bluuebunny/crossref_metadata_2025_split huggingface dataset:
DPDB: a database for the storage, representation and analysis of polymorphism in the Drosophila genus
Authors: Casillas Sònia , Petit Natalia , Barbadilla Antonio 
Published: October 2005

Abstract
Motivation: Polymorphism studies are one of the main research areas of this genomic era. To date, however, no comprehensive secondary databases have been designed to provide searchable collections of polymorphic sequences with their associated diversity measures.
Results: We define a data model for the storage, representation and analysis of genotypic and haplotypic data. Under this model we have created DPDB, ‘Drosophila Polymorphism Database’, a web site that provides a daily updated repository of all well-annotated polymorphic sequences in the Drosophila genus. It allows the search for any polymorphic set according to different parameter values of nucleotide diversity, linkage disequilibrium and codon bias. For data collection, analysis and updating we use PDA, a pipeline that automates the process of sequence retrieval, grouping, alignment and estimation of nucleotide diversity from Genbank sequences in different functional regions. The web site also includes analysis tools for sequence comparison and the estimation of genetic diversity, a page with real-time statistics of the database contents, a help section and a collection of selected links.
Availability: DPDB is freely available at http://dpdb.uab.es and can be downloaded via FTP.
Contact: antonio.barbadilla@uab.es
Design of a description language for generating wrapper to collect biological data
Authors: Lim Myungeun , Chung Myunggeun , Bae Myungnam , Park Sunhee 
Published: October 2005

Abstract
Summary: The biological data are scattered in various areas with various formats and they are changing continuously. Therefore, data integration becomes an important issue to provide researcher a dynamic access of data. In the data integration process, the method of extracting heterogeneous data dynamically from the data source is an essential part. Data extraction method using wrapper can provide flexibility and extensibility to an integration system.
Contact: melim@etri.re.kr
The fragment assembly string graph
Authors: Myers Eugene W. 
Published: October 2005

Abstract
We present a concept and formalism, the string graph, which represents all that is inferable about a DNA sequence from a collection of shotgun sequencing reads collected from it. We give time and space efficient algorithms for constructing a string graph given the collection of overlaps between the reads and, in particular, present a novel linear expected time algorithm for transitive reduction in this context. The result demonstrates that the decomposition of reads into kmers employed in the de Bruijn graph approach described earlier is not essential, and exposes its close connection to the unitig approach we developed at Celera. This paper is a preliminary piece giving the basic algorithm and results that demonstrate the efficiency and scalability of the method. These ideas are being used to build a next-generation whole genome assembler called BOA (Berkeley Open Assembler) that will easily scale to mammalian genomes.
Contact: gene@eecs.berkeley.edu
Association Cluster Detector: a tool for heuristic detection of significance clusters in whole-genome scans
Authors: Marquès-Bonet Tomàs , Lao Oscar , Goertsches Robert , Comabella Manuel , Montalban Xavier , Navarro Arcadi 
Published: October 2005

Abstract
Summary: Whole genome scans analyze large sets of genetic markers, mainly single nucleotide polymorphisms, over the entire genome in order to find variants and regions associated with complex traits so these can be further investigated. Analyzing the results of such scans becomes difficult due to multiple testing problems and to the genomic distributions of recombination, linkage disequilibrium and true associations, which generate an extremely complex network of dependences between markers. Here we present Association Cluster Detector (ACD), a simple tool aiming to ease the analysis of the results of whole genome scans. ACD facilitates correction for multiple tests using several standard procedures and implements a sliding-window heuristic method that helps in detecting potentially interesting candidate regions by exploiting the property of non-random distribution of significantly associated markers.
Availability: The tool can be downloaded from http://www.upf.es/cexs/recerca/bioevo/softanddata.htm
Contact: arcadi.navarro@upf.edu
Data-adaptive test statistics for microarray data
Authors: Mukherjee Sach , Roberts Stephen J. , van der Laan Mark J. 
Published: October 2005

Abstract
Motivation: An important task in microarray data analysis is the selection of genes that are differentially expressed between different tissue samples, such as healthy and diseased. However, microarray data contain an enormous number of dimensions (genes) and very few samples (arrays), a mismatch which poses fundamental statistical problems for the selection process that have defied easy resolution.
Results: In this paper, we present a novel approach to the selection of differentially expressed genes in which test statistics are learned from data using a simple notion of reproducibility in selection results as the learning criterion. Reproducibility, as we define it, can be computed without any knowledge of the ‘ground-truth’, but takes advantage of certain properties of microarray data to provide an asymptotically valid guide to expected loss under the true data-generating distribution. We are therefore able to indirectly minimize expected loss, and obtain results substantially more robust than conventional methods. We apply our method to simulated and oligonucleotide array data.
Availability: By request to the corresponding author.
Contact: sach@robots.ox.ac.uk
Model-P: a basecalling method for resequencing microarrays of diploid samples
Authors: Zhan Yiping , Kulp David 
Published: October 2005

Abstract
Motivation: Basecalling is a critical step of the analysis of DNA resequencing microarray data for single nucleotide polymorphism discovery and genotyping. For microarrays hybridized with DNA derived from diploid organisms, basecalling with high accuracy at high call rates is a challenging task. Current methods sometimes do not produce satisfactory results.
Results: We explored using physical models based on the sequences of the probe and the target to predict feature intensities in resequencing microarrays. Based on these intensity-predicting models, a new basecalling method (Model-P), which takes into consideration the expected feature intensities for different potential genotypes, was developed. Model-P is shown to have better performance at high call rates compared with ABACUS, the current state-of-the-art method, on a test dataset and on relatively AT-rich regions.
Availability: Model-P is available upon request.
Contact: dkulp@cs.umass.edu
Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E.Coli
Authors: Simão E. , Remy E. , Thieffry D. , Chaouiya C. 
Published: October 2005

Abstract
Motivation: The integrated dynamical modelling of mixed metabolic/genetic networks constitutes one of the challenges of systems biology. Furthermore, as most of available data about genetic and metabolic regulations are qualitative, there is a pressing need for rigorous qualitative mathematical approaches.
Results: On the basis of two established formalisms, the logical modelling of genetic regulatory networks and the Petri net modelling of metabolic networks, we propose a systematic approach for the modelling of regulated metabolic networks. This approach leans on previous work defining a systematic procedure to translate logical regulatory graphs into standard (discrete) Petri nets (PNs). This approach is illustrated by the qualitative modelling of the biosynthesis of tryptophan (Trp) in Escherichia coli, taking into account two types of regulatory feedbacks: the direct inhibition of the first enzyme of the pathway by the final product of the pathway, and the transcriptional inhibition of the Trp operon by the Trp–repressor complex. On the basis of this integrated PN model, we further indicate how available dynamical analysis tools can be applied to obtain significant insights in the behaviour of the system.
Availability: The software GINsim for the logical modelling of genetic regulatory networks together with the PN model of the regulated Trp biosynthesis pathway are available at: http://gin.univ-mrs.fr/GINsim.
Contact: chaouiya@ibdm.univ-mrs.fr
RNA secondary structural alignment with conditional random fields
Authors: Sato Kengo , Sakakibara Yasubumi 
Published: October 2005

Abstract
Motivation: The computational identification of non-coding RNA regions on the genome is currently receiving much attention. However, it is essentially harder than gene-finding problems for protein-coding regions because non-coding RNA sequences do not have strong statistical signals. Since comparative sequence analysis is effective for non-coding RNA detection, efficient computational methods are expected for structural alignment of RNA sequences. Several methods have been proposed to accomplish the structural alignment tasks for RNA sequences, and we found that one of the most important points is to estimate an accurate score matrix for calculating structural alignments.
Results: We propose a novel approach for RNA structural alignment based on conditional random fields (CRFs). Our approach has some specific features compared with previous methods in the sense that the parameters for structural alignment are estimated such that the model can most probably discriminate between correct alignments and incorrect alignments, and has the generalization ability so that a satisfiable score matrix can be obtained even with a small number of sample data without overfitting. Experimental results clearly show that the parameter estimation with CRFs can outperform all the other existing methods for structural alignments of RNA sequences. Furthermore, structural alignment search based on CRFs is more accurate for predicting non-coding RNA regions than the other scoring methods. These experimental results strongly support our discriminative method employing CRFs to estimate the score matrix parameters.
Availability: The program which is implemented in C++ is available at http://phmmts.dna.bio.keio.ac.jp/ under the GNU public license.
Contact: satoken@bio.keio.ac.jp
Implementing the iHOP concept for navigation of biomedical literature
Authors: Hoffmann Robert , Valencia Alfonso 
Published: October 2005

Abstract
Motivation: The World Wide Web has profoundly changed the way in which we access information. Searching the internet is easy and fast, but more importantly, the interconnection of related contents makes it intuitive and closer to the associative organization of human memory. However, the information retrieval tools currently available to researchers in biology and medicine lag far behind the possibilities that the layman has come to expect from the internet.
Results: By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource. iHOP (Information Hyperlinked over Proteins) is an online service that provides this gene-guided network as a natural way of accessing millions of PubMed abstracts and brings all the advantages of the internet to scientific literature research. Navigating across interrelated sentences within this network is closer to human intuition than the use of conventional keyword searches and allows for stepwise and controlled acquisition of information. Moreover, this literature network can be superimposed upon experimental interaction data to facilitate the simultaneous analysis of novel and existing knowledge. The network presented in iHOP currently contains5 million sentences and 40 000 genes from Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Danio rerio, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli.
Availability: iHOP is freely accessible at http://www.pdg.cnb.uam.es/UniPub/iHOP/
Contact: hoffmann@cbio.mskcc.org
Supplementary Information: Supplementary data are available at Bioinformatics online.
Detection and characterization of two strains of Grapevine fanleaf nepovirus in Tunisia
Authors: Fattouch S. , Acheche H. , M’hirsi S. , Marrakchi M. , Marzouki N. 
Published: October 2005

The nematode‐borne Grapevine fanleaf nepovirus (GFLV) causes severe degeneration of grapevines in vineyards worldwide. In a recent survey of the sanitary status of grapevine plants in north Tunisian vineyards, we were interested to study the polymorphism of GFLV. Purified virus, from mechanically inoculated Chenopodium quinoa, was used to produce anti‐GFLV antiserum, which specifically recognized GFLV in different Tunisian grapevine samples using the DAS‐ELISA technique. Positive samples were subjected to oligoprobe‐RT‐PCR to amplify a 606 bp region of the viral coat protein sequence. PCR products used for RFLP analysis after digestion with endonuclease AluI produced 3 restriction profiles. RFLP data allowed clear distinction of two GFLV strains in Tunisia. The nucleotide sequence of the PCR‐generated amplicons from each strain was determined showing 93.4% identity at the nucleic acid level and 97.5% similarity at the aminoacid sequence level compared to the previously characterized GFLV‐F13 French isolate. This paper is the first report on molecular variability of GFLV in Tunisia.
First report ofPythium diclinumin Morocco
Authors: El Androusse A. , El Aissami A. , Rahouti M. , Lahlou H. , Bouloud A. , Murandi F. Seigle 
Published: October 2005

Pythium diclinumwas isolated from a reservoir near the city of Rabat (Morocco). This is the first report of its presence in this country. Taxonomic and morphological details of the fungus are presented. The isolate grew on potato carrot agar (PCA) containing various concentrations of NaCl, up to 700 mm. Pathogenicity of the Moroccan isolate was demonstratedin vitroon lucerne seeds and seedlings.
Ecological stoichiometry in freshwater benthic ecosystems: an introduction
Authors: FROST PAUL C. , CROSS WYATT F. , BENSTEAD JONATHAN P. 
Published: October 2005

Summary1. Ecological stoichiometry is a conceptual framework that considers how the balance of energy and elements affects and is affected by organisms in the environment. This perspective has seen recent development primarily in marine and freshwater pelagic ecosystems but its widescale application to freshwater benthic ecosystems remains limited.2. This paper briefly introduces the concept of ecological stoichiometry, its potential application to freshwater benthic ecosystems, and it provides an overview of a series of papers that use a stoichiometric approach to illustrate the utility of this concept for studying a range of central questions about benthic ecosystems.3. Papers in this issue include a detailed description of the elemental composition of stream benthic invertebrates, an analysis of the algal content of and its effects on C : P stoichiometry of periphyton, two reports exploring the stoichiometry of stromatolites and their snail consumers in a stream fed by thermal springs, an examination of the stoichiometric effects on stream periphyton and macroinvertebrates of slight nutrient enrichment resulting from treated sewage effluents, a study of nutrient release ratios and their control from crayfish and snails, a paper addressing the stoichiometric effects on fish and plankton that result from benthic food subsidies to fish, a study of the stoichiometry of tree leaves and litter and floodplain arthropods in the riparian zone of the Rio Grande, and a synthesis examining the current state and future potential of benthic stoichiometry.4. The insights from these and other studies suggest that ecological stoichiometry has great potential to guide scientific thought and resolve long‐standing problems in ecology. Increasing use of this stoichiometric perspective should thus lead to a deeper understanding of important ecological processes in freshwater benthic ecosystems.
Diet quality affects egg size and number but does not reduce maternal antibody transmission in Japanese quailCoturnix japonica
Authors: GRINDSTAFF JENNIFER L. , DEMAS GREGORY E. , KETTERSON ELLEN D. 
Published: October 2005

SummaryThe ability to resist infection is an important component of survival and lifetime reproductive success. Mounting and maintaining an immunological defence is assumed to be energetically costly and nutritional resources expended on immune function may induce trade‐offs with other energetically expensive functions, including reproduction. Resource limitation may even have transgenerational effects on immune function during reproduction because mothers are the primary source of humoral immunity in young vertebrates.To determine whether protein restriction affects humoral immunity, either within or across generations, we fed adult Japanese quailCoturnix japonicaisocaloric diets containing either the recommended protein content for reproducing adults (20%), or a low protein diet (12%).Females fed the low protein diet weighed less than control females and produced fewer eggs that were smaller in size. However, dietary treatment did not affect the antibody response to a novel antigen (SRBCs) or immunoglobulin concentration (IgG = IgY) in either females or their eggs.This suggests that the magnitude of the humoral immune response is either not constrained by protein availability or that birds can compensate for low dietary protein intake when fedad libitum. Maternal protein reserves may be catabolized to support egg production and antibody formation under protein restriction such that only very severe malnutrition would affect immune function. Future work should address whether other resources mediate the trade‐off between immunity and reproduction or whether other components of the immune response are impacted by resource limitation.
Significance of the dorsal zigzag pattern of Vipera latastei gaditana against avian predators
Authors: NISKANEN MARTTI , MAPPES JOHANNA 
Published: October 2005

Summary

Aposematism is an antipredatory strategy in which prey animals conspicuously signal their noxiousness to potential predators. This successful strategy is based on avoidance learning of predators.
Most species in the viperid genus Vipera have a characteristic dorsal zigzag pattern. It has previously been suggested that the dorsal zigzag pattern of Vipera berus (the adder) has a cryptic function and thus makes the snake less conspicuous to avian predators. However, a recent experiment suggested that the pattern may function as an aposematic signal rather than being cryptic, and therefore induces active avoidance in avian predators.
We conducted a field experiment in Doñana national park in Spain, testing whether the zigzag pattern gives survival value to Vipera latastei gaditana against avian predators. We used two sizes of plasticine models with a zigzag pattern vs. without a zigzag pattern to record attacks by avian predators. The background was controlled (white vs. natural) to exclude the possibility that one morph would be more cryptic to predators than the other one. We also tested size‐dependent mortality against the signalling and nonsignalling snakes as aposematic signal is expected to enhance the survival of the aposematic species in a size‐dependent manner.
Predation pressure against snakes was severe, and on average 39% of models were attacked. Coloration did not enhance the survival of juvenile‐sized zigzag‐patterned snakes, but significantly increased the survival of adult‐sized zigzag‐patterned snakes on both backgrounds.
Our results provide further support for the aposematism hypothesis of zigzag‐patterned noxious snakes, although the advantage due to disruptive coloration is not mutually exclusive.
Formulating a general statistical model for Betula spp. invasion of lowland heath ecosystems
Authors: MANNING P. , PUTWAIN P. D. , WEBB N. R. 
Published: October 2005

Summary
Numerous studies describe thresholds at which transitions between alternate ecosystem states occur but few quantitatively delimit these conditions and present them in simple frameworks that are of use in ecosystem management. Previous research on heathland ecosystems has provided a site‐specific statistical model that describes the determinants of the threshold point in heath–scrub vegetation transition, but the wider applicability, and thus utility, of this model was unknown.
Multi‐site experimental manipulations were conducted to assess whether a consistent set of factors limited the recruitment of Betula species into heathland vegetation. Data were pooled and used to fit a single general statistical model. The applicability of this model to a wider range of environments was tested using two independent data sets.
The identity of the factors controlling Betula colonization, which include Betula seed bank density, phosphorus (P) availability and disturbance effects, were broadly similar between sites, but the strength of their effect varied widely.
The general model (explained deviance 59·8%) described Betula seedling densities as a function of biomass and necromass density, vegetation height, Betula seed bank density, P availability and soil water content. These relationships were complex, with numerous interaction and polynomial terms.
Although the model was derived from data from a single community type it was reasonably accurate in the prediction of seedling densities over a wider range of heath conditions. However, data capable of validating predictions of high seedling densities were not available.
Synthesis and applications. The apparent success of the general statistical model suggests that an approach incorporating multi‐site experiments and statistical modelling can facilitate our understanding of ecosystem state transitions and inform the management of invasive species. By describing Betula invasion as a function of variables that are simple, general descriptions of the environment, the model can potentially inform management in a wide range of conditions. The results suggest that heaths close to seed sources and in the degenerate state of the dwarf shrub cycle are the most vulnerable to invasion, and management should target such sites as a priority. At regional scales, these conditions are probably most common in high soil phosphorus sorption capacity areas, where management should be prioritized.