bluuebunny/crossref_metadata_2025_split huggingface dataset:
The synthetic TRH analogue taltirelin exerts modality‐specific antinociceptive effects via distinct descending monoaminergic systems
Authors: Tanabe M , Tokuda Y , Takasu K , Ono K , Honda M , Ono H 
Published: January 2007

Background and purpose:Exogenously administered thyrotropin‐releasing hormone (TRH) is known to exert potent but short‐acting centrally‐mediated antinociceptive effects. We sought to investigate the mechanisms underlying these effects using the synthetic TRH analogue taltirelin, focusing on the descending monoaminergic systems in mice.Experimental approach:The mice received systemic or local injections of taltirelin combined with either central noradrenaline (NA) or 5‐hydroxytryptamine (5‐HT) depletion by 6‐hydroxydopamine (6‐OHDA) or DL‐p‐chlorophenylalanine (PCPA), respectively, or blockade of their receptors. The degree of antinociception was determined using the tail flick and tail pressure tests.Key results:Subcutaneously (s.c.) administered taltirelin exhibited dose‐dependent antinociceptive effects in the tail flick and tail pressure tests. These effects appeared to be primarily supraspinally mediated, since intracerebroventricularly (i.c.v.) but not intrathecally (i.t.) injected taltirelin generated similar effects. Depletion of central NA abolished only the analgesic effect of taltirelin (s.c. and i.c.v.) on mechanical nociception. By contrast, depletion of central 5‐HT abolished only its analgesic effect on thermal nociception. Intraperitoneal (i.p.) and i.t. injection of the α2‐adrenoceptor antagonist yohimbine respectively reduced the analgesic effect of taltirelin (s.c. and i.c.v.) on mechanical nociception. By contrast, the 5‐HT1Areceptor antagonist WAY‐100635 (i.p. and i.t.) reduced the effect of taltirelin (s.c. and i.c.v.) on thermal nociception. Neither the 5‐HT2receptor antagonist ketanserin nor the opioid receptor antagonist naloxone altered the antinociceptive effect of taltirelin.Conclusions and Implications:These findings suggest that taltirelin activates the descending noradrenergic and serotonergic pain inhibitory systems, respectively, to exert its analgesic effects on mechanical and thermal nociception.British Journal of Pharmacology(2007)150, 403–414. doi:10.1038/sj.bjp.0707125
Guidelines on information requirements for import and release of invertebrate biological control agents in European countries.
Authors: Bigler F. , Bale J. S. , Cock M. J. W. , Dreyer H. , Greatrex R. , Kuhlmann U. , Loomans A. J. M. , Lenteren J. C. van 
Published: January 2007

Abstract
Several international documents have been published in recent years with the objective of providing guidance to industry, biocontrol practitioners and competent national regulatory authoritieson the regulatory framework for the import and release of invertebrate biological control agents(IBCAs). As the scope and the level of detail given in these documents were diverse in many respects, it has been difficult for all stakeholders to apply such guidelines, and to integrate them in a harmonized way into national regulatory documents. At the request of several stakeholders, the International Organization for Biological Control of Noxious Animals and Plants/West Palaearctic Regional Section (IOBC/WPRS) organized an initiative with the objective of merging all relevant international documents into one document, to provide more specific guidance, and to harmonizethe regulation of IBCAs in European countries and in other countries of the IOBC/WPRS. This document consists of five sections which together form comprehensive guidelines specifying the information required for regulating import and release of IBCAs.
Control of fish lactococcosis: efficacy of vaccination procedures.
Authors: Romalde J. L. , Ravelo C. , Toranzo A. E. 
Published: January 2007

Abstract
The aim of this review is to give a comprehensive overview of the current status of vaccination against lactococcosis. Presented are the effectiveness and duration of protection in rainbow trout and yellowtail, two of the fish species that are most affected by this disease, obtained with a variety of vaccines developed by different research groups. In addition, recent advances obtained in our laboratory with two distinct approaches, adjuvanted vaccines and oral booster vaccination, as well as the availability of commercial vaccines are also discussed.
Reproduction and production performance of Moroccan sheep breeds.
Authors: Boujenane I 
Published: January 2007

Abstract
The Moroccan sheep population consists of several breeds. The most important breeds are the Dman, Timahdite, Béni Guil, Sardi, Béni Ahsen and Boujaâd. With regard to reproduction performance, these breeds could be divided into two groups. The Dman breed reaches puberty at an early age, has a long breeding season, a short postpartum anoestrus and a high prolificacy. The other local breeds are not prolific and have a limited breeding season. All the breeds perform similarly in terms of the growth traits. Nevertheless, the Sardi breed has a slightly higher growth rate and good carcass characteristics, while the Dman has a moderate growth rate. Milk yield of local breeds is low, but milk composition is in line with that of other sheep breeds. The milk production is, in general, sufficient to nurse one lamb. Except for the Dman breed that has a low fleece weight, the other breeds have similar and moderate fleece weights. However, wool quality of local sheep is poor.
Incremental window-based protein sequence alignment algorithms
Authors: Rangwala Huzefa , Karypis George 
Published: January 2007

AbstractMotivation: Protein sequence alignment plays a critical role in computational biology as it is an integral part in many analysis tasks designed to solve problems in comparative genomics, structure and function prediction, and homology modeling.Methods: We have developed novel sequence alignment algorithms that compute the alignment between a pair of sequences based on short fixed- or variable-length high-scoring subsequences. Our algorithms build the alignments by repeatedly selecting the highest scoring pairs of subsequences and using them to construct small portions of the final alignment. We utilize PSI-BLAST generated sequence profiles and employ a profile-to-profile scoring scheme derived from PICASSO.Results: We evaluated the performance of the computed alignments on two recently published benchmark datasets and compared them against the alignments computed by existing state-of-the-art dynamic programming-based profile-to-profile local and global sequence alignment algorithms. Our results show that the new algorithms achieve alignments that are comparable with or better than those achieved by existing algorithms. Moreover, our results also showed that these algorithms can be used to provide better information as to which of the aligned positions are more reliable—a critical piece of information for comparative modeling applications.Contact: rangwala@cs.umn.eduSupplementary information:
A supervised approach for identifying discriminating genotype patterns and its application to breast cancer data
Authors: Yosef Nir , Yakhini Zohar , Tsalenko Anya , Kristensen Vessela , Børresen-Dale Anne-Lise , Ruppin Eytan , Sharan Roded 
Published: January 2007

AbstractMotivation: Large-scale association studies, investigating the genetic determinants of a phenotype of interest, are producing increasing amounts of genomic variation data on human cohorts. A fundamental challenge in these studies is the detection of genotypic patterns that discriminate individuals exhibiting the phenotype under study from individuals that do not posses it. The difficulty stems from the large number of single nucleotide polymorphism (SNP) combinations that have to be tested. The discrimination problem becomes even more involved when additional high-throughput data, such as gene expression data, are available for the same cohort.Results: We have developed a graph theoretic approach for identifying discriminating patterns (DPs) for a given phenotype in a genotyped population. The method is based on representing the SNP data as a bipartite graph of individuals and their SNP states, and identifying fully connected subgraphs of this graph that relate individuals enriched for a given phenotypic group. The method can handle additional data types such as expression profiles of the genotyped population. It is reminiscent of biclustering approaches with the crucial difference that its search process is guided by the phenotype under consideration in a supervised manner. We tested our approach in simulations and on real data. In simulations, our method was able to retrieve planted patterns with high success rate. We then applied our approach to a dataset of 72 breast cancer patients with available gene expression profiles, genotyped over 695 SNPs. We detected several DPs that were highly significant with respect to various clinical phenotypes, and investigated the groups of patients and the groups of genes they defined. We found the patient groups to be highly enriched for other phenotypes and to display expression coherency among their profiles. The gene groups displayed functional coherency and involved genes with known role in cancer, providing additional support to their involvement.Availability: The program is available upon request.Contact: roded@post.tau.ac.il
TOPP—the OpenMS proteomics pipeline
Authors: Kohlbacher Oliver , Reinert Knut , Gröpl Clemens , Lange Eva , Pfeifer Nico , Schulz-Trieglaff Ole , Sturm Marc 
Published: January 2007

AbstractMotivation: Experimental techniques in proteomics have seen rapid development over the last few years. Volume and complexity of the data have both been growing at a similar rate. Accordingly, data management and analysis are one of the major challenges in proteomics. Flexible algorithms are required to handle changing experimental setups and to assist in developing and validating new methods. In order to facilitate these studies, it would be desirable to have a flexible ‘toolbox’ of versatile and user-friendly applications allowing for rapid construction of computational workflows in proteomics.Results: We describe a set of tools for proteomics data analysis—TOPP, The OpenMS Proteomics Pipeline. TOPP provides a set of computational tools which can be easily combined into analysis pipelines even by non-experts and can be used in proteomics workflows. These applications range from useful utilities (file format conversion, peak picking) over wrapper applications for known applications (e.g. Mascot) to completely new algorithmic techniques for data reduction and data analysis. We anticipate that TOPP will greatly facilitate rapid prototyping of proteomics data evaluation pipelines. As such, we describe the basic concepts and the current abilities of TOPP and illustrate these concepts in the context of two example applications: the identification of peptides from a raw dataset through database search and the complex analysis of a standard addition experiment for the absolute quantitation of biomarkers. The latter example demonstrates TOPP's ability to construct flexible analysis pipelines in support of complex experimental setups.Availability: The TOPP components are available as open-source software under the lesser GNU public license (LGPL). Source code is available from the project website atContact: oliver.kohlbacher@uni-tuebingen.de
Using median sets for inferring phylogenetic trees
Authors: Bernt Matthias , Merkle Daniel , Middendorf Martin 
Published: January 2007

AbstractMotivation: Algorithms for phylogenetic tree reconstruction based on gene order data typically repeatedly solve instances of the reversal median problem (RMP) which is to find for three given gene orders a fourth gene order (called median) with a minimal sum of reversal distances. All existing algorithms of this type consider only one median for each RMP instance even when a large number of medians exist. A careful selection of one of the medians might lead to better phylogenetic trees.Results: We propose a heuristic algorithm amGRP for solving the multiple genome rearrangement problem (MGRP) by repeatedly solving instances of the RMP taking all medians into account. Algorithm amGRP uses a branch-and-bound method that branches over medians from a selected subset of all medians for each RMP instance. Different heuristics for selecting the subsets have been investigated. To show that the medians for RMP vary strongly with respect to different properties that are likely to be relevant for phylogenetic tree reconstruction, the set of all medians has been investigated for artificial datasets and mitochondrial DNA (mtDNA) gene orders. Phylogenetic trees have been computed for a large set of randomly generated gene orders and two sets of mtDNA gene order data for different animal taxa with amGRP and with two standard approaches for solving the MGRP (GRAPPA-DCM and MGR). The results show that amGRP outperforms both other methods with respect to solution quality and computation time on the test data.Availability: The source code of amGRP, additional results and the test instances used in this paper are freely available from the authors.Contact: merkle@informatik.uni-leipzig.de
Discovering tightly regulated and differentially expressed gene sets in whole genome expression data
Authors: Ye Chun , Eskin Eleazar 
Published: January 2007

AbstractMotivation: Recently, a new type of expression data is being collected which aims to measure the effect of genetic variation on gene expression in pathways. In these datasets, expression profiles are constructed for multiple strains of the same model organism under the same condition. The goal of analyses of these data is to find differences in regulatory patterns due to genetic variation between strains, often without a phenotype of interest in mind. We present a new method based on notions of tight regulation and differential expression to look for sets of genes which appear to be significantly affected by genetic variation.Results: When we use categorical phenotype information, as in the Alzheimer's and diabetes datasets, our method finds many of the same gene sets as gene set enrichment analysis. In addition, our notion of correlated gene sets allows us to focus our efforts on biological processes subjected to tight regulation. In murine hematopoietic stem cells, we are able to discover significant gene sets independent of a phenotype of interest. Some of these gene sets are associated with several blood-related phenotypes.Availability: The programs are available by request from the authors.Contact: cye@bioinf.ucsd.edu
Merging microarray cell synchronization experiments through curve alignment
Authors: Hermans Filip , Tsiporkova Elena 
Published: January 2007

AbstractMotivation: The validity of periodic cell cycle regulation studies in plants is seriously compromised by the relatively poor quality of cell synchrony that is achieved for plant suspension cultures in comparison to yeast and mammals. The present state-of-the-art plant synchronization techniques cannot offer a complete cell cycle coverage and moreover a considerable loss of cell synchrony may occur toward the end of the sampling. One possible solution is to consider combining multiple datasets, produced by different synchronization techniques and thus covering different phases of the cell cycle, in order to arrive at a better cell cycle coverage.Results: We propose a method that enables pasting expression profiles from different plant cell synchronization experiments and results in an expression curve that spans more than one cell cycle. The optimal pasting overlap is determined via a dynamic time warping alignment. Consequently, the different expression time series are merged together by aggregating the corresponding expression values lying within the overlap area. We demonstrate that the periodic analysis of the merged expression profiles produces more reliable p-values for periodicity. Subsequent Gene Ontology analysis of the results confirms that merging synchronization experiments is a more robust strategy for the selection of potentially periodic genes. Additional validation of the proposed algorithm on yeast data is also presented.Availability: Results, benchmark sets and scripts are freely available at our website:Contact: elena.tsiporkova@ugent.be, fiher@psb.ugent.be
Prediction and simulation of motion in pairs of transmembrane α-helices
Authors: Enosh Angela , Fleishman Sarel J. , Ben-Tal Nir , Halperin Dan 
Published: January 2007

AbstractMotivation: Motion in transmembrane (TM) proteins plays an essential role in a variety of biological phenomena. Thus, developing an automated method for predicting and simulating motion in this class of proteins should result in an increased level of understanding of crucial physiological mechanisms. We have developed an algorithm for predicting and simulating motion in TM proteins of the α-helix bundle type. Our method employs probabilistic motion-planning techniques to suggest possible collision-free motion paths. The resulting paths are ranked according to the quality of the van der Waals interactions between the TM helices. Our algorithm considers a wide range of degrees of freedom (dofs) involved in the motion, including external and internal moves. However, in order to handle the vast dimensionality of the problem, we employ some constraints on these dofs in a way that is unlikely to rule out the native motion of the protein. Our algorithm simulates the motion, including all the dofs, and automatically produces a movie that demonstrates it.Results: Overexpression of the RTK ErbB2 was implicated in causing a variety of human cancers. Recently, a molecular mechanism for rotation-coupled activation of the receptor was suggested. We applied our algorithm to investigate the TM domain of this protein, and compared our results with this mechanism. A motion pathway that was similar to the proposed mechanism ranked first, and motions with partial overlap to this pathway followed in rank order. In addition, we conducted a negative-control computational-experiment using Glycophorin A. Our results confirmed the immobility of this TM protein, resulting in degenerate paths comprising native-like conformations.Supplementary information: Supplementary data are available atContact: angela@post.tau.ac.il
Novel solutions of the Helmholtz equation and their application to diffraction
Authors: Budaev Bair V , Bogy David B 
Published: January 2007

This paper presents a series of novel representations for the solutions of the Helmholtz equation in a broad class of wedge-like domains including those with curvilinear, non-flat faces. These representations are obtained by an original method which combines ray theory with the probabilistic approach to partial differential equations and uses a specific technique to deal with a need for analytical continuation of the specified boundary function. The main results are reminiscent of the standard Feynman–Kac formula but differ in that the averaging over solutions of stochastic differential equations is replaced by averaging over the trajectories of a new two-scale random motion introduced here.
The paper focuses on the development of the solutions and for this reason it includes only a brief outline of numerous applications, consequences, extensions and variations of the method, which include, but are not limited to, problems of diffraction and scattering, problems in three-dimensional domains and problems of wave propagation in non-homogeneous media.
Human resources and scientific output in Brazilian science
Authors: Leta Jacqueline 
Published: January 2007

PurposeThe present study aims to overview Brazilian human resources and scientific output in astronomy, immunology and oceanography during the last decade.Design/methodology/approachData on human resources and on scientific output were obtained from the Brazilian database, the Directory of Research Groups. Scientific outputs were also analysed from a set of journals catalogued by the Institute for Scientific Information: the 20 journals with the largest number of articles in 2003.FindingsCompared with the other two fields, the number of Brazilian researchers in astronomy has not grown from 1997‐2002, but they are the most qualified and more than 90 per cent of them have a PhD degree. Most astronomy publications are in international journals and they are well cited. The most cited astronomy papers are on international topics, but this is not true for the oceanography papers.Research limitations/implicationsThese data are derived from a particular set of publications and should be interpreted as trends rather than as definitive.Originality/valueThis study, which covers three fields with different structures and traditions, provides a snapshot of some features of the whole of Brazilian science, and will provide evidence for new science policies.
Journals used for the publication of English psychiatry, surgery and paediatrics research
Authors: Jones Teresa , Hanney Steve , Buxton Martin , Rippon Isla 
Published: January 2007

PurposeTo identify the papers, and publishing journals, describing psychiatry, surgery and paediatrics research funded by the National Health Service (NHS) in the UK. To make comparisons with non‐NHS research and examine the journal impact factors, and importance to clinicians, of journals publishing the most NHS research. To consider the implications, including those for research assessment.Design/methodology/approachExisting databases were examined: the research outputs database (ROD), which contains information on UK biomedical papers; NHS ROD, which contains details of papers on ROD funded by the NHS; lists of journal impact factors. These were combined with selective findings from surveys conducted to identify journals read and viewed as important for clinical practice by psychiatrists, surgeons and paediatricians.FindingsIn each specialty many papers publish NHS‐funded research and they out‐number the non‐NHS papers in the ROD. They appear in a wide range of journals but in each specialty one journal is clearly the most used. The impact factors of journals publishing the most NHS research vary considerably. In each specialty the journal containing most NHS publications is widely perceived to be important by clinicians.Research limitations/implicationsMuch NHS‐funded research is also funded by other bodies. Clinician survey response rates were between 38 per cent and 47 per cent. The analysis could be extended to other specialties.Practical implicationsPapers published in the few journals in each specialty that are viewed as important by clinicians could be given additional credit in assessments.Originality/valueThis paper describes outputs from NHS research and shows how assessment could be extended.