bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predictors of adherence and contamination in a randomized trial of exercise in colorectal cancer survivors
Authors: Courneya Kerry S. , Friedenreich Christine M. , Quinney H. Arthur , Fields Anthony L.A. , Jones Lee W. , Fairey Adrian S. 
Published: March 2004

AbstractThe purpose of this study was to examine predictors of exercise adherence (i.e. exercise in the intervention group) and exercise contamination (i.e. exercise in the control group) in a randomized controlled trial of home‐based exercise in colorectal cancer survivors. At baseline, 102 participants completed measures of the theory of planned behavior, personality, past exercise, exercise stage of change, physical fitness, and medical/demographics and then were randomly assigned in a 2:1 ratio to an exercise (n=69) or control (n=33) group. Exercise was monitored weekly for 16 weeks using self‐reports by telephone. Ninety‐three (91%) participants completed the trial. Adherence was 76% in the exercise group and contamination was 52% in the control group. Hierarchical stepwise regression analyses indicated that baseline exercise stage of change (β=0.35; p=0.001), employment status (β=−0.28; p=0.010), treatment protocol (β=−0.26; p=0.018), and perceived behavioral control (β=0.20; p=0.055) explained 39.6% of the variance in exercise adherence. Intentions (β=0.36; p=0.049) and baseline exercise stage of change (β=0.30; p=0.095) explained 29.9% of the variance in exercise contamination. These findings may have implications for conducting clinical trials of exercise in colorectal cancer survivors and for promoting exercise to colorectal cancer survivors outside of clinical trials. Copyright © 2004 John Wiley & Sons, Ltd.
Androgen receptor polymorphisms and risk of biochemical failure among prostatectomy patients
Authors: Strom Sara S. , Gu Yun , Zhang Hui , Troncoso Patricia , Babaian Richard J. , Pettaway Curtis A. , Shete Sanjay , Spitz Margaret R. , Logothetis Christopher J. 
Published: March 2004

AbstractBackgroundLittle is known about the role of inherited genotypes in prostate cancer (PC) progression. This prospective study evaluated the predictive value of androgen receptor (AR) polymorphisms (CAG and GGC repeats) among prostatectomy patients.MethodsWe studied 354 patients registered at M. D. Anderson Cancer Center from 1991 to 2001. Kaplan–Meier and Cox proportional hazard analyses were used.ResultsDuring an average follow‐up of 56 months, 66 (19%) post‐prostatectomy patients experienced biochemical failure (BF). Patients with higher CAG repeats (CAG ≥ 24) had significantly longer BF‐free survival (BFFS) than those with fewer repeats (CAG ≤ 23) (P = 0.04). Higher CAG repeats were significantly associated with lower BF risk among Whites and African Americans. Among Whites, longer CAG repeats (relative risk (RR) = 0.45,P = 0.03) and Gleason score ≥8 (RR = 19.33,P = 0.005) remained significant BFFS predictors in multivariate analysis. GGC repeats were not associated with BF.ConclusionsOur data showed that an inherited polymorphism (CAG repeats) in the AR is related to differences in genetic susceptibility to BF, supporting the hypothesis that increased AR activity may play a role in PC progression. © 2004 Wiley‐Liss, Inc.
Mutational analysis of PINX1 in hereditary prostate cancer
Authors: Hawkins Gregory A. , Chang Bao‐Li , Zheng S. Lilly , Isaacs Sarah D. , Wiley Kathleen E. , Bleecker Eugene R. , Walsh Patrick. C. , Meyers Deborah A. , Xu Jianfeng , Isaacs William B. 
Published: March 2004

AbstractBackgroundTelomerase activity is increased in most tumors. PinX1 has recently been identified as a critical component in regulating telomerase activity. The PinX1 gene is located within chromosomal region 8p22‐23, a region associated with LOH and potentially linked to increased prostate cancer risk.MethodsPINX1 was re‐sequenced in 159 hereditary prostate cancer (HPC) probands. Four non‐synonymous coding variants were genotyped in 159 HPC families.ResultsThirty‐nine polymorphisms were identified in the HPC screening panel. Ten coding polymorphisms were identified, seven (Gln50His, Leu91Met, Gln206His, Arg215Ile, Thr220Ala, Ser254Cys, and Glu414Ala) of which were non‐synonymous. The most common variants Thr220Ala and Ser254Cys were not significantly over‐transmitted from affected parent to affected offspring.ConclusionsBased on these results, we conclude that PINX1 is not a major factor for HPC risk. © 2004 Wiley‐Liss, Inc.
Ultrahigh resolution drug design. II. Atomic resolution structures of human aldose reductase holoenzyme complexed with fidarestat and minalrestat: Implications for the binding of cyclic imide inhibitors
Authors: El‐Kabbani Ossama , Darmanin Connie , Schneider Thomas R. , Hazemann Isabelle , Ruiz Federico , Oka Mitsuru , Joachimiak Andrzejj , Schulze‐Briese Clemens , Tomizaki Takashi , Mitschler Andre , Podjarny Alberto 
Published: March 2004

AbstractThe X‐ray structures of human aldose reductase holoenzyme in complex with the inhibitors Fidarestat (SNK‐860) and Minalrestat (WAY‐509) were determined at atomic resolutions of 0.92 Å and 1.1 Å, respectively. The hydantoin and succinimide moieties of the inhibitors interacted with the conserved anion‐binding site located between the nicotinamide ring of the coenzyme and active site residues Tyr48, His110, and Trp111. Minalrestat's hydrophobic isoquinoline ring was bound in an adjacent pocket lined by residues Trp20, Phe122, and Trp219, with the bromo‐fluorobenzyl group inside the “specificity” pocket. The interactions between Minalrestat's bromo‐fluorobenzyl group and the enzyme include the stacking against the side‐chain of Trp111 as well as hydrogen bonding distances with residues Leu300 and Thr113. The carbamoyl group in Fidarestat formed a hydrogen bond with the main‐chain nitrogen atom of Leu300. The atomic resolution refinement allowed the positioning of hydrogen atoms and accurate determination of bond lengths of the inhibitors, coenzyme NADP+ and active‐site residue His110. The 1′‐position nitrogen atom in the hydantoin and succinimide moieties of Fidarestat and Minalrestat, respectively, form a hydrogen bond with the Nϵ2 atom of His 110. For Fidarestat, the electron density indicated two possible positions for the H‐atom in this bond. Furthermore, both native and anomalous difference maps indicated the replacement of a water molecule linked to His110 by a Cl‐ion. These observations suggest a mechanism in which Fidarestat is bound protonated and becomes negatively charged by donating the proton to His110, which may have important implications on drug design. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Polyproline II helix is the preferred conformation for unfolded polyalanine in water
Authors: Mezei Mihaly , Fleming Patrick J. , Srinivasan Rajgopal , Rose George D. 
Published: March 2004

AbstractDoes aqueous solvent discriminate among peptide conformers? To address this question, we computed the solvation free energy of a blocked, 12‐residue polyalanyl‐peptide in explicit water and analyzed its solvent structure. The peptide was modeled in each of 4 conformers: α‐helix, antiparallel β‐strand, parallel β‐strand, and polyproline II helix (PII). Monte Carlo simulations in the canonical ensemble were performed at 300 K using the CHARMM 22 forcefield with TIP3P water. The simulations indicate that the solvation free energy of PII is favored over that of other conformers for reasons that defy conventional explanation. Specifically, in these 4 conformers, an almost perfect correlation is found between a residue's solvent‐accessible surface area and the volume of its first solvent shell, but neither quantity is correlated with the observed differences in solvation free energy. Instead, solvation free energy tracks with the interaction energy between the peptide and its first‐shell water. An additional, previously unrecognized contribution involves the conformation‐dependent perturbation of first‐shell solvent organization. Unlike PII, β‐strands induce formation of entropically disfavored peptide:water bridges that order vicinal water in a manner reminiscent of the hydrophobic effect. The use of explicit water allows us to capture and characterize these dynamic water bridges that form and dissolve during our simulations. Proteins 2004. © 2004 Wiley‐Liss, Inc.
On the functional significance of electron density protein structure alignments
Authors: Constans Pere 
Published: March 2004

AbstractElectron density protein alignments are analyzed in terms of their underlying similarity measure, the density overlap. These alignments are conceptually unrelated to biochemical structural elements and, therefore, are appropriate in structure‐only similarity studies. The analysis is focused on the low sequence similarity subset of protein domains. A remarkable association is found between simple, density overlap measures and the expert designed Structural Classification of Proteins (SCOP) for which functional and evolutive analogies prevail. The association found validates the functional significance of electron density alignments. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.
Discrimination of single amino acid mutations of the p53 protein by means of deterministic singularities of recurrence quantification analysis
Authors: Porrello Alessandro , Soddu Silvia , Zbilut Joseph P. , Crescenzi Marco , Giuliani Alessandro 
Published: March 2004

Abstractp53 is mutated in roughly 50% of all human tumors, predominantly in the DNA‐binding domain codons. Structural, biochemical, and functional studies have reported that the different p53 mutants possess a broad range of behaviors that include the elimination of the tumor‐suppression function of wild‐type protein, the acquisition of dominant‐negative function over the wild‐type form, and the establishment of gain‐of‐function activities. The contribution of each of these types of mutations to tumor progression, grade of malignancy, and response to anticancer treatments has been so far analyzed only for a few “hot‐spots.” In an attempt to identify new approaches to systematically characterize the complete spectrum of p53 mutations, we applied recurrence quantification analysis (RQA), a non‐linear signal analysis technique, to p53 primary structure. Moving from the study of the p53 hydrophobicity pattern, which revealed important similarities with the singular deterministic structuring of prions, we could statistically discriminate, on a pure amino acid sequence basis, between experimentally characterized DNA‐contact defective and conformational p53 mutants with a very high percentage of success. This result indicates that RQA is a mathematical tool particularly advantageous for the development of a database of p53 mutations that integrates epidemiological data with structural and functional categorizations. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.
Apolipoprotein E‐low density lipoprotein receptor binding: Study of protein–protein interaction in rationally selected docked complexes
Authors: Prévost Martine , Raussens Vincent 
Published: March 2004

AbstractApolipoprotein E (apoE) is an important protein involved in lipid metabolism due to its interaction with members of the low‐density lipoprotein receptor (LDLR) family. To further understand the molecular basis for this receptor‐binding activity, an apoE fragment containing the receptor binding region (residues 135–151) was docked onto the fifth LDLR ligand binding repeat (LR5) by computational methods. A subset of structures generated by the docking was rationally selected on the grounds of experimental data combined with modeling and was used for further analysis.The application and comparison of two different experimental structures for the apoE fragment underlines the local structural changes occurring in apoE when switching from a receptor‐inactive to a receptor‐active conformation. The body of interactions occurring at the interface between the two proteins is in very good agreement with the biochemical data available for both apoE and LDLR. Charged residues are involved in numerous ionic interactions and might therefore be important for the specificity of the interaction between apoE and LR5. In addition, the interface also features a tryptophan and a stacking of histidine residues, revealing that the association between the two proteins is not entirely governed by ionic interactions. In particular, the presence of histidine residues in the interface gives a structural basis for the pH‐regulated release mechanism of apoE in the endosomes. The proposed molecular basis for apoE binding to LDLR could aid the design of strategies for targeting alterations in lipid transport and metabolism. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Recognition of coarse‐grained protein tertiary structure
Authors: Lezon Timothy , Banavar Jayanth R. , Maritan Amos 
Published: March 2004

AbstractA model of the protein backbone is considered in which each residue is characterized by the location of its Cα atom and one of a discrete set of conformal (ϕ, ψ) states. We investigate the key differences between a description that offers a locally precise fit to known backbone structures and one that provides a globally accurate fit to protein structures. Using a statistical scoring scheme and threading, a protein's local best‐fit conformation is highly recognizable, but its global structure cannot be directly determined from an amino acid sequence. The incorporation of information about the conformal states of neighboring residues along the chain allows one to accurately translate the local structure into a global structure. We present a two‐step algorithm, which recognizes up to 95% of the tested protein native‐state structures to within a 2.5 Å root mean square deviation. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.
Fmoc‐based chemical synthesis and selective binding to supercoiled DNA of the p53 C‐terminal segment and its phosphorylated and acetylated derivatives
Authors: Teruya Kenta , Murphy Angela C. , Burlin Tom , Appella Ettore , Mazur Sharlyn J. 
Published: March 2004

AbstractThe C‐terminal domain of p53 comprises a linker, the tetramerization domain and the regulatory domain, and contains at least seven sites of potential post‐translational modification. An improved strategy was developed for the synthesis of large peptides that contain phosphorylated amino acids and p53(303–393), a 91‐amino acid peptide, and three post‐translationally modified derivatives were synthesized through the sequential condensation of three partially protected segments. Peptide thiolesters were prepared using the sulfonamide‐based ‘safety‐catch’ resin approach and employing Fmoc‐based solid‐phase peptide synthesis. At the N‐terminus of the middle building block, a photolabile protecting group, 3,4‐dimethoxy‐6‐nitrobenzyloxycarbonyl, was incorporated to differentiate the N‐terminal amino group from the side‐chain amino groups. Two sequential couplings were accomplished following this protection strategy. The synthetic products, p53(303–393) and its phosphorylated or acetylated derivatives, exhibited the ability to bind specifically to supercoiled DNA, which is one of the characteristics of this domain. Published in 2004 by the European Peptide Society and John Wiley & Sons, Ltd.
First‐principles periodic and semiempirical cyclic cluster calculations for single oxygen vacancies in crystalline Al2O3
Authors: Janetzko Florian , Evarestov Robert A. , Bredow Thomas , Jug Karl 
Published: March 2004

AbstractSingle neutral and positively charged oxygen vacancies (F and F+ centers) in α‐Al2O3 are investigated using the supercell model (SCM) at the Hartree‐Fock (HF) and density functional theory (DFT) level and the cyclic cluster model (CCM) implemented in the semiempirical MSINDO method. Results of supercell and cyclic cluster calculations for the cohesive energy of the perfect Al2O3 crystal are compared with the experimental value for the heat of atomization. The defect formation energy of the unrelaxed F center is calculated with the SCM. The CCM is used to calculate the defect formation energy of the F and the F+ centers. Relaxation effects for the nearest neighbors (NN) and the next‐nearest neighbors (NNN) of the F and F+ centers are investigated. The obtained values are compared to other theoretical literature data. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Photoelectric emission from quantum well wire: effect of broadening
Authors: Mutsuddi I. , Bose C. , Sarkar C. K. 
Published: March 2004

AbstractWe investigate the photoemission from quasi‐one‐dimensional electron gas (Q1DEG) formed in a quantum wire in the presence of energy level broadening arising due to electron impurity interactions in a real system. The effect of broadening has been incorporated in analogy of energy level broadening observed in a bulk semiconductor subjected to a quantizing magnetic field. Inclusion of broadening is found to be responsible for the lowering of photoemission, as expected, due to enhanced scattering. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Thickness dependence of the dielectric function of ferroelectric thin films
Authors: Wesselinowa J. M. , Trimper S. 
Published: March 2004

AbstractA Green's function technique for a modified Ising model in a transverse field is applied, which allows to calculate the real and the imaginary parts of the dielectric function ϵ(k, E) for ferroelectric thin films. Compared to bulk materials the frequency of the soft‐mode in thin film is reduced whereas the damping is enhanced. The dependence of ϵ(k, E) on temperature and film thickness is obtained for k = 0 numerically. It is demonstrated, that the maximum of the dielectric function decreases with decreasing film thickness. The temperature, where the dielectric function offers a maximum, can decrease or increase depending on the strength of the surface transverse field and the exchange interaction parameter. Due to stronger damping effects in thin films the peak in the dielectric function becomes more diffuse when the film thickness decreases. The results are in reasonable qualitative agreement with experimental data for different ferroelctrics. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Horizontal line nodes in superconducting Sr2RuO4
Authors: Litak G. , Annett J. F. , Györffy B. L. , Wysokiński K. I. 
Published: March 2004

AbstractSuperconductivity in Sr2RuO4 is one of the most interesting phenomena in current condensed matter physics, since it is revealed to be a triplet‐pairing state. Our Editor's Choice [1] considers an important problem related to the type of order parameter in this material.The position of line nodes on the Fermi surface, as evident from recent measurements, has been determined for various scenarios shown in the cover picture. Using these models, the temperature dependence of heat capacity and penetration depth has been calculated for easy comparison with experiments.The first author, Grzegorz Litak, is assistant professor at Technical University of Lublin and visiting scientist at the Max Planck Institute in Dresden. He is working on the effect of disorder on correlated and exotic superconductors, nonlinear dynamics, and superconductivity in strontium ruthenate. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Neural Network Selection Mechanism for BDD Construction
Authors: Bartlett L. M. 
Published: March 2004

AbstractThe binary decision diagram (BDD) methodology is the latest approach used to improve the analysis of the fault ree diagram, which gives a qualitative and quantitative assessment of specified risks. To convert the fault tree into the necessary BDD format requires the basic events of the tree to be placed in an ordering. The ordering of the basic events is critical to the resulting size of the BDD, and ultimately affects the performance and benefits of this technique. A number of heuristic approaches have been developed to produce an optimal ordering permutation for a specific tree, however they do not always yield a minimal BDD structure for all trees. Latest research considers a neural network approach used to select the ‘best’ ordering permutation from a given set of alternatives. To use this approach characteristics are taken from the fault tree as guidelines to selection of the appropriate ordering permutation. This paper looks at a new method of using the Jacobian matrix to choose the most desired characteristics from the fault tree, which will aid the neural network selection procedure. Copyright © 2004 John Wiley & Sons, Ltd.
Calculating the Failure Intensity of a Non‐coherent Fault Tree Using the BDD Technique
Authors: Beeson Sally , Andrews John 
Published: March 2004

AbstractThis paper considers a technique for calculating the unconditional failure intensity of any given non‐coherent fault tree. Conventional fault tree analysis (FTA) techniques involve the evaluation of lengthy series expansions and approximations are unavoidable even for moderate sized fault trees. The binary decision diagram (BDD) technique overcomes some of the shortfalls of conventional FTA techniques enabling efficient and exact quantitative analysis of both coherent and non‐coherent fault trees. Copyright © 2004 John Wiley & Sons, Ltd.
Bayesian Estimation from Censored Data with Incomplete Information
Authors: Phillips M. J. 
Published: March 2004

AbstractPhillips and Sweeting (Journal of the Royal Statistical Society B 1996; 58:775–783) considered estimation of the parameter of the exponential distribution with censored failure time data when there is incomplete knowledge of the censoring times. It was shown that, under particular models for the censoring mechanism and censoring errors, it will usually be safe to ignore such errors provided they are not expected to be too large. The results depended on using an inverted Gamma model for the conditional distribution of the concomitant variable which provided the supplementary information used when the failure times were censored. The effect of alternative assumptions about knowledge of the censoring values on the estimation of failure rate is investigated through the use of Bayesian analysis. By putting prior distributions on the critical parameters of the censoring mechanism it is possible to incorporate and investigate the influence of the use of prior knowledge. Copyright © 2004 John Wiley & Sons, Ltd.
Linear and nonlinear feature of electronic excitation energy in carbon chains HC2n+1H and HC2nH
Authors: Zhang Congjie , Cao Zexing , Wu Haishun , Zhang Qianer 
Published: March 2004

AbstractDensity functional theory has been used to investigate the geometries, bonding, and vibrational frequencies of HC2nH (n = 1–13) and HC2n+1H (n = 2–12). Vertical excitation energies for the X1Σ → 11Σ transition of HC2nH (n = 1–5) and for the X3Σ → 13Σ transition of HC2n+1H (n = 2–5) have been calculated by the time‐dependent density functional theory and ab initio second‐order multiconfiguration perturbation method, respectively. On the basis of the present calculations, explicit expressions for the size dependence of excitation energy in linear polyynes HC2n+1H and HC2n+1H are suggested. Such analytical λ − n relationships show good agreement with experimental observations. Theoretical investigations of relevant excited states demonstrate that distinct linear and nonlinear spectroscopic features in such polyynes can be ascribed to similarity and difference in bonding between the ground and excited states in HC2n+1H and HC2nH. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Approximate atomic calculations and stability of negative ions with a modified Thomas–Fermi–Dirac model
Authors: Porras Ignacio , Moya Andrés 
Published: March 2004

AbstractBy means of an improved modified Thomas–Fermi–Dirac approach we obtain fair shell‐averaged total energies of atoms and ions. In particular, stable single‐charged negative ions can be described with this method. In addition, the possibility of developing hybrid schemes with this method coupled to quantum mechanical calculations for the evaluation of quantities such as ionization potentials is also investigated. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004