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  • 1
    Publication Date: 2014-12-31
    Description: Without any doubt XML is currently a de facto standard for data representation. Its popularity is given by the fact that it is well-defined, easy-to-use, and, at the same time, sufficiently expressive. However, most of XML documents are still created without the respective description of their structure, i.e. an XML schema. Since the knowledge of XML schema is crucial for various data processing approaches as well as a standard optimization tool, approaches to (semi-)automatic inference of XML schema become an interesting research problem. Recently, there have been introduced several approaches that improve particular steps of the inference process. The problem is how to compare such approaches, how to find the optimal ones and how to join them to get the best possible result. In this paper, we introduce jInfer , a general framework for XML schema inference. It represents an easily extensible tool that enables one to implement, test and compare new modules of the inference process. Since the compulsory parts of the process, such as parsing of XML data, visualization of automata, transformation of automata to XML schema languages, etc. are implemented, the user can focus purely on the research and the improved aspect of the inference process. We describe not only the framework, but the area of schema inference in general, including related work and open problems.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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  • 2
    Publication Date: 2012-12-27
    Description: Author(s): J. Preclíková, M. Kozák, D. Fregenal, Ø. Frette, B. Hamre, B. T. Hjertaker, J. P. Hansen, and L. Kocbach We study Rydberg wave packets produced by pairs of time separated femtosecond laser pulses. The time separation ranges from femtosecond to picosecond time scales. The wave packets consist predominantly of f states of principal quantum numbers n =22–32 in Li. With a direct analysis of the field ioniza... [Phys. Rev. A 86, 063418] Published Wed Dec 26, 2012
    Keywords: Atomic and molecular processes in external fields, including interactions with strong fields and short pulses
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
    Topics: Physics
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  • 3
    Publication Date: 2014-09-30
    Description: Author(s): A. F. Kravets, Yu. I. Dzhezherya, A. I. Tovstolytkin, I. M. Kozak, A. Gryshchuk, Yu. O. Savina, V. A. Pashchenko, S. L. Gnatchenko, B. Koop, and V. Korenivski Interlayer exchange coupling in strong/weak/strong ferromagnetic multilayers is investigated as a function of external magnetic field and temperature, with the focus on the magnetization switching near the Curie transition in the spacer composed of a diluted ferromagnet of concentration paramagnetic... [Phys. Rev. B 90, 104427] Published Mon Sep 29, 2014
    Keywords: Magnetism
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 4
    Publication Date: 2014-07-16
    Description: The Journal of Physical Chemistry B DOI: 10.1021/jp5047485
    Electronic ISSN: 1520-5207
    Topics: Chemistry and Pharmacology , Physics
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  • 5
    Publication Date: 2014-04-08
    Description: Author(s): J. Preclíková, M. Kozák, D. Fregenal, and J. P. Hansen We propose a method for measuring velocities of atoms or molecules in a gas phase based on time-resolved laser experiments. Two intensity gratings of electromagnetic field with variable time delay τ are created by interfering of four laser pulses. Using first-order perturbation theory, we show that ... [Phys. Rev. A 89, 043406] Published Mon Apr 07, 2014
    Keywords: Atomic and molecular processes in external fields, including interactions with strong fields and short pulses
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
    Topics: Physics
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  • 6
  • 7
    Publication Date: 2018-09-19
    Description: Hmga2 is dispensable for pancreatic cancer development, metastasis, and therapy resistance Hmga2 is dispensable for pancreatic cancer development, metastasis, and therapy resistance, Published online: 18 September 2018; doi:10.1038/s41598-018-32159-x Hmga2 is dispensable for pancreatic cancer development, metastasis, and therapy resistance
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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  • 8
    Publication Date: 2016-03-17
    Description: Pyruvate and acetyl-coenzyme A, located at the interface between glycolysis and TCA cycle, are important intermediates in yeast metabolism and key precursors for industrially relevant products. Rational engineering of their supply requires knowledge of compensatory reactions that replace predominant pathways when these are inactivated. This study investigates effects of individual and combined mutations that inactivate the mitochondrial pyruvate-dehydrogenase (PDH) complex, extramitochondrial citrate synthase (Cit2) and mitochondrial CoA-transferase (Ach1) in Saccharomyces cerevisiae . Additionally, strains with a constitutively expressed carnitine shuttle were constructed and analyzed. A predominant role of the PDH complex in linking glycolysis and TCA cycle in glucose-grown batch cultures could be functionally replaced by the combined activity of the cytosolic PDH bypass and Cit2. Strongly impaired growth and a high incidence of respiratory deficiency in pda1 ach1 strains showed that synthesis of intramitochondrial acetyl-CoA as a metabolic precursor requires activity of either the PDH complex or Ach1 . Constitutive overexpression of AGP2 , HNM1 , YAT2 , YAT1 , CRC1 and CAT2 enabled the carnitine shuttle to efficiently link glycolysis and TCA cycle in l -carnitine-supplemented, glucose-grown batch cultures. Strains in which all known reactions at the glycolysis-TCA cycle interface were inactivated still grew slowly on glucose, indicating additional flexibility at this key metabolic junction.
    Print ISSN: 1567-1356
    Electronic ISSN: 1567-1364
    Topics: Biology
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  • 9
    Publication Date: 2006-06-24
    Description: Posttranslational arginylation is critical for mouse embryogenesis, cardiovascular development, and angiogenesis, but its molecular effects and the identity of proteins arginylated in vivo are unknown. We found that beta-actin was arginylated in vivo to regulate actin filament properties, beta-actin localization, and lamella formation in motile cells. Arginylation of beta-actin apparently represents a critical step in the actin N-terminal processing needed for actin functioning in vivo. Thus, posttranslational arginylation of a single protein target can regulate its intracellular function, inducing global changes on the cellular level, and may contribute to cardiovascular development and angiogenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Karakozova, Marina -- Kozak, Marina -- Wong, Catherine C L -- Bailey, Aaron O -- Yates, John R 3rd -- Mogilner, Alexander -- Zebroski, Henry -- Kashina, Anna -- P41 RR11823-09/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2006 Jul 14;313(5784):192-6. Epub 2006 Jun 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Animal Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16794040" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/*metabolism/ultrastructure ; Actins/chemistry/*metabolism ; Aminoacyltransferases/genetics/metabolism ; Animals ; Arginine/chemistry/*metabolism ; *Cell Movement ; Cell Shape ; Cell Size ; Fibroblasts ; Immunoprecipitation ; Isoelectric Point ; Mass Spectrometry ; Mice ; Protein Binding ; Protein Isoforms/chemistry/metabolism ; Pseudopodia/metabolism/ultrastructure
    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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  • 10
    Publication Date: 2014-08-15
    Description: CHARGE syndrome is a multiple anomaly disorder in which patients present with a variety of phenotypes, including ocular coloboma, heart defects, choanal atresia, retarded growth and development, genitourinary hypoplasia and ear abnormalities. Despite 70-90% of CHARGE syndrome cases resulting from mutations in the gene CHD7, which encodes an ATP-dependent chromatin remodeller, the pathways underlying the diverse phenotypes remain poorly understood. Surprisingly, our studies of a knock-in mutant mouse strain that expresses a stabilized and transcriptionally dead variant of the tumour-suppressor protein p53 (p53(25,26,53,54)), along with a wild-type allele of p53 (also known as Trp53), revealed late-gestational embryonic lethality associated with a host of phenotypes that are characteristic of CHARGE syndrome, including coloboma, inner and outer ear malformations, heart outflow tract defects and craniofacial defects. We found that the p53(25,26,53,54) mutant protein stabilized and hyperactivated wild-type p53, which then inappropriately induced its target genes and triggered cell-cycle arrest or apoptosis during development. Importantly, these phenotypes were only observed with a wild-type p53 allele, as p53(25,26,53,54)(/-) embryos were fully viable. Furthermore, we found that CHD7 can bind to the p53 promoter, thereby negatively regulating p53 expression, and that CHD7 loss in mouse neural crest cells or samples from patients with CHARGE syndrome results in p53 activation. Strikingly, we found that p53 heterozygosity partially rescued the phenotypes in Chd7-null mouse embryos, demonstrating that p53 contributes to the phenotypes that result from CHD7 loss. Thus, inappropriate p53 activation during development can promote CHARGE phenotypes, supporting the idea that p53 has a critical role in developmental syndromes and providing important insight into the mechanisms underlying CHARGE syndrome.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4192026/" 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/PMC4192026/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Van Nostrand, Jeanine L -- Brady, Colleen A -- Jung, Heiyoun -- Fuentes, Daniel R -- Kozak, Margaret M -- Johnson, Thomas M -- Lin, Chieh-Yu -- Lin, Chien-Jung -- Swiderski, Donald L -- Vogel, Hannes -- Bernstein, Jonathan A -- Attie-Bitach, Tania -- Chang, Ching-Pin -- Wysocka, Joanna -- Martin, Donna M -- Attardi, Laura D -- 1F31CA167917-01/CA/NCI NIH HHS/ -- F31 CA167917/CA/NCI NIH HHS/ -- R01 CA140875/CA/NCI NIH HHS/ -- R01 DC009410/DC/NIDCD NIH HHS/ -- R01 GM095555/GM/NIGMS NIH HHS/ -- R01 HL118087/HL/NHLBI NIH HHS/ -- R01HL121197/HL/NHLBI NIH HHS/ -- England -- Nature. 2014 Oct 9;514(7521):228-32. doi: 10.1038/nature13585. Epub 2014 Aug 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Radiation Oncology, Division of Radiation and Cancer Biology, Stanford University School of Medicine, Stanford, California 94305, USA. ; 1] Department of Radiation Oncology, Division of Radiation and Cancer Biology, Stanford University School of Medicine, Stanford, California 94305, USA [2] Cardiovascular Research Center and Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA (C.A.B.); Department of Medicine, University of Central Florida, Orlando, Florida 32827, USA (M.M.K.); Department of Emergency Medicine, Oregon Health and Science University, Portland, Oregon 97239, USA (T.M.J.). ; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA. ; Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA. ; Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA. ; Department of Otolaryngology, The University of Michigan Medical School, Ann Arbor, Michigan 48109, USA. ; Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA. ; 1] Departement de Genetique, Hopital Necker-Enfants Malades, APHP, 75015 Paris, France [2] Unite INSERM U1163, Universite Paris Descartes-Sorbonne Paris Cite, Institut Imagine, 75015 Paris, France. ; Krannert Institute of Cardiology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA. ; 1] Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA [2] Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA. ; 1] Department of Pediatrics, The University of Michigan Medical School, Ann Arbor, Michigan 48109, USA [2] Department of Human Genetics, The University of Michigan Medical School, Ann Arbor, Michigan 48109, USA. ; 1] Department of Radiation Oncology, Division of Radiation and Cancer Biology, Stanford University School of Medicine, Stanford, California 94305, USA [2] Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25119037" target="_blank"〉PubMed〈/a〉
    Keywords: Abnormalities, Multiple/genetics/*metabolism ; Alleles ; Animals ; Apoptosis/genetics ; CHARGE Syndrome/*genetics/*metabolism ; Cell Cycle Checkpoints/genetics ; Craniofacial Abnormalities/genetics/metabolism ; DNA-Binding Proteins/deficiency/genetics/metabolism ; Ear/abnormalities ; Embryo, Mammalian/abnormalities/metabolism ; Female ; Fibroblasts ; Gene Deletion ; Heterozygote ; Humans ; Male ; Mice ; Mutant Proteins/metabolism ; *Phenotype ; Promoter Regions, Genetic/genetics ; Tumor Suppressor Protein p53/*genetics/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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