| 11. |
- Kim, Tae-Yun, et al.
(author)
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3D Texture Analysis in Renal Cell Carcinoma Tissue Image Grading
- 2014
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In: Computational & Mathematical Methods in Medicine. - : Hindawi Publishing Corporation. - 1748-670X .- 1748-6718. ; 2014, s. 536217:1-12
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Journal article (peer-reviewed)abstract
- One of the most significant processes in cancer cell and tissue image analysis is the efficient extraction of features for grading purposes. This research applied two types of three-dimensional texture analysis methods to the extraction of feature values from renal cell carcinoma tissue images, and then evaluated the validity of the methods statistically through grade classification. First, we used a confocal laser scanning microscope to obtain image slices of four grades of renal cell carcinoma, which were then reconstructed into 3D volumes. Next, we extracted quantitative values using a 3D gray level cooccurrence matrix (GLCM) and a 3D wavelet based on two types of basis functions. To evaluate their validity, we predefined 6 different statistical classifiers and applied these to the extracted feature sets. In the grade classification results, 3D Haar wavelet texture features combined with principal component analysis showed the best discrimination results. Classification using 3D wavelet texture features was significantly better than 3D GLCM, suggesting that the former has potential for use in a computer-based grading system.
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| 12. |
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| 13. |
- Lee, Sang Hoon, 1982-, et al.
(author)
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Global organization of protein complexome in the yeast Saccharomyces cerevisiae
- 2011
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In: BMC Systems Biology. - : BioMed Central. - 1752-0509. ; 5:126, s. 15-
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Journal article (peer-reviewed)abstract
- Background: Proteins in organisms, rather than act alone, usually form protein complexes to perform cellular functions. We analyze the topological network structure of protein complexes and their component proteins in the budding yeast in terms of the bipartite network and its projections, where the complexes and proteins are its two distinct components. Compared to conventional protein-protein interaction networks, the networks from the protein complexes show more homogeneous structures than those of the binary protein interactions, implying the formation of complexes that cause a relatively more uniform number of interaction partners. In addition, we suggest a new optimization method to determine the abundance and function of protein complexes, based on the information of their global organization. Estimating abundance and biological functions is of great importance for many researches, by providing a quantitative description of cell behaviors, instead of just a "catalogues" of the lists of protein interactions.Results: With our new optimization method, we present genome-wide assignments of abundance and biological functions for complexes, as well as previously unknown abundance and functions of proteins, which can provide significant information for further investigations in proteomics. It is strongly supported by a number of biologically relevant examples, such as the relationship between the cytoskeleton proteins and signal transduction and the metabolic enzyme Eno2's involvement in the cell division process.Conclusions: We believe that our methods and findings are applicable not only to the specific area of proteomics, but also to much broader areas of systems biology with the concept of optimization principle.
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| 14. |
- Lee, Sang Hoon, 1982-, et al.
(author)
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Googling social interactions : web search engine based social network construction
- 2010
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In: PLoS ONE. - : Public Library of Science. - 1932-6203. ; 5:7, s. e11233-
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Journal article (peer-reviewed)abstract
- Social network analysis has long been an untiring topic of sociology. However, until the era of information technology, the availability of data, mainly collected by the traditional method of personal survey, was highly limited and prevented large-scale analysis. Recently, the exploding amount of automatically generated data has completely changed the pattern of research. For instance, the enormous amount of data from so-called high-throughput biological experiments has introduced a systematic or network viewpoint to traditional biology. Then, is “high-throughput” sociological data generation possible? Google, which has become one of the most influential symbols of the new Internet paradigm within the last ten years, might provide torrents of data sources for such study in this (now and forthcoming) digital era. We investigate social networks between people by extracting information on the Web and introduce new tools of analysis of such networks in the context of statistical physics of complex systems or socio-physics. As a concrete and illustrative example, the members of the 109th United States Senate are analyzed and it is demonstrated that the methods of construction and analysis are applicable to various other weighted networks.
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| 15. |
- Lee, Sang Hoon, 1982-, et al.
(author)
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Neutral theory of chemical reaction networks
- 2012
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In: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 14, s. 033032-
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Journal article (peer-reviewed)abstract
- To what extent do the characteristic features of a chemical reaction network reflect its purpose and function? In general, one argues that correlations between specific features and specific functions are key to understanding a complex structure. However, specific features may sometimes be neutral and uncorrelated with any system-specific purpose, function or causal chain. Such neutral features are caused by chance and randomness. Here we compare two classes of chemical networks: one that has been subjected to biological evolution (the chemical reaction network of metabolism in living cells) and one that has not (the atmospheric planetary chemical reaction networks). Their degree distributions are shown to share the very same neutral system-independent features. The shape of the broad distributions is to a large extent controlled by a single parameter, the network size. From this perspective, there is little difference between atmospheric and metabolic networks; they are just different sizes of the same random assembling network. In other words, the shape of the degree distribution is a neutral characteristic feature and has no functional or evolutionary implications in itself; it is not a matter of life and death.
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| 16. |
- Lessard, Christopher J., et al.
(author)
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Identification of IRF8, TMEM39A, and IKZF3-ZPBP2 as Susceptibility Loci for Systemic Lupus Erythematosus in a Large-Scale Multiracial Replication Study
- 2012
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In: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 90:4, s. 648-660
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Journal article (peer-reviewed)abstract
- Systemic lupus erythematosus (SLE) is a chronic heterogeneous autoimmune disorder characterized by the loss of tolerance to self-antigens and dysregulated interferon responses. The etiology of SLE is complex, involving both heritable and environmental factors. Candidate-gene studies and genome-wide association (GWA) scans have been successful in identifying new loci that contribute to disease susceptibility; however, much of the heritable risk has yet to be identified. In this study, we sought to replicate 1,580 variants showing suggestive association with SLE in a previously published GWA scan of European Americans; we tested a multiethnic population consisting of 7,998 SLE cases and 7,492 controls of European, African American, Asian, Hispanic, Gullah, and Amerindian ancestry to find association with the disease. Several genes relevant to immunological pathways showed association with SLE. Three loci exceeded the genome-wide significance threshold: interferon regulatory factor 8 (IRF8; rs11644034; p(meta-Euro) = 2.08 x 10(-10)), transmembrane protein 39A (TMEM39A; rs1132200; p(meta-all) 8.62 x 10(-9)), and 17q21 (rs1453560; p(meta-all) = 3.48 x 10(-10)) between IKAROS family of zinc finger 3 (AIOLOS; IKZF3) and zona pellucida binding protein 2 (ZPBP2). Fine mapping, resequencing, imputation, and haplotype analysis of IRF8 indicated that three independent effects tagged by rs8046526, rs450443, and rs4843869, respectively, were required for risk in individuals of European ancestry. Eleven additional replicated effects (5 x 10(-8) < p(meta-Euro) < 9.99 x 10(-5)) were observed with CFHR1, CADM2, LOC730109/IL12A, LPP, LOC63920, SLU7, ADAMTSL1, C10orf64, OR8D4 FAM19A2, and STXBP6. The results of this study increase the number of confirmed SLE risk loci and identify others warranting further investigation.
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| 17. |
- Niculaes, Claudiu, et al.
(author)
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Phenylcoumaran Benzylic Ether Reductase Prevents Accumulation of Compounds Formed under Oxidative Conditions in Poplar Xylem
- 2014
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In: The Plant Cell. - : Oxford University Press (OUP). - 1040-4651 .- 1532-298X. ; 26:9, s. 3775-3791
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Journal article (peer-reviewed)abstract
- Phenylcoumaran benzylic ether reductase (PCBER) is one of the most abundant proteins in poplar (Populus spp) xylem, but its biological role has remained obscure. In this work, metabolite profiling of transgenic poplar trees downregulated in PCBER revealed both the in vivo substrate and product of PCBER. Based on mass spectrometry and NMR data, the substrate was identified as a hexosylated 8-5-coupling product between sinapyl alcohol and guaiacylglycerol, and the product was identified as its benzyl-reduced form. This activity was confirmed in vitro using a purified recombinant PCBER expressed in Escherichia coli. Assays performed on 20 synthetic substrate analogs revealed the enzyme specificity. In addition, the xylem of PCBER-downregulated trees accumulated over 2000-fold higher levels of cysteine adducts of monolignol dimers. These compounds could be generated in vitro by simple oxidative coupling assays involving monolignols and cysteine. Altogether, our data suggest that the function of PCBER is to reduce phenylpropanoid dimers in planta to form antioxidants that protect the plant against oxidative damage. In addition to describing the catalytic activity of one of the most abundant enzymes in wood, we provide experimental evidence for the antioxidant role of a phenylpropanoid coupling product in planta.
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| 18. |
- Reddy, A. Satyanarayana, et al.
(author)
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Ultrathin titania coating for high-temperature stable SiO(2)/Pt nanocatalysts
- 2011
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In: Chemical Communications. - : Royal Society of Chemistry (RSC). - 1359-7345 .- 1364-548X. ; 47, s. 8412-8414
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Journal article (peer-reviewed)abstract
- The facile synthesis of silica supported platinum nanoparticles with ultrathin titania coating to enhance metal-support interactions suitable for high temperature reactions is reported, as thermal and structure stability of metal nanoparticles is important for catalytic reactions.
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| 19. |
- Wåhlin, Anna, 1970, et al.
(author)
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Variability of Warm Deep Water Inflow in a Submarine Trough on the Amundsen Sea Shelf
- 2013
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In: Journal of Physical Oceanography. - 0022-3670 .- 1520-0485. ; 43:10, s. 2054-2070
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Journal article (peer-reviewed)abstract
- The ice shelves in the Amundsen Sea are thinning rapidly, and the main reason for their decline appears to be warm ocean currents circulating below the ice shelves and melting these from below. Ocean currents transportwarm densewater ontothe shelf,channeledby bathymetric troughs leadingto the deep inner basins. A hydrographic mooring equipped with an upward-looking ADCP has been placed in one of these troughs on the central Amundsen shelf. The two years (2010/11) of mooring data are here used to characterize the inflow of warm deep water to the deep shelf basins. During both years, the warm layer thickness and temperature peaked in austral fall. The along-trough velocity is dominated by strong fluctuations that do not vary in the vertical. These fluctuations are correlated with the local wind, with eastward wind over the shelf and shelf break giving flow toward the ice shelves. In addition, there is a persistent flow of dense lower Circumpolar Deep Water (CDW) toward the ice shelves in the bottom layer. This bottom-intensified flow appears to be driven by buoyancy forces rather than the shelfbreak wind. The years of 2010 and 2011 were characterized by a comparatively stationary Amundsen Sea low, and hence there were no strong eastward winds during winter that could drive an upwelling of warm water along the shelf break. Regardless of this, there was a persistent flow of lower CDW in the bottom layer during the two years. The average heat transport toward the ice shelves in the trough was estimated from the mooring data to be 0.95 TW.
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| 20. |
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