AA2024‐T351 (AlCuMg) aerospace alloys were compared. For LSM, a KrF excimer laser (248 nm) was used, with variation of the number of pulses received per unit area. After LSM, the specimens were anodised at a constant voltage of 12 V in 0.46 M H2SO4 for different times from 4 to 20 min, followed by sealing in boiling water for 30 min. Material characterisation, in terms of surface morphology, microstructural and laser‐induced phase transformations, was performed using scanning and transmission electron microscopies (TEMs). The corrosion behaviour was evaluated using the ASTM G34‐01 EXCO test at 25 °C for 6 h. The results showed that excimer LSM, used as a pre‐treatment prior to anodising, greatly improved the anodising performance, through the dissolution of intermetallic phases in the near‐surface alloy. Further, different exfoliation susceptibility was observed by comparing both alloys, being strongly dependent on the presence and distribution of the main constituent phases, e.g. T1 (Al2CuLi) and S (Al2CuMg) phases, for AA2050‐T8 and AA2024‐T351, respectively. Copyright © 2009 John Wiley & Sons, Ltd.
Estimation of the effect size in meta‐analysis with few studies
Authors: Longford Nicholas T. 
Published: December 2009

AbstractMeta‐analysis is often conducted with only a small number of studies. Adjustments of the (restricted) maximum likelihood estimator of the effect size are derived and their gains in efficiency are explored. The proposed estimators are applied to three sets of studies. Copyright © 2009 John Wiley & Sons, Ltd.
Effect of age‐dependent exposure to lead on hepatotoxicity and nephrotoxicity in male rats
Authors: Berrahal Alya Annabi , Lasram Montassar , El Elj Naziha , Kerkeni Abdelhamid , Gharbi Najoua , El‐Fazâa Saloua 
Published: December 2009

AbstractLead is known to induce a broad range of physiological, biochemical, and behavioral dysfunctions in laboratory animals and humans. This includes age‐specific variations in absorption, retention, and tissue distribution of lead. This study was carried out to investigate the effects of chronic exposure to lead (50 mg/L) on liver and kidneys of two different age groups of male rats treated with lead from delivery until puberty period (40 days) and postpuberty period (65 days). For this purpose, the concentrations of thiobarbituric acid reactive substance (TBARS), total thiol groups (SH), and superoxide dismutase (SOD) activity were measured in the liver and kidney of rats. Renal function was analyzed by determining creatinine, acid uric, and urea. Plasma activities of alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, and albumin were determined spectrophotometrically to evaluate hepatic function. These markers of damage were determined to assess the level of toxicity in these animals. Our results clearly show that the administration of lead produces oxidative damage in liver and kidney, as strongly suggested by the significant increase in TBARS, decrease in total SH, and the alteration of SOD activity. In young lead‐exposed animals, lead‐induced perturbations on the synthetic function of the liver and the kidney were more pronounced. However, nephropathy is evident for adult lead‐exposed animals. It is concluded that lead induces severe hepatic and renal toxicity, which depends on the age of the animals and the target organ. © 2009 Wiley Periodicals, Inc. Environ Toxicol 26: 68–78, 2011.
A study of the subchronic effects of arsenic exposure on the liver tissues ofLabeo rohitausing Fourier transform infrared technique
Authors: Palaniappan PL.R M. , Vijayasundaram V. , Prabu S. Milton 
Published: December 2009

AbstractIn this work, an attempt has been made to study the subchronic effects of arsenic exposure on the biochemical composition; mainly proteins of the liver tissues ofLabeo rohitafingerlings by using Fourier transform infrared (FT‐IR) spectroscopic technique. The study was carried out using a Perkin Elmer‐Spectrum Rx1 spectrometer. Because of arsenic exposure, significant reductions in the intensity as well as area of amide bands have been observed in the liver tissues. The decreased intensity of the amide bands could be interpreted as the result of alteration of the protein synthesis due to the high affinity of metal compounds towards different amino acid residues of proteins. Further,meso‐2, 3‐dimercaptosuccinic acid (DMSA) treatment shows the recovery of the protein content in the liver tissues. To confirm that the changes observed are only due to the bio‐accumulation of arsenic, the concentration of arsenic in the liver tissues ofLabeo rohitawas determined by using Inductively Coupled Plasma‐Optical Emission Spectrometry (ICP‐OES). It is observed that the arsenic level in the control tissues is found to be below detectable limit, whereas the arsenic exposed liver shows an accumulation of 66.68 ± 0.43 μg/g and DMSA treatment reduces the arsenic content to 17.96 ± 0.19 μg/g. In conclusion, this study gives clear evidence that the use of FT‐IR spectroscopy is a powerful approach to achieve more insight into the protein alterations caused by arsenic. © 2009 Wiley Periodicals, Inc. Environ Toxicol, 2011.
Three‐dimensional multiplanar ultrasound is a valuable tool in the study of the fetal profile in the second trimester of pregnancy
Authors: De Jong‐Pleij E. A. P. , Ribbert L. S. M. , Tromp E. , Bilardo C. M. 
Published: December 2009

AbstractObjectivesTo evaluate the additional value of three‐dimensional (3D) multiplanar ultrasound in the examination of the fetal profile.MethodsTwo 3D volumes of the fetal head were obtained from 84 fetuses at 22 to 29 weeks' gestation. The volumes were taken starting at the midsagittal plane with the fetus facing the transducer. The success rate and acquisition time to obtain each volume and display the exact midsagittal plane by 3D multiplanar ultrasound were analyzed. The correction angles from the original two‐dimensional (2D) profile view to the exact midsagittal plane were noted. Of six measurements, related to the fetal nose and jaws, the success rate and the intraobserver reproducibility between the 2D and the 3D multiplanar ultrasound were compared.ResultsIn 81 (96.4%) cases we succeeded in obtaining a profile volume, 70% of the volumes being obtained within 10 min. It was possible to define by multiplanar mode the exact midsagittal plane in less than 1 min. The mean rotation necessary to obtain the exact midsagittal plane with 3D multiplanar mode was significantly larger around the y‐axis (11.9°) than around the z‐axis (4.3°) of the fetus. For between 5 and 12% of the six measurements under investigation it was not possible to obtain values with 2D ultrasound. However, 3D ultrasound made these measurements possible in at least one volume. The intraobserver reproducibility was higher with 3D multiplanar ultrasound than with 2D ultrasound, this difference being statistically significant for five of the six measurements.Conclusions3D multiplanar ultrasound improves the topographic depiction of the midsagittal profile view, enables correct measurement of anatomical details and improves intraobserver reproducibility. 3D multiplanar ultrasound is a powerful instrument for investigating the fetal profile. Copyright © 2009 ISUOG. Published by John Wiley & Sons, Ltd.
James Ensor's pigment use: artistic and material evolution studied by means of portable X‐ray fluorescence spectrometry
Authors: Snickt Geert Van der , Janssens Koen , Schalm Olivier , Aibéo Cristina , Kloust Hauke , Alfeld Matthias 
Published: December 2009

AbstractIn this paper, portable X‐ray fluorescence spectrometry (PXRF) was employed as a screening tool for determining and comparing the pigment use in a large series of paintings by the Belgian artist James Ensor (1860–1949). Benefits and drawbacks of PXRF as a method, and the instrument employed, are discussed from a practical, conservation and instrumental perspective. Regardless of several restrictions due to the set‐up and/or the analytical method, it appeared feasible to document the evolution with time in Ensor's use of inorganic pigments and to correlate this technical evolution with stylistic developments, Nevertheless, it became clear that a full identification of all materials present can only be done by means of the analysis of (cross‐sectioned) samples. Copyright © 2009 John Wiley & Sons, Ltd.
Differential effects of hydrogen peroxide and ascorbic acid on the aerobic thermosensitivity of yeast cells grown under aerobic and anoxic conditions
Authors: Moraitis Christos , Curran Brendan P. G. 
Published: December 2009

AbstractWe have previously demonstrated that in aerobically‐grown cells of the yeast Saccharomyces cerevisiae, hydrogen peroxide (H2O2) increases and ascorbic acid decreases cellular thermosensitivity, as determined by the inducibility of a heat shock (HS)‐reporter gene. In this work, we reveal that the aerobic thermosensitivity of anaerobically‐grown yeast cells also increases in the presence of H2O2, albeit differentially between cells with two different lipid profiles. In comparison to aerobically‐grown fermenting cells treated with the same H2O2 concentration, both these types of anaerobically‐grown cells were found to be considerably less sensitive to aerobic heat shock and considerably more thermotolerant. Paradoxically, and in contrast to ascorbate‐pretreated aerobically‐grown yeast cells, when anaerobically‐grown cells were heat‐shocked aerobically in the presence of the same ascorbic acid concentration, they exhibited increased thermosensitivity and decreased intrinsic thermotolerance with respect to their untreated counterparts. These findings are discussed with respect to what is currently known about the redox and physiological status of yeast cells grown aerobically and cells reoxygenated following anoxic growth. Copyright © 2009 John Wiley & Sons, Ltd.