Genome-wide association tests by using block information in family data

Abstract By applying an association test to analyze the data sets from Genetic Analysis Workshop 15 Problem 3, we compare power using different haplotype-block information. The results from using both of the two different coding schemes show that the test using tight blocks with limited haplotype diversity within each block is more powerful than that using evenly spaced blocks, and the latter is more powerful than that using single-marker blocks. By using carefully chosen haplotype blocks, the power of association tests may be enhanced.http://deepblue.lib.umich.edu/bitstream/2027.42/117371/1/12919_2007_Article_2513.pd

Altitudinal Patterns of Leaf Traits and Leaf Allometry in Bamboo Pleioblastus amarus

Awareness of local-scale variation in leaf traits for a single species and the relationships between these traits and their dependence on altitude might be essential for extrapolating ecophysiological processes from the leaf to the ecosystem level. While altitudinal patterns of leaf traits have been extensively studied in a number of species, little is known about such patterns in bamboos. We analyzed leaf functional traits and leaf allometric relationships of Pleioblastus amarus at three different altitudes (200, 400, and 800 m). With increasing altitude, most functional traits, including leaf length, width, perimeter, area, dry weight, and water content, decreased significantly, while the leaf length:width ratio exhibited a marked increase, resulting in a tendency toward narrow leaves. Specific leaf area first increased, and then decreased, while the change in leaf dry matter content showed the opposite trend. Leaf area was positively correlated with leaf length, leaf width and leaf perimeter, but negatively correlated with the leaf length:width ratio. With increasing altitude, the slopes of these relationships for leaf area first increased, and then decreased. Leaf biomass was positively correlated with leaf length, width, perimeter, and area, with the slopes of the relationships being the same at all altitudes. Thus, the leaves of this bamboo species at middle altitude have the highest specific leaf area and lowest leaf dry matter content. Our findings suggest that this bamboo species has a big potential of growth and morphological plasticity

Nitrogen-doped TiO₂ for promoting CO₂ activation towards methanol synthesis over Cu-based catalyst

Creating surface oxygen vacancy (Ov) is key to enrich catalytically active metal-oxide interfaces to promote CO2 activation and thus facilitating methanol synthesis via CO2 hydrogenation. This study shows that nitrogen (N) doping of TiO2 could achieve this, and the bimetallic CuGa supported on N doped TiO2 (CuGa/TiO2-N0.5) attained the improved methanol yield compared to the undoped counterpart (CuGa/TiO2, 1.2 g gCu−1 h−1 vs. 0.75 g gCu−1 h−1 at 300 °C). The combined characterization, such as high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM), X-ray absorption spectroscopy (XAS), and CO/H2 temperature-programmed reduction (CO/H2-TPR), reveals that incorporation of N species in crystalline rutile TiO2 promoted O2 formation, being beneficial to promote CO2 activation. High-pressure in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) combining steady-state isotope transient kinetic analysis (SSITKA, with H2/D2 isotopic exchange) was conducted, and the results suggest that the hydrogenation of formates bound on the supported Cu species is the rate-limiting step, while in situ DRIFTS experiments with CO2-H2 switching specifically demonstrate that the formation of Cu-bound formates on CuGa/TiO2-N0.5 is facilitated by the improved CO2 interaction affinity induced by N doping. In addition, relevant findings by in situ DRIFTS-MS studies (temperature-programmed surface reaction and CO2-CO switching) also suggest that, during CO2 hydrogenation, H2 and CO (by-product) could possibly react with surface weak oxygen species to regenerate weak surface OV maintaining the catalyst's activity

Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes

BACKGROUND: Due to the high cost and low reproducibility of many microarray experiments, it is not surprising to find a limited number of patient samples in each study, and very few common identified marker genes among different studies involving patients with the same disease. Therefore, it is of great interest and challenge to merge data sets from multiple studies to increase the sample size, which may in turn increase the power of statistical inferences. In this study, we combined two lung cancer studies using micorarray GeneChip(®), employed two gene shaving methods and a two-step survival test to identify genes with expression patterns that can distinguish diseased from normal samples, and to indicate patient survival, respectively. RESULTS: In addition to common data transformation and normalization procedures, we applied a distribution transformation method to integrate the two data sets. Gene shaving (GS) methods based on Random Forests (RF) and Fisher's Linear Discrimination (FLD) were then applied separately to the joint data set for cancer gene selection. The two methods discovered 13 and 10 marker genes (5 in common), respectively, with expression patterns differentiating diseased from normal samples. Among these marker genes, 8 and 7 were found to be cancer-related in other published reports. Furthermore, based on these marker genes, the classifiers we built from one data set predicted the other data set with more than 98% accuracy. Using the univariate Cox proportional hazard regression model, the expression patterns of 36 genes were found to be significantly correlated with patient survival (p < 0.05). Twenty-six of these 36 genes were reported as survival-related genes from the literature, including 7 known tumor-suppressor genes and 9 oncogenes. Additional principal component regression analysis further reduced the gene list from 36 to 16. CONCLUSION: This study provided a valuable method of integrating microarray data sets with different origins, and new methods of selecting a minimum number of marker genes to aid in cancer diagnosis. After careful data integration, the classification method developed from one data set can be applied to the other with high prediction accuracy

Projected near-term changes of temperature extremes in Europe and China under different aerosol emissions

This study assesses near-term future changes in temperature extremes over China and Europe in scenarios with two very different anthropogenic aerosol (AA) pathways from 2016 to 2049: a maximum technically feasible aerosol reduction (MTFR), and a current legislation aerosol scenario (CLE), both with greenhouses gas forcing following RCP 4.5. Simulations with a fully coupled atmosphere-ocean model HadGEM3-GC2 show that there is an increase in hot extremes and a decrease in cold extremes relative to the present day (1995-2014) over China and Europe in both scenarios. However, the magnitude of the changes in both hot and cold extremes depends strongly on the AA pathway. The AA reduction in MTFR amplifies the changes in temperature extremes relative to CLE, and accounts for 40% and 30% of the projected changes in temperature extremes relative to present day over China and Europe respectively. Thus, this study suggests that future and current policy decisions about AA emissions have the potential for a large near-term impact on temperature extremes

Opportunity for marine fisheries reform in China

China's 13th Five-Year Plan, launched in March 2016, provides a sound policy platform for the protection of marine ecosystems and the restoration of capture fisheries within China's exclusive economic zone. What distinguishes China among many other countries striving for marine fisheries reform is its size- accounting for almost one-fifth of global catch volume-and the unique cultural context of its economic and resource management. In this paper, we trace the history of Chinese government priorities, policies, and outcomes related to marine fisheries since the 1978 Economic Reform, and examine how the current leadership's agenda for "ecological civilization" could successfully transform marine resource management in the coming years. We show how China, like many other countries, has experienced a decline in the average trophic level of its capture fisheries during the past few decades, and how its policy design, implementation, and enforcement have influenced the status of its wild fish stocks. To reverse the trend in declining fish stocks, the government is introducing a series of new programs for sustainable fisheries and aquaculture, with greater traceability and accountability in marine resource management and area controls on coastal development. As impressive as these new plans are on paper, we conclude that serious institutional reforms will be needed to achieve a true paradigm shift in marine fisheries management in China. In particular, we recommend new institutions for science-based fisheries management, secure fishing access, policy consistency across provinces, educational programs for fisheries managers, and increasing public access to scientific data.Additional co-authors: Yingqi Zhou, Ping Zhuang, and Rosamond L. Naylo