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  • 1
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    DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-06
    Description: Large amounts of epigenomic data are generated under the umbrella of the International Human Epigenome Consortium, which aims to establish 1000 reference epigenomes within the next few years. These data have the potential to unravel the complexity of epigenomic regulation. However, their effective use is hindered by the lack of flexible and easy-to-use methods for data retrieval. Extracting region sets of interest is a cumbersome task that involves several manual steps: identifying the relevant experiments, downloading the corresponding data files and filtering the region sets of interest. Here we present the DeepBlue Epigenomic Data Server, which streamlines epigenomic data analysis as well as software development. DeepBlue provides a comprehensive programmatic interface for finding, selecting, filtering, summarizing and downloading region sets. It contains data from four major epigenome projects, namely ENCODE, ROADMAP, BLUEPRINT and DEEP. DeepBlue comes with a user manual, examples and a well-documented application programming interface (API). The latter is accessed via the XML-RPC protocol supported by many programming languages. To demonstrate usage of the API and to enable convenient data retrieval for non-programmers, we offer an optional web interface. DeepBlue can be openly accessed at http://deepblue.mpi-inf.mpg.de .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Genes expressed in human tumor endothelium (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-08-19
    Description: To gain a molecular understanding of tumor angiogenesis, we compared gene expression patterns of endothelial cells derived from blood vessels of normal and malignant colorectal tissues. Of over 170 transcripts predominantly expressed in the endothelium, 79 were differentially expressed, including 46 that were specifically elevated in tumor-associated endothelium. Several of these genes encode extracellular matrix proteins, but most are of unknown function. Most of these tumor endothelial markers were expressed in a wide range of tumor types, as well as in normal vessels associated with wound healing and corpus luteum formation. These studies demonstrate that tumor and normal endothelium are distinct at the molecular level, a finding that may have significant implications for the development of anti-angiogenic therapies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉St Croix, B -- Rago, C -- Velculescu, V -- Traverso, G -- Romans, K E -- Montgomery, E -- Lal, A -- Riggins, G J -- Lengauer, C -- Vogelstein, B -- Kinzler, K W -- CA57345/CA/NCI NIH HHS/ -- CA62924/CA/NCI NIH HHS/ -- CGAP S98-146A/PHS HHS/ -- New York, N.Y. -- Science. 2000 Aug 18;289(5482):1197-202.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Johns Hopkins Oncology Center, Howard Hughes Medical Institute, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10947988" target="_blank"〉PubMed〈/a〉
    Keywords: Biomarkers, Tumor ; Cell Separation ; Cells, Cultured ; Colon/*blood supply/metabolism ; Colorectal Neoplasms/*blood supply/genetics/metabolism/pathology ; Corpus Luteum/blood supply/metabolism ; Endothelium, Vascular/cytology/*metabolism/pathology ; Extracellular Matrix Proteins/genetics ; Female ; Gene Expression ; *Gene Expression Profiling ; Humans ; Intestinal Mucosa/blood supply/cytology/pathology ; Neoplasms/blood supply/genetics/metabolism ; Neovascularization, Pathologic/*genetics ; Neovascularization, Physiologic/genetics ; RNA, Messenger/genetics/metabolism ; Rectum/*blood supply/metabolism ; Tumor Cells, Cultured
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    A phosphatase associated with metastasis of colorectal cancer (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-10-13
    Description: To gain insights into the molecular basis for metastasis, we compared the global gene expression profile of metastatic colorectal cancer with that of primary cancers, benign colorectal tumors, and normal colorectal epithelium. Among the genes identified, the PRL-3 protein tyrosine phosphatase gene was of particular interest. It was expressed at high levels in each of 18 cancer metastases studied but at lower levels in nonmetastatic tumors and normal colorectal epithelium. In 3 of 12 metastases examined, multiple copies of the PRL-3 gene were found within a small amplicon located at chromosome 8q24.3. These data suggest that the PRL-3 gene is important for colorectal cancer metastasis and provide a new therapeutic target for these intractable lesions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Saha, S -- Bardelli, A -- Buckhaults, P -- Velculescu, V E -- Rago, C -- St Croix, B -- Romans, K E -- Choti, M A -- Lengauer, C -- Kinzler, K W -- Vogelstein, B -- CA 62924/CA/NCI NIH HHS/ -- CA43460/CA/NCI NIH HHS/ -- CA57345/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2001 Nov 9;294(5545):1343-6. Epub 2001 Oct 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, The Oncology Center, Department of Surgery, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11598267" target="_blank"〉PubMed〈/a〉
    Keywords: Adenoma/enzymology/genetics/pathology ; Chromosome Mapping ; Chromosomes, Human, Pair 8 ; Colon/enzymology ; Colorectal Neoplasms/*enzymology/*genetics/pathology ; Gene Amplification ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Gene Library ; Humans ; Immediate-Early Proteins/*genetics/metabolism ; Intestinal Mucosa/enzymology ; Neoplasm Metastasis/*genetics ; Neoplasm Proteins ; Neoplasm Staging ; Polymerase Chain Reaction ; Protein Tyrosine Phosphatases/*genetics/metabolism ; Rectum/enzymology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Tankyrase inhibition stabilizes axin and antagonizes Wnt signalling (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-09-18
    Description: The stability of the Wnt pathway transcription factor beta-catenin is tightly regulated by the multi-subunit destruction complex. Deregulated Wnt pathway activity has been implicated in many cancers, making this pathway an attractive target for anticancer therapies. However, the development of targeted Wnt pathway inhibitors has been hampered by the limited number of pathway components that are amenable to small molecule inhibition. Here, we used a chemical genetic screen to identify a small molecule, XAV939, which selectively inhibits beta-catenin-mediated transcription. XAV939 stimulates beta-catenin degradation by stabilizing axin, the concentration-limiting component of the destruction complex. Using a quantitative chemical proteomic approach, we discovered that XAV939 stabilizes axin by inhibiting the poly-ADP-ribosylating enzymes tankyrase 1 and tankyrase 2. Both tankyrase isoforms interact with a highly conserved domain of axin and stimulate its degradation through the ubiquitin-proteasome pathway. Thus, our study provides new mechanistic insights into the regulation of axin protein homeostasis and presents new avenues for targeted Wnt pathway therapies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Shih-Min A -- Mishina, Yuji M -- Liu, Shanming -- Cheung, Atwood -- Stegmeier, Frank -- Michaud, Gregory A -- Charlat, Olga -- Wiellette, Elizabeth -- Zhang, Yue -- Wiessner, Stephanie -- Hild, Marc -- Shi, Xiaoying -- Wilson, Christopher J -- Mickanin, Craig -- Myer, Vic -- Fazal, Aleem -- Tomlinson, Ronald -- Serluca, Fabrizio -- Shao, Wenlin -- Cheng, Hong -- Shultz, Michael -- Rau, Christina -- Schirle, Markus -- Schlegl, Judith -- Ghidelli, Sonja -- Fawell, Stephen -- Lu, Chris -- Curtis, Daniel -- Kirschner, Marc W -- Lengauer, Christoph -- Finan, Peter M -- Tallarico, John A -- Bouwmeester, Tewis -- Porter, Jeffery A -- Bauer, Andreas -- Cong, Feng -- England -- Nature. 2009 Oct 1;461(7264):614-20. doi: 10.1038/nature08356. Epub 2009 Sep 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19759537" target="_blank"〉PubMed〈/a〉
    Keywords: Axin Protein ; Cell Division/drug effects ; Cell Line ; Cell Line, Tumor ; Colorectal Neoplasms/drug therapy/metabolism ; Heterocyclic Compounds, 3-Ring/pharmacology ; Humans ; Proteasome Endopeptidase Complex/metabolism ; Protein Binding ; Proteomics ; Repressor Proteins/chemistry/*metabolism ; Signal Transduction/*drug effects ; Tankyrases/*antagonists & inhibitors/metabolism ; Transcription, Genetic/drug effects ; Ubiquitin/metabolism ; Ubiquitination ; Wnt Proteins/*antagonists & inhibitors/metabolism ; beta Catenin/antagonists & inhibitors/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 5
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    Glucose deprivation contributes to the development of KRAS pathway mutations in tumor cells (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-08-08
    Description: Tumor progression is driven by genetic mutations, but little is known about the environmental conditions that select for these mutations. Studying the transcriptomes of paired colorectal cancer cell lines that differed only in the mutational status of their KRAS or BRAF genes, we found that GLUT1, encoding glucose transporter-1, was one of three genes consistently up-regulated in cells with KRAS or BRAF mutations. The mutant cells exhibited enhanced glucose uptake and glycolysis and survived in low-glucose conditions, phenotypes that all required GLUT1 expression. In contrast, when cells with wild-type KRAS alleles were subjected to a low-glucose environment, very few cells survived. Most surviving cells expressed high levels of GLUT1, and 4% of these survivors had acquired KRAS mutations not present in their parents. The glycolysis inhibitor 3-bromopyruvate preferentially suppressed the growth of cells with KRAS or BRAF mutations. Together, these data suggest that glucose deprivation can drive the acquisition of KRAS pathway mutations in human tumors.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2820374/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2820374/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yun, Jihye -- Rago, Carlo -- Cheong, Ian -- Pagliarini, Ray -- Angenendt, Philipp -- Rajagopalan, Harith -- Schmidt, Kerstin -- Willson, James K V -- Markowitz, Sandy -- Zhou, Shibin -- Diaz, Luis A Jr -- Velculescu, Victor E -- Lengauer, Christoph -- Kinzler, Kenneth W -- Vogelstein, Bert -- Papadopoulos, Nickolas -- CA43460/CA/NCI NIH HHS/ -- CA62924/CA/NCI NIH HHS/ -- R37 CA043460/CA/NCI NIH HHS/ -- R37 CA043460-27/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2009 Sep 18;325(5947):1555-9. doi: 10.1126/science.1174229. Epub 2009 Aug 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ludwig Center for Cancer Genetics and Therapeutics and Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19661383" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line, Tumor ; Cell Proliferation ; Colorectal Neoplasms/*genetics/metabolism ; Gene Expression Regulation, Neoplastic ; Gene Targeting ; *Genes, ras ; Glucose/*metabolism ; Glucose Transporter Type 1/genetics/metabolism ; Glycolysis/drug effects ; Humans ; Lactic Acid/metabolism ; Mice ; Mice, Nude ; *Mutation ; Neoplasm Transplantation ; Oligonucleotide Array Sequence Analysis ; Proto-Oncogene Proteins B-raf/*genetics ; Pyruvates/pharmacology ; Transplantation, Heterologous
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    Cancer. An unstable liaison (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-04-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lengauer, Christoph -- New York, N.Y. -- Science. 2003 Apr 18;300(5618):442-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA. lengauer@jhmi.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12702865" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Chromosome Aberrations ; Chromosomes/*genetics/physiology ; Colorectal Neoplasms/genetics ; DNA (Cytosine-5-)-Methyltransferase/genetics/metabolism ; *DNA Methylation ; DNA Repair ; Gene Silencing ; Genes, Neurofibromatosis 1 ; Genes, p53 ; Humans ; *Loss of Heterozygosity ; Lymphoma, T-Cell/genetics ; Mice ; Mutation ; Neoplasms/*genetics ; Recombination, Genetic ; Sarcoma/genetics ; Soft Tissue Neoplasms/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
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    Requirement for p53 and p21 to sustain G2 arrest after DNA damage (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-11-20
    Description: After DNA damage, many cells appear to enter a sustained arrest in the G2 phase of the cell cycle. It is shown here that this arrest could be sustained only when p53 was present in the cell and capable of transcriptionally activating the cyclin-dependent kinase inhibitor p21. After disruption of either the p53 or the p21 gene, gamma radiated cells progressed into mitosis and exhibited a G2 DNA content only because of a failure of cytokinesis. Thus, p53 and p21 appear to be essential for maintaining the G2 checkpoint in human cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bunz, F -- Dutriaux, A -- Lengauer, C -- Waldman, T -- Zhou, S -- Brown, J P -- Sedivy, J M -- Kinzler, K W -- Vogelstein, B -- CA 43460/CA/NCI NIH HHS/ -- CA 57345/CA/NCI NIH HHS/ -- CA 62924/CA/NCI NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1998 Nov 20;282(5393):1497-501.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Howard Hughes Medical Institute and The Johns Hopkins Oncology Center, 424 North Bond Street, Baltimore, MD 21231, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9822382" target="_blank"〉PubMed〈/a〉
    Keywords: Apoptosis ; CDC2 Protein Kinase/antagonists & inhibitors/metabolism ; Cell Line ; Cyclin B/metabolism ; Cyclin B1 ; Cyclin-Dependent Kinase Inhibitor p21 ; Cyclins/genetics/*physiology ; DNA/analysis ; *DNA Damage ; *G2 Phase/drug effects ; Gamma Rays ; Gene Expression Regulation ; Genes, p53 ; Humans ; Mitosis ; Mutation ; Nocodazole/pharmacology ; Tumor Cells, Cultured ; Tumor Suppressor Protein p53/*physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 8
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    Mutations of GTBP in genetically unstable cells (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-06-30
    Description: The molecular defects responsible for tumor cell hypermutability in humans have not yet been fully identified. Here the gene encoding a G/T mismatch-binding protein (GTBP) was localized to within 1 megabase of the related hMSH2 gene on chromosome 2 and was found to be inactivated in three hypermutable cell lines. Unlike cells defective in other mismatch repair genes, which display widespread alterations in mononucleotide, dinucleotide, and other simple repeated sequences, the GTBP-deficient cells showed alterations primarily in mononucleotide tracts. These results suggest that GTBP is important for maintaining the integrity of the human genome and document molecular defects accounting for variation in mutator phenotype.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Papadopoulos, N -- Nicolaides, N C -- Liu, B -- Parsons, R -- Lengauer, C -- Palombo, F -- D'Arrigo, A -- Markowitz, S -- Willson, J K -- Kinzler, K W -- CA35494/CA/NCI NIH HHS/ -- CA47527/CA/NCI NIH HHS/ -- CA62924/CA/NCI NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1995 Jun 30;268(5219):1915-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Johns Hopkins Oncology Center, Baltimore, MD 21231, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7604266" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Chromosome Mapping ; Chromosomes, Human, Pair 2 ; Codon ; Colorectal Neoplasms/*genetics ; Colorectal Neoplasms, Hereditary Nonpolyposis/genetics ; DNA Repair/*genetics ; DNA, Neoplasm/*genetics ; DNA, Satellite/genetics ; DNA-Binding Proteins/*genetics ; *Frameshift Mutation ; Genetic Markers ; Germ-Line Mutation ; Humans ; Molecular Sequence Data ; Tumor Cells, Cultured
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
    Electronic Resource
    Electronic Resource
    PC-Rietveld Plus, A Comprehensive Rietveld Analysis Package for PC (1993)
    s.l. ; Stafa-Zurich, Switzerland
    Materials science forum Vol. 133-136 (Jan. 1993), p. 287-292 
    Details
    ISSN: 1662-9752
    Source: Scientific.Net: Materials Science & Technology / Trans Tech Publications Archiv 1984-2008
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Type of Medium: Electronic Resource
    URL: http://www.tib-hannover.de/fulltexts/2011/0528/02/00/transtech_doi~10.4028%252Fwww.scientific.net%252FMSF.133-136.287.pdf
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  • 10
    Electronic Resource
    Electronic Resource
    Painting of human chromosomes with probes generated from hybrid cell lines by PCR with Alu and L1 primers (1990)
    Springer
    Human genetics 〈Berlin〉 86 (1990), S. 1-6 
    Details
    ISSN: 1432-1203
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary Specific amplification of human sequences of up to several kb length has recently been accomplished in man-hamster and man-mouse somatic hybrid cell DNA by IRS-PCR (interspersed repetitive sequence — polymerase chain reaction). This approach is based on oligonucleotide primers that anneal specifically to human Alu- or L1-sequences and allows the amplification of any human sequences located between adequately spaced, inverted Alu- or L1-blocks. Here, we demonstrate that probe pools generated from two somatic hybrid cell lines by Alu- and L1-PCR can be used for chromosome painting in normal human lymphocyte metaphase spreads by chromosomal in situ suppression (CISS-) hybridization. The painted chromosomes and chromosome subregions directly represent the content of normal and deleted human chromosomes in the two somatic hybrid cell lines. The combination of IRS-PCR and CISS-hybridization will facilitate and improve the cytogenetic analysis of somatic hybrid cell panels, in particular, in cases where structurally aberrant human chromosomes or human chromosome segments involved in interspecies translocations cannot be unequivocally identified by classical banding techniques. Moreover, this new approach will help to generate probe pools for the specific delineation of human chromosome subregions for use in cytogenetic diagnostics and research without the necessity of cloning.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00205163
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