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  • 1
    Call number: M120:162
    Pages: 235 p. : ill.
    Edition: 3. Aufl.
    ISBN: 9783832172039
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    M120:162 departmental collection or stack – please contact the library
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  • 2
    Keywords: GROWTH ; PROTEIN ; DIFFERENTIATION ; DNA ; DATABASE ; INTERFACE ; W2H
    Abstract: In high throughput sequence analysis, it is often necessary to combine the results of contemporary bioinformatics tools, because no individual tool alone computes all the requested information. ESTAnnotator is a tool for the high throughput annotation of expressed sequence tags (ESTs) by automatically running a collection of bioinformatics applications. In the first step, a quality check is performed and repeats, vector parts and low quality sequences are masked. Then successive steps of database searching and EST clustering are performed. Already known transcripts present within mRNA and genomic DNA reference databases are identified. Subsequently, tools for the clustering of anonymous ESTs, and for further database searches at the protein level, are applied. Finally, the outputs of each individual tool are gathered and the relevant results presented in a descriptive summary. ESTAnnotator was already successfully applied for the systematic identification and characterisation of novel human genes involved in cartilage/bone formation, growth, differentiation and homeostasis. ESTAnnotator is available at http://genome.dkfz-heidelberg.de, contact: genome@dkfz.de
    Type of Publication: Journal article published
    PubMed ID: 12824401
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  • 3
    Keywords: Germany ; TOOL ; PROTEIN ; COMPLEX ; COMPLEXES ; DNA ; INTERVENTION ; PREDICTION ; WEB ; QUESTIONNAIRE ; ANNOTATION ; GENOME DATABASE ; PROTEIN DATA ; RESOURCE ; SEQUENCE DATABASE
    Abstract: The Helmholtz Network for Bioinformatics (HNB) is a joint venture of eleven German bioinformatics research groups that offers convenient access to numerous bioinformatics resources through a single web portal. The 'Guided Solution Finder' which is available through the HNB portal helps users to locate the appropriate resources to answer their queries by employing a detailed, tree-like questionnaire. Furthermore, automated complex tool cascades ('tasks'), involving resources located on different servers, have been implemented, allowing users to perform comprehensive data analyses without the requirement of further manual intervention for data transfer and re-formatting. Currently, automated cascades for the analysis of regulatory DNA segments as well as for the prediction of protein functional properties are provided
    Type of Publication: Journal article published
    PubMed ID: 14734319
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  • 4
    Keywords: Germany ; CLASSIFICATION ; INFORMATION ; TOOL ; SITE ; CLONING ; GENOME ; PROTEIN ; PROTEINS ; TIME ; SEQUENCE ; SIGNAL ; VARIANTS ; ASSAY ; DATABASE ; LOCALIZATION ; PREDICTION ; SELECTION ; REJECTION ; SEQUENCE-ANALYSIS ; HUMAN GENES ; FUNCTIONAL GENOMICS ; CDNAS ; FEATURES ; PROGRAM ; RE ; VARIANT ; assembly ; databases ; ANNOTATION ; CPG ISLANDS ; FULL-LENGTH HUMAN ; ASSAYS ; HIGH-THROUGHPUT ; TESTS ; GENOMIC DNA ; genomic ; SIGNALS ; E ; SET ; transcriptome ; POLYADENYLATION
    Abstract: Background: The German cDNA Consortium has been cloning full length cDNAs and continued with their exploitation in protein localization experiments and cellular assays. However, the efficient use of large cDNA resources requires the development of strategies that are capable of a speedy selection of truly useful cDNAs from biological and experimental noise. To this end we have developed a new high-throughput analysis tool, CAFTAN, which simplifies these efforts and thus fills the gap between large-scale cDNA collections and their systematic annotation and application in functional genomics. Results: CAFTAN is built around the mapping of cDNAs to the genome assembly, and the subsequent analysis of their genomic context. It uses sequence features like the presence and type of PolyA signals, inner and flanking repeats, the GC-content, splice site types, etc. All these features are evaluated in individual tests and classify cDNAs according to their sequence quality and likelihood to have been generated from fully processed mRNAs. Additionally, CAFTAN compares the coordinates of mapped cDNAs with the genomic coordinates of reference sets from public available resources ( e. g., VEGA, ENSEMBL). This provides detailed information about overlapping exons and the structural classification of cDNAs with respect to the reference set of splice variants. The evaluation of CAFTAN showed that is able to correctly classify more than 85% of 5950 selected "known protein-coding" VEGA cDNAs as high quality multi-or single-exon. It identified as good 80.6% of the single exon cDNAs and 85% of the multiple exon cDNAs. The program is written in Perl and in a modular way, allowing the adoption of this strategy to other tasks like EST-annotation, or to extend it by adding new classification rules and new organism databases as they become available. We think that it is a very useful program for the annotation and research of unfinished genomes. Conclusion: CAFTAN is a high-throughput sequence analysis tool, which performs a fast and reliable quality prediction of cDNAs. Several thousands of cDNAs can be analyzed in a short time, giving the curator/scientist a first quick overview about the quality and the already existing annotation of a set of cDNAs. It supports the rejection of low quality cDNAs and helps in the selection of likely novel splice variants, and/or completely novel transcripts for new experiments
    Type of Publication: Journal article published
    PubMed ID: 17064411
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  • 5
    Keywords: ENVIRONMENT ; Germany ; SYSTEM ; BASE ; FLOW ; bioinformatics ; INTERFACE ; W2H
    Abstract: The W3H task framework allows the execution of compound jobs utilizing the description of work and data flows in a heterogeneous bioinformatics environment using meta-data information. By means of these descriptions, the task system can schedule the necessary execution of applications available in the environment, depending on rules specified in the meta- data. By integrating this task framework into the publicly available web interface W2H, similarly based on meta-data, web access and data management are immediately available for each task description. Authors of task descriptions can base their work on the underlying classes and objects to be able to describe dependency rules between previously independent applications. The result of a compound task is given as XML data that is translated according to XSLT data into web pages or plain text to report the result of the task to the user. Availability: Within the HUSAR environment at DKFZ http: Hgenome.dkfz-heidelberg.de/. Contact: P.Ernst@dkfz.de
    Type of Publication: Journal article published
    PubMed ID: 12538250
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  • 6
    Keywords: CANCER ; COMBINATION ; Germany ; INFORMATION ; SITE ; SITES ; GENES ; PROTEIN ; TIME ; DOMAIN ; BIOLOGY ; MOLECULAR-BIOLOGY ; ACID ; ELEMENT ; IDENTIFICATION ; ELEMENTS ; DATABASE ; bioinformatics ; INTERFACE ; SECONDARY STRUCTURE ; PROJECT ; molecular biology ; molecular ; RE ; FAMILIES ; SOFTWARE ; ANNOTATION ; SUPPLEMENT ; HOMOLOGY ; analysis ; methods ; cancer research ; ACCESS ; ENGLAND ; in combination ; ENSEMBL ; FUNCTIONAL-ANALYSIS ; PIPELINES ; SECONDARY STRUCTURE PREDICTION
    Abstract: The wealth of transcript information that has been made publicly available in recent years has led to large pools of individual web sites offering access to bioinformatics software. However, finding out which services exist, what they can or cannot do, how to use them and how to feed results from one service to the next one in the right format can be very time and resource consuming, especially for non-experts. Automating this task, we present a suite of protein annotation pipelines (tasks) developed at the German Cancer Research Centre (DKFZ) oriented to protein annotation by homology (ProtSweep), by domain analysis (DomainSweep), and by secondary structure elements (2Dsweep). The aim of these tasks is to perform an exhaustive structural and functional analysis employing a wide variety of methods in combination with the most updated public databases. The three servers are available for academic users at the HUSAR open server http://genius.embnet.dkfz-heidelberg.de/menu/biounit/open-husar/
    Type of Publication: Journal article published
    PubMed ID: 17526514
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  • 7
    ISSN: 1432-1041
    Keywords: Key words Asthma therapy ; Corticosteroids; hospitalisation ; case-control study ; compliance ; attitude ; behaviour
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Medicine
    Notes: Abstract Background: The relationship between therapy and adverse outcome in asthma is debated especially for naturally occurring situations. This is due in part to insufficient information regarding actual use of medications. Objective: This study was conducted to clarify the relationship between actual intake of anti-asthma drugs and asthma hospitalisation, considered as an outcome. Methods: A case-control study was performed. Patients hospitalised for an asthma exacerbation were matched to community controls identified in surrounding general practices. Patients were questioned to identify prior use of anti-asthma medications, level of use of inhaled corticosteroids and attitude towards therapy. Results: Twenty-three cases and 31 matched controls were interviewed. Cases tended to have more severe asthma than controls, as judged by more frequent use of oral corticosteroids. Cases tended to make more frequent use of oral xanthines and inhaled anticholinergics, but the proportion of patients using inhaled β2-adrenoceptor agonists and inhaled corticosteroids was similar in both groups. Use of lower doses of inhaled corticosteroids was associated with an increased risk of hospitalisation, while higher dosage was associated with␣decreased risk. Cases and controls differed as to their answers to a questionnaire concerning attitudes: cases expressed less interest in optimal usage of inhaled␣corticosteroids than controls; they also expressed more confidence in inhaled β2-agonists. When both risks were combined, overconfidence in β2-agonists and suboptimal use of inhaled steroids, the relationship with hospitalisation was significant (OR 5.5, 95% CI 1.1; 26.1). Conclusion: The results suggest that patients' attitudes to inhaled corticosteroids and actual consumption of these medications are directly related to adverse outcome in asthma.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Virchows Archiv 359 (1973), S. 185-200 
    ISSN: 1432-2307
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Description / Table of Contents: Zusammenfassung Bei 2 Patienten im Alter von 3 8/12 bzw. 27 Jahren entwickelte sich nach Anlegen eines ventriculo-atrialen Shunt eine diffuse Glomerulonephritis mit nephrotischem Syndrom. Die Entfernung des Shunt führte beim ersten Patienten zu einer raschen Besserung und beim zweiten Patienten zu einer kompletten Heilung des Nierenleidens. Das anfänglich tiefe Serumkomplement (β1C) normalisierte sich. Bei dem Kinde konnte aus dem Liquor und vom Ventil Staphylococcus albus gezüchtet werden. Bei dem erwachsenen Patienten blieben die Kulturen steril. Beim ersten Patienten ergab die Nierenbiopsie vor Entfernung des Shunt eine diffuse intra- und extracapilläre Glomerulonephritis, Typ III (subakute Glomerulonephritis), beim zweiten eine diffuse intracapilläre proliferative und exsudative Glomerulonephritis. Bei beiden Patienten wurde 22, bzw. 7 Monate nach Entfernung des Shunt eine zweite Biopsie entnommen. Beim ersten Fall waren rund die Hälfte der Glomeruli hyalinisiert. Die übrigen zeigten mäßig ausgeprägte segmentäre Läsionen. Halbmonde waren keine mehr nachweisbar. Beim zweiten Patienten bestand nach 7 Monaten noch eine deutliche mesangiale Proliferation mit Lobulierung der Glomeruli. Immunfluorescenzmikroskopisch konnte in beiden Fällen in den Glomerulusschlingen IgG, IgM und β1C in grob granulärer Form nachgewiesen werden. Elektronenmikroskopisch fanden sich bei beiden Patienten auch in der zweiten Biopsie subendotheliale Ablagerungen. Die nach einem infizierten ventriculo-atrialen Shunt auftretende Glomerulonephritis ist mit großer Wahrscheinlichkeit durch Immunkomplexe bedingt. Da durch Entfernung des Shunt das Antigen sofort entfernt werden kann, ist selbst bei schweren Nierenläsionen eine weitgehende Besserung möglich.
    Notes: Summary Diffuse glomerulonephritis with the nephrotic syndrome was observed in two patients aged 3 years 8 months and 27 years, both of whom had ventriculo-atrial shunts. Removal of the shunts resulted in marked improvement in the first and complete recovery in the second patient. Serum β1C-globulin concentrations were initially low and returned to normal values. Cultures taken from cerebrospinal fluid and valve grew Staphylococcus albus in the pediatric patient and were negative in the adult patient. Initial renal biopsies obtained immediately before shunt removal showed diffuse intra- and extracapillary glomerulonephritis type III (crescent formation in over 90 percent of the glomeruli) in the first patient, and diffuse intracapillary proliferative and exudative glomerulonephritis in the second patient. Repeat biopsies were performed, on the first patient 22 months, and on the second patient 7 months after shunt removal. In the first patient, half of the glomeruli were sclerosed, and the others exhibited slight mesangial proliferation with some capsular adhesions. The repeat renal biopsy from the adult patient showed mesangial proliferation with lobulation. Immunofluorescence studies in both patients revealed positive staining in a coarsely granular pattern against IgG, IgM, and β1C globulin. On electron microscopy, subendothelial deposits were still visible in the second biopsies of both patients. Glomerulonephritis associated with infected ventriculo-atrial shunt is probably mediated by antigen-antibody complexes. Recovery is possible in spite of severe renal lesions since the antigen can be eliminated at once by removal of the shunt.
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 1365-2036
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Medicine
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 1432-0851
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary The influence of immunotherapy with high dose (50×106 units/m2) recombinant leukocyte A interferon on blood monocyte functions was studied in eight patients with bronchogenic carcinoma. Monocyte chemotactic responsiveness (MCR) was initially depressed (9.8±1.6 cells/field) compared to healthy controls (17.6±5.1 cells/field), P〈0.01. Recombinant interferon was administered three times weekly, and after 7 days a significant improvement in chemotaxis was observed (16.6±3.0 cells/field), P〈0.05. The MCR remained normal until cessation of interferon therapy (〉1 month). Phagocytic and candidacidal activities were normal in the patients and were not influenced by treatment with interferon. In conclusion, high dose recombinant interferon given to cancer patients caused a normalization of defective blood monocyte chemotaxis, which persisted for 〉1 month.
    Type of Medium: Electronic Resource
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