bluuebunny/crossref_metadata_2025_split huggingface dataset:
Linkage and QTL mapping for Sus scrofa chromosome 14
Authors: Dragos‐Wendrich M. , Sternstein I. , Brunsch C. , Moser G. , Bartenschlager H. , Reiner G. , Geldermann H. 
Published: December 2003

SummaryThe Sus scrofa chromosome 14 (SSC14) linkage maps, constructed using eight markers in three F2‐families based on Wild Boar (W), Meishan (M) and Pietrain (P) crosses, were similar for the different families. The detected quantitative trait loci (QTLs) explained up to 8.2% of the F2 phenotypic variance for carcass traits. They were located in the interval SW540 to SW2488 (containing the candidate loci ACTN2 and ACTA1) in the M × P and W × P families. A QTL for body weight at 35 days was mapped close to the candidate locus ACTN2 in the W × M family. In comparison with Pietrain QTL alleles, the effects of Meishan and Wild Boar alleles reduced meat content.
Linkage and QTL mapping for Sus scrofa chromosome 15
Authors: Kuryl J. , Pierzchala M. , Hojny J. , Reiner G. , Bartenschlager H. , Moser G. , Geldermann H. 
Published: December 2003

SummaryThe Sus scrofa chromosome 15 (SSC15) linkage maps were produced with six markers in three F2 families based on Wild Boar (W), Meishan (M) and Pietrain (P) crosses. The maps were similar for the different families, with a higher rate of maternal recombination than paternal only in the M × P family. Quantitative trait loci (QTLs) for carcass composition (dressing yield, lean cuts and fat depth) explained up to 9% of F2 phenotypic variance in the W × P family and mapped near the marker S0148 (0 cM). Similar QTLs for fat depth were observed in the W × M family, where a minor QTL for dressing yield was mapped in the interval EAG–SW964 (approximately at 25 cM). No SSC15 QTL was found in the M × P family.
Linkage and QTL mapping for Sus scrofa chromosome 16
Authors: Pierzchala M. , Kuryl J. , Reiner G. , Bartenschlager H. , Moser G. , Geldermann H. 
Published: December 2003

SummaryLinkage maps of Sus scrofa chromosome 16 (SSC16) were produced using five markers and three F2 families based on Wild Boar (W), Meishan (M) and Pietrain (P) crosses. The maps were similar for the different families and in agreement with published maps. Quantitative trait loci (QTLs) for fattening, growth, meat quality and stress resistance were found in the M × P and W × P families, but not in the W × M family. QTLs for fattening and growth were mapped to the proximal end of SSC16, whereas QTLs for meat quality were located centrally or distally. The QTLs explained up to 5.9% of the F2 phenotypic variance.
Linkage and QTL mapping for Sus scrofa chromosome 17
Authors: Pierzchala M. , Cieslak D. , Reiner G. , Bartenschlager H. , Moser G. , Geldermann H. 
Published: December 2003

SummaryLinkage and QTL maps of Sus scrofa chromosome 17 (SSC17) were analysed with five markers and in three F2 families based on Wild Boar (W), Meishan (M) and Pietrain (P) crosses. The maps were similar across the three families and agree well with published maps. In the M × P family, new quantitative trait loci (QTLs) for growth and fat deposition were located in the vicinity of GHRH, whereas in the W × P family one minor QTLs for daily gain was detected. No QTL was found in the W × M family.
Linkage and QTL mapping for Sus scrofa chromosome X
Authors: Cepica S. , Reiner G. , Bartenschlager H. , Moser G. , Geldermann H. 
Published: December 2003

SummaryThe Sus scrofa chromosome X (SSCX) linkage and QTL maps, based on 11 markers, were investigated in F2 families generated from Wild Boar (W), Meishan (M) and Pietrain (P) crosses. The linkage maps were similar for the three families and to the published USDA‐MARC.2 linkage map. Strongly supported quantitative trait loci (QTLs) for growth, fattening, meat quality and weight of head were mapped in the proximal part of SSCX of the M × P and W × P families, whilst QTLs for fat deposition and muscling mainly were assigned to the mid part of SSCX in the W × M and M × P families. The QTLs explained up to 13.7% of F2 phenotypic variance. Meishan QTL alleles led to increased fatness traits, while those of Pietrain tended to increased carcass and meat weights and to decreased meat quality.
Mesoscale regulation comes from the bottom‐up: intertidal interactions between consumers and upwelling
Authors: Nielsen Karina J. , Navarrete Sergio A. 
Published: December 2003

AbstractTheory suggests that variation in resource supply should propagate up trophic webs influencing plant–herbivore interactions and abundances. Community regulation models have been tested in several ecosystems, but benthic marine ecologists have largely overlooked bottom‐up factors except at the largest spatial scales. We used naturally occurring variation in nutrient supply associated with upwelling intensity (over 10s of kilometre) to test community regulation models. Higher upwelling intensity was strongly associated with increased abundance of late‐successional, corticated algae, which in turn had apparent negative effects on ephemeral algae. Corticated algae were resistant to extant levels of herbivory. As a result, corticated algae were more abundant at sites of high upwelling intensity, while ephemeral algae were more abundant at sites of low upwelling intensity. We speculate that human removal of large grazers that can feed on corticated algae may interact with natural variation in nutrient supply to shift community structure over mesoscales.
Quantifying mortality of tropical rain forest trees using high‐spatial‐resolution satellite data
Authors: Clark David B. , Castro Carlomagno Soto , Alvarado Luis Diego Alfaro , Read Jane M. 
Published: December 2003

AbstractAssessment of forest responses to climate change is severely hampered by the limited information on tree death on short temporal and broad spatial scales, particularly in tropical forests. We used 1‐m resolution panchromatic IKONOS and 0.7‐m resolution QuickBird satellite data, acquired in 2000 and 2002, respectively, to evaluate tree death rates at the La Selva Biological Station in old‐growth Tropical Wet Forest in Costa Rica, Central America. Using a calibration factor derived from ground inspection of tree deaths predicted from the images, we calculated a landscape‐scale annual exponential death rate of 2.8%. This corresponds closely to data for all canopy‐level trees in 18 forest inventory plots, each of 0.5 ha, for a mostly‐overlapping 2‐year period (2.8% per year). This study shows that high‐spatial‐resolution satellite data can now be used to measure old‐growth tropical rain forest tree death rates, suggesting many new avenues for tropical forest ecology and global change research.
Trade‐offs in community ecology: linking spatial scales and species coexistence
Authors: Kneitel Jamie M. , Chase Jonathan M. 
Published: December 2003

AbstractTrade‐offs in species performances of different ecological functions is one of the most common explanations for coexistence in communities. Despite the potential for species coexistence occurring at local or regional spatial scales, trade‐offs are typically approached at a single scale. In recent years, ecologists have increasingly provided evidence for the importance of community processes at both local and regional spatial scales. This review summarizes the theoretical predictions for the traits associated with trade‐offs under different conditions and at different spatial scales. We provide a spatial framework for understanding trade‐offs, coexistence and the supportive empirical evidence. Predictions are presented that link the patterns of diversity observed to the patterns of trade‐offs that lead to coexistence at different spatial scales. Recent evidence for the evolution of trade‐offs under different conditions is provided which explores both laboratory microcosm studies and phylogenetic tests. Examining trade‐offs within a spatial framework can provide a strong approach to understanding community structure and dynamics, while explaining patterns of species diversity.
Ecological conditions during winter predict arrival date at the breeding quarters in a trans‐Saharan migratory bird
Authors: Saino Nicola , Szép Tibor , Romano Maria , Rubolini Diego , Spina Fernando , Møller Anders Pape 
Published: December 2003

AbstractWe studied variation in arrival date to the breeding colonies in Italy of a trans‐Saharan migratory bird, the barn swallowHirundo rustica, in relation to variation in ecological conditions, as reflected by the normalized difference vegetation index (NDVI), in the winter quarters. Arrival date of old but not young individuals captured during consecutive breeding seasons was earlier after winters with favourable conditions. Change in arrival date in relation to change in NDVI was similar in the two sexes. Change in arrival date significantly and positively predicted change in breeding date. As a result of increased frequency of second broods determined by earlier arrival, the number of fledged offspring per season was larger after African winters with good in comparison to poor ecological conditions for barn swallows. This is the first study demonstrating phenotypic plasticity in migration phenology of a long‐distance migratory bird in relation to ecological conditions during wintering.
A comprehensive framework for global patterns in biodiversity
Authors: Ricklefs Robert E. 
Published: December 2003

AbstractThe present study proposes to reconcile the different spatial and temporal scales of regional species production and local constraint on species richness. Although interactions between populations rapidly achieve equilibrium and limit membership in ecological communities locally, these interactions occur over heterogeneous environments within large regions, where the populations of species are stably regulated through competition and habitat selection. Consequently, exclusion of species from a region depends on long‐term regional‐scale environmental change or evolutionary change among interacting populations, bringing species production and extinction onto the same scale and establishing a link between local and regional processes.
Annotation pattern of ESTs from Spodoptera frugiperda Sf9 cells and analysis of the ribosomal protein genes reveal insect-specific features and unexpectedly low codon usage bias
Authors: Landais I. , Ogliastro M. , Mita K. , Nohata J. , López-Ferber M. , Duonor-Cérutti M. , Shimada T. , Fournier P. , Devauchelle G. 
Published: December 2003

Abstract
Motivation: A whole set of Expressed Sequence Tags (ESTs) from the Sf9 cell line of Spodoptera frugiperda is presented here for the first time. By this way we want to identify both conserved and specific genes of this pest species. We also expect from this analysis to find a class of protein sequences providing a tool to explore genomic features and phylogeny of Lepidoptera.
Results: The ESTs display both housekeeping as well as developmentally regulated genes, and a high percentage of sequences with unknown function. Among the identified ORFs, almost all ribosomal proteins (RPs) were found with high EST redundancy and hence sequence accuracy. The codon usage found among RP genes is in average surprisingly much less biased in Lepidoptera than in other organisms. Other Spodoptera genes also displayed a low bias, suggesting a general genome expression feature in this Lepidoptera. We also found that the L35A and L36 RP sequences, respectively, display 40 and 10 amino-acid insertions, both being present only in insects. Sequence analysis suggests that they are probably not subjected to a strong selective pressure and may be good phylogenetic markers for Lepidoptera. Most interestingly, the Lepidoptera sequences of 9 RP genes displayed a specific signature different from the canonical one. We conclude that the RP family allows valuable comparative genomics and phylogeny of Lepidoptera.
Availability: All EST sequence data are available from the private ‘Spodo-Base’ upon request.
The MUSC DNA Microarray Database
Authors: Argraves Gary L. , Barth Jeremy L. , Argraves W. Scott 
Published: December 2003

Abstract
Summary: The Medical University of South Carolina (MUSC) DNA Microarray Database is a web-accessible archive of DNA microarray data. The database was developed using the DNA microarray project/data management system, μArrayDB. Annotations for each DNA microarray project and associated cRNA target information are stored in a MySQL relational database and linked to array hybridization data (raw and normalized). At the discretion of investigators, data are placed into the public domain where they can be interrogated and downloaded through a web browser. In addition to serving as an online resource of gene expression data, the MUSC DNA Microarray Database is a model for other academic DNA microarray data repositories.
Availability: Browsing and downloading of MUSC DNA Microarray Database information can be done after registration at http://proteogenomics.musc.edu/pss/home.php.
MREPATT: detection and analysis of exact consecutive repeats in genomic sequences
Authors: Roset Roman , Subirana Juan A. , Messeguer Xavier 
Published: December 2003

Abstract
We have developed a program to determine the number, length and position of exact consecutive repeats of short sequences in DNA fragments or whole genomes. The program also gives the statistical significance of results by comparing them with those expected for a random sequence generated according to a Markovian model.
Availability: MREPATT can be accessed on line at http://www.lsi.upc.es/~alggen under the RESEARCH and SEARCH links.
Efficient estimation of emission probabilities in profile hidden Markov models
Authors: Ahola Virpi , Aittokallio Tero , Uusipaikka Esa , Vihinen Mauno 
Published: December 2003

Abstract
Motivation: Profile hidden Markov models provide a sensitive method for performing sequence database search and aligning multiple sequences. One of the drawbacks of the hidden Markov model is that the conserved amino acids are not emphasized, but signal and noise are treated equally. For this reason, the number of estimated emission parameters is often enormous. Focusing the analysis on conserved residues only should increase the accuracy of sequence database search.
Results: We address this issue with a new method for efficient emission probability (EEP) estimation, in which amino acids are divided into effective and ineffective residues at each conserved alignment position. A practical study with 20 protein families demonstrated that the EEP method is capable of detecting family members from other proteins with sensitivity of 98% and specificity of 99% on the average, even if the number of free emission parameters was decreased to 15% of the original. In the database search for TIM barrel sequences, EEP recognizes the family members nearly as accurately as HMMER or Blast, but the number of false positive sequences was significantly less than that obtained with the other methods.
Availability: The algorithms written in C language are available on request from the authors.
gff2aplot: Plotting sequence comparisons
Authors: Abril Josep F. , Guigó Roderic , Wiehe Thomas 
Published: December 2003

Abstract
Summary: gff2aplot is a program to visualize the alignment of two sequences together with their annotations. Input for the program consists of single or multiple files in GFF-format which specify the alignment coordinates and annotation features of both sequences. Output is in PostScript format of any size. The features to be displayed are highly customizable to meet user specific needs. The program serves to generate print-quality images for comparative genome sequence analysis.
Availability: gff2aplot is freely available under the GNU software licence and can be downloaded from the address specified below.
Supplementary information: http://genome.imim.es/software/gfftools/GFF2APLOT.html
caCORE: A common infrastructure for cancer informatics
Authors: Covitz Peter A. , Hartel Frank , Schaefer Carl , De Coronado Sherri , Fragoso Gilberto , Sahni Himanso , Gustafson Scott , Buetow Kenneth H. 
Published: December 2003

Abstract
Motivation:Sites with substantive bioinformatics operations are challenged to build data processing and delivery infrastructure that provides reliable access and enables data integration. Locally generated data must be processed and stored such that relationships to external data sources can be presented. Consistency and comparability across data sets requires annotation with controlled vocabularies and, further, metadata standards for data representation. Programmatic access to the processed data should be supported to ensure the maximum possible value is extracted. Confronted with these challenges at the National Cancer Institute Center for Bioinformatics, we decided to develop a robust infrastructure for data management and integration that supports advanced biomedical applications.
Results: We have developed an interconnected set of software and services called caCORE. Enterprise Vocabulary Services (EVS) provide controlled vocabulary, dictionary and thesaurus services. The Cancer Data Standards Repository (caDSR) provides a metadata registry for common data elements. Cancer Bioinformatics Infrastructure Objects (caBIO) implements an object-oriented model of the biomedical domain and provides Java, Simple Object Access Protocol and HTTP–XML application programming interfaces. caCORE has been used to develop scientific applications that bring together data from distinct genomic and clinical science sources.
Availability: caCORE downloads and web interfaces can be accessed from links on the caCORE web site (http://ncicb.nci.nih.gov/core). caBIO software is distributed under an open source license that permits unrestricted academic and commercial use. Vocabulary and metadata content in the EVS and caDSR, respectively, is similarly unrestricted, and is available through web applications and FTP downloads.
Supplementary information: http://ncicb.nci.nih.gov/core/publications contains links to the caBIO 1.0 class diagram and the caCORE 1.0 Technical Guide, which provide detailed information on the present caCORE architecture, data sources and APIs. Updated information appears on a regular basis on the caCORE web site (http://ncicb.nci.nih.gov/core).
MUTAGEN: Multi-User Tool for Annotating GENomes
Authors: Brügger Kim , Redder Peter , Skovgaard Marie 
Published: December 2003

Abstract
Summary: MUTAGEN is a free prokaryotic annotation system. It offers the advantages of genome comparison, graphical sequence browsers, search facilities and open-source for user-specific adjustments. The web-interface allows several users to access the system from standard desktop computers. The Sulfolobus acidocaldarius genome, and several plasmids and viruses have so far been analysed and annotated using MUTAGEN.
Availability: MUTAGEN is released as open-source software under GPL. The code is available for download and/or contribution at http://dac.molbio.ku.dk/bioinformatics/MUTAGEN/
GoFigure: Automated Gene Ontology™ annotation
Authors: Khan Salim , Situ Gang , Decker Keith , Schmidt Carl J. 
Published: December 2003

Abstract
Summary: We have developed a web tool to predict Gene Ontology (GO) terms. The tool accepts an input DNA or protein sequence, and uses BLAST to identify homologous sequences in GO annotated databases. A graph is returned to the user via email.
Availability: The tool is freely available at: http://udgenome.ags.udel.edu/frm_go.html/
SEMEDA: ontology based semantic integration of biological databases
Authors: Köhler Jacob , Philippi Stephan , Lange Matthias 
Published: December 2003

Abstract
Motivation: Many molecular biological databases are implemented on relational Database Management Systems, which provide standard interfaces like JDBC and ODBC for data and metadata exchange. By using these interfaces, many technical problems of database integration vanish and issues related to semantics remain, e.g. the use of different terms for the same things, different names for equivalent database attributes and missing links between relevant entries in different databases.
Results: In this publication, principles and methods that were used to implement SEMEDA (Semantic Meta Database) are described. Database owners can use SEMEDA to provide semantically integrated access to their databases as well as to collaboratively edit and maintain ontologies and controlled vocabularies. Biologists can use SEMEDA to query the integrated databases in real time without having to know the structure or any technical details of the underlying databases.
Availability: SEMEDA is available at http://www-bm.ipk-gatersleben.de/semeda/. Database providers who intend to grant access to their databases via SEMEDA are encouraged to contact the authors.
Metabolic pathways in three dimensions
Authors: Rojdestvenski Igor 
Published: December 2003

Abstract
Motivation: Currently a substantial research effort is devoted to automated representation of metabolic and gene networks. Automatic visualization plays a significant role in such efforts, and becomes an important problem on its own. Graphical visualization of metabolic pathways has to be information dense and not ‘overloaded’, recognizable and unified, close to traditional and algebraically consistent. The use of three-dimensional ‘virtual reality’ visualizations may help to understand better the intricate topology of metabolic and regulatory networks.
Results: A system of visualizing metabolic networks as graphs in three-dimensional space by means of Virtual Reality Modeling Language (VRML) is presented. The system is based on an XML-compliant MNV (‘Metabolic Network Visualizer’) language, and comprises MNV language standard and parser, MNV to VRML translator, and interactive pathway constructor, all unified by the HTML graphic user interface.
Availability: The MNV can be accessed in viewer mode at http://www.patronov.net/sciencevr/mnv/indexview.html or in constructor mode at http://www.patronov.net/sciencevr/mnv/indexmake.html
Supplementary information: The figures for the paper as well as the Appendices may be found at http://www.patronov.net/sciencevr/mnv/screenshots.html
Accelerating screening of 3D protein data with a graph theoretical approach
Authors: Frömmel Cornelius , Gille Christoph , Goede Andrean , Gröpl Clemens , Hougardy Stefan , Nierhoff Till , Preißner Robert , Thimm Martin 
Published: December 2003

Abstract
Motivation: The Dictionary of Interfaces in Proteins (DIP) is a database collecting the 3D structure of interacting parts of proteins that are called patches. It serves as a repository, in which patches similar to given query patches can be found. The computation of the similarity of two patches is time consuming and traversing the entire DIP requires some hours. In this work we address the question of how the patches similar to a given query can be identified by scanning only a small part of DIP. The answer to this question requires the investigation of the distribution of the similarity of patches.
Results: The score values describing the similarity of two patches can roughly be divided into three ranges that correspond to different levels of spatial similarity. Interestingly, the two iso-score lines separating the three classes can be determined by two different approaches. Applying a concept of the theory of random graphs reveals significant structural properties of the data in DIP. These can be used to accelerate scanning the DIP for patches similar to a given query. Searches for very similar patches could be accelerated by a factor of more than 25. Patches with a medium similarity could be found 10 times faster than by brute-force search.
PRIMEX: rapid identification of oligonucleotide matches in whole genomes
Authors: Lexa Matej , Valle Giorgio 
Published: December 2003

Abstract
Summary: PRIMEX (PRImer Match EXtractor) can detect oligonucleotide sequences in whole genomes, allowing for mismatches. Using a word lookup table and server functionality, PRIMEX accepts queries from client software and returns matches rapidly. We find it faster and more sensitive than currently available tools.
Availability: Running applications and source code have been made available at http://bioinformatics.cribi.unipd.it/primex