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  • Molecular Diversity Preservation International  (45)
  • Oxford University Press  (29)
  • 1
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    Microstructure and Mechanical Strength of Attritor-Milled and Spark Plasma Sintered Mg-4Y-3Nd Alloy (2020)
    Molecular Diversity Preservation International
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    Publication Date: 2020-07-03
    Description: Gas-atomized powder of an Mg-4Y-3Nd magnesium alloy was attritor-milled at room temperature in an argon atmosphere for two time periods—1.5 and 5 h. Subsequently, the gas-atomized powder as well as both of the milled powders were spark plasma sintered at four temperatures, 400, 450, 500, and 550 °C, for 3 min. The effect of the milling on the powder particles’ morphology and the microstructure of the consolidated samples were studied by advanced microscopy techniques. The effect of the microstructural changes, resulting from the pre-milling and the sintering temperature, on the mechanical strength was investigated in compression along and perpendicular to the sintering load direction. Both the compression yield strength and ultimate compression strength were significantly affected by the grain size refinement, residual strain, secondary phase particles, and porosity. The results showed that attritor-milling imposed severe deformation to the powder particles, causing a significant grain size refinement in all of the consolidated samples. However, 1.5 h of milling was insufficient to achieve uniform refinement, and these samples also exhibited a distinctive anisotropy in the mechanical properties. Only a negligible anisotropy and superior yield strength were observed in the samples sintered from 5 h milled powder, whereas the ultimate strength was lower than that of the samples sintered from the gas-atomized powder.
    Electronic ISSN: 2073-4352
    Topics: Physics
    Published by Molecular Diversity Preservation International
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  • 2
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    xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model (2015)
    Oxford University Press
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    Publication Date: 2015-09-22
    Description: Motivation: Integrative network analysis methods provide robust interpretations of differential high-throughput molecular profile measurements. They are often used in a biomedical context—to generate novel hypotheses about the underlying cellular processes or to derive biomarkers for classification and subtyping. The underlying molecular profiles are frequently measured and validated on animal or cellular models. Therefore the results are not immediately transferable to human. In particular, this is also the case in a study of the recently discovered interleukin-17 producing helper T cells (Th17), which are fundamental for anti-microbial immunity but also known to contribute to autoimmune diseases. Results: We propose a mathematical model for finding active subnetwork modules that are conserved between two species. These are sets of genes, one for each species, which (i) induce a connected subnetwork in a species-specific interaction network, (ii) show overall differential behavior and (iii) contain a large number of orthologous genes. We propose a flexible notion of conservation, which turns out to be crucial for the quality of the resulting modules in terms of biological interpretability. We propose an algorithm that finds provably optimal or near-optimal conserved active modules in our model. We apply our algorithm to understand the mechanisms underlying Th17 T cell differentiation in both mouse and human. As a main biological result, we find that the key regulation of Th17 differentiation is conserved between human and mouse. Availability and implementation: xHeinz, an implementation of our algorithm, as well as all input data and results, are available at http://software.cwi.nl/xheinz and as a Galaxy service at http://services.cbib.u-bordeaux2.fr/galaxy in CBiB Tools. Contact: gunnar.klau@cwi.nl Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 3
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    Robustness and accuracy of functional modules in integrated network analysis (2012)
    Oxford University Press
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    Publication Date: 2012-07-06
    Description: Motivation: High-throughput molecular data provide a wealth of information that can be integrated into network analysis. Several approaches exist that identify functional modules in the context of integrated biological networks. The objective of this study is 2-fold: first, to assess the accuracy and variability of identified modules and second, to develop an algorithm for deriving highly robust and accurate solutions. Results: In a comparative simulation study accuracy and robustness of the proposed and established methodologies are validated, considering various sources of variation in the data. To assess this variation, we propose a jackknife resampling procedure resulting in an ensemble of optimal modules. A consensus approach summarizes the ensemble into one final module containing maximally robust nodes and edges. The resulting consensus module identifies and visualizes robust and variable regions by assigning support values to nodes and edges. Finally, the proposed approach is exemplified on two large gene expression studies: diffuse large B-cell lymphoma and acute lymphoblastic leukemia. Contact: marcus.dittrich@biozentrum.uni-wuerzburg.de or tobias.mueller@biozentrum.uni-wuerzburg.de Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 4
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    THOC5 controls 3'end-processing of immediate early genes via interaction with polyadenylation specific factor 100 (CPSF100) (2014)
    Oxford University Press
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    Publication Date: 2014-11-07
    Description: Transcription of immediate early genes (IEGs) in response to extrinsic and intrinsic signals is tightly regulated at multiple stages. It is known that untranslated regions of the RNA can play a role in these processes. Here we show that THOC5, a member of the TREX (transcription/export) complex, plays a role in expression of only a subset of constitutively active genes, however transcriptome analysis reveals that more than 90% of IEG were not induced by serum in THOC5 depleted cells. Furthermore, THOC5 depletion does not influence the expression of the most rapidly induced IEGs, e.g. Fos and Jun . One group of THOC5 target genes, including Id1 , Id3 and Wnt11 transcripts, were not released from chromatin in THOC5 depleted cells. Genes in another group, including Myc and Smad7 transcripts, were released with shortening of 3'UTR by alternative cleavage, and were spliced but export was impaired in THOC5 depleted cells. By interactome analysis using THOC5 as bait, we show that upon stimulation with serum THOC5 forms a complex with polyadenylation-specific factor 100 (CPSF100). THOC5 is required for recruitment of CPSF100 to 3'UTR of THOC5 target genes. These data suggest the presence of a novel mechanism for the control of IEG response by THOC5 via 3'end-processing.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Effects of small particle numbers on long-term behaviour in discrete biochemical systems (2014)
    Oxford University Press
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    Publication Date: 2014-08-27
    Description: Motivation: The functioning of many biological processes depends on the appearance of only a small number of a single molecular species. Additionally, the observation of molecular crowding leads to the insight that even a high number of copies of species do not guarantee their interaction. How single particles contribute to stabilizing biological systems is not well understood yet. Hence, we aim at determining the influence of single molecules on the long-term behaviour of biological systems, i.e. whether they can reach a steady state. Results: We provide theoretical considerations and a tool to analyse Systems Biology Markup Language models for the possibility to stabilize because of the described effects. The theory is an extension of chemical organization theory, which we called discrete chemical organization theory. Furthermore we scanned the BioModels Database for the occurrence of discrete chemical organizations. To exemplify our method, we describe an application to the Template model of the mitotic spindle assembly checkpoint mechanism. Availability and implementation: http://www.biosys.uni-jena.de/Services.html . Contact: bashar.ibrahim@uni-jena.de or dittrich@minet.uni-jena.de Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 6
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    Transcriptional landscape and essential genes of Neisseria gonorrhoeae (2014)
    Oxford University Press
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    Publication Date: 2014-09-17
    Description: The WHO has recently classified Neisseria gonorrhoeae as a super-bacterium due to the rapid spread of antibiotic resistant derivatives and an overall dramatic increase in infection incidences. Genome sequencing has identified potential genes, however, little is known about the transcriptional organization and the presence of non-coding RNAs in gonococci. We performed RNA sequencing to define the transcriptome and the transcriptional start sites of all gonococcal genes and operons. Numerous new transcripts including 253 potentially non-coding RNAs transcribed from intergenic regions or antisense to coding genes were identified. Strikingly, strong antisense transcription was detected for the phase-variable opa genes coding for a family of adhesins and invasins in pathogenic Neisseria , that may have regulatory functions. Based on the defined transcriptional start sites, promoter motifs were identified. We further generated and sequenced a high density Tn5 transposon library to predict a core of 827 gonococcal essential genes, 133 of which have no known function. Our combined RNA-Seq and Tn-Seq approach establishes a detailed map of gonococcal genes and defines the first core set of essential gonococcal genes.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Evolution in an Ancient Detoxification Pathway Is Coupled with a Transition to Herbivory in the Drosophilidae (2014)
    Oxford University Press
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    Publication Date: 2014-08-20
    Description: Chemically defended plant tissues present formidable barriers to herbivores. Although mechanisms to resist plant defenses have been identified in ancient herbivorous lineages, adaptations to overcome plant defenses during transitions to herbivory remain relatively unexplored. The fly genus Scaptomyza is nested within the genus Drosophila and includes species that feed on the living tissue of mustard plants (Brassicaceae), yet this lineage is derived from microbe-feeding ancestors. We found that mustard-feeding Scaptomyza species and microbe-feeding Drosophila melanogaster detoxify mustard oils, the primary chemical defenses in the Brassicaceae, using the widely conserved mercapturic acid pathway. This detoxification strategy differs from other specialist herbivores of mustard plants, which possess derived mechanisms to obviate mustard oil formation. To investigate whether mustard feeding is coupled with evolution in the mercapturic acid pathway, we profiled functional and molecular evolutionary changes in the enzyme glutathione S- transferase D1 (GSTD1), which catalyzes the first step of the mercapturic acid pathway and is induced by mustard defense products in Scaptomyza . GSTD1 acquired elevated activity against mustard oils in one mustard-feeding Scaptomyza species in which GstD1 was duplicated. Structural analysis and mutagenesis revealed that substitutions at conserved residues within and near the substrate-binding cleft account for most of this increase in activity against mustard oils. Functional evolution of GSTD1 was coupled with signatures of episodic positive selection in GstD1 after the evolution of herbivory. Overall, we found that preexisting functions of generalized detoxification systems, and their refinement by natural selection, could play a central role in the evolution of herbivory.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Middle Class, Tradition and the Desi-Realm—Discourses of Alternative Food Networks in Bengaluru, India (2020)
    Molecular Diversity Preservation International
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    Publication Date: 2020-03-31
    Description: It has repeatedly been claimed that persistent traditional agriculture and marketing in countries of the Global South, such as India, are a fruitful basis for the foundation of alternative food networks (AFNs). However, literature on AFNs in the Global South is scarce and it thus remains uncertain how the appropriation of traditional agri-food practices plays out. We conducted semi-structured expert interviews with representatives of 14 AFNs in Bengaluru, India, in order to explore their aims and approaches. We found that there is a high variety of different AFNs in the city. One salient discourse among the representatives was that the agri-food system can be improved by a revitalization of tradition. In this paper, we discuss the implications of this conviction on representatives of AFNs. Traditionalism, we argue, does rather represent a deflection from achieving the stated goals of the AFN, namely the improvement of the livelihood of Indian farmers.
    Electronic ISSN: 2071-1050
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by Molecular Diversity Preservation International
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  • 9
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    Tensor Network Renormalization with Fusion Charges—Applications to 3D Lattice Gauge Theory (2020)
    Molecular Diversity Preservation International
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    Publication Date: 2020-07-12
    Description: Tensor network methods are powerful and efficient tools for studying the properties and dynamics of statistical and quantum systems, in particular in one and two dimensions. In recent years, these methods have been applied to lattice gauge theories, yet these theories remain a challenge in ( 2 + 1 ) dimensions. In this article, we present a new (decorated) tensor network algorithm, in which the tensors encode the lattice gauge amplitude expressed in the fusion basis. This has several advantages—firstly, the fusion basis does diagonalize operators measuring the magnetic fluxes and electric charges associated to a hierarchical set of regions. The algorithm allows therefore a direct access to these observables. Secondly the fusion basis is, as opposed to the previously employed spin network basis, stable under coarse-graining. Thirdly, due to the hierarchical structure of the fusion basis, the algorithm does implement predefined disentanglers. We apply this new algorithm to lattice gauge theories defined for the quantum group SU ( 2 ) k and identify a weak and a strong coupling phase for various levels k . As we increase the level k , the critical coupling g c decreases linearly, suggesting the absence of a deconfining phase for the continuous group SU ( 2 ) . Moreover, we illustrate the scaling behaviour of the Wilson loops in the two phases.
    Electronic ISSN: 2218-1997
    Topics: Physics
    Published by Molecular Diversity Preservation International
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  • 10
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    Increasing the Size-Selectivity in Laser-Based g/h Liquid Flow Synthesis of Pt and PtPd Nanoparticles for CO and NO Oxidation in Industrial Automotive Exhaust Gas Treatment Benchmarking (2020)
    Molecular Diversity Preservation International
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    Publication Date: 2020-08-12
    Description: PtPd catalysts are state-of-the-art for automotive diesel exhaust gas treatment. Although wet-chemical preparation of PtPd nanoparticles below 3 nm and kg-scale synthesis of supported PtPd/Al2O3 are already established, the partial segregation of the bimetallic nanoparticles remains an issue that adversely affects catalytic performance. As a promising alternative, laser-based catalyst preparation allows the continuous synthesis of surfactant-free, solid-solution alloy nanoparticles at the g/h-scale. However, the required productivity of the catalytically relevant size fraction
    Electronic ISSN: 2079-4991
    Topics: Physics
    Published by Molecular Diversity Preservation International
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