bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nuclear–Mitochondrial Epistasis and Drosophila Aging: Introgression of Drosophila simulans mtDNA Modifies Longevity in D. melanogaster Nuclear Backgrounds
Authors: Rand David M , Fry Adam , Sheldahl Lea 
Published: October 2005

Abstract
Under the mitochondrial theory of aging, physiological decline with age results from the accumulated cellular damage produced by reactive oxygen species generated during electron transport in the mitochondrion. A large body of literature has documented age-specific declines in mitochondrial function that are consistent with this theory, but relatively few studies have been able to distinguish cause from consequence in the association between mitochondrial function and aging. Since mitochondrial function is jointly encoded by mitochondrial (mtDNA) and nuclear genes, the mitochondrial genetics of aging should be controlled by variation in (1) mtDNA, (2) nuclear genes, or (3) nuclear–mtDNA interactions. The goal of this study was to assess the relative contributions of these factors in causing variation in Drosophila longevity. We compared strains of flies carrying mtDNAs with varying levels of divergence: two strains from Zimbabwe (&lt;20 bp substitutions between mtDNAs), strains from Crete and the United States (∼20–40 bp substitutions between mtDNAs), and introgression strains of Drosophila melanogaster carrying mtDNA from Drosophila simulans in a D. melanogaster Oregon-R chromosomal background (&gt;500 silent and 80 amino acid substitutions between these mtDNAs). Longevity was studied in reciprocal cross genotypes between pairs of these strains to test for cytoplasmic (mtDNA) factors affecting aging. The intrapopulation crosses between Zimbabwe strains show no difference in longevity between mtDNAs; the interpopulation crosses between Crete and the United States show subtle but significant differences in longevity; and the interspecific introgression lines showed very significant differences between mtDNAs. However, the genotypes carrying the D. simulans mtDNA were not consistently short-lived, as might be predicted from the disruption of nuclear–mitochondrial coadaptation. Rather, the interspecific mtDNA strains showed a wide range of variation that flanked the longevities seen between intraspecific mtDNAs, resulting in very significant nuclear × mtDNA epistatic interaction effects. These results suggest that even “defective” mtDNA haplotypes could extend longevity in different nuclear allelic backgrounds, which could account for the variable effects attributable to mtDNA haplogroups in human aging.
Convergence to the Island-Model Coalescent Process in Populations With Restricted Migration
Authors: Matsen Frederick A , Wakeley John 
Published: October 2005

Abstract
In this article we apply some graph-theoretic results to the study of coalescence in a structured population with migration. The graph is the pattern of migration among subpopulations, or demes, and we use the theory of random walks on graphs to characterize the ease with which ancestral lineages can traverse the habitat in a series of migration events. We identify conditions under which the coalescent process in populations with restricted migration, such that individuals cannot traverse the habitat freely in a single migration event, nonetheless becomes identical to the coalescent process in the island migration model in the limit as the number of demes tends to infinity. Specifically, we first note that a sequence of symmetric graphs with Diaconis–Stroock constant bounded above has an unstructured Kingman-type coalescent in the limit for a sample of size two from two different demes. We then show that circular and toroidal models with long-range but restricted migration have an upper bound on this constant and so have an unstructured-migration coalescent in the limit. We investigate the rate of convergence to this limit using simulations.
Detection of Genes for Ordinal Traits in Nuclear Families and a Unified Approach for Association Studies
Authors: Zhang Heping , Wang Xueqin , Ye Yuanqing 
Published: October 2005

Abstract
There is growing interest in genomewide association analysis using single-nucleotide polymorphisms (SNPs), because traditional linkage studies are not as powerful in identifying genes for common, complex diseases. Tests for linkage disequilibrium have been developed for binary and quantitative traits. However, since many human conditions and diseases are measured in an ordinal scale, methods need to be developed to investigate the association of genes and ordinal traits. Thus, in the current report we propose and derive a score test statistic that identifies genes that are associated with ordinal traits when gametic disequilibrium between a marker and trait loci exists. Through simulation, the performance of this new test is examined for both ordinal traits and quantitative traits. The proposed statistic not only accommodates and is more powerful for ordinal traits, but also has similar power to that of existing tests when the trait is quantitative. Therefore, our proposed statistic has the potential to serve as a unified approach to identifying genes that are associated with any trait, regardless of how the trait is measured. We further demonstrated the advantage of our test by revealing a significant association (P = 0.00067) between alcohol dependence and a SNP in the growth-associated protein 43.
Drosophila Poly(ADP-Ribose) Glycohydrolase Mediates Chromatin Structure and SIR2-Dependent Silencing
Authors: Tulin Alexei , Naumova Natalia M , Menon Ammini K , Spradling Allan C 
Published: October 2005

Abstract
Protein ADP ribosylation catalyzed by cellular poly(ADP-ribose) polymerases (PARPs) and tankyrases modulates chromatin structure, telomere elongation, DNA repair, and the transcription of genes involved in stress resistance, hormone responses, and immunity. Using Drosophila genetic tools, we characterize the expression and function of poly(ADP-ribose) glycohydrolase (PARG), the primary enzyme responsible for degrading protein-bound ADP-ribose moieties. Strongly increasing or decreasing PARG levels mimics the effects of Parp mutation, supporting PARG's postulated roles in vivo both in removing ADP-ribose adducts and in facilitating multiple activity cycles by individual PARP molecules. PARP is largely absent from euchromatin in PARG mutants, but accumulates in large nuclear bodies that may be involved in protein recycling. Reducing the level of either PARG or the silencing protein SIR2 weakens copia transcriptional repression. In the absence of PARG, SIR2 is mislocalized and hypermodified. We propose that PARP and PARG promote chromatin silencing at least in part by regulating the localization and function of SIR2 and possibly other nuclear proteins.
Variation in Mutation Dynamics Across the Maize Genome as a Function of Regional and Flanking Base Composition
Authors: Morton Brian R , Bi Irie V , McMullen Michael D , Gaut Brandon S 
Published: October 2005

Abstract
We examine variation in mutation dynamics across a single genome (Zea mays ssp. mays) in relation to regional and flanking base composition using a data set of 10,472 SNPs generated by resequencing 1776 transcribed regions. We report several relationships between flanking base composition and mutation pattern. The A + T content of the two sites immediately flanking the mutation site is correlated with rate, transition bias, and GC → AT pressure. We also observe a significant CpG effect, or increase in transition rate at CpG sites. At the regional level we find that the strength of the CpG effect is correlated with regional A + T content, ranging from a 1.7-fold increase in transition rate in relatively G + C-rich regions to a 2.6-fold increase in A + T-rich regions. We also observe a relationship between locus A + T content and GC → AT pressure. This regional effect is in opposition to the influence of the two immediate neighbors in that GC → AT pressure increases with increasing locus A + T content but decreases with increasing flanking base A + T content and may represent a relationship between genome location and mutation bias. The data indicate multiple context effects on mutations, resulting in significant variation in mutation dynamics across the genome.
High temperature sorption separation of air for producing oxygen‐enriched CO2 stream
Authors: Yang Qing , Lin Y. S. , Bülow Martin 
Published: October 2005

AbstractA new high temperature sorption process for production of oxygen‐enriched carbon dioxide stream through air separation with carbon dioxide as the purge gas is reported. The process is based on a fixed‐bed packed with a perovskite‐type strontium‐iron doped lanthanum cobaltite, as the sorbent, operated in 500–900°C. Oxygen is adsorbed by the perovskite‐type sorbent with air being fed. An oxygen‐enriched carbon dioxide stream is obtained when the fixed‐bed is regenerated with carbon dioxide as the desorption gas. A specific carbonation‐reaction mechanism for the O2‐desorption process and a complete reverse reaction during the O2‐sorption process are identified with the evidences of XRD and TGA analysis. A study of the sorption process kinetics over a temperature range of 600–800°C was conducted by fixed‐bed sorption/desorption and TGA experiments. Both desorption and sorption processes exhibit a high reaction rate in an initial stage followed by a slower rate in a second stage. A remarkable separation efficiency was observed at 800°C. The new process offers potential for applications in a number of processes including in the efficient and environmentally benign oxyfuel coal combustion process for power generation. © 2005 American Institute of Chemical Engineers AIChE J, 2006
A comparative study on aldol‐type condensation reactions of cyclic, acyclic and substituted cyclic ketones by the W(CO)6/CCl4/UV system
Authors: Altıntaş B. , Bozkurt Ç. 
Published: October 2005

AbstractAldol‐type condensation reactions of a number of cyclic, acyclic and substituted cyclic ketones were investigated using the W(CO)6/CCl4/UV system. The progress of the reactions was followed by IR and GC‐MS techniques. The cyclic ketone derivatives with β‐ and γ‐substituent gave the expected condensation products. However, the α‐substituted cyclic, acyclic and unsubstituted cyclic ketones with rings larger than six did not. Formation of [W]–ketone complexes with all of the ketones used was observed by FTIR. With respect to our studies, a mechanism involving an intermediate seven‐coordinate tungsten complex has been proposed. Copyright © 2005 John Wiley & Sons, Ltd.
Assessment of the conformational features of vasoactive intestinal peptide in solution by limited proteolysis experiments
Authors: Stiuso Paola , Marabotti Anna , Facchiano Angelo , Lepretti Marilena , Dicitore Alessandra , Ferranti Pasquale , Cartenì Maria 
Published: October 2005

AbstractThe structural features of vasoactive intestinal peptide (VIP) and of its Gln16‐diaminopropane derivative (VIP‐DAP) in solution were investigated by limited proteolysis experiments with trypsin and thermolysin. The proteolysis of the native peptide by both proteinases takes place near the residues in positions 12 and 21/22, suggesting that these amino acids are embedded in segments more flexible than the rest of the molecule. VIP‐DAP appears to be more resistant to the proteolytic attack of trypsin, indicating that the derivatization in position 16 is able to stabilize the structure of the peptide. Moreover, the analysis of the mass spectra of the proteolytic mixtures supports the evidence that the derivatization is also able to protect Met17 against oxidation. From these data it can be concluded that VIP in solution under physiological conditions is characterized by the presence of segments with secondary structure, linked together by “hinge” regions that confer flexibility to the peptide, whereas VIP‐DAP is embedded in a more rigid conformation, more suitable to receptor interaction. © 2005 Wiley Periodicals, Inc. Biopolymers 81: 110–119, 2006This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Synthesis and Proinflammatory Properties of Muramyl Tripeptides Containing Lysine and Diaminopimelic Acid Moieties
Authors: Roychowdhury Abhijit , Wolfert Margreet A. , Boons Geert‐Jan 
Published: October 2005

AbstractThe unusual amino acid diaminopimelic acid (DAP) was prepared by cross metathesis of appropriately protected vinyl glycine and allyl glycine derivatives. Catalytic hydrogenation of the cross‐coupling product resulted in reduction of the double bond and the removal of protecting groups. The resulting compounds were appropriately protected for the polymer‐supported and solution‐phase synthesis of muramyl tripeptides 2 and 3, which differ in the amidation of the α‐carboxylic acids of the isoglutamine and DAP moieties. Muramyl dipeptide (1, MDP), the DAP‐containing muramyl tripeptide 3, and the lysine‐containing muramyl tripeptides 4 and 5 induced TNF‐α gene expression without TNF‐α protein production in a human monocytic cell line. The observed block in translation could be removed by co‐incubation with LPS, resulting in an apparent synergistic effect. Compound 2 did not induce TNF‐α gene expression, neither did it exhibit a synergistic effect with LPS; this indicates that amidation of the α‐carboxylic acids of the isoglutamine and DAP moieties results in a loss of biological activity. It is proposed that amidation of α‐carboxylic acids is a strategy that may be used by pathogens to avoid detection by the innate immune system. Furthermore, the pattern recognition receptors Nod1 and Nod2 have been implicated in the possible induction of a synergistic effect of muropeptides with LPS.
An Enantiomeric Nanoscale Architecture Obtained from a Pseudoenantiomeric Aggregate: Covalent Fixation of Helical Chirality Formed in Self‐Assembled Discotic Triazine Triamides by Chiral Amplification
Authors: Ishi‐i Tsutomu , Kuwahara Rempei , Takata Akihiko , Jeong Yeonhwan , Sakurai Kazuo , Mataka Shuntaro 
Published: October 2005

AbstractCovalent fixation of a chiral helical structure which is created in a self‐assembling system by a chiral‐amplification method based on the sergeants/soldiers principle is reported. Disk‐shaped triazine triamides self‐assembled to form columnar‐type helical aggregates through π‐stacking interactions among the central triphenyltriazine moieties, hydrogen‐bonding interactions among the amide groups, and van der Waals interactions among the alkyl groups in nonpolar solvents such as hexane, octane, toluene, and p‐xylene. When the achiral triazine triamide soldier component is mixed with a tiny amount of the chiral triazine triamide sergeant component, control of the intrinsic supramolecular helicity of the self‐assembled soldier component by the sergeant component leads to chiral amplification and formation of a pseudoenantiomeric aggregate with only one handedness of the helix. The helicity can be preserved by ring‐closing olefin metathesis polymerization mediated by Grubbs catalyst when an achiral component with terminal olefinic groups forms the pseudoenantiomeric aggregate in the presence of a tiny amount of the chiral component without olefinic groups. After polymerization and removal of the chiral component, the polymeric architecture obtained from the achiral soldier component is optically active and thus can be regarded as an enantiomeric object in which the chiral information transferred from the chiral sergeant component is preserved. The nanoscale chiral structure is fixed perfectly, as indicated by CD spectroscopic evidence obtained in a polar THF medium at high temperature and low concentration. AFM and TEM observations show a nanoscale fibrous structure with a diameter of 2–4 nm, which corresponds to the molecular size of the triazine triamide monomer.
X‐Folders: documents on the move
Authors: Rossi D. 
Published: October 2005

AbstractX‐Folders is a software environment for multi‐party document‐based processes that aims at supporting the implementation of workflows involving multiple users that interact by means of documents stored in special, reactive, folders: the X‐Folders. A reaction in X‐Folders is a program whose control flow depends on the status of the folder and whose actions are invocations of local services (that can be used to interact with the documents in the folders) or of services exposed by external components. The actions performed by the actors and the reactions fired by the system flow in a sequence that drives to the accomplishment of the workflow process coordinating humans and software components using documents. Copyright © 2005 John Wiley & Sons, Ltd.
BisPNA Targeting to DNA: Effect of Neutral Loop on DNA Duplex Strand Invasion by aepPNA‐N7G/aepPNA‐C Substituted Peptide Nucleic Acids
Authors: Shirude Pravin S. , Kumar Vaijayanti A. , Ganesh Krishna N. 
Published: October 2005

AbstractN7‐Alkyl‐substituted guanine (N7G) as a CH+ mimic has been introduced into aminoethylglycyl PNA (aegPNA) forming a hairpin through a neutral linker derived from bis(tetraethylene) glycol (teg‐teg). These form pH‐independent PNA2:DNA triplexes with complementary DNA sequences. The introduction of chiral, cationic aminoethylprolyl (aep) units with C and the CH+ mimic N7G in the backbone of the hairpin bisPNAs with a neutral teg‐teg linker, influenced the recognition of complementary DNA in an orientation‐selective manner. Fluorescence assay was used to examine the process of strand invasion of the target DNA duplex by the modified hairpin bisPNAs with the neutral teg linker and comparison of results of previous studies employing cationic linkers suggested the triplex formation to be a two‐step process, with the preferred formation of HG bonds in the first step. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)
Adhesion enhancement of steel fibers to acrylic bone cement through a silane coupling agent
Authors: Kotha S. P. , Lieberman M. , Vickers A. , Schmid S. R. , Mason J. J. 
Published: October 2005

AbstractThe use of a silane coupling agent (methacryloxypropyl‐trichlorosilane) to improve the mechanical properties of steel fiber‐reinforced acrylic bone cements was assessed. Changes to the tensile and fracture properties of bone cements reinforced with silane‐coated or uncoated 316L stainless steel fibers of different aspect ratios were studied. Contact‐angle measurements indicated that the coupling agent coats the metal surface through room temperature treatments in a short time (within 2 h). Push‐out tests indicated that the interfacial shear strength of silane‐coated 316L stainless steel rods is 141% higher than the uncoated rods. The elastic moduli, ultimate stresses, and fracture toughness of the silane‐coated, steel fiber‐reinforced bone cements are significantly higher than the bone cements reinforced with uncoated steel fibers. There were no differences in the tensile mechanical properties of the silane‐coated or uncoated, steel fiber‐reinforced cements after aging in a physiological saline solution, indicating that the bonding effectiveness is decreased by the intrusion of water at the metal–polymer interface. Because of possible biocompatibility issues with leaching of the silane coupling agent and no long‐term mechanical benefit in simulated aging experiments, the use of these agents is not recommended for in vivo use. © 2005 Wiley Periodicals, Inc. J Biomed Mater Res, 2006
Production and transport logistics scheduling with two transport mode choices
Authors: Wang Haiyan , Lee Chung‐Yee 
Published: October 2005

AbstractThis paper considers a new class of scheduling problems arising in logistics systems in which two different transportation modes are available at the stage of product delivery. The mode with the shorter transportation time charges a higher cost. Each job ordered by the customer is first processed in the manufacturing facility and then transported to the customer. There is a due date for each job to arrive to the customer. Our approach integrates the machine scheduling problem in the manufacturing stage with the transportation mode selection problem in the delivery stage to achieve the global maximum benefit. In addition to studying the NP‐hard special case in which no tardy job is allowed, we consider in detail the problem when minimizing the sum of the total transportation cost and the total weighted tardiness cost is the objective. We provide a branch and bound algorithm with two different lower bounds. The effectiveness of the two lower bounds is discussed and compared. We also provide a mathematical model that is solvable by CPLEX. Computational results show that our branch and bound algorithm is more efficient than CPLEX. © 2005 Wiley Periodicals, Inc. Naval Research Logistics, 2005
Design, syntheses, and characterization of new thermoplastic polyureas based on 3,4‐ethylenedioxythiophene
Authors: Ojha Uma P. , Ramesh C. , Kumar Anil 
Published: October 2005

AbstractNew thermoplastic polyureas labeled PUn (n = 2, 3, 4, 6, 7, 9, or 10), based on 3,4‐ethylenedioxythiophene (EDOT) with flexible aliphatic spacers, were synthesized and characterized for the first time. EDOT was chosen as a replacement for the aromatic phenyl group in conventional thermoplastics based on urea linkages to improve solubility without compromising the thermal properties. As synthesized, all the samples exhibited a semicrystalline nature. The glass‐transition and melting temperatures showed a strong dependence on the spacer length. A comparison of the thermal properties of these polyureas with the corresponding phenyl analogues indicated that EDOT was a viable heteroatomic analogue of the phenyl group to be inserted into the main‐chain polyureas without hampering their thermal stability. The polyureas with spacer lengths greater than hexamethylene formed transparent gels in N‐methylpyrrolidone, 1,1,2,2‐tetrachloroethane, and dimethyl sulfoxide. The molecular packing of the polyureas was assigned with wide‐angle X‐ray diffraction studies. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 5823–5830, 2005
New generic leak frequencies for process equipment
Authors: Spouge John 
Published: October 2005

AbstractThe likelihood of leaks from process equipment is a key input to any quantitative risk assessment (QRA) of process plant. This paper describes a new source of generic leak frequencies and reviews the challenges in using it for QRA.Established leak frequencies for onshore process equipment are poor in quality because they are based on old data sources of unknown provenance, judgmentally modified. Recent data from offshore process activities provide a high‐quality data set, which appears to show that the established frequencies are much too low. Much of this discrepancy arises from the QRA practice of modeling only the most hazardous leak scenarios. Recognizing the practical difficulty of changing QRA practice to match new data, the present paper therefore describes a method of analyzing the new data to obtain leak frequencies for specific modeled scenarios.Leaks are divided into three scenarios, allowing analysts to use frequencies for only those scenarios that are compatible with their QRA outflow modeling. Standardized leak frequencies have been developed for different types of process equipment, using leak frequency functions to ensure that consistent, nonzero frequencies are available for any equipment type and hole size. The results are consistent with traditional onshore leak frequencies, while also being traceable to specific incidents among the modern high‐quality offshore leak data. © 2005 American Institute of Chemical Engineers Process Saf Prog, 2005