Estimation of l0 Norm Penalized Models: A Statistical Treatment.

Fitting penalized models for the purpose of merging the estimation and model selection problem has become commonplace in statistical practice. Of the various regularization strategies that can be leveraged to this end, the use of the l0 norm to penalize parameter estimation poses the most daunting model fitting task. In fact, this particular strategy requires an end user to solve a non-convex NP-hard optimization problem irregardless of the underlying data model. For this reason, the use of the l0 norm as a regularization strategy has been woefully under utilized. To obviate this difficulty, a strategy to solve such problems that is generally accessible by the statistical community is developed. The approach can be adopted to solve l0 norm penalized problems across a very broad class of models, can be implemented using existing software, and is computationally efficient. The performance of the method is demonstrated through in-depth numerical experiments and through using it to analyze several prototypical data sets.

The detection of a de novo allele of the Glu-1Dx gene in wheat-rye hybrid offspring.

KEY MESSAGE: This study provides a link between a de novo gene and novel phenotype in wheat-rye hybrids that can be used as a model for induced de novo genetic variation. Wide hybridization can produce de novo DNA variation that may cause novel phenotypes. However, there is still a lack of specific links between changed genes and novel phenotypes in wide hybrids. The well-studied high-molecular-weight glutenin subunit (HMW-GS) genes in tribe Triticeae provide a useful model for addressing this issue. In this study, we investigated the feasibility of a wheat-rye hybridization method for inducing de novo phenotypes using the Glu-1Dx2.2 subunit as an example. We developed three hexaploid wheat lines with normal fertility and a Glu-1Dx2.2 variant, named Glu-1Dx2.2 (v) , derived from three F1 hybrids. The wild-type Glu-1Dx2.2 has two direct repeats of 295 bp length separated by an intervening 101 bp in its central repetitive region. In the mutant Glu-1Dx2.2 (v) , one copy of the repeats and the intervening sequence were deleted, probably through homology-dependent illegitimate recombination (IR). This study provides a direct link between a de novo allele and novel phenotype. Our results indicate that the wheat-rye method may be a useful tool to induce de novo genetic variations that broaden the genetic diversity for wheat improvement.

Optimizing rice yield, quality and nutrient use efficiency through combined application of nitrogen and potassium.

Reasonable nitrogen (N) and potassium (K) application rates can effectively improve fertilizer use efficiency, rice yield and quality. A two-year field experiment was conducted with combined application of three N rates (135, 180, and 225 kg ha-1, denoted as N1-N3) and four K rates (0, 90, 135, and 180 kg ha-1, denoted as K0-K3) using super indica hybrid rice cultivar Yixiangyou (YXY) 2115 to explore the effects of co-application of N and K on rice growth and development. The results indicated that the combined application of N and K had significantly interactive effects on dry matter (DM) accumulation, nutrients absorption, N harvest index (NHI), K harvest index (KHI), spikelets per panicle and most rice quality indexes. The highest total DM accumulation (17998.17-19432.47 kg ha-1) at maturity stage was obtained under N3K2. The effect of co-application of N and K on nutrients absorption and utilization varied between the two years and within each year. The highest total N and K accumulations at maturity stage were observed under N3K1 and N3K2, respectively, while the highest N recovery efficiency (NRE) and K recovery efficiency (KRE) were observed under N1K3. High expression levels of N and K metabolism-related genes in rice grains were observed under N3K2 or N3K3, consistent with N and K uptake. Co-application of N and K increased rice yield significantly and the highest yield (6745.02-7010.27 kg ha-1) was obtained under N2K2. As more N was gradually applied, rice appearance quality improved but milling, cooking and eating quality decreased. Although appropriate application of K could improve rice milling, cooking and eating quality, it reduced appearance quality. The optimal milling, cooking and eating quality were obtained under N1K2, while the best appearance quality was obtained under N3K0. Overall, a combination of 135-210 kg ha-1 N and 115-137 kg ha-1 K application rates was recommended for achieving relatively higher yield and better quality in rice production.

Responses of Yield and Photosynthetic Characteristics of Rice to Climate Resources under Different Crop Rotation Patterns and Planting Methods.

Climate is the most important environmental factor influencing yield during rice growth and development. To investigate the relationships between climate and yield under different crop rotation patterns and planting methods, three typical rotation patterns (vegetable-rice (V), rape-rice (R), and wheat-rice (W)) and two mechanical planting methods (mechanical transplanting (T1) and mechanical direct seeding (T2)) were established. The results showed that compared to the V rotation pattern, the average daily temperature (ADT) during the sowing to heading stage increased under both R and W rotation patterns, which significantly shortened the growth period. Thus, the effective accumulated temperature (EAT), photosynthetic capacity, effective panicle (EP), and spikelet per panicle (SP) under R and W rotation patterns significantly decreased, leading to reductions in grain yield (GY). VT2 had a higher ratio of productive tillers (RPT), relative chlorophyll content (SPAD), leaf area index (LAI), and net photosynthetic rate (Pn) than those of VT1, which significantly increased panicle dry matter accumulation (DMA), resulting in an increase in GY. Although RT2 and WT2 had a higher RPT than those of RT1 and WT1, the GY of RT1 and WT1 decreased due to the significant reductions in EAT and photosynthetic capacity. Principal component analysis (PCA) showed that the comprehensive score for different rotation patterns followed the order of V > R > T with VT2 ranking first. The structural equation model (SEM) showed that EAT and ADT were the most important climate factors affecting yield, with total effects of 0.520 and -0.446, respectively. In conclusion, mechanical direct seeding under vegetable-rice rotation pattern and mechanical transplanting under rape-rice or wheat-rice rotation pattern were the rice-planting methods that optimized the climate resources in southwest China.

Effects of water stress on starch synthesis and accumulation of two rice cultivars at different growth stages.

Rice is a water intensive crop and soil water conditions affect rice yield and quality. However, there is limited research on the starch synthesis and accumulation of rice under different soil water conditions at different growth stages. Thus, a pot experiment was conducted to explore the effects of IR72 (indica) and Nanjing (NJ) 9108 (japonica) rice cultivars under flood-irrigated treatment (CK, 0 kPa), light water stress treatment (L, -20 ± 5 kPa), moderate water stress treatment (M, -40 ± 5 kPa) and severe water stress treatment (S, -60 ± 5 kPa) on the starch synthesis and accumulation and rice yield at booting stage (T1), flowering stage (T2) and filling stage (T3), respectively. Under LT treatment, the total soluble sugar and sucrose contents of both cultivars decreased while the amylose and total starch contents increased. Starch synthesis-related enzyme activities and their peak activities at mid-late growth stage increased as well. However, applying MT and ST treatments produced the opposite effects. The 1000-grain weight of both cultivars increased under LT treatment while the seed setting rate increased only under LT3 treatment. Compared with CK, water stress at booting stage decreased grain yield. The principal component analysis (PCA) showed that LT3 got the highest comprehensive score while ST1 got lowest for both cultivars. Furthermore, the comprehensive score of both cultivars under the same water stress treatment followed the trend of T3 > T2 > T1, and NJ 9108 had a better drought-resistant ability than IR72. Compared with CK, the grain yield under LT3 increased by 11.59% for IR72 and 16.01% for NJ 9108, respectively. Overall, these results suggested that light water stress at filling stage could be an effective method to enhance starch synthesis-related enzyme activities, promote starch synthesis and accumulation and increase grain yield.

Vectorial total variation regularisation of orientation distribution functions in diffusion weighted MRI.

We propose a model for simultaneous Orientation Distribution Function (ODF) reconstruction and regularisation. The ODFs are represented by real spherical harmonic functions, and we propose to solve the spherical harmonic coefficients of the ODFs, with spatial regularisation by minimising the Vectorial Total Variation (VTV) of the coefficients. The proposed model also incorporates angular regularisation of the ODFs using Laplace-Beltrami operator on the unit sphere. A modified primal-dual hybrid gradient algorithm is applied to solve the model efficiently. The experimental results indicate better directional structures of reconstructed ODFs.