bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthesis and properties of a new fluorine‐containing polybenzimidazole for high‐temperature fuel‐cell applications
Authors: Chuang Shih‐Wei , Hsu Steve Lien‐Chung 
Published: June 2006

AbstractAn amorphous, organosoluble, fluorine‐containing polybenzimidazole (PBI) was synthesized from 3,3′‐diaminobenzidine and 2,2‐bis(4‐carboxyphenyl)hexafluoropropane. The polymer was soluble in N‐methylpyrrolidinone and dimethylacetamide and had an inherent viscosity of 2.5 dL/g measured in dimethylacetamide at a concentration of 0.5 g/dL. The 5% weight loss temperature of the polymer was 520 °C. Proton‐conducting PBI membranes were prepared via solution casting and doped with different amounts of phosphoric acid. In the methanol permeability measurement, the PBI membranes showed much better methanol barrier ability than a Nafion membrane. The proton conductivity of the acid‐doped PBI membranes increased with increasing temperatures and concentrations of phosphoric acid in the polymer. The PBI membranes showed higher proton conductivity than a Nafion 117 membrane at high temperatures. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 4508–4513, 2006
Synthesis and characterization of liquid‐crystalline block copolymers with cyanoterphenyl moieties by atom transfer radical polymerization
Authors: Lee Kuan‐Wei , Wei Kung‐Hwa , Lin Hong‐Cheu 
Published: June 2006

AbstractA series of new mesomorphic block copolymers composedofdifferentmacroinitiators, including poly(ethylene oxide), polystyrene, and poly(ethylene oxide)‐b‐polystyrene,and polymethacrylate with a pendent cyanoterphenyl group were synthesized through atom transfer radical polymerization. The number‐average molecular weights of the three diblock copolymers, determined by gel permeation chromatography, were 10,254, 9,772, and 15,632 g mol−1, and their polydispersity indices were 1.17, 1.28, and 1.34. The mesomorphic and optical properties of all the block copolymers were investigated, and they possessed a smectic A phase with mesophasic ranges wider than 100 °C. Moreover, X‐ray diffraction patterns provided evidence of the smectic A phase and the corresponding interdigitated packing of all the polymers. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 4593–4602, 2006
Fluorene copolymers containing bithiophene/2,5‐ or 2,6‐pyridine units: A study of their optical, electrochemical, and electroluminescence properties
Authors: Jung Young Kwan , Lee Jaemin , Lee Sang Kyu , Cho Hoon‐Je , Shim Hong‐Ku 
Published: June 2006

AbstractTwo alternating copolymers, poly[(2,5‐di(2‐thienyl)‐pyridine‐5,5′‐diyl)‐alt‐(9,9‐dioctylfluorene‐2,7‐diyl)], PFO‐TPy25T, and poly[(2,6‐di(2‐thienyl)‐pyridine‐5,5′‐diyl)‐alt‐(9,9‐dioctylfluorene‐2,7‐diyl)], PFO‐TPy26T, were synthesized by the Pd‐catalyzed Suzuki polymerization method. The pyridine units are present as trimeric monomers in these copolymers and have different connectivities to their two neighboring thiophenes, para‐ and meta‐linkages. We investigated the variations in the optical and electrochemical properties of the copolymers that arise from these different connectivities. The two polymers exhibit 5% weight loss above 410 °C and high glass transition temperatures (Tg: 113 °C for PFO‐TPy25T, 142 °C for PFO‐TPy26T). The UV–vis absorption maximum peaks of PFO‐TPy25T and PFO‐TPy26T in the solid state were found to be 449 and 398 nm respectively, with photoluminescence maximum peaks in the solid state of 573 and 490 nm respectively. Using cyclic voltammetry, we determined their energy band gaps: 3.08 eV for PFO‐TPy25T and 3.49 eV for PFO‐TPy25T. The cyclic voltammetry study of these polymers revealed that there are some differences. The electroluminescence (EL) properties of the copolymers were measured for the device configuration of ITO/PEDOT/polymers/Ca/Al. The device fabricated with the polymer containing 2,5‐pyridine exhibits pale orange emission, whereas the device fabricated with the polymer containing 2,6‐pyridine exhibits pale blue emission. The EL device fabricated with PFO‐TPy25T has a higher brightness (2010 cd/m2) and external quantum efficiency (0.1%) than the PFO‐TPy26T device (260 cd/m2, 0.008%), because it has a smaller energy barrier to the injection of charges from PEDOT and Ca into the HOMO and LUMO levels. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 4611–4620, 2006
Synthesis and Characterization of Energetic 1,2‐Bis(Oxyamino)Ethane Salts
Authors: Hawkins Tommy , Hall Leslie , Tollison Kerri , Brand Adam , McKay Milton , Drake Gregory W. 
Published: June 2006

AbstractThe synthesis, characterization, theoretical calculations, and safety studies of energetic salts based on 1,2‐bis(oxyamino)ethane, (H2NOCH2CH2ONH2), were carried out. The salts were characterized by vibrational (infrared, Raman), multinuclear NMR studies (1H, 13C), differential scanning calorimetry (DSC), elemental analysis, and initial safety testing (impact and friction sensitivity). Single crystal X‐ray diffraction studies were carried out on the mono‐perchlorate and the double nitrate salts, revealing the expected structures.
Scaling of the Shaped Charge Jet Break‐Up Time
Authors: Hirsch Eitan 
Published: June 2006

AbstractSince the formula for the shaped charge jet break‐up time was published on 1979 many attempts were made to interpret it and to make its use more efficient. It is shown herein that the Vpl parameter depends on the ratio of the liner thickness to the charge explosive diameter by the formula: 1/Vpl=13.9−101⋅(TL/CD), where TL is the liner thickness, CD is the explosive charge diameter and the numbers are for a published set of measurements with an OFE copper liner driven by COMP‐B explosive. To find how the numbers used in this formula change with the liner material and its metallurgical state and with the type of explosive, measurements should be made as prescribed herein. An attempt to begin explaining this formula is made in the discussion.
Modification/oxidation of GaAs surface in electrolytes for cell‐culture bio‐sensing devices
Authors: Ozasa Kazunari , Nemoto Shigeyuki , Hara Masahiko , Maeda Mizuo 
Published: June 2006

AbstractThe surface modification/oxidation of GaAs substrates in electrolytes has been investigated from the viewpoint of bio‐sensing devices using AlGaAs/GaAs high‐electron‐mobility‐transistor (HEMT) structures, where the cell culture directly on a bare gate‐surface is intended for a high sensitivity to cell‐viabilities such as adhesion or cell‐cell interaction, through nitric‐oxide concentration or charged‐peptide chemisorption. Although GaAs surface (gate surface of HEMT) was oxidized even in pure water under room light, we found that the oxide layer is not formed in the dark or removed with the existence of small amounts of NaH2PO4 (0.8 mM) in the solution. The photo‐excited oxidation and its etching by NaH2PO4 are discussed as well as the temporal change of the HEMT performance in solution. Cell adhesion on a bare GaAs surface was poor, but a surface modification by fibrionectin improved the cell adhesion, comparable to that on the conventional cell‐culture dishes. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electronic conductivity and structural distortion at the interface between insulators SrTiO3 and LaAlO3
Authors: Maurice J.‐L. , Carrétéro C. , Casanove M.‐J. , Bouzehouane K. , Guyard S. , Larquet É. , Contour J.‐P. 
Published: June 2006

AbstractWhen insulator LaAlO3 is grown by epitaxy onto a TiO2‐terminated {100} surface of insulator SrTiO3, the system obtained has a metallic character. This phenomenon has been associated with an electrostatic frustration at the interface, as {100} surfaces of SrTiO3 are neutral while those of LaAlO3 are polar, but its microscopic mechanism is not quite understood. Here, we present a structural characterisation of this interface by aberration‐corrected transmission electron microscopy. The unit cells at the interface appear elongated: we discuss this distortion in terms of electrostatic charge and extra carriers at the interface. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Parallel Manipulation of Bifunctional DNA Molecules on Structured Surfaces Using Kinesin‐Driven Microtubules
Authors: Dinu Cerasela Zoica , Opitz Jörg , Pompe Wolfgang , Howard Jonathon , Mertig Michael , Diez Stefan 
Published: June 2006

AbstractWe have developed a technique to manipulate bifunctional DNA molecules: One end is thiolated to bind to a patterned gold surface and the other end is biotinylated to bind to a microtubule gliding over a kinesin‐coated surface. We found that DNA molecules can be stretched and overstretched between the gold pads and the motile microtubules, and that they can form dynamic networks. This serves as a proof‐of‐principle that biological machineries can be used in vitro to accomplish the parallel formation of structured DNA templates that will have applications in biophysics and nanoelectronics.
Succinic semialdehyde dehydrogenase (SSADH) deficiency: Molecular analysis in a South American family
Authors: Lemes Aida , Blasi Paola , Gonzales Gabriel , Russi Maria E. , Quadrelli Roberto , Novelletto Andrea , Malaspina Patrizia 
Published: June 2006

SummaryWe report the clinical, biochemical and molecular findings on the first documented patient with 4‐hydroxybutyric aciduria (4‐HBA, McKusick 271980) from Uruguay. The patient displayed a severe picture and turned out to be homozygous for a mutation (c.1226G < A) previously shown to be associated with null enzyme activity.
Transcript mapping with high-density oligonucleotide tiling arrays
Authors: Huber Wolfgang , Toedling Joern , Steinmetz Lars M. 
Published: June 2006

Abstract
Motivation: High-density DNA tiling microarrays are a powerful tool for the characterization of complete transcriptomes. The two major analytical challenges are the segmentation of the hybridization signal along genomic coordinates to accurately determine transcript boundaries and the adjustment of the sequence-dependent response of the oligonucleotide probes to achieve quantitative comparability of the signal between different probes.
Results: We describe a dynamic programming algorithm for finding a globally optimal fit of a piecewise constant expression profile along genomic coordinates. We developed a probe-specific background correction and scaling method that employs empirical probe response parameters determined from reference hybridizations with no need for paired mismatch probes. This combined analysis approach allows the accurate determination of dynamical changes in transcription architectures from hybridization data and will help to study the biological significance of complex transcriptional phenomena in eukaryotic genomes.
Availability: R package tilingArray at .
Contact: huber@ebi.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
A reference database for circular dichroism spectroscopy covering fold and secondary structure space
Authors: Lees Jonathan G. , Miles Andrew J. , Wien Frank , Wallace B. A. 
Published: June 2006

AbstractMotivation: Circular Dichroism (CD) spectroscopy is a long-established technique for studying protein secondary structures in solution. Empirical analyses of CD data rely on the availability of reference datasets comprised of far-UV CD spectra of proteins whose crystal structures have been determined.This article reports on the creation of a new reference dataset which effectively covers both secondary structure and fold space, and uses the higher information content available in synchrotron radiation circular dichroism (SRCD) spectra to more accurately predict secondary structure than has been possible with existing reference datasets. It also examines the effects of wavelength range, structural redundancy and different means of categorizing secondary structures on the accuracy of the analyses. In addition, it describes a novel use of hierarchical cluster analyses to identify protein relatedness based on spectral properties alone. The databases are shown to be applicable in both conventional CD and SRCD spectroscopic analyses of proteins. Hence, by combining new bioinformatics and biophysical methods, a database has been produced that should have wide applicability as a tool for structural molecular biology.Contact: b.wallace@mail.cryst.bbk.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.
Additional Gene Ontology structure for improved biological reasoning
Authors: Myhre Simen , Tveit Henrik , Mollestad Torulf , Lægreid Astrid 
Published: June 2006

Abstract
Motivation: The Gene Ontology (GO) is a widely used terminology for gene product characterization in, for example, interpretation of biology underlying microarray experiments. The current GO defines term relationships within each of the independent subontologies: molecular function, biological process and cellular component. However, it is evident that there also exist biological relationships between terms of different subontologies. Our aim was to connect the three subontologies to enable GO to cover more biological knowledge, enable a more consistent use of GO and provide new opportunities for biological reasoning.
Results: We propose a new structure, the Second Gene Ontology Layer, capturing biological relations not directly reflected in the present ontology structure. Given molecular functions, these paths identify biological processes where the molecular functions are involved and cellular components where they are active. The current Second Layer contains 6271 validated paths, covering 54% of the molecular functions of GO and can be used to render existing gene annotation sets more complete and consistent. Applying Second Layer paths to a set of 4223 human genes, increased biological process annotations by 24% compared to publicly available annotations and reproduced 30% of them.
Availability: The Second GO is publicly available through the GO Annotation Toolbox (GOAT.no):
Contact: astrid.lagreid@ntnu.no
Increasing confidence of protein interactomes using network topological metrics
Authors: Chen Jin , Hsu Wynne , Lee Mong Li , Ng See-Kiong 
Published: June 2006

Abstract
Motivation: Experimental limitations in high-throughput protein–protein interaction detection methods have resulted in low quality interaction datasets that contained sizable fractions of false positives and false negatives. Small-scale, focused experiments are then needed to complement the high-throughput methods to extract true protein interactions. However, the naturally vast interactomes would require much more scalable approaches.
Results: We describe a novel method called IRAP* as a computational complement for repurification of the highly erroneous experimentally derived protein interactomes. Our method involves an iterative process of removing interactions that are confidently identified as false positives and adding interactions detected as false negatives into the interactomes. Identification of both false positives and false negatives are performed in IRAP* using interaction confidence measures based on network topological metrics. Potential false positives are identified amongst the detected interactions as those with very low computed confidence values, while potential false negatives are discovered as the undetected interactions with high computed confidence values. Our results from applying IRAP* on large-scale interaction datasets generated by the popular yeast-two-hybrid assays for yeast, fruit fly and worm showed that the computationally repurified interaction datasets contained potentially lower fractions of false positive and false negative errors based on functional homogeneity.
Availability: The confidence indices for PPIs in yeast, fruit fly and worm as computed by our method can be found at our website
Contact: skng@i2r.a-star.edu.sg
Supplementary information: Supplementary data are available at Bioinformatics online.
A lock-and-key model for protein–protein interactions
Authors: Morrison Julie L. , Breitling Rainer , Higham Desmond J. , Gilbert David R. 
Published: June 2006

Abstract
Motivation: Protein–protein interaction networks are one of the major post-genomic data sources available to molecular biologists. They provide a comprehensive view of the global interaction structure of an organism's proteome, as well as detailed information on specific interactions. Here we suggest a physical model of protein interactions that can be used to extract additional information at an intermediate level: It enables us to identify proteins which share biological interaction motifs, and also to identify potentially missing or spurious interactions.
Results: Our new graph model explains observed interactions between proteins by an underlying interaction of complementary binding domains (lock-and-key model). This leads to a novel graph-theoretical algorithm to identify bipartite subgraphs within protein–protein interaction networks where the underlying data are taken from yeast two-hybrid experimental results. By testing on synthetic data, we demonstrate that under certain modelling assumptions, the algorithm will return correct domain information about each protein in the network. Tests on data from various model organisms show that the local and global patterns predicted by the model are indeed found in experimental data. Using functional and protein structure annotations, we show that bipartite subnetworks can be identified that correspond to biologically relevant interaction motifs. Some of these are novel and we discuss an example involving SH3 domains from the Saccharomyces cerevisiae interactome.
Availability: The algorithm (in Matlab format) is available (see )
Contact: jmorriso@dcs.gla.ac.uk
Supplementary information: Supplementary data are available at .
Overconfidence in wargames: experimental evidence on expectations, aggression, gender and testosterone
Authors: Johnson Dominic D.P , McDermott Rose , Barrett Emily S , Cowden Jonathan , Wrangham Richard , McIntyre Matthew H , Peter Rosen Stephen 
Published: June 2006

SummaryOverconfidence has long been noted by historians and political scientists as a major cause of war. However, the origins of such overconfidence, and sources of variation, remain poorly understood. Mounting empirical studies now show that mentally healthy people tend to exhibit psychological biases that encourage optimism, collectively known as ‘positive illusions’. Positive illusions are thought to have been adaptive in our evolutionary past because they served to cope with adversity, harden resolve, or bluff opponents. Today, however, positive illusions may contribute to costly conflicts and wars. Testosterone has been proposed as a proximate mediator of positive illusions, given its role in promoting dominance and challenge behaviour, particularly in men. To date, no studies have attempted to link overconfidence, decisions about war, gender, and testosterone. Here we report that, in experimental wargames: (i) people are overconfident about their expectations of success; (ii) those who are more overconfident are more likely to attack; (iii) overconfidence and attacks are more pronounced among males than females; and (iv) testosterone is related to expectations of success, but not within gender, so its influence on overconfidence cannot be distinguished from any other gender specific factor. Overall, these results constitute the first empirical support of recent theoretical work linking overconfidence and war.
Phylogeographical history of the widespread meadow fescue (Festuca pratensis Huds.) inferred from chloroplast DNA sequences
Authors: Fjellheim Siri , Rognli Odd Arne , Fosnes Kjetil , Brochmann Christian 
Published: June 2006

AbstractAim  Here we explore the variation in chloroplast DNA (cpDNA) in a widespread Eurasian diploid forage grass, meadow fescue (Festuca pratensis Huds.), to address its phylogeographical history. In particular, we aim to answer whether the post‐glacial migration routes of meadow fescue are associated with the spread of agriculture or concurrent with well‐documented natural migration pathways from glacial refugia.Location  A total of 56 Eurasian accessions of F. pratensis were analysed, representing the entire native distribution area as well as non‐native areas in northernmost Europe.Methods  Based on initial sequencing of 10 non‐coding cpDNA regions, three regions were sequenced for all F. pratensis accessions. For reference, three closely related species [the diploid Lolium perenne L. and the polyploids Festuca arundinacea Schreb. and Festuca gigantea (L.) Vill.] were also sequenced, as well as the more distantly related Festuca ovina L. Divergence times were estimated assuming a simple molecular clock, calibrated using a previously published estimate of 9 Myr for the divergence between fine‐leaved (F. ovina) and broad‐leaved fescues (F. pratensis, F. arundinacea and F. gigantea).Results  Limited, but geographically structured, cpDNA variation was observed in F. pratensis. Three haplotypes, estimated to have diverged 0.16 Ma, were identified: one western European (A), one with a wide eastern distribution from central‐eastern Europe into Asia (B) and one Caucasian (C). The haplotypes of the polyploids and L. perenne were estimated to have diverged from haplotype A in F. pratensis 0.8–1.3 Ma.Main conclusions  We found no definite evidence for migration of the diploid F. pratensis associated with the spread of agriculture from the Fertile Crescent after the last glaciation. The distinct geographical structuring of the present‐day variation in cpDNA can rather be explained by northwards expansion of the western haplotype from an Iberian refugium, expansion of the eastern haplotype from an unlocated (south‐)eastern refugium and glacial survival without subsequent expansion from a Caucasian refugium. The high level of cpDNA divergence observed between this diploid and the polyploids which have probably been derived from it may suggest that the very low level of cpDNA variation in the diploid is caused by a recent bottleneck. Today, F. pratensis is widespread in the open agricultural landscape but appears otherwise confined to naturally open habitats such as river banks, and its populations may have been decimated when dense forests dominated in the previous interglacial.