bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dispersive and long‐time behavior of oscillations in lattices
Authors: Path Carsten , Mielke Alexander 
Published: January 2007

AbstractWe study the long‐time dynamics of oscillations in lattices of infinitely many particles interacting via harmonic springs and adumbrate how decay rates for the displacements are proved analytically applying methods for oscillatory integrals. After recapitulating the results of an infinite chain with nearest‐neighbour interaction, we highlight the differences to the case of next‐nearest‐neighbour interaction. Finally we give an outlook on the two dimensional lattice with nearest‐neighbour interaction where more complicated singularities occur. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Prandtl's Mixing Length Model ‐ Revisited
Authors: Obermeier Frank 
Published: January 2007

AbstractThe paper is concerned with a modification of Prandtl's mixing length model of Reynolds stresses in fully developed turbulent channel flows. Here it is a well established fact that Prandtl's model falls short to describe the Reynolds stresses correctly very close to the wall. Furthermore, the resulting solution of the time averaged velocity fails to describe the channel flow correctly from the wall to its center. To overcome these shortcomings, the only characteristic mixing length in Prandtl's model is replaced by separate mixing lengths for velocity fluctuations parallel to the wall and normal to the wall, respectively. The modified model describes the mean velocity, all Reynolds stresses, and the functional dependence between Reynolds number based on the mean velocity and the one based on the friction velocity. For all Reynolds numbers these results ‐ and corresponding results for the production terms of Reynolds stresses and the energy balance of the mean flow ‐ agree quantitatively with experimental data and with data obtained by numerical simulations. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Variability in annual recruitment success as a determinant of long-term and large-scale variation in annual production of intertidal Wadden Sea mussels (Mytilus edulis)
Authors: Beukema J. J. , Dekker R. 
Published: January 2007

AbstractTo understand the background of the strong variation and recent decline of stocks and production of mussels (Mytilus edulis) on tidal flats of the Wadden Sea, we analysed long-term (twice-annual for 26 years) and multi-station (15 sites) estimates of numbers, mean individual weights, biomass, and annual production on Balgzand, a 50-km2tidal-flat area in the westernmost part of the Wadden Sea (The Netherlands). Somatic production was estimated from summed growth increments of soft tissues per half-year period and expressed in ash-free dry mass (AFDM). In adults, positive values in spring/summer regularly alternated with negative values in autumn/winter, when up to ∼25% (mean: 14%) of individual weight gains in the preceding season were lost. No weight losses were observed during the first winter of the life of mussels. The 26-year mean of net somatic tissue production P amounted to 5.5 g AFDM m−2 a−1at a mean biomass B of 3.2 g AFDM m−2; the ratioP/Bvaried strongly with age composition of the mussel population and ranged between 0.5 and 3.0 a−1(mean: 1.7). Within the restricted areas of mussel beds, mean biomass and annual production values were two orders of magnitude higher. In the Wadden Sea, mussel beds cover a typical 1% of extensive tidal flat areas. Numerical densities of recruits showed straight-line relationships with subsequent life-time year-class production. Once recruits had reached an age of ∼10 months, their numbers predicted subsequent production within narrow limits. Production per recruit averaged 0.21 g AFDM for 10-mo recruits and was not related to recruit density. Local variation in annual production varied strongly, with maximal values between mid-tide and low-tide level, where recruitment was also maximal. Production per recruit was higher at low than at high intertidal levels. Frequently failing recruitment is indicated as the main cause of declining mussel stocks in the Wadden Sea. As in other bivalve species, a declining frequency of the occurrence of cold winters appears to govern declining recruitment success and consequently declining production.
Recent advances in amino acid and organic acid metabolism
Authors: Leonard J. V. 
Published: January 2007

SummaryThis paper focuses on the three areas in this field in which there have been advances in amino acid and organic acid metabolism. These are the description of glutamine synthetase deficiency, the elucidation of the mechanism of pyridoxine‐dependent convulsions, and a hypothesis to explain the neurological complications of some organic acidaemias.
Characterization of retinaldehyde dehydrogenase‐2 induction in NG2‐positive glia after spinal cord contusion injury
Authors: Kern Johanna , Schrage Kirsten , Koopmans Guido C. , Joosten Elbert A. , McCaffery Peter , Mey Jörg 
Published: January 2007

AbstractThe transcriptional activator retinoic acid (RA) supports axonal regeneration of several neuronal cell populations in vitro, and it has been suggested that its receptor RARβ2 may be used to support axonal regeneration in the adult mammalian spinal cord. We have previously shown that spinal cord injury induces activity of the RA synthesizing enzyme retinaldehyde dehydrogenase (RALDH)2 in NG2‐positive cells. This report quantifies the increase of RALDH2 protein in the injured spinal cord and characterizes the RALDH2/NG2 expressing cells probably as a unique RA synthesizing subpopulation of activated oligodendrocyte precursors or “polydendrocytes”. In the uninjured spinal cord low levels of RALDH2 are present in oligodendrocytes as well as in the meninges and in blood vessels. Following injury there is a significant increase in RALDH2 in these latter two tissues and, given that the RALDH2/NG2 positive cells are clustered in the same area, this implies that these are specific foci of RA synthesis. It is presumed that these cells release RA in a paracrine fashion in the region of the wound; however, the RALDH2/NG2‐immunoreactive cells expressed the retinoid receptors RARα, RARβ, RXRα and RXRβ, suggesting that RA also serves an autocrine function.
Evolution of the field of operations management
Authors: Sprague Linda G. 
Published: January 2007

AbstractThis Special Issue of the Journal of Operations Management consists of 16 articles by 26 authors covering Operations Managements (OM) topics and issues from the 16th century to the 21st with predictions for the future. While it does not pretend to be comprehensive, it is representative of the types of subjects of inquiry through out this historical period in what could be considered OM. This introduction attempts to put the papers in context, and concludes with comments about what might be considered fundamental concepts which, taken as a set, can be seen as the foundations of Operations Management today.
A behavioural approach to adolescents in trouble
Authors: Brown Barrie J. 
Published: January 2007

Attempts by the mental health professions to find effective prevention or treatment programmes for adolescents with severe conduct disorders have been marked by failure, and by a number of swings in preferred practice which currently have been given expression in the form of various kinds of intervention within the community of the delinquent adolescent—Special Family Placement and Intermediate Treatment for example. Before rejecting current resources however, in particular residential treatment, the question has to be asked how might such resources deal effectively with delinquency? It is suggested that the use of a behavioural model has particular relevance to the delivery of services within the residential sector since it offers a consistent theoretical framework for understanding both the aetiology and the management of such problems. The behaviour model is concerned with controlling behaviour, but not necessarily in a sense of imposing social control on others. Behavioural methods of treatment may be used to control others but are equally useful in the hands of practitioners seeking to foster self‐determination and maturity in his client.The most relevant form of behavioural treatment within the residential setting is the Token Economy since it is a technique which can be incorporated into the culture and the life of all the people who live in the residential setting. This paper describes one example of a Token Economy, focusing on the three essential components of any successful use of token economy techniques; firstly involving the clients themselves in the management of their own programmes, secondly, the establishment of a system of token reinforcement which can be gradually faded as the clients are able to respond more and more to the intrinsic value of their newly acquired skills and thirdly an effective feedback and training system for staff and children of their performance in the programme.Preliminary results from this programme, the Gilbey House Token Economy Management Scheme, indicate that the initial aim of the programme (to achieve rapid and extensive expansion in the repertoire of skills of the boys in the unit) has been, broadly speaking, achieved. The Gilbey House programme, however, is only at its first stage—defining a treatment technology. What is now required is to achieve the second stage of its development, establishing clear cut evidence of its efficacy through a controlled comparative evaluation.
Numerical response of a helminth community in the course of a multi-annual abundance cycle of the Water Vole (Arvicola terrestris)
Authors: CERQUEIRA D. , DELATTRE P. , DE SOUSA B. , GABRION C. , MORAND S. , QUERE J. P. 
Published: January 2007

SUMMARYThe impact of parasitism on population dynamics is determined in part by the numerical responses of parasites during population fluctuations of their hosts. Vole populations fluctuate in multi-annual cycles allowing such responses to be studied over successive phases of population growth, abundance and decline. We investigate how a helminth community (5 nematode and 7 cestode species) evolved over a full 6-year Water Vole (Arvicola terrestris) population cycle. Brillouin and individual parasite species richness (IPSR) indices were used to measure the numerical response of the parasite community. We report a correlation between levels of parasite intensity and vole population cycle phases. Both indices were consistently higher during pre-decline and decline phases for male and female voles alike. The numerical response of the parasite community suggests that populations may be regulated by parasitism and that studies of this mechanism should allow both for the cyclic or non-cyclic character of the host populations and for the response of the broadest possible set of the local parasite community.
Growth-hormone-releasing peptide 6 (GHRP6) prevents oxidant cytotoxicity and reduces myocardial necrosis in a model of acute myocardial infarction
Authors: Berlanga Jorge , Cibrian Danay , Guevara Luis , Dominguez Heberto , Alba Jose S. , Seralena Alina , Guillén Gerardo , López-Mola Ernesto , López-Saura Pedro , Rodriguez Alberto , Perez Brumny , Garcia Diana , Vispo Nelson S. 
Published: January 2007

Therapies aimed at enhancing cardiomyocyte survival following myocardial injury are urgently required. As GHRP6 [GH (growth hormone)-releasing peptide 6] has been shown to stimulate GH secretion and has beneficial cardiovascular effects, the aim of the present study was to determine whether GHRP6 administration reduces myocardial infarct size following acute coronary occlusion in vivo. Female Cuban Creole pigs were anaesthetized, monitored and instrumented to ensure a complete sudden left circumflex artery occlusion for 1 h, followed by a 72 h reperfusion/survival period. Animals were screened clinically before surgery and assigned randomly to receive either GHRP6 (400 μg/kg of body weight) or normal saline. Hearts were processed, and the area at risk and the infarct size were determined. CK-MB (creatine kinase MB) and CRP (C-reactive protein) levels and pathological Q-wave-affected leads were analysed and compared. Evaluation of the myocardial effect of GHRP6 also included quantitative histopathology, local IGF-I (insulin-growth factor-I) expression and oxidative stress markers. GHRP6 treatment did not have any influence on mortality during surgery associated with rhythm and conductance disturbances during ischaemia. Infarct mass and thickness were reduced by 78% and 50% respectively, by GHRP6 compared with saline (P&lt;0.01). More than 50% of the GHRP6-treated pigs did not exhibit pathogological Q waves in any of the ECG leads. Quantitative histopathology and CK-MB and CRP serum levels confirmed the reduction in GHRP6-mediated necrosis (all P&lt;0.05). Levels of oxidative stress markers suggested that GHRP6 prevented myocardial injury via a decrease in reactive oxygen species and by the preservation of antioxidant defence systems (all P&lt;0.05). Myocardial IGF-I transcription was not amplified by GHRP6 treatment compared with the increase induced by the ischaemic episode in relation to expression in intact hearts (P&lt;0.01). In conclusion, GHRP6 exhibits antioxidant effects which may partially contribute to reduce myocardial ischaemic damage.
Simulating multiplexed SNP discovery rates using base-specific cleavage and mass spectrometry
Authors: Böcker Sebastian 
Published: January 2007

AbstractMotivation: Single Nucleotide Polymorphisms (SNPs) are believed to contribute strongly to the genetic variability in living beings, and SNP and mutation discovery are of great interest in today's Life Sciences. A comparatively new method to discover such polymorphisms is based on base-specific cleavage, where resulting cleavage products are analyzed by mass spectrometry (MS). One particular advantage of this method is the possibility of multiplexing the biochemical reactions, i.e. examining multiple genomic regions in parallel. Simulations can help estimating the performance of a method for polymorphism discovery, and allow us to evaluate the influence of method parameters on the discovery rate, and also to investigate whether the method is well suited for a certain genomic region.Results: We show how to efficiently conduct such simulations for polymorphism discovery using base-specific cleavage and MS. Simulating multiplexed polymorphism discovery leads us to the problem of uniformly drawing a multiplex. Given a multiset of natural numbers we want to uniformly draw a subset of fixed cardinality so that the elements sum up to some fixed total length. We show how to enumerate multiplex layouts using dynamic programming, which allows us to uniformly draw a multiplex.Contact: boecker@minet.uni-jena.de
A novel pattern recognition algorithm to classify membrane protein unfolding pathways with high-throughput single-molecule force spectroscopy
Authors: Marsico Annalisa , Labudde Dirk , Sapra Tanuj , Muller Daniel J. , Schroeder Michael 
Published: January 2007

AbstractMotivation: Misfolding of membrane proteins plays an important role in many human diseases such as retinitis pigmentosa, hereditary deafness and diabetes insipidus. Little is known about membrane proteins as there are only very few high-resolution structures. Single-molecule force spectroscopy is a novel technique, which measures the force necessary to pull a protein out of a membrane. Such force curves contain valuable information on the protein structure, conformation, and inter- and intra-molecular forces. High-throughput force spectroscopy experiments generate hundreds of force curves including spurious ones and good curves, which correspond to different unfolding pathways. Manual analysis of these data is a bottleneck and source of inconsistent and subjective annotation.Results: We propose a novel algorithm for the identification of spurious curves and curves representing different unfolding pathways. Our algorithm proceeds in three stages: first, we reduce noise in the curves by applying dimension reduction; second, we align the curves with dynamic programming and compute pairwise distances and third, we cluster the curves based on these distances. We apply our method to a hand-curated dataset of 135 force curves of bacteriorhodopsin mutant P50A. Our algorithm achieves a success rate of 81% distinguishing spurious from good curves and a success rate of 76% classifying unfolding pathways. As a result, we discuss five different unfolding pathways of bacteriorhodopsin including three main unfolding events and several minor ones. Finally, we link folding barriers to the degree of conservation of residues. Overall, the algorithm tackles the force spectroscopy bottleneck and leads to more consistent and reproducible results paving the way for high-throughput analysis of structural features of membrane proteins.Contact: annalisa.marsico@biotec.tu-dresden.de
EBIMed—text crunching to gather facts for proteins from Medline
Authors: Rebholz-Schuhmann Dietrich , Kirsch Harald , Arregui Miguel , Gaudan Sylvain , Riethoven Mark , Stoehr Peter 
Published: January 2007

AbstractSummary: To allow efficient and systematic retrieval of statements from Medline we have developed EBIMed, a service that combines document retrieval with co-occurrence-based analysis of Medline abstracts. Upon keyword query, EBIMed retrieves the abstracts from EMBL-EBI's installation of Medline and filters for sentences that contain biomedical terminology maintained in public bioinformatics resources. The extracted sentences and terminology are used to generate an overview table on proteins, Gene Ontology (GO) annotations, drugs and species used in the same biological context. All terms in retrieved abstracts and extracted sentences are linked to their entries in biomedical databases. We assessed the quality of the identification of terms and relations in the retrieved sentences. More than 90% of the protein names found indeed represented a protein. According to the analysis of four protein–protein pairs from the Wnt pathway we estimated that 37% of the statements containing such a pair mentioned a meaningful interaction and clarified the interaction of Dkk with LRP. We conclude that EBIMed improves access to information where proteins and drugs are involved in the same biological process, e.g. statements with GO annotations of proteins, protein–protein interactions and effects of drugs on proteins.Availability: Available atSupplementary Data: Supplementary Data are available at Bioinformatics online.Contact: Rebholz@ebi.ac.uk
ISIS: interaction sites identified from sequence
Authors: Ofran Yanay , Rost Burkhard 
Published: January 2007

AbstractMotivation: Large-scale experiments reveal pairs of interacting proteins but leave the residues involved in the interactions unknown. These interface residues are essential for understanding the mechanism of interaction and are often desired drug targets. Reliable identification of residues that reside in protein–protein interface typically requires analysis of protein structure. Therefore, for the vast majority of proteins, for which there is no high-resolution structure, there is no effective way of identifying interface residues.Results: Here we present a machine learning-based method that identifies interacting residues from sequence alone. Although the method is developed using transient protein–protein interfaces from complexes of experimentally known 3D structures, it never explicitly uses 3D information. Instead, we combine predicted structural features with evolutionary information. The strongest predictions of the method reached over 90% accuracy in a cross-validation experiment. Our results suggest that despite the significant diversity in the nature of protein–protein interactions, they all share common basic principles and that these principles are identifiable from sequence alone.Contact: yanay.ofran@columbia.edu
Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates
Authors: Ninio Matan , Privman Eyal , Pupko Tal , Friedman Nir 
Published: January 2007

AbstractDistance-based methods for phylogeny reconstruction are the fastest and easiest to use, and their popularity is accordingly high. They are also the only known methods that can cope with huge datasets of thousands of sequences. These methods rely on evolutionary distance estimation and are sensitive to errors in such estimations. In this study, a novel Bayesian method for estimation of evolutionary distances is developed. The proposed method enables the use of a sophisticated evolutionary model that better accounts for among-site rate variation (ASRV), thereby improving the accuracy of distance estimation. Rate variations are estimated within a Bayesian framework by extracting information from the entire dataset of sequences, unlike standard methods that can only use one pair of sequences at a time. We compare the accuracy of a cascade of distance estimation methods, starting from commonly used methods and moving towards the more sophisticated novel method. Simulation studies show significant improvements in the accuracy of distance estimation by the novel method over the commonly used ones. We demonstrate the effect of the improved accuracy on tree reconstruction using both real and simulated protein sequence alignments. An implementation of this method is available as part of the SEMPHY package.Contact: talp@tau.ac.il
Simultaneous alignment and annotation ofcis-regulatory regions
Authors: Bais Abha Singh , Grossmann Steffen , Vingron Martin 
Published: January 2007

AbstractMotivation: Current methods that annotate conserved transcription factor binding sites in an alignment of two regulatory regions perform the alignment and annotation step separately and combine the results in the end. If the site descriptions are weak or the sequence similarity is low, the local gap structure of the alignment poses a problem in detecting the conserved sites. It is therefore desirable to have an approach that is able to simultaneously consider the alignment as well as possibly matching site locations.Results: With SimAnn we have developed a tool that serves exactly this purpose. By combining the annotation step and the alignment of the two sequences into one algorithm, it detects conserved sites more clearly. It has the additional advantage that all parameters are calculated based on statistical considerations. This allows for its successful application with any binding site model of interest. We present the algorithm and the approach for parameter selection and compare its performance with that of other, non-simultaneous methods on both simulated and real data.Availability: A command-line based C++ implementation of SimAnn is available from the authors upon request. In addition, we provide Perl scripts for calculating the input parameters based on statistical considerations.Contact: bais@molgen.mpg.de