bluuebunny/crossref_metadata_2025_split huggingface dataset:
Force calculations in automated docking: Enzyme–substrate interactions in Fusarium oxysporum Cel7B
Authors: Mulakala Chandrika , Reilly Peter J. 
Published: September 2005

AbstractAutoDock is a small‐molecule docking program that uses an energy function to score docked ligands. Here AutoDock's grid‐based method for energy evaluation was exploited to evaluate the force exerted by Fusarium oxysporum Cel7B on the atoms of docked cellooligosaccharides and a thiooligosaccharide substrate analog. Coupled with the interaction energies evaluated for each docked ligand, these forces give insight into the dynamics of the ligand in the active site, and help to elucidate the relative importance of specific enzyme–substrate interactions in stabilizing the substrate transition‐state conformation. The processive force on the docked substrate in the F. oxysporum Cel7B active site is less than half of that on the docked substrate in the Hypocrea jecorina Cel7A active site. Hydrogen bonding interactions of the enzyme with the C2 hydroxyl group of the glucosyl residue in subsite −2 and with the C3 hydroxyl group of the glucosyl residue in subsite +1 are the most significant in stabilizing the distorted1, 4B transition‐state conformation of the glucosyl residue in subsite −1. The force calculations also help to elucidate the mechanism that prevents the active site from fouling. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Superlattice ordering in SrFeO3–δ: Electron microscopy and diffraction study
Authors: Schott Stefanie , Jia Zhihong , Schaper Andreas K. , Thangadurai Venkataraman , Weppner Werner , Schmid‐Beurmann Peter 
Published: September 2005

AbstractThe oxygen‐deficient SrFeO2.74 phase of quenched samples is located within the miscibility gap of the SrFeO3–δ perovskite system, and exhibits a manifold vacancy ordering pattern at room temperature. We have studied the complex ordering by high‐resolution electron microscopy, and by electron and X‐ray diffraction. New principal superlattice structures have been identified by electron diffraction which can be of relevance for the electronic and magnetic properties of this respective perovskite system. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Configuration of twins in glass‐embedded silver nanoparticles of various origin
Authors: Hofmeister H. , Dubiel M. , Tan G. L. , Schicke K.‐D. 
Published: September 2005

AbstractStructural characterization using high resolution electron microscopy and diffractogram analysis of silver nanoparticles embedded in glass by various routes of fabrication was aimed at revealing the characteristic features of twin faults occuring in such particles. Nearly spherical silver nanoparticles well below 10 nm size embedded in commercial soda‐lime silicate float glass have been fabricated either by silver/sodium ion exchange or by Ag+ ion implantation. Twinned nanoparticles, besides single crystalline species, have frequently been observed for both fabrication routes, mainly at sizes above 5 nm, but also at smaller sizes, even around 1 nm. The variety of particle forms comprises single crystalline particles of nearly cuboctahedron shape, particles containing single twin faults, and multiply twinned particles containing parallel twin lamellae, or cyclic twinned segments arranged around axes of fivefold symmetry. Parallel twinning is distinctly favoured by ion implantation whereas cyclic twinning preferably occurs upon ion exchange processing. Regardless of single or repeated twinning, parallel or cyclic twin arrangement, one may classify simple twin faults of regular atomic configuration and compound twin faults whose irregular configuration consists of additional planar defects like associated stacking faults or secondary twin faults. Besides, a particular superstructure composed of parallel twin lamellae of only three atomic layers thickness is observed. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Coordination of transition‐metals in glasses from high‐resolution electron energy‐loss spectroscopy
Authors: Höche Thomas , Heyroth Frank , Grodzicki Michael , van Aken Peter A. 
Published: September 2005

AbstractTwo fresnoitic glasses (2BaO–TiO2–2GeO2 and 2SrO–TiO2–2SiO2) are studied by high‐resolution electron energy‐loss spectroscopy in the transmission electron microscope. It is shown that coordination fingerprinting using the electron energy‐loss near‐edge structure (being widely used in crystalline compounds bearing transition metals) can also be applied to amorphous matter. In particular, respective ratios of fourfold, fivefold, and sixfold co‐ordinated Ti4+ are verified for both glasses in comparison to earlier X‐ray photoemission measurements. The results demonstrate that – sufficiently high spectral resolution given – electron energy‐loss spectroscopy in the transmission electron microscope is an extremely promising and powerful technique for atomistic‐structure studies of amorphous materials. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Multiple‐textured gallium nitride prepared by ion beam assisted molecular beam epitaxy
Authors: Gerlach Jürgen W. , Höche Thomas 
Published: September 2005

AbstractA gallium nitride bilayer was deposited on Al2O3(0001) by low‐energy nitrogen ion beam assisted molecular beam epitaxy using two different ion energies. First, the ion energy was chosen such that a thin film consisting of a mixture of wurtzitic and zincblende polytypes of GaN could be deposited. For the covering second layer, the ion energy was lowered to obtain optimum growth conditions for single‐polytype wurtzitic GaN. The resulting bilayer was investigated by X‐ray diffraction and transmission electron microscopy and found to contain no less than nine differently oriented types of crystallites possessing well‐defined orientation relationships. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Nitrogen substitutions in GaAs(001) surfaces: Density‐functional supercell calculations of the surface stability
Authors: Jenichen Arndt , Engler Cornelia , Leibiger Gunnar , Gottschalch Volker 
Published: September 2005

AbstractThe structures and energies of various probable reconstruction patterns of the GaAs(001) surface with restricted nitrogen substitution on arsenic positions are calculated using periodic supercells and the density‐functional method. In dependence on chemical potentials of arsenic and nitrogen the most stable structures and compositions of the surface are obtained: Under extreme As‐rich conditions the N‐free c(4 × 4) reconstruction is the preferred arrangement. Under Ga‐rich conditions the ζ(4 × 2) reconstruction builds in variously high N‐substituted structures (especially parallel coupled (GaN)n chains), which can lead to a GaN phase (phase separation). In the transition region between the Ga‐ and As‐rich limits the α2(2 × 4) but also the β2(2 × 4) reconstruction form structures with restricted nitrogen substitution. The high stability of restricted substitutions predestinates the region between the Ga‐ and As‐rich conditions for the growth of GaAsN alloys. The blueshift of the band gap during the annealing of the grown bulk can be explained by the transformation of the grown (GaN)n chains, which are also formed in this region (in the β(2 × 4) reconstruction), to the thermodynamically most stable bulk structures. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Proton stopping data from experiment and theory
Authors: Kalbitzer S. 
Published: September 2005

AbstractProton stopping cross‐sections in several solid and gaseous targets have been calculated by applying the Bethe–Bloch formalism to each electron shell. In addition, binary collision kinetics for both proton and electron in motion have been taken into account. The calculations closely match experimental data on C and Si by us and on He and Ne by TRIM. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Phonon polariton modes in porous III–V semiconductors
Authors: Wilson K. S. Joseph , Navaneethakrishnan K. 
Published: September 2005

AbstractThe phonon polariton modes in the bulk porous III–V semiconductor materials like GaP and GaAs are investigated for different porosity values. Their behavior under an external hydrostatic pressure is also studied. The frequencies of the various modes shift to higher values. The model has been extended to the case of self assembled GaP quantum dots (QDOTs) in GaAs matrix. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Chromium ions in alkali lead borotellurite glasses – An EPR and optical study
Authors: Sreekanth Chakradhar R. P. , Lakshmana Rao J. , Sivaramaiah G. , Gopal N. O. 
Published: September 2005

AbstractChromium ions doped 90 Na2B4O7 + (9 – x)PbO + 1TeO2 and 90 K2B4O7 + (9 – x)PbO + 1TeO2 (x = 3, 4, 5, 6, 7 and 8 mol%) glasses have been studied by using Electron Paramagnetic Resonance (EPR) and optical absorption techniques. The EPR spectra exhibit a broad resonance signal at g = 4.65 and a narrow resonance signal at g = 1.97. The resonance at g = 4.65 can be attributed to isolated Cr3+ ions in rhombic symmetry subjected to strong crystal field effects and the resonance at g = 1.97 is due to Cr5+ ions. The EPR spectra have also been studied at different temperatures (153–393 K). The number of spins (N) participating in the resonance is measured as a function of temperature and the activation energy is calculated. The exchange coupling constant J between chromium ions is calculated. The optical absorption spectrum exhibits bands characteristic of Cr3+ ions in an octahedral symmetry. The optical band gap (Eopt) and Urbach energies (ΔE) have been calculated for all the glass samples and it is observed that Eopt decreases and ΔE increases with increase of chromium content. This has been explained as due to the creation of additional localized states with chromium doping, which overlap and extend in the mobility gap of the glass matrix. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Self‐consistent calculation for energy band profiles and energy levels of cubic quantum dots
Authors: Lee Johnson , Spector Harold N. , Chou Wu Ching 
Published: September 2005

AbstractWe have performed a self‐consistent calculation for the energy band profiles and energy levels of cubic quantum dots, solving both the Schrödinger and Poisson's equations. In particular, we examined the effect of doping on these levels both in the presence and absence of a positive test charge. We found that the number of levels the cubic dot supported depended on the size of the dot, and that the energy of the levels decreased in the presence of a positive test charge. Moreover, we found that the energy levels of both the singlet and triplet states in the dot increased with the doping density. The quasi‐Fermi level was found to be lower in the presence of a positive test charge than in its absence, and the quasi‐Fermi level increased sharply with increasing doping density both in the absence and presence of the test charge. With very high doping the Fermi level is located in the barrier while with low doping the Fermi level is located down below the ground state energy which implies that the probability of finding an electron in a dot is very small. We also find that at high doping levels the lowest energy states are no longer confined in the dot. The potential energy profile was found to be dramatically affected by both the doping and the presence of a positive test charge. The profile was found to become asymmetric when the test charge was displaced from the center of the dot. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Synthesis and characterization of aluminum–polyaniline thin films and membranes
Authors: Liu Yan , O'Keefe Matthew J. , Beyaz Ayse , Schuman Thomas P. 
Published: September 2005

AbstractPolyaniline (PAni) films of different intrinsic oxidation states, including emeraldine salt, emeraldine base and leucoemeraldine base, were synthesized. Free‐standing membranes and thin film bilayers of aluminum–polyaniline were fabricated by magnetron sputter deposition of aluminum onto polyaniline films. Aluminum–polyaniline samples were analyzed by transmission electron microscopy (TEM) to investigate the microstructures of specimens, including cross‐sectional TEM micrographs of the metal‐polyaniline interfacial structure not previously reported in the literature. Auger electron spectroscopy (AES) and X‐ray photoelectron spectroscopy (XPS) were employed to study the chemical bonding and interaction between deposited aluminum and polyaniline at the interface. Results indicated that the intrinsic oxidation state of the polyaniline influenced the chemistry of the aluminum–polyaniline interface. Distinct interaction between aluminum and polyaniline in the emeraldine salt‐form was observed. However, there was no evidence of direct interactions of the aluminum with emeraldine base and leucoemeraldine base polyaniline. Copyright © 2005 John Wiley & Sons, Ltd.
Retracted: Nanobubbles influence on BSA adsorption on mica surface
Authors: Wu Zhihua , Zhang Xuehua , Zhang Xiaodong , Li Gang , Sun Jielin , Zhang Yi , Li Minqian , Hu Jun 
Published: September 2005

AbstractRetraction: The following article from the Surface and Interface Anlysis, 'Nanobubbles influence on BSA adsorption on mica surface' by Wu ZH, Zhang XH, Zhang XD, Li G, Sun J, Zhang Y, Li M and Hu J, published online on 1 September 2005 in Wiley InterScience (www.interscience.com) and in print Volume 37 Issue 10 pages 797‐801, 2005, has been retracted by agreement between the authors, the journal's Editor‐in‐Chief Professor John F. Watts and John Wiley & Sons, Ltd. The retraction has been agreed due to the article being subsequently published in Volume 38 Issue 6, pages 990‐995 of the journal as part of a Special Issue entitled 'Chinese‐German Forum on Fundamentals and Technological Perspectives of Nanoscience 26‐30 September 2004, Beijing, China.'
Bayesian neural networks for bivariate binary data: an application to prostate cancer study
Authors: Chakraborty Sounak , Ghosh Malay , Maiti Tapabrata , Tewari Ashutosh 
Published: September 2005

AbstractProstate cancer is one of the most common cancers in American men. The cancer could either be locally confined, or it could spread outside the organ. When locally confined, there are several options for treating and curing this disease. Otherwise, surgery is the only option, and in extreme cases of outside spread, it could very easily recur within a short time even after surgery and subsequent radiation therapy. Hence, it is important to know, based on pre‐surgery biopsy results how likely the cancer is organ‐confined or not.The paper considers a hierarchical Bayesian neural network approach for posterior prediction probabilities of certain features indicative of non‐organ confined prostate cancer. In particular, we find such probabilities for margin positivity (MP) and seminal vesicle (SV) positivity jointly. The available training set consists of bivariate binary outcomes indicating the presence or absence of the two. In addition, we have certain covariates such as prostate specific antigen (PSA), gleason score and the indicator for the cancer to be unilateral or bilateral (i.e. spread on one or both sides) in one data set and gene expression microarrays in another data set. We take a hierarchical Bayesian neural network approach to find the posterior prediction probabilities for a test and validation set, and compare these with the actual outcomes for the first data set. In case of the microarray data we use leave one out cross‐validation to access the accuracy of our method. We also demonstrate the superiority of our method to the other competing methods through a simulation study. The Bayesian procedure is implemented by an application of the Markov chain Monte Carlo numerical integration technique. For the problem at hand, our Bayesian bivariate neural network procedure is shown to be superior to the classical neural network, Radford Neal's Bayesian neural network as well as bivariate logistic models to predict jointly the MP and SV in a patient in both the data sets as well as in the simulation study. Copyright © 2005 John Wiley & Sons, Ltd.
Inferences on the within‐subject coefficient of variation
Authors: Tian Lili 
Published: September 2005

AbstractThe within‐subject coefficient of variation (WCV) is widely used as a measure of precision and reproducibility of data in medical and biological science. In this paper, generalized confidence intervals and tests for a single WCV is developed using the concept of generalized pivots under the assumption of one‐way random effect model. This approach is further extended to two‐sample cases. The resulting procedures are easy to compute and have good properties in term of coverage probabilities and type‐I error control at small sample sizes. The proposed methods are illustrated by a real life example. Copyright © 2005 John Wiley & Sons, Ltd.
A New Knot Technique for Vessel Ligatures
Authors: Botet Xavier , Surinyach Santiago , Molinas Joan 
Published: September 2005

AbstractA new technique for ligating vessels and similar structures that offers more security is described. The aim of the study was to test whether this hypothesis was correct. Six different types of knots, including the one described in this article were compared by a strength‐testing study. The knots were tied on a silicon tube through which a constant air flow of 795.10 mmHg of pressure circulated. Tension of 2 kg was then applied to both loose ends of the suture filament (polyglyconate n°1 gauge) for 25 seconds. Then, 15 seconds after the tension was released an overpressure of 2250.31 mmHg was applied to the system. Two computerized pressure sensors were applied to both ends of the tube.The newly described knot reached the highest strangulating force (997.63 mmHg) and had the highest resistance to slippage.From these results, we conclude that the new knot is far more secure for vessel and duct ligature and that it represents a new and useful tool for surgeons in both open and laparoscopic surgery.
Nerve‐sparing Axillary Dissection Using the da Vinci Surgical System
Authors: Lim Susan M.L. , Kum Cheng K. , Lam Foong L. 
Published: September 2005

AbstractThis is an initial report of a new method of axillary dissection via a periareolar incision and an 8 mm incision in the axilla with the da Vinci Surgical System. The 10× magnification and three‐dimensional image, together with the versatility and precision of the robotic telemanipulators, has enabled us to perform nerve‐sparing axillary dissection in four patients with invasive ductal carcinoma of the breast undergoing segmental (conservative) excision and level II axillary dissection. The time for the robotic axillary dissection ranged from 30 to 105 minutes (average 70.5 minutes). The average number of lymph nodes retrieved was 13 (11, 11, 13, and 17, respectively). Postoperatively all four patients recovered well and were discharged the next day. The robotic system can enhance the surgeon’s ability by providing a high‐definition, magnified, three‐dimensional view of the operative field, intuitively controlled articulating instruments, and elimination of tremors; and it has potential benefits for the patient.
Do Antimicrobial Susceptibility Patterns of Colonic Isolates of Bacteroides Species Change after Antibiotic Prophylaxis with Cefoxitine during Elective Abdominal Surgery?
Authors: (Toprak) Nurver Ülger , Güllüoğlu Bahadır M. , Çakıcı Özlem , Akin M. Levhi , Demirkalem Pakize , Çelenk Tuncay , Söyletir Güner 
Published: September 2005

AbstractThe objectives of the study were to investigate and compare the susceptibility profiles of preoperative and postoperative intestinal Bacteroides fragilis and Bacteroides thetaiotaomicron strains against antimicrobials to evaluate their resistance development patterns due to prophylactic antibiotic administration. Preoperative and postoperative stool samples were obtained from patients undergoing elective abdominal surgery with a “clean‐contaminated” wound categorization. All patients received cefoxitin 2 g as prophylaxis. Isolates of Bacteroides species were identified. Susceptibility tests against ampicillin, piperacillin, cefoxitin, clindamycin, chloramphenicol, metronidazole, imipenem, and amoxicillin‐clavulanate were performed. Stool samples were collected from 40 patients at two settings: before and after the operation. Most of the patients (53%) were operated on because of colorectal carcinoma and underwent surgery that included colectomy or anterior resection. Bacteroidesfragilis and Bacteroides thetaiotaomicron were isolated in both samples obtained from 22 and 34 patients, respectively. In the present study 95% to 100%, 50% to 74%, 46% to 64%, and 18% to 35% of preoperatively isolated Bacteroides species were resistant to ampicillin, cefoxitin, clindamycin, and piperacillin, respectively. Although there were no statistically significant difference, postoperative strains were more resistant than preoperative isolates, and the resistance rates were found to be 95% to 100%, 55% to 82%, 46% to 86%, and 37% to 41%, respectively. Both Bacteroides species isolated from all specimens before and after the surgery were uniformly susceptible to amoxicillin‐clavulanate, imipenem, metronidazol, and chloramphenicol.Our data revealed that Bacteroides strains revealed high resistance to ampicillin, cefoxitin, piperacillin, and clindamycin. Metronidazole, imipenem, and amoxicillin‐clavulanate seem highly effective against both Bacteroides species. Cefoxitin prophylaxis did not significantly increase the resistance patterns against antimicrobial agents.
The meaning of smoking as health and social risk in adolescence
Authors: Tilleczek Kate C. , Hine Donald W. 
Published: August 2005

ABSTRACTThis investigation describes what smoking means to adolescents, and attempts to better understand it as a rite of passage. Applying a social ontology to an often‐individualized issue, interviews were conducted with 20 adolescent smokers between the ages of 13 and 19. Results show that adolescents possess detailed information about the risks of smoking. Both age and gender differentiated the meanings of smoking which were found to be both positive and negative. Valence inconsistency increased with age. Results are interpreted within a cultural, developmental framework and suggest reconstructing smoking risks as potentially positive. Implications for research and prevention are discussed.
The association between the Lie scale of the Maudsley personality inventory and striatal dopamine D2/D3 receptor availability of healthy Chinese community subjects
Authors: Huang Chieh Liang , Yang Yen Kuang , Chu Ching Lin , Lee I Hui , Yeh Tzung Lieh , Chen Po See , Chiu Nan Tsing 
Published: September 2005

AbstractThe present study examined the relationship between the Lie scale scores and striatal D2/D3 receptor availability with respect to the cerebellum in 42 healthy community volunteers in Taiwan using single photon emission computed tomography (SPECT) with [123I]iodo-benzoaminde (IBZM). Even after controlling of age and educational level, subjects' Lie scale scores of the Maudsley personality inventory correlate negatively with D2/D3 receptor availability. Individual with higher Lie scale scores may have higher impulsivity due to lower dopaminergic availability.