bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional restraints on the patterns of amino acid substitutions: Application to sequence–structure homology recognition
Authors: Chelliah Vijayalakshmi , Blundell Tom , Mizuguchi Kenji 
Published: September 2005

AbstractAmino acid residues that are involved in functional interactions in proteins have strong evolutionary pressure to remain unchanged and consequently their substitution patterns are different from those that are noninteracting. To characterize and quantify the differences between amino acid substitution patterns due to structural restraints and those under functional restraints, we have made a comparative analysis of families of homologous proteins. Residues classified as having the same amino acid type, secondary structure, accessibility, and side‐chain hydrogen bonds are shown to be better conserved if they are close to the active site. We have focused on enzyme families for this analysis since they have functional sites that are easily defined by their catalytic residues. We have derived new sets of environment‐specific substitution tables, which we term function‐dependent environment‐specific substitution tables, where amino acid residues are classified according to their distance from the functional sites. The residues that are within a distance of 9 Å from the active site have distinct amino acid substitution patterns when compared to the other sites. The function‐dependent environment‐specific substitution tables have been tested using the sequence–structure homology recognition program FUGUE and the results compared with the recognition performance obtained using the standard environment‐specific substitution tables. Significant improvements are obtained in both recognition performance and alignment accuracy using the function‐dependent environment‐specific substitution tables (P‐value = 0.02, according to the Wilcoxon signed rank test for alignment accuracy). The alignments near the active site are greatly improved with pronounced improvements at lower percentage identities (less than 30%). Proteins 2005. © 2005 Wiley‐Liss, Inc.
Multiple display of a protein domain on a bacterial polymeric scaffold
Authors: Craig P. O. , Berguer P. M. , Ainciart N. , Zylberman V. , Thomas M. G. , Tosar L. J. Martinez , Bulloj A. , Boccaccio G. L. , Goldbaum F. A. 
Published: September 2005

AbstractThe multiple display of protein domains on polymeric scaffolds is an emerging technology for many applications. BLS is a highly immunogenic protein that has an oligomeric structure formed by a 17.2 kDa subunit arranged as a dimer of pentamers. Here we describe the production as well as the structural, functional, and immunological properties of a 9 kDa double‐stranded RNA‐binding domain (RBD3) fused to the structure of BLS. We demonstrate that the BLS and RBD3 modules are stably and independently folded in the structure of the chimera and form a decameric structure of 255 kDa as the native BLS oligomers. The polymeric display of RBD3 in the structure of BLS increases the dsRNA binding strength of this domain both in vitro and in vivo, and also enhances its immunogenicity to the point that it breaks the tolerance of mice to the RBD3 self‐antigen. Our results underscore the BLS display strategy as a powerful tool for biotechnological and therapeutic applications. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Capsicum oleoresin: development of an in‐soil repellent for pocket gophers
Authors: Sterner Ray T , Shumake Stephen A , Gaddis Stanley E , Bourassa Jean B 
Published: September 2005

AbstractA pre‐ and post‐monitoring study was conducted of the potential use of capsicum oleoresin as an in‐soil repellent for northern pocket gophers (Thomomys talpoides). Pocket gophers were captured in irrigated alfalfa (Medicago sativa L), affixed with radio transmitters, and monitored daily for location. Six plots (4.87 × 4.87 m) each were randomly assigned to capsicum oleoresin and soybean oil treatments; these were set up based upon the centers of initial core areas of gophers. Mean (±SD) volumes of capsicum oleoresin and water and soybean oil and water mixtures (10 + 90 by volume) dispensed onto plots equaled 178.5 (±4.7) and 175.7 (±14.0) liters, respectively. Movements (m) of the radio‐transmitted gophers from plot centers were computed for four daily readings (i.e., 0801–1000, 1101–1300, 1501–1700 and 1801–2000 h). Spectrophotometric analysis of soil samples from capsicum oleoresin plots validated the presence of capsicum on plots and the absence of capsicum on placebo‐ and off‐plot locations. Analysis of variance for movement distances of gophers yielded a Date main effect [F(11, 103) = 2.08, P ≤ 0.03] and a Date × Reading (time) interaction [F(32, 299) = 3.21, P ≤ 0.01]. Results showed that gophers were located farther from plot centers for the 0801–1000 and 1501–1700 h telemetry readings for ≤3 days post‐chemical application—a probable ‘disturbance’ effect rather than a chemical‐induced avoidance. In a prior laboratory study, capsicum oleoresin and soil treatments of 1.5% w/w capsicum caused nearly a 50% decrease in soil contact time by gophers relative to placebo‐exposed control animals. This implies that procedural variables warrant revision before abandoning this approach. The potential for soil insertion of repellents as a technique for expelling pocket gophers from territories and some methodological changes for future research of the technique are discussed. Published in 2005 for SCI by John Wiley & Sons, Ltd.
Improved performance of InGaN/GaN blue light‐emitting diodes with a SiO2/TiO2 Bragg reflector
Authors: Chen Lung‐Chien , Feng Hui‐Ching 
Published: September 2005

AbstractInGaN/GaN blue light‐emitting diodes (LEDs) on sapphire substrates with a SiO2/TiO2 Bragg reflector were fabricated. The deposited SiO2/TiO2 Bragg reflectors exhibit a high reflectivity of up to nearly 96.9% at about 460 nm. When the InGaN/GaN LEDs with a SiO2/TiO2 Bragg reflectors were operated at a forward current of 20 mA at room temperature, the peak wavelength, the light output power, and the external quantum efficiency were measured to be 470 nm, 5.91 mW, and 11.21%, respectively. The light output power was as high as 15.33 mW at the forward current of 100 mA. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Scaling relations, virial theorem, and energy densities for long‐range and short‐range density functionals
Authors: Toulouse Julien , Gori‐Giorgi Paola , Savin Andreas 
Published: September 2005

AbstractDecomposition of the Coulomb electron–electron interaction into a long‐range and a short‐range part is described within the framework of density functional theory, deriving some scaling relations and the corresponding virial theorem. We study the behavior of the local density approximation in the high‐density limit for the long‐range and the short‐range functionals by carrying out a detailed analysis of the correlation energy of a uniform electron gas interacting via a long‐range‐only electron–electron repulsion. Possible definitions of exchange and correlation energy densities are discussed and clarified with some examples. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Electronic structure and stability of BP clusters: theoretical calculations for (BP)n (n = 2–4)
Authors: Qu Yuhui , Ma Wanyong , Bian Xiufang , Tang Hongwei , Tian Weixing 
Published: September 2005

AbstractThe geometry, electronic configurations, harmonic vibrational frequencies, and stability of the structural isomers of boron phosphide clusters have been investigated using density functional theory (DFT). CCSD(T) calculations show that the lowest‐energy structures are cyclic (IIt, IVs) with Dnh symmetry for dimers and trimers. The caged structure for B4P4 lie higher in energy than the monocyclic structure with D2d symmetry (VIs). The B–P bond dominates the structures for many isomers, so that one preferred dissociation channel is loss of the BP monomer. The hybridization and chemical bonding in the different structures are also discussed. Comparisons with boron nitride clusters, the ground state structures of BnPn (n = 2, 3) clusters are analogous to those of their corresponding BnNn (n = 2, 3) counterparts. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Robust trend tests for genetic association using matched case‐control design
Authors: Zheng Gang , Tian Xin 
Published: September 2005

AbstractTrend tests for genetic association using a matched case‐control design are studied, which allows for a variable number of controls per case. However, the tests depend on the scores based on the underlying genetic model, thus it may result in substantial loss of power when the model is misspecified. Since the mode of inheritance may be unknown for complex diseases, robust trend tests in matched case‐control studies are developed. Simulation is conducted to compare the trend tests and the robust trend tests under various genetic models. The results are applied to detect candidate‐gene association using an example from a case‐control aetiologic study of sarcoidosis. Published in 2005 by John Wiley & Sons, Ltd.
A symmetrized vector potential‐vorticity formulation of the Stokes system and its Finite Element Discretization
Authors: Ruas V. , Trales P.R. 
Published: September 2005

AbstractThe aim of this paper is to study a formulation of the Stokes system in a bounded three‐dimensional domain, expressed in terms of the vorticity and a vector potential, whose gradient is fully prescribed on the boundary of the domain. The formulation is based on an uncoupling technique following principles similar to those exploited by Glowinski & Pironneau [7] in the case of the stream function‐vorticity formulation of the two‐dimensional Stokes system. A solution scheme of the resulting system using special classes of finite elements is given.
Large‐scale simulations of acoustic‐structure interaction using the fast multipole BEM
Authors: Gaul L. , Fischer M. 
Published: September 2005

AbstractFor the simulation of acoustic‐structure interaction problems, the coupled field equations must be solved. The structure is commonly discretized using finite elements, whereas for the acoustic field the boundary element method (BEM) is favorable. A mortar BEM‐FEM coupling algorithm is developed that allows the combination of non‐conforming meshes. The high flexibility for the choice of discretizations offers a high efficiency, since specialized shape functions and adaptive mesh refinement can be used in the subdomains. The mortar coupling algorithm yields a saddle point problem that is solved using a preconditioned inexact Uzawa algorithm. The iterative solver enables the use of the fast multipole BEM and thus coupled simulations on large boundary element models.
Thursdays with Marion: The Therapist's Tale
Authors: Sobel Susan 
Published: September 2005

AbstractWe who work with people with chronic and/or terminal illnesses are often confounded about what we ought to do and what we can do for those who suffer. This paper presents a case study of my work with Marion who began therapy after her presymptomatic testing for HD to address her depression and anxiety. The approach we took is a narrative one. The impact of illness on existing family stories is described followed by an examination of the premises of a narrative model. The case description demonstrates the collaborative nature of the therapy. Some thoughts on the role of the therapist in this model are offered.
Communication Analysis of BRCA1 Genetic Counseling
Authors: Ellington Lee , Roter Debra , Dudley William N. , Baty Bonnie J. , Upchurch Renn , Larson Susan , Wylie Jean E. , Smith Ken R. , Botkin Jeffrey R. 
Published: September 2005

AbstractIn this study, we apply an existing medical communication coding system to BRCA1 genetic counseling sessions, describe the session dynamics, and explore variation in session communication. The sample was comprised of 167 members of an identified BRCA1 kindred whose pretest counseling session was audiotaped and coded using Roter's Interaction Analysis System (RIAS). Three certified genetic counselors followed a research protocol that dictated areas to be covered in the counseling session. We found that it was feasible to code long, protocol driven BRCA1 sessions in a quantitative manner without the use of transcripts and capture the dialogue of all session participants. These findings support the use of RIAS in genetic counseling research. Our results indicate that these BRCA1 sessions were predominantly educational in nature with minimal dialogue devoted to psychosocial issues. We found that participant gender, presence of a client companion, and counselor identity influence session communication.
Conflict resolution patterns and longevity of adolescent romantic couples: A 2‐year follow‐up study
Authors: Shulman Shmuel , Tuval‐Mashiach Rivka , Levran Elisheva , Anbar Shmuel 
Published: September 2005

ABSTRACTThis study examined the predictors of longevity among 40 late adolescent romantic couples (mean age males=17.71 years; mean age females=17.18 years). Subjects were given a revealed differences task where they were asked to solve their disagreements. The joint task was recorded, transcribed and analysed by two raters. At 3, 6, 9, 12, 18, and 24 months after this procedure, partners were contacted by telephone and asked whether their relationship was still intact. A cluster analysis was performed on couples’ interaction indices and yielded three distinctive conflict resolution patterns. TheDownplayingpattern was characterized by a high tendency to minimize the conflict. The relationships of the adolescents displaying this pattern stayed intact for a period of 9 months. Half of them were still together after 24 months. Theadolescents displaying the Integrativepattern, which shows a good ability to negotiate differences tended to stay together over a period of 24 months. Those showing theConflictivepattern, characterized by a confrontative interaction, were separated by the 3 months follow‐up. Results are discussed within the context of developmental perspectives of conflict resolution tendencies and adolescent romance.
A proof of a generalization of Deligne’s conjecture
Authors: Varshavsky Yakov 
Published: September 2005

The goal of this paper is to give a simple proof of Deligne’s conjecture on the Lefschetz trace formula (proven by Fujiwara) and to generalize it to the situation appearing in the forthcoming joint paper with D. Kazhdan. Our proof holds in the realm of ordinary algebraic geometry and does not use rigid geometry.
A note on using permutation-based false discovery rate estimates to compare different analysis methods for microarray data
Authors: Xie Yang , Pan Wei , Khodursky Arkady B. 
Published: September 2005

AbstractMotivation: False discovery rate (FDR) is defined as the expected percentage of false positives among all the claimed positives. In practice, with the true FDR unknown, an estimated FDR can serve as a criterion to evaluate the performance of various statistical methods under the condition that the estimated FDR approximates the true FDR well, or at least, it does not improperly favor or disfavor any particular method. Permutation methods have become popular to estimate FDR in genomic studies. The purpose of this paper is 2-fold. First, we investigate theoretically and empirically whether the standard permutation-based FDR estimator is biased, and if so, whether the bias inappropriately favors or disfavors any method. Second, we propose a simple modification of the standard permutation to yield a better FDR estimator, which can in turn serve as a more fair criterion to evaluate various statistical methods.Results: Both simulated and real data examples are used for illustration and comparison. Three commonly used test statistics, the sample mean, SAM statistic and Student's t-statistic, are considered. The results show that the standard permutation method overestimates FDR. The overestimation is the most severe for the sample mean statistic while the least for the t-statistic with the SAM-statistic lying between the two extremes, suggesting that one has to be cautious when using the standard permutation-based FDR estimates to evaluate various statistical methods. In addition, our proposed FDR estimation method is simple and outperforms the standard method.Contact: yangxie@biostat.umn.ed
Profile-based direct kernels for remote homology detection and fold recognition
Authors: Rangwala Huzefa , Karypis George 
Published: September 2005

Abstract
Motivation: Protein remote homology detection is a central problem in computational biology. Supervised learning algorithms based on support vector machines are currently one of the most effective methods for remote homology detection. The performance of these methods depends on how the protein sequences are modeled and on the method used to compute the kernel function between them.
Results: We introduce two classes of kernel functions that are constructed by combining sequence profiles with new and existing approaches for determining the similarity between pairs of protein sequences. These kernels are constructed directly from these explicit protein similarity measures and employ effective profile-to-profile scoring schemes for measuring the similarity between pairs of proteins. Experiments with remote homology detection and fold recognition problems show that these kernels are capable of producing results that are substantially better than those produced by all of the existing state-of-the-art SVM-based methods. In addition, the experiments show that these kernels, even when used in the absence of profiles, produce results that are better than those produced by existing non-profile-based schemes.
Availability: The programs for computing the various kernel functions are available on request from the authors.
Contact: karypis@cs.umn.edu
Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues
Authors: Wachi Shinichiro , Yoneda Ken , Wu Reen 
Published: September 2005

AbstractMotivation: Global protein interaction network (interactome) analysis provides an effective way to understand the relationships between genes. Through this approach, it was demonstrated that the essential genes in yeast tend to be highly connected as well as connected to other highly connected genes. This is in contrast to the genes that are not essential, which share neither of these properties. Using a similar interactome-transcriptome approach, the topological features in the interactome of differentially expressed genes in lung squamous cancer tissues are assessed.Results: This analysis reveals that the genes that are differentially elevated, as obtained from the microarray gene profiling data, in cancer are well connected, whereas the suppressed genes and randomly selected ones are less so. These results support the notion that a topological analysis of cancer genes using protein interaction data will allow the placement of the list of genes, often of the disparate nature, into the global, systematic context of the cell. The result of this type of analysis may provide the rationale for therapeutic targets in cancer treatment.Contact: swachi@ucdavis.eduSupplementary information: Supplementary data for this paper are available on Bioinformatics online.
HapSim: a simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients
Authors: Montana Giovanni 
Published: September 2005

Abstract
We have developed a simulation tool HapSim for the generation of haplotype data. The simulated haplotypes are such that their allele frequencies and linkage disequilibrium coefficients match exactly those estimated in a real sample.
Availability: The program is available as an R package and can be downloaded from
Contact: g.montana@imperial.ac.uk
First Human Exposure of Org 25969, a Novel Agent to Reverse the Action of Rocuronium Bromide
Authors: Gijsenbergh Francois , Ramael Steven , Houwing Natalie , van Iersel Thijs 
Published: September 2005

Background
Acetylcholinesterase inhibitors are widely used for the reversal of neuromuscular blocking agents. However, acetylcholinesterase inhibitors have several side effects and are not effective during profound block. Org 25969 is a modified gamma-cyclodextrin that encapsulates the neuromuscular blocking agent, rocuronium bromide (Esmeron/Zemuron, NV Organon, Oss, The Netherlands), forming a tightly bound complex with an association constant of approximately 10 m. Chemical encapsulation of rocuronium promotes dissociation of rocuronium from the acetylcholine receptor, thereby reversing the neuromuscular block without the side effects associated with acetylcholinesterase inhibitors.

Methods
Twenty-nine healthy male volunteers were enrolled to investigate the safety, pharmacokinetics, and efficacy of Org 25969. In part 1, Org 25969 or placebo was administered to 19 subjects during one to three treatment periods each. In part 2, a further 10 subjects received general anesthesia on two separate occasions, using an intubating dose of 0.6 mg/kg rocuronium. Three minutes after rocuronium administration, Org 25969 or placebo was given in random order. Six doses of 0.1-8.0 mg/kg Org 25969 were evaluated. Neuromuscular block was measured using an acceleromyograph, the TOF-Watch-SX (NV Organon, Oss, The Netherlands).

Results
All adverse events related to Org 25969 treatment were of limited duration and mild intensity, except for a period of paresthesia, seen in one patient receiving 8 mg/kg Org 25969, which was of moderate intensity. No adverse events required any treatment, and all subjects recovered from them. When 8 mg/kg Org 25969 was given, the train-of-four ratio returned to 0.9 within 2 min after its administration. No signs of recurarization were observed.

Conclusions
Org 25969 was both well tolerated and effective in reversing neuromuscular block induced by rocuronium in 29 human volunteers.
Dose-dependent Inhibition of Platelet Function by Acetaminophen in Healthy Volunteers
Authors: Munsterhjelm Edward , Munsterhjelm Nina M. , Niemi Tomi T. , Ylikorkala Olavi , Neuvonen Pertti J. , Rosenberg Per H. 
Published: September 2005

Background
Acetaminophen (paracetamol) is widely used for postoperative analgesia. Its mechanism of action is inhibition of prostaglandin synthesis in the central nervous system, and acetaminophen is traditionally not considered to influence platelet function. The authors studied the dose-dependent inhibition of platelet function by acetaminophen in healthy volunteers.

Methods
Thirteen healthy male volunteers (aged 19-26 yr) were given placebo or 15, 22.5, or 30 mg/kg acetaminophen intravenously in a double-blind, crossover study. Ten and 90 min after infusion, platelet function was assessed by photometric aggregometry and by measuring release of thromboxane B2, analgesia by cold pressor test, and plasma acetaminophen concentrations by high-performance liquid chromatography.

Results
When triggered with 500 microm arachidonic acid, median platelet aggregation (area under the curve) was 25.7, 22.8, 4.1, or 3.6 x 10 area units (P < 0.001) 10 min after placebo or 15, 22.5, or 30 mg/kg acetaminophen, respectively. An increasing concentration of arachidonic acid attenuated the antiaggregatory effect. After 90 min, platelet function was recovering. Release of thromboxane B2 was also dose-dependently inhibited by acetaminophen. Although plasma concentration of acetaminophen increased linearly with the dose, no analgesic effect was detected in the cold pressor test.

Conclusions
Acetaminophen, which is a weak inhibitor of platelet cyclooxygenase 1, has a dose-dependent antiaggregatory effect. This property may become clinically significant in patients with intrinsic or drug-induced impairment of hemostasis.