Smoothing Spline ANOVA Models and their Applications in Complex and Massive Datasets

Complex and massive datasets can be easily accessed using the newly developed data acquisition technology. In spite of the fact that the smoothing spline ANOVA models have proven to be useful in a variety of fields, these datasets impose the challenges on the applications of the models. In this chapter, we present a selected review of the smoothing spline ANOVA models and highlight some challenges and opportunities in massive datasets. We review two approaches to significantly reduce the computational costs of fitting the model. One real case study is used to illustrate the performance of the reviewed methods

Exploring the supersymmetric U(1)B−L×_{B-L} \times U(1)R_{R} model with dark matter, muon g−2g-2 and Z′Z^\prime mass limits

We study the low scale predictions of supersymmetric standard model extended by $U(1)_{B-L}\times U(1)_{R}$ symmetry, obtained from $SO(10)$ breaking via a left-right supersymmetric model, imposing universal boundary conditions. Two singlet Higgs fields are responsible for the radiative $U(1)_{B-L}\times U(1)_{R}$ symmetry breaking, and a singlet fermion $S$ is introduced to generate neutrino masses through inverse seesaw mechanism. The lightest neutralino or sneutrino emerge as dark matter candidates, with different low scale implications. We find that the composition of the neutralino LSP changes considerably depending on the neutralino LSP mass, from roughly half $U(1)_R$ bino, half MSSM bino, to singlet higgsino, or completely dominated by MSSM higgsino. The sneutrino LSP is statistically much less likely, and when it occurs it is a 50-50 mixture of right-handed sneutrino and the scalar $\tilde S$. Most of the solutions consistent with the relic density constraint survive the XENON 1T exclusion curve for both LSP cases. We compare the two scenarios and investigate parameter space points and find consistency with the muon anomalous magnetic moment only at the edge of $2\sigma$ deviation from the measured value. However, we find that the sneutrino LSP solutions could be ruled out completely by strict reinforcement of the recent $Z^\prime$ mass bounds. We finally discuss collider prospects for testing the model

A key ‘foxy’ aroma gene is regulated by homologyinduced promoter indels in the iconic juice grape ‘Concord’

‘Concord’, the most well-known juice grape with a parentage of the North American grape species Vitis labrusca L., possesses a special ‘foxy’ aroma predominantly resulted from the accumulation of methyl anthranilate (MA) in berries. This aroma, however, is often perceived as an undesirable attribute by wine consumers and rarely noticeable in the common table and wine grape species V. vinifera. Here we discovered homology-induced promoter indels as a major genetic mechanism for species-specific regulation of a key ‘foxy’ aroma gene, anthraniloyl-CoA:methanol acyltransferase (AMAT), that is responsible for MA biosynthesis. We found the absence of a 426-bp and/or a 42-bp sequence in AMAT promoters highly associated with high levels of AMAT expression and MA accumulation in ‘Concord’ and other V. labrusca-derived grapes. These promoter variants, all with direct and inverted repeats, were further confirmed in more than 1,300 Vitis germplasm. Moreover, functional impact of these indels was validated in transgenic Arabidopsis. Superimposed on the promoter regulation, large structural changes including exonic insertion of a retrotransposon were present at the AMAT locus in some V. vinifera grapes. Elucidation of the AMAT genetic regulation advances our understanding of the ‘foxy’ aroma trait and makes it genetically trackable and amenable in grapevine breeding

Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops

[EN] The Cucurbitaceae family (cucurbit) includes several economically important crops, such as melon, cucumber, watermelon, pumpkin, squash and gourds. During the past several years, genomic and genetic data have been rapidly accumulated for cucurbits. To store, mine, analyze, integrate and disseminate these large-scale datasets and to provide a central portal for the cucurbit research and breeding community, we have developed the Cucurbit Genomics Database (CuGenDB; http://cucurbitgenomics.org) using the Tripal toolkit. The database currently contains all available genome and expressed sequence tag (EST) sequences, genetic maps, and transcriptome profiles for cucurbit species, as well as sequence annotations, biochemical pathways and comparative genomic analysis results such as synteny blocks and homologous gene pairs between different cucurbit species. A set of analysis and visualization tools and user-friendly query interfaces have been implemented in the database to facilitate the usage of these large-scale data by the community. In particular, two new tools have been developed in the database, a `SyntenyViewer¿ to view genome synteny between different cucurbit species and an `RNA-Seq¿ module to analyze and visualize gene expression profiles. Both tools have been packed as Tripal extension modules that can be adopted in other genomics databases developed using the Tripal system.USDA National Institute of Food and Agriculture Specialty Crop Research Initiative [2015-51181-24285]; US-Israel Binational Agricultural Research and Development Fund [IS-3333-02, IS-3877-06CR and IS-4223-09C]; USDA Agricultural Research Service, and by SNC Laboratoire ASL, de Ruiter Seeds B.V., Enza Zaden B.V., Gautier Semences S.A., Nunhems B.V., Rijk Zwaan B.V., Sakata Seed Inc, Semillas Fito S.A., Seminis Vegetable Seeds Inc, Syngenta Seeds B.V., Takii and Company Ltd, Vilmorin and Cie S.A. and Zeraim Gedera Ltd, all of them as part of the support to the International Cucurbit Genomics Initiative (ICuGI). Funding for open access charge: USDA National Institute of Food and Agriculture.Zheng, Y.; Wu, S.; Bai, Y.; Sun, H.; Jiao, C.; Guo, S.; Zhao, K.... (2018). Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. Nucleic Acids Research. 47(D1):D1128-D1136. https://doi.org/10.1093/nar/gky944SD1128D113647D

A High Resolution Genetic Map Anchoring Scaffolds of the Sequenced Watermelon Genome

As part of our ongoing efforts to sequence and map the watermelon (Citrullus spp.) genome, we have constructed a high density genetic linkage map. The map positioned 234 watermelon genome sequence scaffolds (an average size of 1.41 Mb) that cover about 330 Mb and account for 93.5% of the 353 Mb of the assembled genomic sequences of the elite Chinese watermelon line 97103 (Citrullus lanatus var. lanatus). The genetic map was constructed using an F8 population of 103 recombinant inbred lines (RILs). The RILs are derived from a cross between the line 97103 and the United States Plant Introduction (PI) 296341-FR (C. lanatus var. citroides) that contains resistance to fusarium wilt (races 0, 1, and 2). The genetic map consists of eleven linkage groups that include 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel) and 36 structure variation (SV) markers and spans ∼800 cM with a mean marker interval of 0.8 cM. Using fluorescent in situ hybridization (FISH) with 11 BACs that produced chromosome-specifc signals, we have depicted watermelon chromosomes that correspond to the eleven linkage groups constructed in this study. The high resolution genetic map developed here should be a useful platform for the assembly of the watermelon genome, for the development of sequence-based markers used in breeding programs, and for the identification of genes associated with important agricultural traits

Genomic Characterization of the Guillain-Barre Syndrome-Associated Campylobacter jejuni ICDCCJ07001 Isolate

Campylobacter jejuni ICDCCJ07001 (HS:41, ST2993) was isolated from a Guillain-Barré syndrome (GBS) patient during a 36-case GBS outbreak triggered by C. jejuni infections in north China in 2007. Sequence analysis revealed that the ICDCCJ07001 genome consisted of 1,664,840 base pairs (bp) and one tetracycline resistance plasmid of 44,084 bp. The GC content was 59.29% and 1,579 and 37 CDSs were identified on the chromosome and plasmid, respectively. The ICDCCJ07001 genome was compared to C. jejuni subsp. jejuni strains 81-176, 81116, NCTC11168, RM1221 and C. jejuni subsp. doylei 269.97. The length and organization of ICDCCJ07001 was similar to that of NCTC11168, 81-176 and 81-116 except that CMLP1 had a reverse orientation in strain ICDCCJ07001. Comparative genomic analyses were also carried out between GBS-associated C. jejuni strains. Thirteen common genes were present in four GBS-associated strains and 9 genes mapped to the LOS cluster and the ICDCCJ07001_pTet (44 kb) plasmid was mosaic in structure. Thirty-seven predicted CDS in ICDCCJ07001_pTet were homologous to genes present in three virulence-associated plasmids in Campylobacter: 81-176_pTet, pCC31 and 81-176_pVir. Comparative analysis of virulence loci and virulence-associated genes indicated that the LOS biosynthesis loci of ICDCCJ07001 belonged to type A, previously reported to be associated with cases of GBS. The polysaccharide capsular biosynthesis (CPS) loci and the flagella modification (FM) loci of ICDCCJ07001 were similar to corresponding sequences of strain 260.94 of similar serotype as strain ICDCCJ07001. Other virulence-associated genes including cadF, peb1, jlpA, cdt and ciaB were conserved between the C. jejuni strains examined

Size-induced axial band structure and directional flow of a ternary-size granular material in a 3-D horizontal rotating drum

Differences in the material property of the granular material induce segregation which inevitably influences both natural and industrial processes. To understand the dynamical segregation behavior, the band structure, and also the spatial redistribution of particles induced by the size differences of the particles, a ternary-size granular mixture in a three-dimensional rotating drum operating in the rolling flow regime is numerically simulated using the discrete element method. The results demonstrate that (i) the axial bands of the medium particles are spatially sandwiched in between those of the large and small ones; (ii) the total mass in the active and passive regions is a global parameter independent of segregation; (iii) nearly one-third of all the particles are in the active region, with the small particles having the highest mass fraction; (iv) the axial bands initially appear near the end wall, then become wider and purer in the particular species with time as more axial bands form toward the axial center; and (v) the medium particle type exhibits segregation later and has the narrowest axial bandwidth and least purity in the bands. Compared to the binary-size system, the presence of the medium particle type slightly increases the total mass in the active region, leads to larger mass fractions of the small and large particle types in the active region, and enhances the axial segregation in the system. The results obtained in the current work provide valuable insights regarding size segregation, and band structure and formation in the rotating drum with polydisperse particles.NRF (Natl Research Foundation, S’pore)Published versio

Characterization of the OFP Gene Family and its Putative Involvement of Tuberous Root Shape in Radish

The shape of the tuberous root, a very important quality trait, varies dramatically among radish cultivars. Ovate family proteins (OFPs) are plant-specific proteins that regulate multiple aspects of plant growth and development. To investigate the possible role of OFPs in radish tuberous root formation, 35 putative RsOFPs were identified from radish, and their expression patterns were detected during tuberous root development in six different radish cultivars. Phylogenetically, RsOFP2.3 clustered together with AtOFP1 and other members of this family that are known to regulate organ shape. Moreover, RsOFP2.3 expression was negatively correlated with tuberous root elongation after the cortex splitting stage, which made this gene the top candidate for the involvement of tuberous root shape. To further characterize the function of RsOFP2.3, it was ectopically expressed in Arabidopsis. RsOFP2.3 overexpression in Arabidopsis led to multiple phenotypical changes, especially the decreased length and increased width of the hypocotyl. Furthermore, RsOFP2.3 expression was induced by all the five classic plant hormones except ethylene, and it was most sensitive to exogenous gibberellic acid treatment. We also found that RsOFP2.3 was localized in the cytoplasm. Taken together, our results suggested the possible involvement for RsOFP2.3 in suppressing radish tuberous root elongation and that it encodes a functional protein which mainly inhibits the elongation of Arabidopsis aerial organs

Attentive SOLO for Sonar Target Segmentation

Imaging sonar systems play an important role in underwater target detection and location. Due to the influence of reverberation noise on imaging sonar systems, the task of sonar target segmentation is a challenging problem. In order to segment different types of targets in sonar images accurately, we proposed the gated fusion-pyramid segmentation attention (GF-PSA) module. Specifically, inspired by gated full fusion, we improved the pyramid segmentation attention (PSA) module by using gated fusion to reduce the noise interference during feature fusion and improve segmentation accuracy. Then, we improved the SOLOv2 (Segmenting Objects by Locations v2) algorithm with the proposed GF-PSA and named the improved algorithm Attentive SOLO. In addition, we constructed a sonar target segmentation dataset, named STSD, which contains 4000 real sonar images, covering eight object categories with a total of 7077 target annotations. The experimental results show that the segmentation accuracy of Attentive SOLO on STSD is as high as 74.1%, which is 3.7% higher than that of SOLOv2