Isolated oxygen defects in 3C- and 4H-SiC: A theoretical study

Ab initio calculations in the local-density approximation have been carried out in SiC to determine the possible configurations of the isolated oxygen impurity. Equilibrium geometry and occupation levels were calculated. Substitutional oxygen in 3C-SiC is a relatively shallow effective mass like double donor on the carbon site (O-C) and a hyperdeep double donor on the Si site (O-Si). In 4H-SiC O-C is still a double donor but with a more localized electron state. In 3C-SiC O-C is substantially more stable under any condition than O-Si or interstitial oxygen (O-i). In 4H-SiC O-C is also the most stable one except for heavy n-type doping. We propose that O-C is at the core of the electrically active oxygen-related defect family found by deep level transient spectroscopy in 4H-SiC. The consequences of the site preference of oxygen on the SiC/SiO2 interface are discussed

Knowledge-based energy functions for computational studies of proteins

This chapter discusses theoretical framework and methods for developing knowledge-based potential functions essential for protein structure prediction, protein-protein interaction, and protein sequence design. We discuss in some details about the Miyazawa-Jernigan contact statistical potential, distance-dependent statistical potentials, as well as geometric statistical potentials. We also describe a geometric model for developing both linear and non-linear potential functions by optimization. Applications of knowledge-based potential functions in protein-decoy discrimination, in protein-protein interactions, and in protein design are then described. Several issues of knowledge-based potential functions are finally discussed.Comment: 57 pages, 6 figures. To be published in a book by Springe

The genetic architecture of the human cerebral cortex

INTRODUCTION The cerebral cortex underlies our complex cognitive capabilities. Variations in human cortical surface area and thickness are associated with neurological, psychological, and behavioral traits and can be measured in vivo by magnetic resonance imaging (MRI). Studies in model organisms have identified genes that influence cortical structure, but little is known about common genetic variants that affect human cortical structure. RATIONALE To identify genetic variants associated with human cortical structure at both global and regional levels, we conducted a genome-wide association meta-analysis of brain MRI data from 51,665 individuals across 60 cohorts. We analyzed the surface area and average thickness of the whole cortex and 34 cortical regions with known functional specializations. RESULTS We identified 306 nominally genome-wide significant loci (P < 5 × 10−8) associated with cortical structure in a discovery sample of 33,992 participants of European ancestry. Of the 299 loci for which replication data were available, 241 loci influencing surface area and 14 influencing thickness remained significant after replication, with 199 loci passing multiple testing correction (P < 8.3 × 10−10; 187 influencing surface area and 12 influencing thickness). Common genetic variants explained 34% (SE = 3%) of the variation in total surface area and 26% (SE = 2%) in average thickness; surface area and thickness showed a negative genetic correlation (rG = −0.32, SE = 0.05, P = 6.5 × 10−12), which suggests that genetic influences have opposing effects on surface area and thickness. Bioinformatic analyses showed that total surface area is influenced by genetic variants that alter gene regulatory activity in neural progenitor cells during fetal development. By contrast, average thickness is influenced by active regulatory elements in adult brain samples, which may reflect processes that occur after mid-fetal development, such as myelination, branching, or pruning. When considered together, these results support the radial unit hypothesis that different developmental mechanisms promote surface area expansion and increases in thickness. To identify specific genetic influences on individual cortical regions, we controlled for global measures (total surface area or average thickness) in the regional analyses. After multiple testing correction, we identified 175 loci that influence regional surface area and 10 that influence regional thickness. Loci that affect regional surface area cluster near genes involved in the Wnt signaling pathway, which is known to influence areal identity. We observed significant positive genetic correlations and evidence of bidirectional causation of total surface area with both general cognitive functioning and educational attainment. We found additional positive genetic correlations between total surface area and Parkinson’s disease but did not find evidence of causation. Negative genetic correlations were evident between total surface area and insomnia, attention deficit hyperactivity disorder, depressive symptoms, major depressive disorder, and neuroticism. CONCLUSION This large-scale collaborative work enhances our understanding of the genetic architecture of the human cerebral cortex and its regional patterning. The highly polygenic architecture of the cortex suggests that distinct genes are involved in the development of specific cortical areas. Moreover, we find evidence that brain structure is a key phenotype along the causal pathway that leads from genetic variation to differences in general cognitive function

A Conceptual Framework for Understanding the Strengths of Black Youths

The strengths of Black youths lie in their abilities to resist the barriers that they encounter in the various environments in which they exist. Yet the media and social science literature have defined the youths in terms of the pathology of their environments rather than focusing on the assets that Black youths use in such environments. Thus, terms such as inner city , urban , and at-risk are used as proxies for the youths' personality attributes and themes, such as violence, substance abuse, school underachievement, and family instability are used to define their life experiences. In doing so, the literature suggests that the negative behaviors that it ascribes to Black youths are normative in actuality. In this article, a new framework for understanding the assets of Black youths is provided. The framework highlights the role of racial socialization in the youths' development of strengths that allow them to cope effectively with barriers