bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unique Tissue‐Specific Cell Cycle in Physcomitrella
Authors: Schween G. , Gorr G. , Hohe A. , Reski R. 
Published: March 2003

Abstract: The moss Physcomitrella patens (Hedw.) B.S.G. is a novel tool in plant functional genomics as it has an inimitable high gene targeting efficiency facilitating the establishment of gene/function relationships.Here we report, based on flow cytrometric (FCM) data, that the basic nuclear DNA content per cell of Physcomitrella is 0.53 pg, equating to a genome size of 1 C = 511 Mbp. Furthermore, we describe a unique tissue‐specific cell cycle change in this plant. Young plants consisting of only one cell type (chloronema) displayed one single peak of fluorescence in FCM analyses. As soon as the second cell type (caulonema) developed from chloronema, a second peak of fluorescence at half the intensity of the previous one became detectable, indicating that caulonema cells were predominantly at the G1/S transition, whereas chloronema cells were mainly accumulating at the G2/M transition. This conclusion was validated by further evidence: i) The addition of ammonium tartrate arrested Physcomitrella in the chloronema state and in G2/M. ii) Two different developmental mutants, known to be arrested in the chloronema/caulonema transition, remained in G2/M, regardless of age and treatment. iii) The addition of auxin or cytokinin induced the formation of caulonema, as well as decreasing the amount of cells in G2/M phase. Additionally, plant growth regulators promoted endopolyploidisation.Thus, cell cycle and cell differentiation are closely linked in Physcomitrella and effects of plant hormones and environmental factors on both processes can be analysed in a straight forward way. We speculate that this unique tissue‐specific cell cycle arrest may be the reason for the uniquely high rate of homologous recombination found in the Physcomitrella nuclear DNA.
Engene: the processing and exploratory analysis of gene expression data
Authors: García de la Nava Jorge , Santaella Daniel Franco , Alba Jesús Cuenca , Carazo José María , Trelles Oswaldo , Pascual-Montano Alberto 
Published: March 2003

Abstract
Summary: Engene is a versatile, and platform-independent web tool for exploratory analysis of gene expression data that aims at storing, visualizing and processing large sets of gene expression patterns.
Availability: Access to engene is available on request at http://www.engene.cnb.uam.es
Contact: pascual@cnb.uam.es
* To whom correspondence should be addressed.
The Z curve database: a graphic representation of genome sequences
Authors: Zhang Chun-Ting , Zhang Ren , Ou Hong-Yu 
Published: March 2003

Abstract
Motivation: Genome projects for many prokaryotic and eukaryotic species have been completed and more new genome projects are being underway currently. The availability of a large number of genomic sequences for researchers creates a need to find graphic tools to study genomes in a perceivable form. The Z curve is one of such tools available for visualizing genomes. The Z curve is a unique three-dimensional curve representation for a given DNA sequence in the sense that each can be uniquely reconstructed given the other. The Z curve database for more than 1000 genomes have been established here.
Results: The database contains the Z curves for archaea, bacteria, eukaryota, organelles, phages, plasmids, viroids and viruses, whose genomic sequences are currently available. All the 3-dimensional Z curves and their three component curves are stored in the database. The applications of the Z curve database on comparative genomics, gene prediction, computation of G+C content with a windowless technique, prediction of replication origins and terminations of bacterial and archaeal genomes and study of local deviations from the Chargaff Parity Rule 2 etc. are presented in detail. The Z curve database reported here is a treasure trove in which biologists could find useful biological knowledge.
Availability: The Z curve database is freely available at the website: http://tubic.tju.edu.cn/zcurve/
Contact: ctzhang@tju.edu.cn
* To whom correspondence should be addressed.
DigiNorthern, digital expression analysis of query genes based on ESTs
Authors: Wang Jianxin , Liang Ping 
Published: March 2003

Abstract
Summary: DigiNorthern (DN) is a web-based tool for virtually displaying expression profiles of query genes based on EST sequences. Two utilities are available: DN1 takes one query gene and quantitatively display its expression levels in tissues/organs that express the gene with comparison between normal and neoplastic status of each tissue; DN2 takes two sequences as query genes and compares their expression profiles side by side.
Availability: DN is currently available for analyses of human and mouse genes and is accessible at http://falcon.roswellpark.org/DN. Options for other species may become available in future depending on user’s request and EST data availability.
Contact: ping.liang@roswellpark.org
* To whom correspondence should be addressed.
Mapping multiple co-sequenced T-DNA integration sites
within the Arabidopsis genome
Authors: Presting Gernot G. 
Published: March 2003

Abstract
Motivation: Insertion mutagenesis, using transgenes or endogenous transposons, is a popular method for generating null mutations (knockouts) in model organisms. Insertions are mapped to specific genes by amplifying (via TAIL-PCR) and sequencing genomic regions flanking the inserted DNA. The presence of multiple TAIL-PCR templates in one sequencing reaction results in chimeric sequence of intermittently low quality. Standard processing of this sequence by applying Phred quality requirements results in loss of informative sequence, whereas not trimming low-quality sequence causes inclusion of low-complexity homopolymers from the ends of sequence runs. Accurate mapping of the flanking sequences is complicated by the presence of gene families.
Results: Methods for extracting informative regions from sequence traces obtained by sequencing multiple TAIL-PCR fragments in a single reaction are described. The completely sequenced Arabidopsis genome was used to identify informative TAIL-PCR sequence regions. Methods were devised to define and select high quality matches and precisely map each insert to the correct genome location. These methods were used to analyze sequence of TAIL-PCR-amplified flanking regions of the inserts from individual plants in a T-DNA-mutagenized population of Arabidopsis thaliana, and are applicable to similar situations where a reference genome can be used to extract information from poor-quality sequence.
Contact: gernot@genome.clemson.edu
Supplementary information: Tables of the calculated T-DNA insertion sites and supplementary data are available at http://www.tmri.org/pages/collaborations/garlic_files/Bioinfo.html
* To whom correspondence should be addressed.
PedNavigator: a pedigree drawing servlet for large and
inbred populations
Authors: Mancosu Gianmaria , Ledda Giuseppe , Melis Paola M. 
Published: March 2003

Abstract
Summary: PedNavigator is a pedigree drawing application for large and complex pedigrees. It has been developed especially for genetic and epidemiological studies of isolated populations characterized by high inbreeding and multiple matrimonies. PedNavigator is written in Java and is intended as a server-side web application, allowing researchers to ‘walk’ through family ties by point-and-clicking on person’s symbols. The application is able to enrich the pedigree drawings with genotypic and phenotypic information taken from the underlying relational database.
Availability: Available upon request to author.
Contact: mancosu@shardna.it
* To whom correspondence should be addressed.
PCA disjoint models for multiclass cancer analysis using gene
expression data
Authors: Bicciato S. , Luchini A. , Di Bello C. 
Published: March 2003

Abstract
Motivation: Microarray expression profiling appears particularly promising for a deeper understanding of cancer biology and to identify molecular signatures supporting the histological classification schemes of neoplastic specimens. However, molecular diagnostics based on microarray data presents major challenges due to the overwhelming number of variables and the complex, multiclass nature of tumor samples. Thus, the development of marker selection methods, that allow the identification of those genes that are most likely to confer high classification accuracy of multiple tumor types, and of multiclass classification schemes is of paramount importance.
Results: A computational procedure for marker identification and for classification of multiclass gene expression data through the application of disjoint principal component models is described. The identified features represent a rational and dimensionally reduced base for understanding the basic biology of diseases, defining targets for therapeutic intervention, and developing diagnostic tools for the identification and classification of multiple pathological states. The method has been tested on different microarray data sets obtained from various human tumor samples. The results demonstrate that this procedure allows the identification of specific phenotype markers and can classify previously unseen instances in the presence of multiple classes.
Availability: Matlab source codes are available from the authors.
Contact: silvio.bicciato@unipd.it
Supplementary information: http://www.dpci.unipd.it/PersPages/SBicciato/SIMCArray.html
* To whom correspondence should be addressed.
ASAP: automated sequence annotation pipeline for
web-based updating of sequence information with a local dynamic
database
Authors: Kossenkov Andrew , Manion Frank J. , Korotkov Eugene , Moloshok Thomas D. , Ochs Michael F. 
Published: March 2003

Abstract
Summary: The automated sequence annotation pipeline (ASAP) is designed to ease routine investigation of new functional annotations on unknown sequences, such as expressed sequence tags (ESTs), through querying of web-accessible resources and maintenance of a local database. The system allows easy use of the output from one search as the input for a new search, as well as the filtering of results. The database is used to store formats and parameters and information for parsing data from web sites. The database permits easy updating of format information should a site modify the format of a query or of a returned web page.
Availability: Source code is available under the GNU public license at http://bioinformatics.fccc.edu/
Contact: av_kossenkov@fccc.edufj_manion@fccc.edukatrin22@mtu-net.rutd_moloshok@fccc.edum_ochs@fccc.edu
* To whom correspondence should be addressed.
Automatic analysis of DNA microarray images using mathematical morphology
Authors: Angulo Jesús , Serra Jean 
Published: March 2003

Abstract
Motivation: DNA microarrays are an experimental technology which consists in arrays of thousands of discrete DNA sequences that are printed on glass microscope slides. Image analysis is an important aspect of microarray experiments. The aim of this step is to reduce an image of spots into a table with a measure of the intensity for each spot. Efficient, accurate and automatic analysis of DNA spot images is essential in order to use this technology in laboratory routines.
Results: We present an automatic non-supervised set of algorithms for a fast and accurate spot data extraction from DNA microarrays using morphological operators which are robust to both intensity variation and artefacts. The approach can be summarised as follows. Initially, a gridding algorithm yields the automatic segmentation of the microarray image into spot quadrants which are later individually analysed. Then the analysis of the spot quadrant images is achieved in five steps. First, a pre-quantification, the spot size distribution law is calculated. Second, the background noise extraction is performed using a morphological filtering by area. Third, an orthogonal grid provides the first approach to the spot locus. Fourth, the spot segmentation or spot boundaries definition is carried out using the watershed transformation. And fifth, the outline of detected spots allows the signal quantification or spot intensities extraction; in this respect, a noise model has been investigated. The performance of the algorithm has been compared with two packages: ScanAlyze and Genepix, showing its robustness and precision.
Availability: A prototype system integrated in PDI32 (an image processing software for Windows) may be obtained from the authors on request.
Contact: angulo,serra@cmm.ensmp.fr
Supplementary Information: http://cmm.ensmp.fr/~angulo/
* To whom correspondence should be addressed.
GPCR-GRAPA-LIB—a refined library of hidden Markov Models
for annotating GPCRs
Authors: Shigeta Ron , Cline Melissa , Liu Guoying , Siani-Rose Michael A. 
Published: March 2003

Abstract
Summary: GPCR-GRAPA-LIB is a library of HMMs describing G protein coupled receptor families. These families are initially defined by class of receptor ligand, with divergent families divided into subfamilies using phylogenic analysis and knowledge of GPCR function. Protein sequences are applied to the models with the GRAPA curve-based selection criteria. RefSeq sequences for Homo sapiens, Drosophila melanogaster, and Caenorhabditis elegans have been annotated using this approach.
Availability: The HMMs and sequence alignments are available at http://www.affymetrix.com/community/publications/affymetrix/index.affx. Annotation results are available at http://www.affymetrix.com/analysis/index.affx
Contact: ron_shigeta@affymetrix.com
* To whom correspondence should be addressed.
Effective dimension reduction methods for tumor classification
using gene expression data
Authors: Antoniadis A. , Lambert-Lacroix S. , Leblanc F. 
Published: March 2003

Abstract
Motivation: One particular application of microarray data, is to uncover the molecular variation among cancers. One feature of microarray studies is the fact that the number n of samples collected is relatively small compared to the number p of genes per sample which are usually in the thousands. In statistical terms this very large number of predictors compared to a small number of samples or observations makes the classification problem difficult. An efficient way to solve this problem is by using dimension reduction statistical techniques in conjunction with nonparametric discriminant procedures.
Results: We view the classification problem as a regression problem with few observations and many predictor variables. We use an adaptive dimension reduction method for generalized semi-parametric regression models that allows us to solve the‘ curse of dimensionality problem’ arising in the context of expression data. The predictive performance of the resulting classification rule is illustrated on two well know data sets in the microarray literature: the leukemia data that is known to contain classes that are easy ‘separable’ and the colon data set.
Availability: Software that implements the procedures on which this paper focus are freely available at http://www-lmc.imag.fr/SMS/software/microarrays/
Contact: anestis.antoniadis@imag.fr
* To whom correspondence should be addressed.
The estimation of relative site variability among aligned homologous
protein sequences
Authors: Horner D. S. , Pesole G. 
Published: March 2003

Abstract
Motivation: Maximum likelihood-based methods to estimate site by site substitution rate variability in aligned homologous protein sequences rely on the formulation of a phylogenetic tree and generally assume that the patterns of relative variability follow a pre-determined distribution. We present a phylogenetic tree-independent method to estimate the relative variability of individual sites within large datasets of homologous protein sequences. It is based upon two simple assumptions. Firstly that substitutions observed between two closely related sequences are likely, in general, to occur at the most variable sites. Secondly that non-conservative amino acid substitutions tend to occur at more variable sites. Our methodology makes no assumptions regarding the underlying pattern of relative variability between sites.
Results: We have compared, using data simulated under a non-gamma distributed model, the performance of this approach to that of a maximum likelihood method that assumes gamma distributed rates. At low mean rates of evolution our method inferred site by site relative substitution rates more accurately than the maximum likelihood approach in the absence of prior assumptions about the relationships between sequences. Our method does not directly account for the effects of mutational saturation, However, we have incorporated an ‘ ad-hoc’ modification that allows the accurate estimation of relative site variability in fast evolving and saturated datasets.
Availability: A script which implements the methodology described in this paper (written in Biopython) is available from dsh on request.
Contact: graziano.pesole@unimi.it
* To whom correspondence should be addressed.
The Economic and Environmental Implications of Centralized Stock Keeping
Authors: Matthews H. Scott , Hendrickson Chris T. 
Published: March 2003

SummaryRecent changes to the management of inventory and warehousing methods have created significant changes in business processes. These changes have produced economic savings to firms from reduced handling of supplies. The system‐wide impacts of this shift in methods on overall cost and the environment are still unclear, however. Reductions in inventories can provide significant environmental savings. In this article, we analyze the changes in inventory control methods and assess the environmental and cost tradeoffs between increased trucking and more efficient centralized warehouses. We consider the case of consolidating the spare‐parts inventory at U.S. Department of Defense warehouses and discuss similarities to other existing businesses. The case suggests large economic and environmental benefits due to reductions in warehousing expenses, despite higher transportation costs.
Differentiation of stress, metabolism, communication, and defense responses following transplantation
Authors: Mueller Thomas F , Ma Chunyan , Lederer James A , Perkins David L 
Published: March 2003

AbstractThe biological complexity of allograft rejection and alloantigen-independent mechanisms is poorly understood. Therefore, we analyzed four components of the biological response following transplantation by global gene analysis. A comparative and kinetic approach was used to identify gene expression profiles. Biological processes were assigned to genes displaying the largest alterations in expression. Metabolism, stress response, and cell organization were the predominant, biological processes associated with ischemia and systemic stress. Innate and adaptive immune responses induced a transcriptional shift toward defense and cell communication. The kinetic analysis showed a shift from innate toward adaptive responses in the post-transplant course.
Gap-junctional coupling between neutrophils and endothelial cells: a novel modulator of transendothelial migration
Authors: Zahler Stefan , Hoffmann Anke , Gloe Torsten , Pohl Ulrich 
Published: March 2003

Abstract
Communication between leukocytes and endothelial cells is crucial for inflammatory reactions. Paracrine cross-talk and outside-in signaling (via adhesion molecules) have been characterized as communication pathways to date. As leukocytes and endothelial cells express connexins, we considered intercellular communication via gap junctions an intriguing additional concept. We found that gap-junctional coupling between neutrophils and endothelium occurred in a time-dependent, bidirectional manner and was facilitated by adhesion. After blockade of connexins, transmigration of neutrophils through the endothelial layer was enhanced, and the barrier function of cell monolayers was reduced during transmigration. Tumor necrosis factor α decreased coupling. In the presence of connexins, transmigration of neutrophils did not alter permeability. Thus, neutrophils couple to endothelium via gap junctions, functionally modulating transmigration and leakiness. Gap-junctional coupling may be a ovel way of leukocyte-endothelial communication.
β1/β3 integrin ligation is uncoupled from ERK1/ERK2 activation in cytotoxic T lymphocytes
Authors: Puente Lawrence G , Ostergaard Hanne L 
Published: March 2003

Abstract
β3 integrins mediate fibronectin binding and enhanced activation of cytotoxic T lymphocytes (CTL). The intracellular signals initiated by β3 integrins in lymphocytes are not well characterized, but in many cell types, β1 integrin ligation activates mitogen-activated protein (MAP) kinases. In the present study, we find that fibronectin can synergize with very low levels of CD3 stimulation to activate the extracellular signal-regulated kinase (ERK)1 and ERK2 MAP kinases but that fibronectin alone induces no detectable MAP kinase activation in CTL. Surprisingly, antibodies to β1 or β3 integrins were also unable to stimulate MAP kinase activation, suggesting that although β1 integrins are capable of stimulating MAP kinase activation in other cells, they cannot do so in CTL. In CTL, phosphorylation of proline-rich tyrosine kinase 2 downstream of integrin stimulation did not result in recruitment of the adaptor protein Grb2. Additionally, we examined the role of MAP kinases in regulating integrin-mediated adhesion. Anti-CD3-triggered adhesion to fibronectin was largely insensitive to the MAP kinase kinase inhibitor PD98059. Triggered cell-spreading on fibronectin was inhibited by PD98059 but not by U0126. In summary, ligation of β3 integrin by antibodies or fibronectin or of β1 integrin by monoclonal antibodies fails to activate ERK MAP kinases, but integrin ligation synergizes with T cell receptor stimulation upstream of MAP kinases.
Characterization of promoter elements directing Mona/Gads molecular adapter expression in T and myelomonocytic cells: involvement of the AML-1 transcription factor
Authors: Guyot B , Mouchiroud G 
Published: March 2003

Abstract
Monocytic adaptor (Mona, also called Gads) is a molecular adaptor implicated in T cell activation and macrophage differentiation. The objective of this study was to identify elements regulating specific expression of Mona/Gads in human T cell and myelomonocytic cell lines. We first confirmed that the −2000 to +150 genomic region relative to the Mona gene transcription start site is sufficient to direct specific reporter gene expression in T cell lines, Jurkat, and MOLT-4 and in the immature myeloid cell lines, KG1a and RC2A. Deletion analysis and electrophoresis mobility shift assay identified several cis regulatory elements: overlapping initiator sequences, one interferon response factor-2 (IRF-2)-binding site at position −154, one GC box recognized by Sp1 and Sp3 at position −52, and two acute myeloid leukemia (AML)-1 binding sites at positions −70 and −13. Site-directed mutagenesis experiments indicated a key role of AML-1 for driving Mona expression in T cells and myeloid cells, and involvement of Sp1/Sp3 and IRF-2 transcription factors to modulate Mona expression in a cell-specific manner.