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  • 1
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    Testing differential networks with applications to the detection of gene-gene interactions (2015)
    Oxford University Press
    Details
    Publication Date: 2015-05-24
    Description: Model organisms and human studies have yielded increasing empirical evidence that interactions among genes contribute broadly to genetic variation of complex traits. In the presence of gene-gene interactions, the dimensionality of the feature space becomes extremely high relative to the sample size. This poses a significant methodological challenge in the identification of gene-gene interactions. In this paper, by using a Gaussian graphical model framework, we translate the problem of identifying gene-gene interactions associated with a binary trait D into an inference problem on the difference of two high-dimensional precision matrices that summarize the conditional dependence network structures of the genes. We propose a procedure for testing the differential network globally, which is particularly powerful against sparse alternatives. In addition, a multiple testing procedure with false discovery rate control is developed to infer the specific structure of the differential network. Theoretical justification is provided to ensure the validity of the proposed tests, and optimality results are derived under sparsity assumptions. Through a simulation study we demonstrate that the proposed tests maintain the desired error rates under the null hypothesis and have good power under the alternative hypothesis. The methods are applied to a breast cancer gene expression study.
    Print ISSN: 0006-3444
    Electronic ISSN: 1464-3510
    Topics: Biology , Mathematics , Medicine
    Published by Oxford University Press
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  • 2
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    Nonlinear real-life signal detection with a supervised principal components analysis (2007)
    American Institute of Physics
    Details
    Publication Date: 2007-03-01
    Print ISSN: 1054-1500
    Electronic ISSN: 1089-7682
    Topics: Physics
    Published by American Institute of Physics
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  • 3
    Electronic Resource
    Electronic Resource
    Optimization of the Supercritical Fluid Extraction of Natural Vitamin E from Wheat Germ Using Response Surface Methodology (2002)
    Oxford, UK : Blackwell Publishing Ltd
    Journal of food science 67 (2002), S. 0 
    Details
    ISSN: 1750-3841
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Process Engineering, Biotechnology, Nutrition Technology
    Notes: : Natural vitamin E was extracted by supercritical fluid extraction of carbon dioxide (SFE-CO2) from wheat germ. Several SFE-CO2 parameters, such as extracting pressure, extracting temperature, and flow rate of carbon dioxide were examined as the independent variables of central composite rotate design (CCRD). Through the response surface methodology (RSM), the optimal processing conditions were determined and the quadratic response surfaces were drawn from the mathematical models. The results demonstrated that the extracting pressure, temperature, pressure × temperature interaction, and flow rate of CO2 significantly affected the yield of the natural Vitamin E's extraction, while two interactions containing the flow rate of CO2 had no significant effect on the yield of natural vitamin E. The optimal processing conditions of the extraction of natural vitamin E in wheat germ by SFE-CO2 were: extracting pressure 5000 PSI, extracting temperature 316 K, and flow rate of carbon dioxide 1.7 ml/min. Optimum value predicted by RSM for the concentration of natural vitamin E was 2307 mg/100g. Close agreement between experimental and predicted values was obtained.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1365-2621.2002.tb11391.x
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  • 4
    Electronic Resource
    Electronic Resource
    Effects of intraperitoneal injection of cortisol on non-specific immune functions of Ctenopharyngodon idella (2005)
    Oxford, UK; Malden, USA : Blackwell Science Ltd
    Journal of fish biology 67 (2005), S. 0 
    Details
    ISSN: 1095-8649
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: After grass carps Ctenopharyngodon idellus were injected with cortisol, with (CBC) and without (C) a cocoa butter carrier, the effects of both slowly and rapidly acting exogenous cortisol on their non-specific immune functions were investigated. On the one hand, after injection with CBC, the cortisol concentration and lysozyme activity in fish serum were enhanced and were sustained at high levels for a long period (30 days). The killing activity in the serum declined with time, and phagocytosis of head kidney macrophages diminished significantly (P 〈 0·05 or P 〈 0·01). The leukocrit values in the high dose group (31·8 mg cortisol fish−1) increased over time, however, with the maximum average being 5·6% at day 30. The spleen mass index in the high dose group was 0·93 × 10−3 after 30 days, notably lower (P 〈 0·05) than that in the control group. In addition, a decrease in resistance to Aeromonas hydrophila infection in cortisol-treated fish was shown, with the final cumulative mortalities being 54·5 and 66·7% in the low and high dose groups, respectively. On the other hand, there was a decrease in both serum cortisol concentration and lysozyme activity of the experimental fish within 2 weeks after injection with C, where plasma bactericidal activities in the high dose group (31·8 mg cortisol fish−1) were remarkably lower (P 〈 0·01) than those in the control group at each sampling, but were increased slightly over time. The results of which were different from those in the CBC trial. Phagocytic activity of head kidney macrophages and spleen mass index decreased significantly (P 〈 0·05), while there were increases in leukocrit value and cumulative mortality due to A. hydrophila. The results of which were similar to those in the CBC trial. This study indicated that the injection of cortisol depressed the non-specific immune functions of the grass carp and increased its susceptibility to disease.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.0022-1112.2005.00779.x
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  • 5
    Electronic Resource
    Electronic Resource
    Light pressure forces on multi-level atoms in intense polychromatic light fields: a continued fraction approach
    Amsterdam : Elsevier
    Optics Communications 104 (1993), S. 175-184 
    Details
    ISSN: 0030-4018
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Physics
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/0030-4018(93)90126-P
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  • 6
    Electronic Resource
    Electronic Resource
    Somaclonal variation in high tannin sorghums (1990)
    Springer
    Theoretical and applied genetics 79 (1990), S. 737-747 
    Details
    ISSN: 1432-2242
    Keywords: Plant tissue culture ; Somaclonal variation ; Sorghum bicolor
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Genetic variants were found among over 6,000 primary plants (R1) regenerated from embryogenic tissue cultures of eight high tannin sorghums [Sorghum bicolor (L.) Moench]. Field assessment of somaclonal variation has progressed to the R2 population, with over 48,000 R2 seedlings (27,000 plants) in 1,126 rows from 1,055 R1 plants. A total of 43 variant phenotypes was recovered, including several types of chlorophyll deficiencies, dwarfism, short culm, sterility, narrow leaf, and several previously unreported variants, such as ragged leaf, multibranched heads, and Hydra, a developmental variant which produces large numbers of panicles. Variation production greatly depends on parent genotype and appears to increase with increasing time in cultures. The toal average somaclonal variation rate (based per 100 R1 plants) and somaclonal variant frequency (based per 100 R2 plants) estimated in the tested population were 11.3 and 1.6, respectively. Chimerism was found in regenerants. The estimated size of the mutated sector carried by mutant regenerants ranged from the whole plant to less than 3% of a single head. The average proportion of mutated R1 heads carrying large (80%–100%), medium (40%–80%), and small (〈40%) mutated sectors was 38.7%, 26.0% and 35.3%, respectively. Some sector mutations do not appear until the R3 generation. In order to avoid losing variants, the population for selecting somaclonal variation should be as large as possible. Some of these variants found may be useful for further study or for use in breeding programs.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00224238
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  • 7
    Electronic Resource
    Electronic Resource
    Screening for grain polyphenol variants from high-tannin sorghum somaclones (1995)
    Springer
    Theoretical and applied genetics 90 (1995), S. 211-220 
    Details
    ISSN: 1432-2242
    Keywords: Somaclonal variation ; Plant tissue culture ; Polyphenols ; Sorghum bicolor
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Several hundred somaclones established from plants regenerated from embryogenic callus cultures of six high tannin sorghum lines were screened for variants with altered levels of polyphenols in the grain. Grain from over 6000 plants including the R 1 (primary), R2, and R3 generations were analyzed for total phenols, flavan-4-ols, and proanthocyanidins (condensed tannins). Although many variants which had lost the ability to synthesize chlorophyll were found, none of the somaclones tested had lost or greatly reduced the ability to synthesize any of the polyphenols assayed. However, we did observe statistically significant differences in polyphenol concentration between tissue culture-derived R1 plants and the parental controls. In the R2 generation the proportion of somaclones which differed significantly from the parents varied from 47% to 68% depending upon genotype. The average somaclonal variation rate and somaclonal variant frequency estimated in the tested population for the three polyphenol characteristics ranged from 37.3% to 40.7% and 5.3% to 7.8%, respectively. Variants with decreased levels of polyphenols were usually epigenetic and reverted back to normal levels in subsequent generations, but those with increased levels usually persisted after two meiotic cycles, indicating they are heritable. Variants with polyphenol levels increased up to 80% or decreased by 30% were selected for in the R3 generation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00222204
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  • 8
    Electronic Resource
    Electronic Resource
    Study of photoreaction in dichromated gelatin by laser photoacoustic technique (1997)
    Springer
    Applied physics 64 (1997), S. 377-381 
    Details
    ISSN: 1432-0649
    Keywords: PACS: 78.20Hp; 82.80KQ; 82.50
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract.  An experimental method to study the photochemical reaction in solid-state dichromated gelatin during exposure is proposed, in which two laser sources with different wavelengths are used to induce photoreaction and to excite photoacoustic signal, respectively. This method is to obtain the real-time characteristics during the formation of the photoreaction product. The curve is fitted using the Rosencwaig-Gersho (R-G) theory and chemical kinetics. The reaction order and the rate of reaction may be obtained by fitting the parameters. The results show that photochemical reaction in dichromated gelatin conforms to the mechanism suggested by Watanable-Westheimer, and the photosensitivity of the samples, prepared under different conditions, is dependent on the initial concentration of photoactive ions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s003400050187
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  • 9
    Electronic Resource
    Electronic Resource
    Semi-classical theory of laser cooling in two dimensions (1999)
    Springer
    The European physical journal 7 (1999), S. 269-278 
    Details
    ISSN: 1434-6079
    Keywords: PACS. 32.80.Pj Optical cooling of atoms; trapping
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract: We present a semi-classical theory of the light pressure force for atoms interacting with a two-dimensional laser field. Unlike previous 2D theory, ours is valid for general atomic level and laser field configurations. We show that striking new features appear in the velocity-dependent force arising from the multi-dimensionality. Finally, we describe in detail the novel numerical technique used in the calculation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s100530050569
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  • 10
    Electronic Resource
    Electronic Resource
    The electronic structure of Keggin anion (PW12O40)3- and catalytic properties (1992)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 44 (1992), S. 1015-1025 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The electronic structure of the Keggin anion (PW12O40)3- has been calculated by the DV-Xα method. The nature of the chemical bonds of the Keggin anion and the relationship between electronic structure and catalytic behavior are discussed. At the same time, the difference in electronic structure and the relationship in catalytic behavior between (PW12O40)3- and (PMo12O40)3- are compared. © 1992 John Wiley & Sons, Inc.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560440606
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