bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generation of Reactive Oxygen and Antioxidant Species by Hydrodynamically Stressed Suspensions of Morinda citrifolia
Authors: Jeffers Paul , Kerins Sinead , Baker C. Jacyn , Kieran Patricia M. 
Published: November 2006

AbstractThe generation of reactive oxygen species (ROS) by plant cell suspension cultures, in response to the imposition of both biotic and abiotic stress, is well‐documented. This study investigated the generation of hydrogen peroxide by hydrodynamically stressed cultures of Morinda citrifolia, over a 5‐h period post‐stress imposition. Suspensions were exposed to repeated passages through a syringe, under laminar flow conditions, corresponding to cumulative energy dissipation levels of approximately 3–6 J kg‐1. Extracellular hydrogen peroxide was detected using a luminol‐based chemiluminescence assay. The addition of exogenous hydrogen peroxide facilitated the detection of low levels of hydrogen peroxide in the presence of antioxidants. Immediately after shear exposure, there was evidence of significant antioxidative capacity in the sheared cell cultures, which potentially masked any oxidative burst (OB), but which decreased over the following 40 min. This antioxidative capacity was determined to derive from the shearing process. Trials in which ground cellular debris was added to control suspensions suggested that some of the antioxidative capacity observed in stressed suspensions was directly associated with debris generated by the shearing process. Using UV‐vis spectrophotometry and HPLC, stress‐related increases in the levels of phenolic compounds were detected in suspension filtrates. Under the stress conditions investigated, maximum hydrogen peroxide levels of 11.5 μM were observed, 5 h after shear exposure. This study emphasizes the importance of considering both oxidative and antioxidative capacities as part of a holistic approach to the determination of the OB in hydrodynamically stressed plant cell suspension cultures.
Multivariate Characterization of Hydrogen Balmer Emission in Cataclysmic Variables
Authors: Sarty Gordon E. , Wu Kinwah 
Published: November 2006

AbstractThe ratios of hydrogen Balmer emission line intensities in cataclysmic variables are signatures of the physical processes that produce them. To quantify those signatures relative to classifications of cataclysmic variable types, we applied the multivariate statistical analysis methods of principal components analysis and discriminant function analysis to the spectroscopic emission data set of Williams (1983). The two analysis methods reveal two different sources of variation in the ratios of the emission lines. The source of variation seen in the principal components analysis was shown to be correlated with the binary orbital period. The source of variation seen in the discriminant function analysis was shown to be correlated with the equivalent width of the Hβ line. Comparison of the data scatterplot with scatterplots of theoretical models shows that Balmer line emission from T CrB systems is consistent with the photoionization of a surrounding nebula. Otherwise, models that we considered do not reproduce the wide range of Balmer decrements, including ‘inverted’ decrements, seen in the data.
Triaxial versus Spherical Dark Matter Halo Profiles
Authors: Knebe Alexander , Wießner Volkmar 
Published: November 2006

AbstractWhen analyzing dark matter halos forming in cosmological n-body simulations, it is common practice to obtain the density profile utilizing spherical shells. However, it is also known that the systems under investigation are far from spherically symmetric but, rather, follow a triaxial mass distribution. In this study we present an estimator for the error introduced by spherically averaging an elliptical mass distribution. We systematically investigate the differences arising when using a triaxial density profile under the assumption of spherical symmetry. We show that the variance in the density can be as large as 50% in the outer parts of dark matter halos for extreme (but still credible) axis ratios of 0.55: 0.67: 1. The inner parts are less affected but still show a scatter at the 16% level for these prolate systems. For more moderate ellipticities, i.e. axis ratios of 0.73: 0.87: 1, the error is smaller but still as large as 10–20% depending on distance. We further provide a simple formula that allows estimation of this variance as a function of radius for arbitrary axis ratios. We conclude that highly prolate and/or oblate systems are better fit by analytical profiles that take into account the triaxial nature of cosmological objects.
Galactic Anisotropy of Cosmic Ray Intensity Observed by an Air Shower Experiment
Authors: Bahmanabadi Mahmud , Ghomi Mehdi Khakian , Sheidaei Farzaneh , Samimi Jalal 
Published: November 2006

AbstractWe have monitored multi-TeV cosmic rays by a small air shower array in Tehran (35°43′ N, 51°20′ E, 1200 m = 890 g cm−2). More than 1.1 × 106 extensive air shower events were recorded. These observations enabled us to analyse sidereal variation of the galactic cosmic ray intensity. The observed sidereal daily variation is compared to the expected variation which includes the Compton–Getting effect due to the motion of the earth in the Galaxy. In addition to the Compton–Getting effect, an anisotropy has been observed which is due to a unidirectional anisotropy of cosmic ray flow along the Galactic arms.
ARIA2: Automated NOE assignment and data integration in NMR structure calculation
Authors: Rieping Wolfgang , Habeck Michael , Bardiaux Benjamin , Bernard Aymeric , Malliavin Thérèse E. , Nilges Michael 
Published: November 2006

AbstractSummary: Modern structural genomics projects demand for integrated methods for the interpretation and storage of nuclear magnetic resonance (NMR) data. Here we present version 2.1 of our program ARIA (Ambiguous Restraints for Iterative Assignment) for automated assignment of nuclear Overhauser enhancement (NOE) data and NMR structure calculation. We report on recent developments, most notably a graphical user interface, and the incorporation of the object-oriented data model of the Collaborative Computing Project for NMR (CCPN). The CCPN data model defines a storage model for NMR data, which greatly facilitates the transfer of data between different NMR software packages.Availability: A distribution with the source code of ARIA 2.1 is freely available atContact: nilges@pasteur.fr
QOMA: quasi-optimal multiple alignment of protein sequences
Authors: Zhang Xu , Kahveci Tamer 
Published: November 2006

AbstractMotivation: We consider the problem of multiple alignment of protein sequences with the goal of achieving a large SP (Sum-of-Pairs) score.Results: We introduce a new graph-based method. We name our method QOMA (Quasi-Optimal Multiple Alignment). QOMA starts with an initial alignment. It represents this alignment using a K-partite graph. It then improves the SP score of the initial alignment through local optimizations within a window that moves greedily on the alignment. QOMA uses two parameters to permit flexibility in time/accuracy trade off: (1) The size of the window for local optimization. (2) The sparsity of the K-partite graph. Unlike traditional progressive methods, QOMA is independent of the order of sequences. The experimental results on BAliBASE benchmarks show that QOMA produces higher SP score than the existing tools including ClustalW, Probcons, Muscle, T-Coffee and DCA. The difference is more significant for distant proteins.Availability: The software is available from the authors upon request.Contact: tamer@cise.ufl.eduSupplementary information: Supplementary material is available at Bioinformatics online.
A predictive model for identifying proteins by a single peptide match
Authors: Higdon Roger , Kolker Eugene 
Published: November 2006

AbstractMotivation: Tandem mass-spectrometry of trypsin digests, followed by database searching, is one of the most popular approaches in high-throughput proteomics studies. Peptides are considered identified if they pass certain scoring thresholds. To avoid false positive protein identification, ≥2 unique peptides identified within a single protein are generally recommended. Still, in a typical high-throughput experiment, hundreds of proteins are identified only by a single peptide. We introduce here a method for distinguishing between true and false identifications among single-hit proteins. The approach is based on randomized database searching and usage of logistic regression models with cross-validation. This approach is implemented to analyze three bacterial samples enabling recovery 68–98% of the correct single-hit proteins with an error rate of &lt;2%. This results in a 22–65% increase in number of identified proteins. Identifying true single-hit proteins will lead to discovering many crucial regulators, biomarkers and other low abundance proteins.Contact: ekolker@biatech.orgSupplementary information: Supplementary Data are available at Bioinformatics online.
Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach
Authors: Steggles L. Jason , Banks Richard , Shaw Oliver , Wipat Anil 
Published: November 2006

AbstractMotivation: New developments in post-genomic technology now provide researchers with the data necessary to study regulatory processes in a holistic fashion at multiple levels of biological organization. One of the major challenges for the biologist is to integrate and interpret these vast data resources to gain a greater understanding of the structure and function of the molecular processes that mediate adaptive and cell cycle driven changes in gene expression. In order to achieve this biologists require new tools and techniques to allow pathway related data to be modelled and analysed as network structures, providing valuable insights which can then be validated and investigated in the laboratory.Results: We propose a new technique for constructing and analysing qualitative models of genetic regulatory networks based on the Petri net formalism. We take as our starting point the Boolean network approach of treating genes as binary switches and develop a new Petri net model which uses logic minimization to automate the construction of compact qualitative models. Our approach addresses the shortcomings of Boolean networks by providing access to the wide range of existing Petri net analysis techniques and by using non–determinism to cope with incomplete and inconsistent data. The ideas we present are illustrated by a case study in which the genetic regulatory network controlling sporulation in the bacterium Bacillus subtilis is modelled and analysed.Availability: The Petri net model construction tool and the data files for the B. subtilis sporulation case study are available atContact: L.J.Steggles@ncl.ac.uk
Homing Devices in Choice of Tort Law: Australian, British, and Canadian Approaches
Authors: Mortensen Reid 
Published: November 2006

AbstractSince 1994, Canada, the United Kingdom and Australia have adopted new choice of law rules for cross-border torts that, in different ways, centre on the application of the law of the place where the tort occurred (thelex loci delicti). All three countries abandoned some species of the rule inPhillips v Eyre, which required some reference to the law of the forum (thelex fori) as well as thelex loci delicti. However, predictions were made that, where possible, courts in these countries would continue to show a strong inclination to apply thelex foriin cross-border tort cases—and would use a range of homing devices to do so. A comprehensive survey and analysis of the cases that have been decided under the Australian, British and Canadianlex loci delictiregimes suggests that courts in these countries do betray a homing instinct, but one that has actually been tightly restrained by appeal courts. Where application of thelex foriwas formally allowed by use of a ‘flexible exception’ in Canada and the United Kingdom, this has been contained by courts of first appeal. Indeed, only the continuing characterization of the assessment of damages as a procedural question in Canada and the United Kingdom, seems to remain as a significant homing device for courts in these countries.
Common Law, Civil Law, and the Single European Market for Insurances
Authors: Rühl Giesela 
Published: November 2006

AbstractFifty years after the foundation of the European Communities, the single market for insurances has not yet become a reality. Despite the harmonization of insurance supervision law, insurance companies still essentially refrain from cross-border activity when it comes to small commercial and consumer risks. Since this finding is usually attributed to the lack of common rules on insurance contracts, this article sets out to lay the foundation for the harmonization of the corresponding national laws. By providing a comparative analysis of two of the most pervasive issues in consumer insurance contract law, the article proves that common law and civil law are not as far apart as commonly assumed. It thus refutes the widely held belief that the insurance contract laws of common law and civil law countries are too different to be harmonized.
BPPred: A Web‐based computational tool for predicting biophysical parameters of proteins
Authors: Geierhaas Christian D. , Nickson Adrian A. , Lindorff‐Larsen Kresten , Clarke Jane , Vendruscolo Michele 
Published: November 2006

AbstractWe exploit the availability of recent experimental data on a variety of proteins to develop a Web‐based prediction algorithm (BPPred) to calculate several biophysical parameters commonly used to describe the folding process. These parameters include the equilibrium m‐values, the length of proteins, and the changes upon unfolding in the solvent‐accessible surface area, in the heat capacity, and in the radius of gyration. We also show that the knowledge of any one of these quantities allows an estimate of the others to be obtained, and describe the confidence limits with which these estimations can be made. Furthermore, we discuss how the kinetic m‐values, or the Beta Tanford values, may provide an estimate of the solvent‐accessible surface area and the radius of gyration of the transition state for protein folding. Taken together, these results suggest that BPPred should represent a valuable tool for interpreting experimental measurements, as well as the results of molecular dynamics simulations.
Vaccinia virus N1L protein resembles a B cell lymphoma‐2 (Bcl‐2) family protein
Authors: Aoyagi Mika , Zhai Dayong , Jin Chaofang , Aleshin Alexander E. , Stec Boguslaw , Reed John C. , Liddington Robert C. 
Published: November 2006

AbstractPoxviruses encode immuno‐modulatory proteins capable of subverting host defenses. The poxvirus vaccinia expresses a small 14‐kDa protein, N1L, that is critical for virulence. We report the crystal structure of N1L, which reveals an unexpected but striking resemblance to host apoptotic regulators of the B cell lymphoma‐2 (Bcl‐2) family. Although N1L lacks detectable Bcl‐2 homology (BH) motifs at the sequence level, we show that N1L binds with high affinity to the BH3 peptides of pro‐apoptotic Bcl‐2 family proteins in vitro, consistent with a role for N1L in modulating host antiviral defenses.
Efficient molecular docking of NMR structures: Application to HIV‐1 protease
Authors: Huang Sheng‐You , Zou Xiaoqin 
Published: November 2006

AbstractDocking ligands into an ensemble of NMR conformers is essential to structure‐based drug discovery if only NMR structures are available for the target. However, sequentially docking ligands into each NMR conformer through standard single‐receptor‐structure docking, referred to as sequential docking, is computationally expensive for large‐scale database screening because of the large number of NMR conformers involved. Recently, we developed an efficient ensemble docking algorithm to consider protein structural variations in ligand binding. The algorithm simultaneously docks ligands into an ensemble of protein structures and achieves comparable performance to sequential docking without significant increase in computational time over single‐structure docking. Here, we applied this algorithm to docking with NMR structures. The HIV‐1 protease was used for validation in terms of docking accuracy and virtual screening. Ensemble docking of the NMR structures identified 91% of the known inhibitors under the criterion of RMSD < 2.0 Å for the best‐scored conformation, higher than the average success rate of single docking of individual crystal structures (66%). In the virtual screening test, on average, ensemble docking of the NMR structures obtained higher enrichments than single‐structure docking of the crystal structures. In contrast, docking of either the NMR minimized average structure or a single NMR conformer performed less satisfactorily on both binding mode prediction and virtual screening, indicating that a single NMR structure may not be suitable for docking calculations. The success of ensemble docking of the NMR structures suggests an efficient alternative method for standard single docking of crystal structures and for considering protein flexibility.
Solution structure of a small protein containing a fluorinated side chain in the core
Authors: Cornilescu Gabriel , Hadley Erik B. , Woll Matthew G. , Markley John L. , Gellman Samuel H. , Cornilescu Claudia C. 
Published: November 2006

AbstractWe report the first high‐resolution structure for a protein containing a fluorinated side chain. Recently we carried out a systematic evaluation of phenylalanine to pentafluorophenylalanine (Phe → F5‐Phe) mutants for the 35‐residue chicken villin headpiece subdomain (c‐VHP), the hydrophobic core of which features a cluster of three Phe side chains (residues 6, 10, and 17). Phe → F5‐Phe mutations are interesting because aryl–perfluoroaryl interactions of optimal geometry are intrinsically more favorable than either aryl–aryl or perfluoroaryl–perfluoroaryl interactions, and because perfluoroaryl units are more hydrophobic than are analogous aryl units. Only one mutation, Phe10 → F5‐Phe, was found to provide enhanced tertiary structural stability relative to the native core (by ∼1 kcal/mol, according to guanidinium chloride denaturation studies). The NMR structure of this mutant, described here, reveals very little variation in backbone conformation or side chain packing relative to the wild type. Thus, although Phe → F5‐Phe mutations offer the possibility of greater tertiary structural stability from side chain–side chain attraction and/or side chain desolvation, the constraints associated with the native c‐VHP fold apparently prevent the modified polypeptide from taking advantage of this possibility. Our findings are important because they complement several studies that have shown that fluorination of saturated side chain carbon atoms can provide enhanced conformational stability.
Analyses of the secretomes of Erwinia amylovora and selected hrp mutants reveal novel type III secreted proteins and an effect of HrpJ on extracellular harpin levels
Authors: NISSINEN RIITTA M. , YTTERBERG A. JIMMY , BOGDANOVE ADAM J. , VAN WIJK KLAAS J. , BEER STEVEN V. 
Published: November 2006

SUMMARY Erwinia amylovora is a plant pathogenic enterobacterium that causes fire blight disease of apple, pear and other rosaceous plants. A type III (T3) secretion system, encoded by clustered, chromosomal hrp genes (hypersensitive response and pathogenicity), is essential for infection, but only a few proteins are known that are secreted through this pathway (the T3 ‘secretome’). We developed an efficient protocol for purification and concentration of extracellular proteins and used it to characterize the T3 secretome of E. amylovora Ea273 by comparing preparations from the wild‐type strain with those from mutants defective in hrp secretion, regulation, or in genes encoding putative T3‐secreted proteins. Proteins were resolved by gel electrophoresis and identified using mass spectrometry and a draft sequence of the E. amylovora genome. Twelve T3‐secreted proteins were identified, including homologues of known effector and helper proteins, and HrpJ, a homologue of YopN of Yersinia pestis. Several previously uncharacterized T3‐secreted proteins were designated as Eops for Erwinia outer proteins. Analysis of the secretome of a non‐polar hrpJ mutant demonstrated that HrpJ is required for accumulation of wild‐type levels of secreted harpins. HrpJ was found to be essential for pathogenesis, and to play a major role in elicitation of the hypersensitive reaction in tobacco.
Semi‐natural grasslands as population sources for pollinating insects in agricultural landscapes
Authors: ÖCKINGER ERIK , SMITH HENRIK G. 
Published: November 2006

SummaryIn intensively farmed agricultural landscapes, many species are confined to very small uncultivated areas such as field margins. However, it has been suggested that these small habitat elements cannot support viable populations of all the species observed there. Instead, species richness and abundance in these small habitat fragments may, at least partly, be dependent on dispersal from larger semi‐natural grassland fragments.We tested this hypothesis for butterflies and bumble bees in 12 independent landscapes in a region of intense agriculture in southern Sweden. In each landscape we surveyed abundance and species richness in one semi‐natural grassland, one linear habitat (uncultivated field margin) adjacent to this (called proximate) and one similar linear habitat (called distant) situated at least 1000 m from the semi‐natural grassland patch.Both species richness and density (individuals per unit area) of butterflies and bumble bees were significantly higher in proximate linear habitats than in distant ones. Moreover, butterfly species richness was higher for a given area in grasslands than in any of the linear habitat types. Butterfly density in grasslands did not differ from that in proximate linear habitats but was lower in distant linear habitats. The effect of isolation on density was stronger for less mobile butterfly species. For bumble bees there was no difference in species richness between grasslands and proximate linear habitats.For at least some of the butterfly species even these relatively small fragments of semi‐natural grasslands act as population sources from which individuals disperse to the surrounding habitats and thereby contribute to higher densities and species richness in adjacent areas. For bumble bees, it is more likely that the grasslands contain a higher density of nests than the surrounding intensively cultivated landscape, and that the density of foraging bumble bees decreases with increasing distance from the nest.Synthesis and application.Habitat fragmentation and intensified agricultural practices are considered to be a threat against services provided by pollinators. In order to sustain the abundance and diversity of insect pollinators in intensively farmed agricultural landscapes, we suggest that preservation of the remaining semi‐natural grasslands or re‐creation of flower‐rich grasslands is essential.