Ranking analysis of F-statistics for microarray data

<p>Abstract</p> <p>Background</p> <p>Microarray technology provides an efficient means for globally exploring physiological processes governed by the coordinated expression of multiple genes. However, identification of genes differentially expressed in microarray experiments is challenging because of their potentially high type I error rate. Methods for large-scale statistical analyses have been developed but most of them are applicable to two-sample or two-condition data.</p> <p>Results</p> <p>We developed a large-scale multiple-group <it>F</it>-test based method, named ranking analysis of <it>F</it>-statistics (RAF), which is an extension of ranking analysis of microarray data (RAM) for two-sample t-test. In this method, we proposed a novel random splitting approach to generate the null distribution instead of using permutation, which may not be appropriate for microarray data. We also implemented a two-simulation strategy to estimate the false discovery rate. Simulation results suggested that it has higher efficiency in finding differentially expressed genes among multiple classes at a lower false discovery rate than some commonly used methods. By applying our method to the experimental data, we found 107 genes having significantly differential expressions among 4 treatments at <0.7% FDR, of which 31 belong to the expressed sequence tags (ESTs), 76 are unique genes who have known functions in the brain or central nervous system and belong to six major functional groups.</p> <p>Conclusion</p> <p>Our method is suitable to identify differentially expressed genes among multiple groups, in particular, when sample size is small.</p

Sister haplotypes and recombination disequilibrium: a new approach to identify associations of haplotypes with complex diseases

Haplotype-based association analysis has several advantages over single-SNP association analysis. However, to date all haplotype-disease associations have not excluded recombination interference among multiple loci and hence some results might be confounded by recombination interference. Association of sister haplotypes with a complex disease, based on recombination disequilibrium (RD) was presented. Sister haplotypes can be determined by translating notation of DNA base haplotypes to notation of genetic genotypes. Sister haplotypes provide haplotype pairs available for haplotype-disease association analysis. After performing RD tests in control and case cohorts, a two-by-two contingency table can be constructed using sister haplotype pair and case-control pair. With this standard two-by-two table, one can perform classical Chi-square test to find statistical haplotype-disease association. Applying this method to a haplotype dataset of Alzheimer disease (AD), association of sister haplotypes containing ApoE3/4 with risk for AD was identified under no RD. Haplotypes within gene IL-13 were not associated with risk for breast cancer in the case of no RD and no association of haplotypes in gene IL-17A with risk for coronary artery disease were detected without RD. The previously reported associations of haplotypes within these genes with risk for these diseases might be due to strong RD and/or inappropriate haplotype pairs

Perovskite-polymer composite cross-linker approach for highly-stable and efficient perovskite solar cells.

Manipulation of grain boundaries in polycrystalline perovskite is an essential consideration for both the optoelectronic properties and environmental stability of solar cells as the solution-processing of perovskite films inevitably introduces many defects at grain boundaries. Though small molecule-based additives have proven to be effective defect passivating agents, their high volatility and diffusivity cannot render perovskite films robust enough against harsh environments. Here we suggest design rules for effective molecules by considering their molecular structure. From these, we introduce a strategy to form macromolecular intermediate phases using long chain polymers, which leads to the formation of a polymer-perovskite composite cross-linker. The cross-linker functions to bridge the perovskite grains, minimizing grain-to-grain electrical decoupling and yielding excellent environmental stability against moisture, light, and heat, which has not been attainable with small molecule defect passivating agents. Consequently, all photovoltaic parameters are significantly enhanced in the solar cells and the devices also show excellent stability

Imaging the Black Hole Silhouette of M87: Implications for Jet Formation and Black Hole Spin

The silhouette cast by the horizon of the supermassive black hole in M87 can now be resolved with the emerging millimeter very-long baseline interferometry (VLBI) capability. Despite being ~2000 times farther away than SgrA* (the supermassive black hole at the center of the Milky-Way and the primary target for horizon-scale imaging), M87's much larger black hole mass results in a horizon angular scale roughly half that of SgrA*'s, providing another practical target for direct imaging. However, unlike SgrA*, M87 exhibits a powerful radio jet, providing an opportunity to study jet formation physics on horizon scales. We employ a simple, qualitatively correct force-free jet model to explore the expected high-resolution images of M87 at wavelengths of 1.3mm and 0.87mm (230GHz and 345GHz), for a variety of jet parameters. We show that future VLBI data will be able to constrain the size of the jet footprint, the jet collimation rate, and the black hole spin. Polarization will further probe the structure of the jet's magnetic field and its effect on the emitting gas. Horizon-scale imaging of M87 and SgrA* will enable for the first time the empirical exploration of the relationship between the mass and spin of a black hole and the characteristics of the gas inflow/outflow around it.Comment: 18 pages, 7 figures, accepted by Ap

Перспективи радонового індикаторного методу у визначенні обводнених інтервалів продуктивних пластів, насичених в'язкою нафтою ( на прикладі Семенівського нафтового родовища)

Рассмотрена возможность использования радонового индикаторного метода для выделения интервалов обводнения в карбонатном разрезе при условии низкоминерализованой пластовой воды. Используется разница в скоростях проникновения носителя радиоактивних изотопов (вода, дизельное топливо) в пласты, насыщенные вязкой нефтью и пластовой водой, за счет разницы фазовых проницаемостей нефтеносной и водоносной частей продуктивного пласта. В водоносной части продуктивных пластов образуется источник радиоактивного излучения большей интенсивности, чем в нефтеносной, за счет объема поступившего индикатора. Интервалы с повышенной радиоактивностью четко выделяются на диаграммах гамма-каротажаIn article the possibility of use the radon indicator's method for allocation of water-encroached intervals in carbonate section under condition of lowmineralized formation water is considered. The difference in speeds of penetration of the carrier radioactive isotopes (water, diesel fuel) in the layers, that saturated by viscous oil and formation water is used, due to a difference in phase permeability of oil and water-saturated parts of a productive layer. In the water-saturated parts of productive layers the source of radioactive radiation of the greater intensity, than in petroliferous is formed, due to volume of the arrived indicator. Intervals with the raised radio-activity are precisely allocated on the gamma-log diagrams

Mesorhizobium septentrionale sp nov and Mesorhizobium temperatum sp nov., isolated from Astragalus adsurgens growing in the northern regions of China

Ninety-five rhizobial strains isolated from Astragalus adsurgens growing in the northern regions of China were classified into three main groups, candidate species 1, 11 and 111, based on a polyphasic approach. Comparative analysis of full-length 16S rRNA gene sequences of representative strains showed that candidate species I and 11 were Mesorhizobium, while candidate species 111, which consisted of non-nodulating strains, was closely related to Agrobacterium tumefaciens. The phylogenetic relationships of the three candidate species and some related strains were also confirmed by the sequencing of glnA genes, which were used as an alternative chromosomal marker. The DNA-DNA relatedness was between 11.3 and 47-1 % among representative strains of candidate species I and 11 and the type strains of defined Mesorhizobium species. Candidate III had DNA relatedness of between 4(.)3 and 25(.)2 % with type strains of Agrobacterium tumefaciens and Agrobacterium rubi. Two novel species are proposed to accommodate candidate species I and 11, Mesorhizobium septentrionale sp. nov. (type strain, SIDW014(T) =CCBAU 11014(T) = HAMBI 2582(T)) and Mesorhizobium temperatum sp. nov. (type strain, SIDW018(T) = CCBAU 11018(T) =HAMBI 2583(T)), respectively. At least two distinct nodA sequences were identified among the strains. The numerically dominant nodA sequence type was most similar to that from the Mesorhizobium tianshanense type strain and was identified in strains belonging to the two novel species as well as other, as yet, undefined genome types. Host range studies indicate that the different nodA sequences correlate with different host ranges. Further comparative studies with the defined Agrobacterium species are needed to clarify the taxonomic identity of candidate species 111

Cloning and characterization of an S-RNase gene in Camellia sinensis

AbstractSelf-incompatibility (SI) prevents inbreeding depression in angiosperms. Camellia sinensis is an important cash crop, but breeding improvements and genetic studies of the plant are hindered by SI. However, the SI mechanism in C. sinensis remains unclear. In this study, a putative S-RNase gene (KU852488) was cloned from C. sinensis. The full-length cDNA of CsS-RNase is 1121bp, which encodes 238 amino acids. It shares the closest relationship with an S-RNase gene (ADA67883.1), which was cloned from a self-incompatibility Citrus reticulata cultivar ‘Wuzishatangju’. The expression level of CsS-RNase in the styles were 3–259 (‘Fuding Dabaicha’) and 5.6–119 (‘Zhongcha108’) times higher than the other tissues, for example petals, pollen grains, filaments and buds. And its expression rose in self-pollinated styles with 24h earlier than cross-pollinated styles. The genotypes of CsS-RNase in 10 cultivars and one breeding line of C. sinensis were analyzed. Totally, 11 polymorphic amino acid residues were identified. A single nucleotide polymorphism (SNP) marker of CsS-RNase was developed. Finally, the CsS-RNase was mapped onto a reference genetic linkage map of tea plant

Real-Time Observation of Iodide Ion Migration in Methylammonium Lead Halide Perovskites

Organic-inorganic metal-halide perovskites (e.g. CH3NH3PbI3-xClx) emerged as a promising opto-electronic material. However, the Shockley–Queisser Limit for the power conversion efficiency (PCE) of perovskite-based photovoltaic devices has still not been reached, which was attributed to non-radiative recombination pathways, as suggested by photoluminescence (PL) inactive (or dark) areas on perovskite films. Although these observations have been related to the presence of ions/defects, the underlying fundamental physics and detailed microscopic processes, concerning trap/defect status, ion migration, etc., still remain poorly understood. Here we utilize correlated wide-field PL microscopy and impedance spectroscopy (IS) on perovskite films to in-situ investigate both the spatial and temporal evolution of these PL inactive areas under external electrical fields. We attribute the formation of PL inactive domains to the migration and accumulation of iodine ions under external fields. Hence we are able to characterize the kinetic processes and determine the drift velocities of these ions. In addition, we show that I2 vapor directly affects the PL quenching of a perovskite film, which provides evidence that the migration/segregation of iodide ions plays an important role in the PL quenching and consequently limits the PCE of organometal halide based perovskite photovoltaic devices