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  • 1
    Publication Date: 2015-12-18
    Description: Motivation: Hodgkin lymphoma (HL) is a type of B-cell lymphoma. To diagnose the subtypes, biopsies are taken and immunostained. The slides are scanned to produce high-resolution digital whole slide images (WSI). Pathologists manually inspect the spatial distribution of cells, but little is known on the statistical properties of cell distributions in WSIs. Such properties would give valuable information for the construction of theoretical models that describe the invasion of malignant cells in the lymph node and the intercellular interactions. Results: In this work, we define and discuss HL cell graphs. We identify CD30 + cells in HL WSIs, bringing together the fields of digital imaging and network analysis. We define special graphs based on the positions of the immunostained cells. We present an automatic analysis of complete WSIs to determine significant morphological and immunohistochemical features of HL cells and their spatial distribution in the lymph node tissue under three different medical conditions: lymphadenitis (LA) and two types of HL. We analyze the vertex degree distributions of CD30 cell graphs and compare them to a null model. CD30 cell graphs show higher vertex degrees than expected by a random unit disk graph, suggesting clustering of the cells. We found that a gamma distribution is suitable to model the vertex degree distributions of CD30 cell graphs, meaning that they are not scale-free. Moreover, we compare the graphs for LA and two subtypes of HL. LA and classical HL showed different vertex degree distributions. The vertex degree distributions of the two HL subtypes NScHL and mixed cellularity HL (MXcHL) were similar. Availability and implementation: The CellProfiler pipeline used for cell detection is available at https://sourceforge.net/projects/cellgraphs/ . Contact: ina.koch@bioinformatik.uni-frankfurt.de Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 2
    ISSN: 1432-0630
    Keywords: PACS: 78.70; 73.40; 75.70
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract.  The coupling of Cr to Fe in stacked Cr/Fe/Cr trilayers is studied by circular magnetic X-ray dichroism using fluorescence yield to monitor the absorption. From the dichroic spectra, we determine the thickness dependent average magnetic coupling of Cr to Fe for Cr layer thicknesses of 1, 2 and 3 ML. We compare our results to new calculated spectra. Additionally, all Cr spectra show significant contributions due to photon scattering processes at the L 2,3 absorption edges, depending on the degree of circular polarization.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    Journal of materials science 10 (1999), S. 519-525 
    ISSN: 1573-4838
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine , Technology
    Notes: Abstract A commercial software package, MAGMASOFT (MAGMA Giessereitechnologie GmbH, Aachen, Germany), was used to study shrinkage and gas porosity in titanium dental castings. A geometrical model for two simplified tooth crowns connected by a connector bar was created. Both mold filling and solidification of this casting model were numerically simulated. Shrinkage porosity was quantitatively predicted by means of a built-in feeding criterion. The risk of gas pore formation was investigated using the numerical filling and solidification results. The results of the numerical simulations were compared with experiments, which were carried out on a centrifugal casting machine with an investment block mold. The block mold was made of SiO2 based slurry with a 1 mm thick Zr2 face coat to reduce metal–mold reactions. Both melting and casting were carried out under protective argon (40 kPa). The finished castings were sectioned and the shrinkage porosity determined. The experimentally determined shrinkage porosity coincided with the predicted numerical simulation results. No apparent gas porosity was found in these model castings. Several running and gating systems for the above model casting were numerically simulated. An optimized running and gating system design was then experimentally cast, which resulted in porosity-free castings. © 1999 Kluwer Academic Publishers
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 1573-4986
    Keywords: Paenibacillus alvei ; secondary cell wall polymer (SCWP) ; surface layer (S-layer) ; peptidoglycan ; NMR spectroscopy ; structure determination
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The peptidoglycan, the secondary cell wall polymer (SCWP), and the surface layer (S-layer) glycoprotein are the major glycosylated cell wall components of Paenibacillus alvei CCM 2051. In this report, the complete structure of the SCWP, its linkage to the peptidoglycan layer, and its physicochemical properties have been investigated. From the combined evidence of chemical and structural analyses together with one- and two-dimensional nuclear magnetic resonance spectroscopy, the following structure of the SCWP-peptidoglycan complex is proposed: [(Pyr4,6)-β-D-Manp NAc-(1→4)-β-D-Glcp NAc-(1→3)]ñ11-(Pyr4,6)-β-D-Manp NAc-(1→4)-α-D-Glcp NAc-(1→O)-PO2-O-PO2-(O→6)-MurNAc- Each disaccharide unit is substituted by 4,6-linked pyruvic acid residues. Under mild acidic conditions, up to 50% of them are lost, leaving non-substituted ManNAc residues. The anionic glycan chains constituting the SCWP are randomly linked via pyrophosphate groups to C-6 of muramic acid residues of the peptidoglycan layer. 31P NMR reveals two signals that, as a consequence of micelle formation, experience different line broadening. Therefore, their integral ratio deviates significantly from 1:1. By treatment with ethylenediaminetetraacetic acid, sodium dodecyl sulfate, and sonication immediately prior to NMR measurement, this ratio approaches unity. The reversibility of this behavior corroborates the presence of a pyrophosphate linker in this SCWP-peptidoglycan complex. In addition to the determination of the structure and linkage of the SCWP, a possible scenario for its biological function is discussed.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Zeitschrift für anorganische Chemie 545 (1987), S. 69-74 
    ISSN: 0044-2313
    Keywords: Chemistry ; Inorganic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Description / Table of Contents: Crystal Structure of Barium Hydride, Determined by Neutron Diffraction Experiments on BaD2A reinvestigation of the structure of BaH2 and BaD2 was performed on powdered samples by X-ray- and neutron diffraction experiments. It is shown, that the hydrogen positions correspond with those in calcium deuteride [1, 2] and not with those proposed by Zintl and Harder [3]. The classification of Barium hydride in the PbCl2 structure type is discussed.
    Notes: Über Röntgen- und Neutronenbeugungsexperimente an pulverförmigen Proben wurde die Kristallstruktur von BaH2 bzw. BaD2 neu bestimmt. Sie entspricht der des Calciumdeuterids [1, 2] und zeigt, daß die seinerzeit von Zintl und Harder [3] angenommenen Wasserstoffpositionen nicht zutreffen. Die Einordnung des Bariumhydrids in die Strukturfamilie des Bleichloridtyps wird diskutiert.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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  • 6
    Publication Date: 2015-12-09
    Description: Flagellin glycosylation impacts, in several documented cases, the functionality of bacterial flagella. The basis of flagellin glycosylation has been studied for various Gram-negative bacteria, but less is known about flagellin glycans of Gram-positive bacteria including Paenibacillus alvei , a secondary invader of honeybee colonies diseased with European foulbrood. Paenibacillus alvei CCM 2051 T swarms vigorously on solidified culture medium, with swarming relying on functional flagella as evidenced by abolished biofilm formation of a non-motile P. alvei mutant defective in the flagellin protein Hag. Here, the glycobiology of the polar P. alvei flagella was investigated. Analysis on purified flagellin demonstrated that the 30-kDa Hag protein (PAV_2c01710) is modified with an O -linked trisaccharide comprised of one hexose and two N -acetyl-hexosamine residues, at three sites of glycosylation. Downstream of the hag gene on the bacterial chromosome, two open reading frames (PAV_2c01630, PAV_2c01640) encoding putative glycosyltransferases were shown to constitute a flagellin glycosylation island. Mutants defective in these genes exhibited altered migration in sodium dodecyl sulfate polyacrylamide gel electrophoresis as well as loss of extracellular flagella production and bacterial motility. This study reveals that flagellin glycosylation in P. alvei is pivotal to flagella formation and bacterial motility in vivo, and simultaneously identifies flagella glycosylation as a second protein O -glycosylation system in this bacterium, in addition to the well-investigated S-layer tyrosine O -glycosylation pathway.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
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  • 7
    Publication Date: 2015-10-31
    Description: Social insects such as ants have evolved collective rather than individual immune defence strategies against diseases and parasites at the level of their societies (colonies), known as social immunity. Ants frequently host other arthropods, so-called myrmecophiles, in their nests. Here, we tested the hypothesis that myrmecophily may partly arise from selection for exploiting the ants’ social immunity. We used larvae of the wax moth Galleria mellonella as ‘model myrmecophiles’ (baits) to test this hypothesis. We found significantly reduced abundance of entomopathogens in ant nests compared with the surrounding environment. Specific entomopathogen groups ( Isaria fumosorosea and nematodes) were also found to be significantly less abundant inside than outside ant nests, whereas one entomopathogen ( Beauveria brongniartii ) was significantly more abundant inside nests. We therefore hypothesize that immunological benefits of entering ant nests may provide us a new explanation of why natural selection acts in favour of such a life-history strategy.
    Keywords: evolution
    Electronic ISSN: 2054-5703
    Topics: Natural Sciences in General
    Published by Royal Society
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  • 8
    Publication Date: 2016-03-17
    Description: Objectives This study aimed to compare visualisation of the vocal cords and performance of intubation by anaesthetists using four different laryngoscopes while wearing full chemical protective equipment. Setting Medical simulation center of a university hospital, department of anaesthesiology. Participants 42 anaesthetists (15 females and 27 males) completed the trial. The participants were grouped according to their professional education as anaesthesiology residents with experience of 〈2 years or 〈5 years, or as anaesthesiology specialists with experience of 〉5 years. Interventions In a manikin scenario, participants performed endotracheal intubations with four different direct and indirect laryngoscopes (Macintosh (MAC), Airtraq (ATQ), Glidescope (GLS) and AP Advance (APA)), while wearing chemical protective gear, including a body suit, rubber gloves, a fire helmet and breathing apparatus. Primary and secondary outcome measures With respect to the manikin, setting time to complete ‘endotracheal intubation’ was defined as primary end point. Glottis visualisation (according to the Cormack-Lehane score (CLS) and impairments caused by the protective equipment, were defined as secondary outcome measures. Results The times to tracheal intubation were calculated using the MAC (31.4 s; 95% CI 26.6 to 36.8), ATQ (37.1 s; 95% CI 28.3 to 45.9), GLS (35.4 s; 95% CI 28.7 to 42.1) and APA (23.6 s; 95% CI 19.1 to 28.1), respectively. Intubation with the APA was significantly faster than with all the other devices examined among the total study population (p〈0.05). A significant improvement in visualisation of the vocal cords was reported for the APA compared with the GLS. Conclusions Despite the restrictions caused by the equipment, the anaesthetists intubated the manikin successfully within adequate time. The APA outperformed the other devices in the time to intubation, and it has been evaluated as an easily manageable device for anaesthetists with varying degrees of experience (low to high), providing good visualisation in scenarios that require the use of chemical protective equipment.
    Keywords: Open access, Anaesthesia, Emergency medicine, Medical education and training
    Electronic ISSN: 2044-6055
    Topics: Medicine
    Published by BMJ Publishing
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  • 9
    Publication Date: 2016-03-19
    Description: Abasic sites (AP-sites) are frequent DNA lesions, arising by spontaneous base hydrolysis or as intermediates of base excision repair (BER). The hemiacetal at the anomeric centre renders them chemically reactive, which presents a challenge to biochemical and structural investigation. Chemically more stable AP-site analogues have been used to avoid spontaneous decay, but these do not fully recapitulate the features of natural AP–sites. With its 3'–phosphate replaced by methylene, the abasic site analogue 3CAPS was suggested to circumvent some of these limitations. Here, we evaluated the properties of 3CAPS in biochemical BER assays with mammalian proteins. 3CAPS-containing DNA substrates were processed by APE1, albeit with comparably poor efficiency. APE1-cleaved 3CAPS can be extended by DNA polymerase β but repaired only by strand displacement as the 5'–deoxyribophosphate (dRP) cannot be removed. DNA glycosylases physically and functionally interact with 3CAPS substrates, underlining its structural integrity and biochemical reactivity. The AP lyase activity of bifunctional DNA glycosylases (NTH1, NEIL1, FPG), however, was fully inhibited. Notably, 3CAPS-containing DNA also effectively inhibited the activity of bifunctional glycosylases on authentic substrates. Hence, the chemically stable 3CAPS with its preserved hemiacetal functionality is a potent tool for BER research and a potential inhibitor of bifunctional DNA glycosylases.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 10
    Publication Date: 2016-02-02
    Description: Motivation: Phosphoproteomics measurements are widely applied in cellular biology to detect changes in signalling dynamics. However, due to the inherent complexity of phosphorylation patterns and the lack of knowledge on how phosphorylations are related to functions, it is often not possible to directly deduce protein activities from those measurements. Here, we present a heuristic machine learning algorithm that infers the activities of kinases from Phosphoproteomics data using kinase–target information from the PhosphoSitePlus database. By comparing the estimated kinase activity profiles to the measured phosphosite profiles, it is furthermore possible to derive the kinases that are most likely to phosphorylate the respective phosphosite. Results: We apply our approach to published datasets of the human cell cycle generated from HeLaS3 cells, and insulin signalling dynamics in mouse hepatocytes. In the first case, we estimate the activities of 118 at six cell cycle stages and derive 94 new kinase–phosphosite links that can be validated through either database or motif information. In the second case, the activities of 143 kinases at eight time points are estimated and 49 new kinase–target links are derived. Availability and implementation: The algorithm is implemented in Matlab and be downloaded from github. It makes use of the Optimization and Statistics toolboxes. https://github.com/marcel-mischnik/IKAP.git . Contact: marcel.mischnik@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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