Mapping Haplotype-haplotype Interactions with Adaptive LASSO

<p>Abstract</p> <p>Background</p> <p>The genetic etiology of complex diseases in human has been commonly viewed as a complex process involving both genetic and environmental factors functioning in a complicated manner. Quite often the interactions among genetic variants play major roles in determining the susceptibility of an individual to a particular disease. Statistical methods for modeling interactions underlying complex diseases between single genetic variants (e.g. single nucleotide polymorphisms or SNPs) have been extensively studied. Recently, haplotype-based analysis has gained its popularity among genetic association studies. When multiple sequence or haplotype interactions are involved in determining an individual's susceptibility to a disease, it presents daunting challenges in statistical modeling and testing of the interaction effects, largely due to the complicated higher order epistatic complexity.</p> <p>Results</p> <p>In this article, we propose a new strategy in modeling haplotype-haplotype interactions under the penalized logistic regression framework with adaptive <it>L</it>₁-penalty. We consider interactions of sequence variants between haplotype blocks. The adaptive <it>L</it>₁-penalty allows simultaneous effect estimation and variable selection in a single model. We propose a new parameter estimation method which estimates and selects parameters by the modified Gauss-Seidel method nested within the EM algorithm. Simulation studies show that it has low false positive rate and reasonable power in detecting haplotype interactions. The method is applied to test haplotype interactions involved in mother and offspring genome in a small for gestational age (SGA) neonates data set, and significant interactions between different genomes are detected.</p> <p>Conclusions</p> <p>As demonstrated by the simulation studies and real data analysis, the approach developed provides an efficient tool for the modeling and testing of haplotype interactions. The implementation of the method in R codes can be freely downloaded from <url>http://www.stt.msu.edu/~cui/software.html</url>.</p

AC Loss Reduction in REBCO Coated Conductors using the Hexagonal Arrangement Cabling Method

High-temperature superconducting (HTS) rare-earth barium copper oxide (REBCO) coated conductors with outstanding critical current density under high fields can help realize a high-field path toward magnetic-confinement fusion. REBCO cabling methods such as conductor on round core (CORC) cables, twisted stacked tape conductor (TSTC) cables, and Rutherford cables are based on the cable-in-conduit conductor (CICC) developed for low-temperature superconducting (LTS) Nb3Sn and Nb-Ti conductors. However, the REBCO coated conductor has challenges in achieving current transposition by twisting due to its ceramic-like mechanical behavior. In addition, it is more sensitive to external perpendicular magnetic fields with its rectangular cross-section than metallic LTS superconductors. In order to solve these issues, a hexagonal arrangement REBCO cabling method with the inherent advantage of mechanical protection and inductance balance is proposed in this paper. The electromagnetic behavior of REBCO coated conductors in the cable is evaluated using H-formulation and T-A formulation-based finite element methods. Results show that AC losses can be reduced using the hexagonal arrangement method compared with non-twisted cables and TSTC cables, which makes it a potentially helpful cabling method for ultra-high-field large-scale applications with high-level inductance balance requirements, especially the central solenoid coils of thermonuclear fusion reactors

Nondestructive Evaluation of Inoculation Effects of AMF and <em>Bradyrhizobium japonicum</em> on Soybean under Drought Stress From Reflectance Spectroscopy

Precise estimation of leaf chlorophyll content (LCC) and leaf water content (LWC) of soybean, using remote sensing technology, provides a new avenue for the nondestructive evaluation of inoculation effects of arbuscular mycorrhizal fungi (AMF) and Bradyrhizobium japonicum (BJ) on soybean growth condition. In this study, a series of pot experiments were conducted in the greenhouse, soybean inoculated with Glomus intraradices (G.i, one of AMF species), G.i and BJ, and non-inoculation were planted under drought stress (DS) and normal irrigation (NI) conditions. Leaf spectra and LCC and LWC were measured on the 28th and 56th days after inoculation. Two new simple ratio (SR) indices, derived from the first derivative spectral reflectance at λ1 nm (Dλ1) and the raw spectral reflectance at λ2 nm (Rλ2), were developed to estimate LCC and LWC. The results indicate that under DS, plants inoculated with G.i had higher LCC and LWC than the non-inoculated plants, followed by the counterparts co-inoculated with G.i and BJ. Linear estimation models, established by the D650/Rred edge and D1680/R680, achieved great improved accuracy for quantifying LCC and LWC of soybean under inoculation and drought stress treatments, with determination of coefficient of 0.63 and 0.76, respectively

Reconstruction of Daily 30 m Data from HJ CCD, GF-1 WFV, Landsat, and MODIS Data for Crop Monitoring

With the recent launch of new satellites and the developments of spatiotemporal data fusion methods, we are entering an era of high spatiotemporal resolution remote-sensing analysis. This study proposed a method to reconstruct daily 30 m remote-sensing data for monitoring crop types and phenology in two study areas located in Xinjiang Province, China. First, the Spatial and Temporal Data Fusion Approach (STDFA) was used to reconstruct the time series high spatiotemporal resolution data from the Huanjing satellite charge coupled device (HJ CCD), Gaofen satellite no. 1 wide field-of-view camera (GF-1 WFV), Landsat, and Moderate Resolution Imaging Spectroradiometer (MODIS) data. Then, the reconstructed time series were applied to extract crop phenology using a Hybrid Piecewise Logistic Model (HPLM). In addition, the onset date of greenness increase (OGI) and greenness decrease (OGD) were also calculated using the simulated phenology. Finally, crop types were mapped using the phenology information. The results show that the reconstructed high spatiotemporal data had a high quality with a proportion of good observations (PGQ) higher than 0.95 and the HPLM approach can simulate time series Normalized Different Vegetation Index (NDVI) very well with R2 ranging from 0.635 to 0.952 in Luntai and 0.719 to 0.991 in Bole, respectively. The reconstructed high spatiotemporal data were able to extract crop phenology in single crop fields, which provided a very detailed pattern relative to that from time series MODIS data. Moreover, the crop types can be classified using the reconstructed time series high spatiotemporal data with overall accuracy equal to 0.91 in Luntai and 0.95 in Bole, which is 0.028 and 0.046 higher than those obtained by using multi-temporal Landsat NDVI data