Sufficient principal component regression for pattern discovery in transcriptomic data

Methods for global measurement of transcript abundance such as microarrays and RNA-seq generate datasets in which the number of measured features far exceeds the number of observations. Extracting biologically meaningful and experimentally tractable insights from such data therefore requires high-dimensional prediction. Existing sparse linear approaches to this challenge have been stunningly successful, but some important issues remain. These methods can fail to select the correct features, predict poorly relative to non-sparse alternatives, or ignore any unknown grouping structures for the features. We propose a method called SuffPCR that yields improved predictions in high-dimensional tasks including regression and classification, especially in the typical context of omics with correlated features. SuffPCR first estimates sparse principal components and then estimates a linear model on the recovered subspace. Because the estimated subspace is sparse in the features, the resulting predictions will depend on only a small subset of genes. SuffPCR works well on a variety of simulated and experimental transcriptomic data, performing nearly optimally when the model assumptions are satisfied. We also demonstrate near-optimal theoretical guarantees.Comment: 26 pages, 9 figures, 9 table

Vertical distributions of non-methane hydrocarbons and halocarbons in the lower troposphere over northeast China

Vertical distributions of air pollutants are crucial for understanding the key processes of atmospheric transport and for evaluating chemical transport models. In this paper, we present measurements of non-methane hydrocarbons (NMHCs) and halocarbons obtained from an intensive aircraft study over northeast (NE) China in summer 2007. Most compounds exhibited a typical negative profile of decreasing mixing ratios with increasing altitude, although the gradients differed with different species. Three regional plumes with enhanced VOC mixing ratios were discerned and characterized. An aged plume transported from the northern part of the densely populated North China Plain (NCP; i.e. Beijing-Tianjin area) showed relatively higher levels of HCFC-22, 1,2-dichloroethane (1,2-DCE) and toluene. In comparison, the plume originating from Korea had higher abundances of CFC-12, tetrachloroethene (C2Cl4) and methyl chloride (CH3Cl), while regional air masses from NE China contained more abundant light alkanes. By comparing these results with the earlier PEM-West B (1994) and TRACE-P (2001) aircraft measurements, continuing declining trends were derived for methyl chloroform (CH3CCl3), tetrachloromethane (CCl4) and C2Cl4 over the greater China-northwestern Pacific region, indicating the accomplishment of China in reducing these compounds under the Montreal protocol. However, the study also provided evidence for the continuing emissions of several halocarbons in China in 2007, such as CFCs (mainly from materials in stock) and HCFCs. © 2011 Elsevier Ltd

Mesoscopic Kondo effect of a quantum dot embedded in an Aharonov-Bohm ring with intradot spin-flip scattering

We study the Kondo effect in a quantum dot embedded in a mesoscopic ring taking into account intradot spin-flip scattering $R$. Based on the finite-$U$ slave-boson mean-field approach, we find that the Kondo peak in the density of states is split into two peaks by this coherent spin-flip transition, which is responsible for some interesting features of the Kondo-assisted persistent current circulating the ring: (1) strong suppression and crossover to a sine function form with increasing $R$; (2) appearance of a "hump" in the $R$-dependent behavior for odd parity. $R$-induced reverse of the persistent current direction is also observed for odd parity.Comment: 7 pages,6 figures, to be published by Europhys. Let

Insect pest management with sex pheromone precursors from engineered oilseed plants

Pheromones have become an environmentally friendly alternative to conventional insecticides for pest control. Most current pheromone-based pest control products target lepidopteran pests of high-value crops, as today’s manufacturing processes cannot yet produce pheromones at low enough costs to enable their use for lower-value crops, especially commodity crops. Camelina sativa seeds genetically modified to express (Z)-11-hexadecenoic acid, a sex pheromone precursor of several moth species, provided the oil from which the precursor was isolated, purified and transformed into the final pheromone. Trap lures containing this pheromone were then assessed for their capacity to manage moth pests in the field. Plant-derived pheromone lures proved equally effective as synthetic pheromone lures in monitoring the diamondback moth, Plutella xylostella, in cabbage and disrupting mating of cotton bollworm, Helicoverpa armigera, in common bean fields. Our study demonstrates the biological efficacy and economic feasibility of pheromone production in plant factories by metabolic engineering of an oilseed crop

Genetic Dissection of Root Angle of Brassica napus in Response to Low Phosphorus

Plant root angle determines the vertical and horizontal distribution of roots in the soil layer, which further influences the acquisition of phosphorus (P) in topsoil. Large genetic variability for the lateral root angle (root angle) was observed in a linkage mapping population (BnaTNDH population) and an association panel of Brassica napus whether at a low P (LP) or at an optimal P (OP). At LP, the average root angle of both populations became smaller. Nine quantitative trait loci (QTLs) at LP and three QTLs at OP for the root angle and five QTLs for the relative root angle (RRA) were identified by the linkage mapping analysis in the BnaTNDH population. Genome-wide association studies (GWASs) revealed 11 single-nucleotide polymorphisms (SNPs) significantly associated with the root angle at LP (LPRA). The interval of a QTL for LPRA on A06 (qLPRA-A06c) overlapped with the confidence region of the leading SNP (Bn-A06-p14439400) significantly associated with LPRA. In addition, a QTL cluster on chromosome C01 associated with the root angle and the primary root length (PRL) in the “pouch and wick” high-throughput phenotyping (HTP) system, the root P concentration in the agar system, and the seed yield in the field was identified in the BnaTNDH population at LP. A total of 87 genes on A06 and 192 genes on C01 were identified within the confidence interval, and 14 genes related to auxin asymmetric redistribution and root developmental process were predicted to be candidate genes. The identification and functional analyses of these genes affecting LPRA are of benefit to the cultivar selection with optimal root system architecture (RSA) under P deficiency in Brassica napus