Laplacian normalization and random walk on heterogeneous networks for disease-gene prioritization

© 2015 Elsevier Ltd. All rights reserved. Random walk on heterogeneous networks is a recently emerging approach to effective disease gene prioritization. Laplacian normalization is a technique capable of normalizing the weight of edges in a network. We use this technique to normalize the gene matrix and the phenotype matrix before the construction of the heterogeneous network, and also use this idea to define the transition matrices of the heterogeneous network. Our method has remarkably better performance than the existing methods for recovering known gene-phenotype relationships. The Shannon information entropy of the distribution of the transition probabilities in our networks is found to be smaller than the networks constructed by the existing methods, implying that a higher number of top-ranked genes can be verified as disease genes. In fact, the most probable gene-phenotype relationships ranked within top 3 or top 5 in our gene lists can be confirmed by the OMIM database for many cases. Our algorithms have shown remarkably superior performance over the state-of-the-art algorithms for recovering gene-phenotype relationships. All Matlab codes can be available upon email request

Salinity effect and seed priming treatments on the germination of Suaeda salsa in the tidal marsh of the Yellow River estuary

The effects of salinity and seed priming treatments (hydropriming, water, KNO3 and KH2PO3) on the germination of the euhalophyte Suaeda salsa in intertidal zone of the Yellow River estuary were investigated. Results show that the seed germination percentage decreased with increasing NaCl concentration, and at the high NaCl level (800 mM), the lowest germination percentage was recorded. At the low NaCl levels, the highest germination rate was observed on day two and the seedling length was promoted slightly. In contrast, the germination delayed and the seedling length decreased at the high salinity. According to the survival functions, we also found that, at the low salinity, the seeds germinated quickly at the initial days and then the germination rate decreased, while few seeds germinated at the initial days at the high salinity. From the results of germination percentage and seedling length, we found that the effect of Yellow river water on germination was similar to the 400 mM NaCl. For priming treatments, the hydropriming has no promotion to the seeds germination, but it promoted the seedling growth at the river water and 400 mM NaCl. Seeds primed with KNO3 could improve the germination at the low salinity, while priming with KH2PO4 could improve the seedling growth at the high salinity, indicating that seed priming with proper nutrient (N, P) solutions could improve the germination or seedling growth as the nutrient (N, P) availability in the soil of S. salsa marsh was very limited.Keywords: Suaeda salsa, germination, salinity, priming, Yellow River estuar

Development of a commercial induction cooker

Author name used in this publication: Y. LuAuthor name used in this publication: K. W. E. ChengAuthor name used in this publication: K. W. ChanAuthor name used in this publication: S. W. ZhaoRefereed conference paper2008-2009 > Academic research: refereed > Refereed conference paperVersion of RecordPublishe

Pre-classification module for an all-season image retrieval system

Author name used in this publication: Zheru ChiAuthor name used in this publication: Dagan FengCentre for Multimedia Signal Processing, Department of Electronic and Information EngineeringRefereed conference paper2007-2008 > Academic research: refereed > Refereed conference paperVersion of RecordPublishe

Regulatory T cells in rheumatoid arthritis showed increased plasticity toward Th17 but retained suppressive function in peripheral blood

OBJECTIVE: Regulatory T cells (Tregs) with the plasticity of producing proinflammatory cytokine IL-17 have been demonstrated under normal and pathogenic conditions. However, it remains unclear whether IL-17-producing Tregs lose their suppressive functions because of their plasticity toward Th17 in autoimmunity. The aim of this study was to investigate IL-17-producing Tregs from patients with rheumatoid arthritis (RA), and characterise their regulatory capacity and clinical significance. METHODS: Foxp3 and IL-17 coexpression were evaluated in CD4 T lymphocytes from RA patients. An in vitro T cell polarisation assay was performed to investigate the role of proinflammatory cytokines in IL-17-producing Treg polarisation. The suppressive function of IL-17-producing Tregs in RA was assessed by an in vitro suppression assay. The relationship between this Treg subset and clinical features in RA patients was analysed using Spearman's rank correlation test. RESULTS: A higher frequency of IL-17-producing Tregs was present in the peripheral blood of RA patients compared with healthy subjects. These cells from peripheral blood showed phenotypic characteristics of Th17 and Treg cells, and suppressed T cell proliferation in vitro. Tregs in RA synovial fluid lost suppressive function. The Th17 plasticity of Tregs could be induced by IL-6 and IL-23. An increased ratio of this Treg subset was associated with decreased levels of inflammatory markers, including the erythrocyte sedimentation rate and C-reactive protein level, in patients with RA. CONCLUSIONS: Increased levels of IL-17-producing Tregs were identified in RA patients. This Treg subset with Th17 plasticity in peripheral blood retained suppressive functions and was associated with milder inflammatory conditions, suggesting that this Treg population works as a negative regulator in RA, but in RA synovial site it may be pathogenic.postprin

Kinetic frustration and the nature of the magnetic and paramagnetic states in iron pnictides and iron chalcogenides

The iron pnictide and chalcogenide compounds are a subject of intensive investigations due to their high temperature superconductivity.\cite{a-LaFeAsO} They all share the same structure, but there is significant variation in their physical properties, such as magnetic ordered moments, effective masses, superconducting gaps and T$_c$. Many theoretical techniques have been applied to individual compounds but no consistent description of the trends is available \cite{np-review}. We carry out a comparative theoretical study of a large number of iron-based compounds in both their magnetic and paramagnetic states. We show that the nature of both states is well described by our method and the trends in all the calculated physical properties such as the ordered moments, effective masses and Fermi surfaces are in good agreement with experiments across the compounds. The variation of these properties can be traced to variations in the key structural parameters, rather than changes in the screening of the Coulomb interactions. Our results provide a natural explanation of the strongly Fermi surface dependent superconducting gaps observed in experiments\cite{Ding}. We propose a specific optimization of the crystal structure to look for higher T$_c$ superconductors.Comment: 5 pages, 3 figures with a 5-page supplementary materia

STUDY ON TOTAL LUMINESCENCE SPECTRA - APPLICATION OF THE MONTE-CARLO METHOD TO 3-DIMENSIONAL SYNCHRONOUS FLUORESCENCE SPECTROMETRY

Three-dimensional synchronous fluorescence spectrometry (TDSFS, a combination of synchronous fluorescence spectrometry and three-dimensional fluorescence spectrometry) is a new method which has been developed recently. The method has usually been used as an efficient tool to select the best Delta lambda value for synchronous fluorescence spectra. This paper studies the sensitivity of the method, which was not been done in the past. The total fluorescence intensity has been used instead of the conventional single point intensity, calculated by the Monte-Carlo method, as the experimental parameter to determine fluorescein and tryptophan. The sensitivity of the total fluorescence method is nearly one hundred times better than that of the single point method. The new method has been used to simultaneously determine naphthalene, pyrene and perylene successfully. The mechanism of the method has also been studied

Phase Separation and Magnetic Order in K-doped Iron Selenide Superconductor

Alkali-doped iron selenide is the latest member of high Tc superconductor family, and its peculiar characters have immediately attracted extensive attention. We prepared high-quality potassium-doped iron selenide (KxFe2-ySe2) thin films by molecular beam epitaxy and unambiguously demonstrated the existence of phase separation, which is currently under debate, in this material using scanning tunneling microscopy and spectroscopy. The stoichiometric superconducting phase KFe2Se2 contains no iron vacancies, while the insulating phase has a \surd5\times\surd5 vacancy order. The iron vacancies are shown always destructive to superconductivity in KFe2Se2. Our study on the subgap bound states induced by the iron vacancies further reveals a magnetically-related bipartite order in the superconducting phase. These findings not only solve the existing controversies in the atomic and electronic structures in KxFe2-ySe2, but also provide valuable information on understanding the superconductivity and its interplay with magnetism in iron-based superconductors