bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hypothesis-driven approach to predict transcriptional units from gene expression data
Authors: Steinhauser Dirk , Junker Björn H. , Luedemann Alexander , Selbig Joachim , Kopka Joachim 
Published: March 2004

Abstract
Motivation: A major issue in computational biology is the reconstruction of functional relationships among genes, for example the definition of regulatory or biochemical pathways. One step towards this aim is the elucidation of transcriptional units, which are characterized by co-responding changes in mRNA expression levels. These units of genes will allow the generation of hypotheses about respective functional interrelationships. Thus, the focus of analysis currently moves from well-established functional assignment through comparison of protein and DNA sequences towards analysis of transcriptional co-response. Tools that allow deducing common control of gene expression have the potential to complement and extend routine BLAST comparisons, because gene function may be inferred from common transcriptional control.
Results: We present a co-clustering strategy of genome sequence information and gene expression data, which was applied to identify transcriptional units within diverse compendia of expression profiles. The phenomenon of prokaryotic operons was selected as an ideal test case to generate well-founded hypotheses about transcriptional units. The existence of overlapping and ambiguous operon definitions allowed the investigation of constitutive and conditional expression of transcriptional units in independent gene expression experiments of Escherichia coli. Our approach allowed identification of operons with high accuracy. Furthermore, both constitutive mRNA co-response as well as conditional differences became apparent. Thus, we were able to generate insight into the possible biological relevance of gene co-response. We conclude that the suggested strategy will be amenable in general to the identification of transcriptional units beyond the chosen example of E.coli operons.
Availability: The analyses of E.coli transcript data presented here are available upon request or at http://csbdb.mpimp-golm.mpg.de/
A tool for gene expression based PubMed search through combining data sources
Authors: Korotkiy Maksym , Middelburg Rutger , Dekker Henk , van Harmelen Frank , Lankelma Jan 
Published: March 2004

Abstract
Summary: We present a new tool for the semi-automated querying of PubMed using a batch of tens to thousands of GenBank accession numbers or UniGene cluster ids. By combining information from UniGene and SWISS-PROT, microGENIE obtains information on the biological relevance of expressed genes, as identified by micro-array experiments, with minimal user intervention and time investment.
Availability: microGENIE is freely available from http://www.cs.vu.nl/microgenie
Supplementary information: The web site above supplies examples of input and output files.
ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure
Authors: Higa R. H. , Montagner A. J. , Togawa R. C. , Kuser P. R. , Yamagishi M. E. B. , Mancini A. L. , Pappas G. , Miura R. T. , Horita L. G. , Neshich G. 
Published: March 2004

Abstract
Summary: A web-based application to analyze protein amino acids conservation—Consensus Sequence (ConSSeq) is presented. ConSSeq graphically represents information about amino acid conservation based on sequence alignments reported in homology-derived structures of proteins. Beyond the relative entropy for each position in the alignment, ConSSeq also presents the consensus sequence and information about the amino acids, which are predominant at each position of the alignment. ConSSeq is part of the STING Millennium Suite and is implemented as a Java Applet.
Availability: http://sms.cbi.cnptia.embrapa.br/SMS/STINGm/consseq/, http://trantor.bioc.columbia.edu/SMS/STINGm/consseq/, http://mirrors.rcsb.org//SMS/STINGm/consseq/, http://www.es.embnet.org/SMS/STINGm/consseq/ and http://www.ar.embnet.org/SMS/STINGm/consseq/
UniProt archive
Authors: Leinonen Rasko , Diez Federico Garcia , Binns David , Fleischmann Wolfgang , Lopez Rodrigo , Apweiler Rolf 
Published: March 2004

Abstract
Summary: UniProt Archive (UniParc) is the most comprehensive, non-redundant protein sequence database available. Its protein sequences are retrieved from predominant, publicly accessible resources. All new and updated protein sequences are collected and loaded daily into UniParc for full coverage. To avoid redundancy, each unique sequence is stored only once with a stable protein identifier, which can be used later in UniParc to identify the same protein in all source databases. When proteins are loaded into the database, database cross-references are created to link them to the origins of the sequences. As a result, performing a sequence search against UniParc is equivalent to performing the same search against all databases cross-referenced by UniParc. UniParc contains only protein sequences and database cross-references; all other information must be retrieved from the source databases.
Availability: http://www.ebi.ac.uk/uniparc/
Phylogenetic trees based on gene content
Authors: Huson Daniel H. , Steel Mike 
Published: March 2004

Abstract
Summary: Comparing gene content between species can be a useful approach for reconstructing phylogenetic trees. In this paper, we derive a maximum-likelihood estimation of evolutionary distance between species under a simple model of gene genesis and gene loss. Using simulated data on a biological tree with 107 taxa (and on a number of randomly generated trees), we compare the accuracy of tree reconstruction using this ML distance measure to an earlier ad hoc distance. We then compare these distance-based approaches to a character-based tree reconstruction method (Dollo parsimony) which seems well suited to the analysis of gene content data. To simplify simulations, we give a formal proof of the well-known ‘fact’ that the Dollo parsimony score is independent of the choice of root. Our results show a consistent trend, with the character-based method and ML distance measure outperforming the earlier ad hoc distance method.
Availability: http://www.ab.informatik.uni-tuebingen.de/software/genecontent/welcome_en.html
Impact of Resection of the Turbinates and the Lateral Nasal Wall on Particle Deposition
Authors: Rozsasi Ajnacska , Leiacker Richard , Rettinger Gerhard , Lindemann Jörg , Keck Tilman 
Published: March 2004

AbstractObjectives/Hypothesis The aim of the investigation was to determine the influence of complete resection of the turbinates and the lateral nasal wall on nasal deposition of particulate matter with an aerodynamic diameter of 10 μm or less (pm10) and its relation to nasal patency and geometry.Study Design Retrospective study.Methods Eight patients were enrolled in the study after unilateral sinus surgery for a unilateral inverted papilloma of the sinuses. Particle deposition from the inhaled and exhaled air was measured by means of a laser particle counter in the nasal valve area and the nasopharynx during nose‐only breathing and nose‐in, mouth‐out breathing. The data on deposited fraction for the operated side were compared with the data for the untreated, healthy side. Rhinomanometry and acoustic rhinometry were performed.Results Particle deposition did not differ significantly between the operated and untreated sides of the nose at both detection sites. No correlation between the deposited fraction and rhinomanometric and rhinometric values was found.Conclusion Radical resection of the turbinates does not seem to disturb particle deposition (pm10) measured in the nose to a significant degree. Factors other than impaction and sedimentation onto the mucosal surface of the turbinates seem to be sufficient for effective particle deposition after radical removal of the turbinates.
Determination of Reactive Oxygen Species in Myringotomized Tympanic Membranes: Effect of Vitamin E Treatment
Authors: Polat Senol , Öztürk Özmen , Üneri Cüneyd , Yüksel Meral , Haklar Goncagül , Bozkurt Süheyla , Küllü Sevgi 
Published: March 2004

AbstractObjectives/Hypothesis Recent studies have established a strong relationship between the development of myringosclerosis and reactive oxygen species (ROS). The aims of the present study were to directly detect ROS in the tympanic membrane and middle ear mucosa of rats by measuring luminol amplified chemiluminescence, to evaluate the changes in the levels of ROS after treatment with vitamin E, and to examine the possible changes in the tympanic membranes otomicroscopically and histologically.Study Design Prospective controlled animal study.Methods Forty healthy Sprague‐Dawley rats were divided into five groups of eight animals each. Animals in all groups except group 1 were bilaterally myringotomized. Group 2 received no treatment, group 3 was treated with topical olive oil, group 4 received topical vitamin E, and group 5 received intramuscular vitamin E. After 24 hours of myringotomy, tympanic membranes were examined otomicroscopically; thereafter, tympanic membranes and middle ear mucosa were peeled off. The right ears of the animals were used for biochemical assay, and the left ears were used for histological study.Results Reactive oxygen species levels were significantly decreased in group 4 with topical application of vitamin E compared with untreated and myringotomized animals in group 2. Reactive oxygen species levels were also decreased in group 5, although the decrease was not statistically significant when compared with groups 2 and 3. Histological studies confirmed sclerotic changes in the untreated myringotomized animals. The tympanic membranes of animals in groups 2 and 3 showed a white, chalk‐like pattern of sclerotic changes, whereas animals in groups 4 and 5, with the exception of two animals in group 5, lacked these changes.Conclusion Although the relationship between the development of myringosclerosis and ROS had been well documented previously, the present study is the first that has directly measured the levels of ROS in the tympanic membrane and middle ear mucosa. These results are relevant because they correlate with histological findings. It has also been demonstrated that topically applied vitamin E is effective in decreasing the ROS levels.
The interaction of streptococcal inhibitor of complement (SIC) and its proteolytic fragments with the human beta defensins
Authors: Fernie‐King Barbara A. , Seilly David J. , Lachmann Peter J. 
Published: March 2004

SummaryStreptococcal inhibitor of complement (SIC) is a 31 kDa extracellular protein produced by a few highly virulent strains of Streptococcus pyogenes (in particular the M1 strain). It has been shown additionally to inhibit four further components of the mucosal innate response—lysozyme, secretory leucocyte proteinase inhibitor, human α‐defensin 1 and the cathelicidin LL‐37 which are all bactericidal against Group A Streptococci (GAS). We now show that SIC also inhibits variably the antibacterial action of hBD‐1, ‐2 and ‐3. By enzyme‐linked immunosorbent assay (ELISA), SIC binds strongly to hBD‐2 and hBD‐3, but not at all to hBD‐1. Investigation of the antimicrobial action of β‐defensins hBD‐1, ‐2 and ‐3 against GAS in two different buffer systems shows that both the killing efficiencies of all three defensins, and the binding of SIC to them, occurs more efficiently in 10 mm Tris buffer than in 10 mm phosphate. The lower ionic strength of the Tris buffer may underlie this effect. hBD‐1 kills the M1 strain of GAS only in 10 mm Tris, but is able to kill an M6 (SIC negative) strain in 10 mm phosphate. The inhibition of hBD‐3 by SIC is clearly of physiological relevance, that of hBD‐2 is likely to be so, but the inhibition of hBD‐1 occurs only at lower ionic strength than is likely to be encountered in vivo. Elastase digestion of SIC yields three major fragments of MW 3·843 kDa comprising residues 1–33 (fragment A); 10·369 kDa comprising residues 34–126 (fragment B); and MW 16·487 kDa, comprising residues 127–273 (fragment C). By ELISA, only fragment B binds to hBD‐2 and hBD‐3 and this may indicate the inhibitory portion of the SIC molecule.
A decrease in the molecular weight of hyaluronic acid in synovial fluid from patients with temporomandibular disorders
Authors: Takahashi Tetsu , Tominaga Kazuhiro , Takano Hiroshi , Ariyoshi Wataru , Habu Manabu , Fukuda Jinichi , Maeda Hiroshi 
Published: March 2004

Background:  The molecular weight (MW) of hyaluronic acid (HA) in joints generally declines in inflammatory arthritis. As inflammation exists in certain temporomandibular disorders (TMD), we measured the MW of HA in synovial fluid (SF) recovered from patients with TMD and compared it with that from normal controls.Methods:  Synovial fluid was obtained from patients with TMD (21 TMJs) and normal controls (5 TMJs). The MW of HA was measured using high‐performance liquid chromatography (HPLC).Results:  In the controls, the MW of HA in SF exceeded the detection limit, 3000 kDa. In contrast, 19 (90.5%) of 21 SF samples from patients showed a decreased MW of HA. The median MW of HA (1570 kDa) in TMD was significantly lower than that in the controls (P < 0.01).Conclusion:  The MW of HA in SF from patients with TMD is decreased.
Association of CTLA‐4 gene polymorphism with oral submucous fibrosis in Taiwan
Authors: Shin Yi‐Ning , Liu Chung‐Ji , Chang Kuo‐Wei , Lee Yann‐Jinn , Liu Hsin‐Fu 
Published: March 2004

Background:  Oral submucous fibrosis (OSF) is an insidious, pre‐cancerous, chronic disease that may affect the entire oral cavity and sometimes extend to the pharynx. It has been reported to be associated with immune function. Cytotoxic T‐lymphocyte‐associated antigen 4 (CTLA‐4; CD (cluster of differentiation) 152) is a negative regulator of T‐lymphocyte activation. Particular genotypes of the locus encoding the CTLA‐4 glycoprotein have been associated with susceptibility to various autoimmune diseases. This study was designed to investigate the role of CTLA‐4 polymorphism in susceptibility to OSF.Methods:  We genotyped 62 patients with OSF and 147 healthy controls for allelic determinants at the exon 1 +49 polymorphism site by restriction fragment length polymorphism. Genotype and phenotype frequencies were evaluated with Chi‐squared test.Results:  The G allele at position +49 of exon 1 was significantly associated with OSF. The frequency of A/A homozygotes was higher in controls than in patients (17.0% vs. 3.2%; χ2 = 7.65, P = 0.02); the G phenotype was more frequent in patients than in controls (96.8% vs. 83.0%; χ2 = 9.31, P = 0.002). Compared with controls, the G allele genotype and phenotype frequencies were increased in patients with OSF.Conclusion:  This is the first report that the CTLA‐4 +49 G allele confers an increased risk of OSF in Taiwan.
Isolation and characterization of a C‐type lectin cDNA specifically expressed in the tip of mouthparts of the flesh fly Sarcophaga peregrina
Authors: Yamamoto‐Kihara M. , Kotani E. 
Published: March 2004

AbstractWe have isolated a novel gene, CLEM 36, of the flesh fly Sarcophaga peregrina, which shows significant homology to the C‐type lectin family. CLEM 36 mRNA was transcribed excessively from the second day after eclosion only in the tip of mouthparts. Whole mount in situ hybridization showed that CLEM 36 mRNA was expressed in the C‐type lectin‐producing tissue (CLPT) located at the entrance of the food canal and between the labellum and haustellum. Immunoblot analysis showed that the mature form of CLEM 36 protein was synthesized in the CLPT, then secreted into saliva. Our results indicate that CLEM 36 protein may play an important role in biological defence against pathogens during the food intake of this insect.
Cloning and characterization of a gut‐specific cathepsin L from the aphid Aphis gossypii
Authors: Deraison C. , Darboux I. , Duportets L. , Gorojankina T. , Rahbé Y. , Jouanin L. 
Published: March 2004

AbstractWe have characterized proteinase activities in gut extracts from the cotton‐melon aphid (Aphis gossypii Glover), an insect feeding strictly on protein‐poor phloem. The major, if not exclusive, intestinal proteinases of this aphid are of the cysteine type. A cDNA has been cloned from a gut library and codes for the cysteine proteinase AgCatL, a cathepsin L‐like cysteine proteinase. The AgCatL protein shows high sequence similarity with mammalian and some arthropod cathepsin L‐like proteinases, but can be reliably distinguished from the secreted (digestive) proteinases identified in other arthropods. AgCatL is widely expressed in aphid intestinal cells. Immunolocalization of AgCatL showed an intense signal at the level of the anterior ‘stomach’ part of the midgut, and especially at intracellular localization. Although the precise role of AgCatL in aphid midgut physiology is still unclear, this enzyme could be involved in the processing of exogenous ingested polypeptides.
Cancer and Cancer Risk in South Australia: What Evidence for a Rural–Urban Health Differential?
Authors: Wilkinson David , Cameron Kate 
Published: March 2004

ABSTRACTObjective:  To determine the extent of evidence for a rural–urban health differential in cancer and cancer risk in South Australia Design:  Secondary analysis and synthesis of data available between 1977 and 2000 from the publications of the South Australian Cancer Registry and reports of population health surveys carried out by the South Australian Department of Human Services. Results:  The mean annual age‐standardised incidence of all forms of cancer combined was about 4% lower for rural residents (265.2 per 100 000 cf. 274.9 per 100 000). Of 31 types of cancer listed, the incidence of three was significantly higher among rural residents, the incidence of eight was significantly higher among urban residents and for 20 types there was no significant difference. Five year case survival for all cancers combined was 52% in both urban and rural residents. Significant survival differences were identified for only 10 cancers and survival for each was higher among urban residents. Melanomas were diagnosed
in situ
more often in the country, but invasive cases tended to be thicker. There was no rural–urban difference in early detection rates for breast cancer or bladder cancer. There were no substantial reported differences in major risk factors and early detection experiences apart from higher rates of smoking in the country. Conclusions:  There is little evidence for substantial or systematic differences in risk factors for, and incidence and early detection of cancers between urban and rural South Australia. However, the apparent consistently poorer survival among rural residents warrants further study. What this paper adds:   It is widely reported that the health status of rural Australians is worse than that of their urban counterparts. There is an apparent increasing gradient in mortality from urban to remote areas of Australia. However, this apparent gradient is not evident for all diseases. This paper seeks to answer the question: is there any difference in the cancer disease experience (incidence, survival and early detection) and cancer risk factors between residents of rural and urban South Australia. Cancer registry data indicate that overall, the incidence of cancer is similar in rural and urban South Australia. The findings on survival differentials are of concern. While overall survival rates are very similar in country and city, and this is encouraging, analysis of individual types of cancer raises some concerns. The registry reports that significant differences in survival were only measured for 10 cancers and for all of these rural residents experienced higher mortality rates.
Educational Needs of Rural and Remote Australian Non‐Specialist Medical Practitioners For Obstetric Ultrasound
Authors: Glazebrook Roz , Manahan Dan , Chater Bruce , Barker Peter , Row David , Steele Brendan , Morris Graham , Cornelius Sally , McLellan Tony 
Published: March 2004

ABSTRACTObjective:  To determine the educational needs of rural and remote non‐specialist Australian doctors for obstetric ultrasound. Design:  Survey design. Setting:  The study surveyed rural and remote doctors practising in a variety of settings including general practice, rural hospitals, Aboriginal communities and flying doctor organisations throughout Australia. Subjects:  Subjects included 314 solo and group practice rural general practitioners, rural hospital medical superintendents, senior medical officers, Aboriginal community controlled health service doctors, flying doctors, rural locums, registrars and two rural obstetricians. A total of 55% of the subjects were general practitioners in group practice. Respondents included 68 (22%) women and 246 (78%) men. Results:  The response rate was 32%. The highest priority areas of need for education included detecting foetal abnormalities and anomalies (19.1%), basic routine ultrasonography (17.17%), placental position (17.17%), dating (17.17%), foetal viability (12.88%) and morphology scan (12.26%). The main areas where doctors stated they lacked confidence included detecting foetal abnormalities (29.09%), basic routine ultrasonography (including machine use), such as, carrying out and interpreting obstetric ultrasound scans (27.27%), morphology scans (16.36%) and placental position (14.54%). Conclusion:  The study showed there was a large unmet need for education in obstetric ultrasound among rural and remote non‐specialist doctors. Information from the needs assessment was used to develop the Australian College of Rural and Remote Medicine national obstetric ultrasound professional development program.What is already known:  The authors could not find any published work on the educational needs of Australian non‐specialist rural and remote doctors for obstetric ultrasound. There is research about the outcome of obstetric ultrasound education for urban family physicians in the USA, but no information about rural doctors’ educational needs or education outcomes. The study needed to be done so that obstetric ultrasound professional development program of the Australian College of Rural and Remote Medicine could be based on the real needs of the target group. What this paper adds:  As a result of this research, there is now information on the educational needs of rural and remote Australian non‐specialist medical practitioners that can be used by education providers to develop quality education programs in obstetric ultrasound.
α6‐Integrin is expressed on germinal centre B cells and modifies growth of a B‐cell line
Authors: Ambrose Helen E. , Wagner Simon D. 
Published: March 2004

SummaryThe production of high‐affinity antibodies requires diversification of the antibody repertoire by somatic hypermutation followed by selection of those B cells bearing the highest affinity antibodies. Whilst many surface molecules that mediate the cell–cell interactions required for germinal centre formation have been identified, little is known of the importance of interactions with components of the extracellular matrix, i.e. fibronectin, collagen and laminin. We demonstrate that the laminin‐binding α6‐integrin is expressed on germinal centre B cells and is induced during the in vitro activation of naïve splenic B cells. A laminin network is demonstrated within the germinal centre. Analysis of an α6‐integrin‐expressing mouse B‐cell line, A20, demonstrates that this molecule is essential for binding to laminin, and that blocking by anti‐α6‐integrin immunoglobulin causes loss of adhesion associated with an increase in proliferation. There is no correlation with changes in BCL‐6 or Blimp‐1 expression, suggesting that α6‐integrin does not play a role in differentiation.