bluuebunny/crossref_metadata_2025_split huggingface dataset:
A graph-theoretic approach to testing associations between disparate sources of functional genomics data
Authors: Balasubramanian Raji , LaFramboise Thomas , Scholtens Denise , Gentleman Robert 
Published: July 2004

Abstract
Motivation: The last few years have seen the advent of high-throughput technologies to analyze various properties of the transcriptome and proteome of several organisms. The congruency of these different data sources, or lack thereof, can shed light on the mechanisms that govern cellular function. A central challenge for bioinformatics research is to develop a unified framework for combining the multiple sources of functional genomics information and testing associations between them, thus obtaining a robust and integrated view of the underlying biology.
Results: We present a graph-theoretic approach to test the significance of the association between multiple disparate sources of functional genomics data by proposing two statistical tests, namely edge permutation and node label permutation tests. We demonstrate the use of the proposed tests by finding significant association between a Gene Ontology-derived predictome and data obtained from mRNA expression and phenotypic experiments for Saccharomyces cerevisiae. Moreover, we employ the graph-theoretic framework to recast a surprising discrepancy presented elsewhere between gene expression and knockout phenotype, using expression data from a different set of experiments.
Availability: An R software package, GraphAT, containing the data and statistical procedures is available from Bioconductor: http://www.bioconductor.org
Reducing storage requirements for biological sequence comparison
Authors: Roberts Michael , Hayes Wayne , Hunt Brian R. , Mount Stephen M. , Yorke James A. 
Published: July 2004

Abstract
Motivation: Comparison of nucleic acid and protein sequences is a fundamental tool of modern bioinformatics. A dominant method of such string matching is the ‘seed-and-extend’ approach, in which occurrences of short subsequences called ‘seeds’ are used to search for potentially longer matches in a large database of sequences. Each such potential match is then checked to see if it extends beyond the seed. To be effective, the seed-and-extend approach needs to catalogue seeds from virtually every substring in the database of search strings. Projects such as mammalian genome assemblies and large-scale protein matching, however, have such large sequence databases that the resulting list of seeds cannot be stored in RAM on a single computer. This significantly slows the matching process.
Results: We present a simple and elegant method in which only a small fraction of seeds, called ‘minimizers’, needs to be stored. Using minimizers can speed up string-matching computations by a large factor while missing only a small fraction of the matches found using all seeds.
Extracting gene pathway relations using a hybrid grammar: the Arizona Relation Parser
Authors: McDonald Daniel M. , Chen Hsinchun , Su Hua , Marshall Byron B. 
Published: July 2004

Abstract
Motivation: Text-mining research in the biomedical domain has been motivated by the rapid growth of new research findings. Improving the accessibility of findings has potential to speed hypothesis generation.
Results: We present the Arizona Relation Parser that differs from other parsers in its use of a broad coverage syntax-semantic hybrid grammar. While syntax grammars have generally been tested over more documents, semantic grammars have outperformed them in precision and recall. We combined access to syntax and semantic information from a single grammar. The parser was trained using 40 PubMed abstracts and then tested using 100 unseen abstracts, half for precision and half for recall. Expert evaluation showed that the parser extracted biologically relevant relations with 89% precision. Recall of expert identified relations with semantic filtering was 35 and 61% before semantic filtering. Such results approach the higher-performing semantic parsers. However, the AZ parser was tested over a greater variety of writing styles and semantic content.
Availability: Relations extracted from over 600 000 PubMed abstracts are available for retrieval and visualization at http://econport.arizona.edu:8080/NetVis/index.html
CRH_Server: an online comparative and radiation hybrid mapping server for the canine genome
Authors: Hitte Christophe , Derrien Thomas , André Catherine , Ostrander Elaine A. , Galibert Francis 
Published: July 2004

Abstract
Summary: CRH_Server is an on line Comparative and Radiation Hybrid mapping Server dedicated to canine genomics. CRH_Server allows users to compute their own RH data using the current canine RH map, and allows comparative dog/human mapping analyses. Finally, it suggests multiple options for storage and queries of the dog RH database.
Availability: http://idefix.univ-rennes1.fr:8080/Dogs/rh-server.html
Supplementary information: All information is available at http://idefix.univ-rennes1.fr:8080/Dogs/help_rh-server.html
Mining HIV protease cleavage data using genetic programming with a sum-product function
Authors: Yang Zheng Rong , Dalby Andrew R. , Qiu Jing 
Published: July 2004

Abstract
Motivation: In order to design effective HIV inhibitors, studying and understanding the mechanism of HIV protease cleavage specification is critical. Various methods have been developed to explore the specificity of HIV protease cleavage activity. However, success in both extracting discriminant rules and maintaining high prediction accuracy is still challenging. The earlier study had employed genetic programming with a min–max scoring function to extract discriminant rules with success. However, the decision will finally be degenerated to one residue making further improvement of the prediction accuracy difficult. The challenge of revising the min–max scoring function so as to improve the prediction accuracy motivated this study.
Results: This paper has designed a new scoring function called a sum–product function for extracting HIV protease cleavage discriminant rules using genetic programming methods. The experiments show that the new scoring function is superior to the min–max scoring function.
Availability: The software package can be obtained by request to Dr Zheng Rong Yang.
Dimension reduction methods for microarrays with application to censored survival data
Authors: Li Lexin , Li Hongzhe 
Published: July 2004

Abstract
Motivation: Recent research has shown that gene expression profiles can potentially be used for predicting various clinical phenotypes, such as tumor class, drug response and survival time. While there has been extensive studies on tumor classification, there has been less emphasis on other phenotypic features, in particular, patient survival time or time to cancer recurrence, which are subject to right censoring. We consider in this paper an analysis of censored survival time based on microarray gene expression profiles.
Results: We propose a dimension reduction strategy, which combines principal components analysis and sliced inverse regression, to identify linear combinations of genes, that both account for the variability in the gene expression levels and preserve the phenotypic information. The extracted gene combinations are then employed as covariates in a predictive survival model formulation. We apply the proposed method to a large diffuse large-B-cell lymphoma dataset, which consists of 240 patients and 7399 genes, and build a Cox proportional hazards model based on the derived gene expression components. The proposed method is shown to provide a good predictive performance for patient survival, as demonstrated by both the significant survival difference between the predicted risk groups and the receiver operator characteristics analysis.
Availability: R programs are available upon request from the authors.
Supplementary information: http://dna.ucdavis.edu/~hli/bioinfo-surv-supp.pdf.
Limited agreement among three global gene expression methods highlights the requirement for non-global validation
Authors: Haverty Peter M. , Hsiao Li-Li , Gullans Steven R. , Hansen Ulla , Weng Zhiping 
Published: July 2004

Abstract
Motivation: DNA microarrays have revolutionized biological research, but their reliability and accuracy have not been extensively evaluated. Thorough testing of microarrays through comparison to dissimilar gene expression methods is necessary in order to determine their accuracy.
Results: We have systematically compared three global gene expression methods on all available histologically normal samples from five human organ types. The data included 25 Affymetrix high-density oligonucleotide array experiments, 23 expressed sequence tag based expression (EBE) experiments and 5 SAGE experiments. The reported gene-by-gene expression patterns showed a wide range of correlations between pairs of methods. This level of agreement was sufficient for accurate clustering of datasets from the same tissue and dissimilar methods, but highlights the need for thorough validation of individual gene expression measurements by alternate, non-global methods. Furthermore, analyses of mRNA abundance distributions indicate limitations in the EBE and SAGE methods at both high- and low-expression levels.
CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data
Authors: Hallin Peter F. , Ussery David W. 
Published: July 2004

Abstract
Summary: Currently, new bacterial genomes are being published on a monthly basis. With the growing amount of genome sequence data, there is a demand for a flexible and easy-to-maintain structure for storing sequence data and results from bioinformatic analysis. More than 150 sequenced bacterial genomes are now available, and comparisons of properties for taxonomically similar organisms are not readily available to many biologists. In addition to the most basic information, such as AT content, chromosome length, tRNA count and rRNA count, a large number of more complex calculations are needed to perform detailed comparative genomics. DNA structural calculations like curvature and stacking energy, DNA compositions like base skews, oligo skews and repeats at the local and global level are just a few of the analysis that are presented on the CBS Genome Atlas Web page. Complex analysis, changing methods and frequent addition of new models are factors that require a dynamic database layout. Using basic tools like the GNU Make system, csh, Perl and MySQL, we have created a flexible database environment for storing and maintaining such results for a collection of complete microbial genomes. Currently, these results counts to more than 220 pieces of information. The backbone of this solution consists of a program package written in Perl, which enables administrators to synchronize and update the database content. The MySQL database has been connected to the CBS web-server via PHP4, to present a dynamic web content for users outside the center. This solution is tightly fitted to existing server infrastructure and the solutions proposed here can perhaps serve as a template for other research groups to solve database issues.
Availability: A web based user interface which is dynamically linked to the Genome Atlas Database can be accessed via www.cbs.dtu.dk/services/GenomeAtlas/
Supplementary information: This paper has a supplemental information page which links to the examples presented: www.cbs.dtu.dk/services/GenomeAtlas/suppl/bioinfdatabase
Interactions between FGF and Wnt signals and Tbx3 gene expression in mammary gland initiation in mouse embryos
Authors: Eblaghie Maxwell C. , Song Soo‐Jin , Kim Jae‐Young , Akita Keiichi , Tickle Cheryll , Jung Han‐Sung 
Published: July 2004

AbstractInteractions between Wnts, Fgfs and Tbx genes are involved in limb initiation and the same gene families have been implicated in mammary gland development. Here we explore how these genes act together in mammary gland initiation. We compared expression of Tbx3, the gene associated with the human condition ulnar–mammary syndrome, expression of the gene encoding the dual‐specificity MAPK phosphatase Pyst1/MKP3, which is an early response to FGFR1 signalling (as judged by sensitivity to the SU5402 inhibitor), and expression of Lef1, encoding a transcription factor mediating Wnt signalling and the earliest gene so far known to be expressed in mammary gland development. We found that Tbx3 is expressed earlier than Lef1 and that Pyst1 is also expressed early but only transiently. Patterns of expression of Tbx3, Pyst1 and Lef1 in different glands suggest that the order of mammary gland initiation is 3, 4, 1, 2 and 5. Consistent with expression of Pyst1 in the mammary gland, we detected expression of Fgfr1b, Fgf8 and Fgf9 in both surface ectoderm and mammary bud epithelium, and Fgf4 and Fgf17 in mammary bud epithelium. Beads soaked in FGF‐8 applied to the flank of mouse embryos, at a stage just prior to mammary bud initiation, induce expression of Pyst1 and Lef1 and maintain Tbx3 expression in flank tissue surrounding the bead. Grafting beads soaked in the FGFR1 inhibitor, SU5402, abolishes Tbx3, Pyst1 and Lef1 expression, supporting the idea that FGFR1 signalling is required for early mammary gland initiation. We also showed that blocking Wnt signalling abolishes Tbx3 expression but not Pyst1 expression. These data, taken together with previous findings, suggest a model in which Tbx3 expression is induced and maintained in early gland initiation by both Wnt and Fgf signalling through FGFR1.
The appearance and distribution of mature T and B cells in the developing immune tissues of the stripe‐faced dunnart (Sminthopsis macroura)
Authors: Old J. M. , Selwood L. , Deane E. M. 
Published: July 2004

AbstractThis paper describes the initial appearance and distribution of mature T and B cells in the developing immune tissues of the stripe‐faced dunnart (Sminthopsis macroura) based on the use of species cross‐reactive antibodies to the lymphocyte cell surface markers CD3, CD5 and CD79b. At birth no mature T or B cells were detected in the liver or bone marrow using anti‐CD3, anti‐CD5 or anti‐CD79b antibodies. T cells were detected in the thymus with anti‐CD3 by day 12 and anti‐CD5 by day 50 postpartum, and T cells in the spleen were detected by day 43 and day 80 postpartum using anti‐CD3 and anti‐CD5, respectively. B cells were observed in the dunnart spleen by 43 days after birth. CD3‐ and CD79b‐positive cells were detected in the lymph nodes by 50 days and CD5 by day 15 after birth, and in the gut‐associated lymphoid tissues by day 50 and anti‐CD5 by day 57 postpartum. The development and distribution of T and B cells in the immune tissues of dunnart pouch young is similar to that described in other marsupial species. Low numbers or absence of mature lymphocytes in immune tissues of early pouch young dunnarts further support the proposition that young marsupials are reliant on non‐specific defence strategies and/or maternal strategies for a significant period of their time of development in the pouch.
Morphological study of the perireticular nucleus in human fetal brains
Authors: Tulay Cumhur Murat , Elevli Levent , Duman Uğur , Sarımehmetoğlu Ayşe , Çavdar Safiye 
Published: July 2004

AbstractThe perireticular nucleus consists of scattered neurons that are located in the internal capsule. The presence of perireticular neurons in the rat, ferret, cat and human has been described previously. Evidence suggests that the perireticular neurons in various species decrease in number with increasing gestation, but in humans this finding has not been supported by quantitative data. This study aimed to investigate (1) the morphology of the human fetal perireticular neurons, (2) the average number of perireticular neurons within the anterior and posterior crus of the internal capsule per unit area, and (3) the magnitude and the stage of neuronal loss in the human perireticular nucleus subsequent to maturation. Nissl‐stained sections of the internal capsule of human fetal brains of 24, 26.5, 32, 35, 37 and 39 weeks of gestation showed a number of clearly distinguishable large perireticular and small microglia cells. A regular increase of both perireticular and microglial cells was observed up to 32 weeks of gestation, after which a dramatic reduction in the number of both perireticular and microglia cells was observed. The average number of perireticular and the microglia cells per unit area, located within the posterior crus, was more than in the anterior crus of the internal capsule. In the adult, no perireticular neurons were detected within the internal capsule. The results show that perireticular neurons are not restricted to the region lateral to the thalamus and medial to the globus pallidus (posterior crus) but are also present at the region lateral to the caudate nucleus and medial to the globus pallidus (anterior crus).
Connections between the facial, vestibular and cochlear nerve bundles within the internal auditory canal
Authors: Özdoğmuş Ömer , Sezen Ozan , Kubilay Utku , Saka Erdinç , Duman Uğur , Şan Tangül , Çavdar Safiye 
Published: July 2004

AbstractThe vestibular, cochlear and facial nerves have a common course in the internal auditory canal (IAC). In this study we investigated the average number of nerve fibres, the average cross‐sectional areas of the nerves and nerve fibres, and the apparent connections between the facial, cochlear and vestibular nerve bundles within the IAC, using light and scanning electron microscopy. The anatomical localization of the nerves within the IAC was not straightforward. The general course showed that the nerves rotated anticlockwise in the right ear from the inner ear end towards the brainstem end and vice versa for the left ear. The average number of fibres forming vestibular, cochlear, and facial nerves was not constant during their courses within the IAC. The superior and the inferior vestibular nerves showed an increase in the number of nerve fibres from the inner ear end towards the brainstem end of the IAC, whereas the facial and the cochlear nerves showed a reduction in the number of fibres. This suggests that some of the superior and inferior vestibular nerve bundles may receive fibres from the facial and/or cochlear nerves. Scanning electron microscopic evaluations showed superior vestibular–facial and inferior vestibular–cochlear connections within the IAC, but no facial–cochlear connections were observed. Connections between the nerves of the IAC can explain the unexpected vestibular disturbances in facial paralysis or persistence of tinnitus after cochlear neurectomy in intractable tinnitus cases. The present study offers morphometric and scanning electron microscopic data on the fibre connections of the nerves of the IAC.
Distribution patterns of immunocompetent cells in the pregnant mouse uteri carrying allogeneic mouse and xenogeneic vole embryos
Authors: Widayati Diah Tri , Ohmori Yasushige , Fukuta Katsuhiro 
Published: July 2004

AbstractMouse and vole embryos were allogeneically and xenogeneically transferred into pseudopregnant CD‐1 and immunodeficient (scid) female mice, and we investigated the distribution of immunocompetent cells, uterine natural killer (uNK) cells, mast cells and macrophages, in the implantation sites on days 6, 7 and 8 of gestation. The survival rate of the vole embryos decreased gradually with increased gestation, but the rate was higher in thesciduteri than in the CD‐1 mice. The number of uNK cells increased markedly at the mesometrial triangle and the outer decidual area in the CD‐1 uteri containing vole embryos; by contrast,sciduteri having vole embryos showed almost the same number as those having mouse embryos. Mast cells were present in large numbers at the myometrium, but rarely in the decidua in all types of pregnant uteri. Cells at the myometrium were more numerous in xenogeneic than in allogeneic transfer. Many mast cells appeared in the inner decidua where xenogeneically transferred vole embryos were dead and aborted. Macrophages were present in the outer decidua and myometria in all types of pregnant uteri, and their distribution pattern did not change even in aborted uterine sites. These results suggest: (1) the response of macrophages to dead embryos is completely inhibited, (2) uNK cells and mast cells increase near dead and aborted embryos, and (3) the increment in uNK cells responding to xenogeneic embryos is suppressed inscidmice, and the suppression may contribute partly to survival of the embryos.
The development and distribution of the interstitial cells of Cajal in the intestine of the equine fetus and neonate
Authors: Fintl C. , Pearson G. T. , Ricketts S. W. , Mayhew I. G. , Hudson N. P. H. 
Published: July 2004

AbstractThis study set out to determine the pattern of development and distribution of the interstitial cells of Cajal (ICC) in the intestinal tract of the equine fetus and neonate. Intestinal tissue samples from 12 naturally aborted equine fetuses and three euthanized neonates were collected and fixed in formalin prior to applying standard immunohistochemical labelling techniques targeting the c‐Kit protein of the ICC. At 6 months of gestation, a network of ICC was present in the myenteric plexus region of both the small and the large intestine. ICC were also present within the circular muscle layer. In the large intestine, a proximal to distal gradient of distribution was evident, with few ICC observed in the more distal parts of the large intestine in the younger fetuses compared with the near‐term animals. A transmural gradient of distribution was also evident within the large intestine, with the most luminal part of the muscularis externa being the last area to be colonized by ICC. This region did not appear fully developed until the early neonatal period. An increased density of ICC was noted throughout the large intestine in the regions of the taenial bands in all animals. This study is the first to describe ICC development and distribution in the equine fetus and neonate.
Development of a new analytical electron microscopy technique to quantify the chemistry of planar defects and to measure accurately solute segregation to grain boundaries
Authors: WALTHER T. 
Published: July 2004

SummaryA new technique of analytical transmission electron microscopy called ConceptEM has been developed for determining highly accurately small amounts of solute or dopant atoms incorporated into well‐defined planar defects such as stacking faults, grain boundaries or interfaces. The method is based on recording series of analytical spectra taken with different electron beam diameters on the same position centred above a defect that is orientated either edge‐on or slightly inclined with respect to the electron beam. It can be applied to energy‐dispersive X‐ray spectroscopy or electron energy‐loss spectroscopy and necessitates only a nano‐probe modus but no scanning unit. Reliability and accuracy have been tested numerically under various conditions using simulations for a specific geometry, as a function of specimen thickness, material, acceleration voltage, collection angle, random beam displacements and solid solubility. The accuracy has been found to be substantially better (by factors of 5–10) than that of any other current standard technique based on single measurements. Our calculations suggest an accuracy in the determination of the Gibbsian solute excess at a special grain boundary down to ±1% of a monolayer, i.e. around ±0.1 atoms nm−2 under typical experimental conditions, with a maximum error about twice as large. The parameter limiting a straightforward analysis is found to be the solid solubility, which itself, however, can be measured accurately by the technique so that it can be taken into account quantitatively and the above‐stated precision is retained.