Deep Feature Screening: Feature Selection for Ultra High-Dimensional Data via Deep Neural Networks

The applications of traditional statistical feature selection methods to high-dimension, low sample-size data often struggle and encounter challenging problems, such as overfitting, curse of dimensionality, computational infeasibility, and strong model assumption. In this paper, we propose a novel two-step nonparametric approach called Deep Feature Screening (DeepFS) that can overcome these problems and identify significant features with high precision for ultra high-dimensional, low-sample-size data. This approach first extracts a low-dimensional representation of input data and then applies feature screening based on multivariate rank distance correlation recently developed by Deb and Sen (2021). This approach combines the strengths of both deep neural networks and feature screening, and thereby has the following appealing features in addition to its ability of handling ultra high-dimensional data with small number of samples: (1) it is model free and distribution free; (2) it can be used for both supervised and unsupervised feature selection; and (3) it is capable of recovering the original input data. The superiority of DeepFS is demonstrated via extensive simulation studies and real data analyses

Analisis Adopsi Inovasi Teknologi Pertanian Berbasis Padi di Sumatera Selatan dalam Perspektif Komunikasi

Analysis of Adoption of Agricultural Technology Innovation Rice-based Farming in Sumatra inthe perspective of communications. Assessment Institute of Agricultural Technology (AIAT) South Sumatrahas produced innovative rice-based farming technology in various agroecosystem. However, adoption ratesare still relatively low. Evaluation of four assessments aimed to identify the factors that predominantly affectthe adoption of technological innovation based local-specific farming rice and to know the level of adoption.This activity is carried out in OKI, East OKU and Banyuasin regencies with 67 respondents interviewedin July-September 2007. The results of this assessment showed that the factors that influence the adoption oftechnological innovations such as the level of selective exposure of technology innovation, cosmopolite,triability, complexity of technology and agricultural extension intensity. The average adoption index for thepacket of rice cultivation technology was 50.32%. As many as 93.02% of respondents have positive perceptionsof the researcher-extension AIAT South Sumatra as the communicator in delivering information technology.Most respondents (80%) expressed a desire to obtain agricultural information generated AIAT South Sumatra.Key words: Adoption, innovation, rice, communication Balai Pengkajian Teknologi Pertanian (BPTP) Sumatera Selatan sudah menghasilkan inovasi teknologipertanian berbasis padi di berbagai agroekosistem. Namun tingkat adopsinya masih relatif rendah. Evaluasi terhadapempat pengkajian ini bertujuan untuk mengidentifikasi faktor-faktor yang dominan mempengaruhi proses adopsiinovasi teknologi pertanian spesifik lokasi berbasis padi dan mengetahui tingkat adopsinya. Kegiatan ini dilakukan diKabupaten OKI, OKU Timur dan Banyuasin dengan mewawancarai 67 orang responden pada bulan Juli – September2007. Berdasarkan hasil analisis deskriptif kualitatif diketahui bahwa (1) adopsi inovasi teknologi budidaya tanamanpadi di Sumatera Selatan dipengaruhi oleh tingkat kebutuhan petani terhadap inovasi teknologi, sifat kekosmopolitanpetani, triabilitas dan kompleksitas teknologi dan intensitas pembinaan, (2) indeks adopsi inovasi petani terhadappaket teknologi budidaya padi kondisinya beragam tergantung pada jenis kegiatan, (3) petani di Sumatera Selatanumumnya memberikan apresiasi positif terhadap peneliti-penyuluh BPTP Sumatera Selatan, terlihat dari tingginyaminat petani untuk mendapatkan berbagai media informasi pertanian BPTP Sumatera Selatan, dan (4) temuankajian ini mengindikasikan faktor komunikasi memegang peran utama yang dapat mempengaruhi adopsi teknologi

The genome evolution and domestication of tropical fruit mango

Background: Mango is one of the world’s most important tropical fruits. It belongs to the family Anacardiaceae, which includes several other economically important species, notably cashew, sumac and pistachio from other genera. Many species in this family produce family-specific urushiols and related phenols, which can induce contact dermatitis. Results: We generate a chromosome-scale genome assembly of mango, providing a reference genome for the Anacardiaceae family. Our results indicate the occurrence of a recent whole-genome duplication (WGD) event in mango. Duplicated genes preferentially retained include photosynthetic, photorespiration, and lipid metabolic genes that may have provided adaptive advantages to sharp historical decreases in atmospheric carbon dioxide and global temperatures. A notable example of an extended gene family is the chalcone synthase (CHS) family of genes, and particular genes in this family show universally higher expression in peels than in flesh, likely for the biosynthesis of urushiols and related phenols. Genome resequencing reveals two distinct groups of mango varieties, with commercial varieties clustered with India germplasms and demonstrating allelic admixture, and indigenous varieties from Southeast Asia in the second group. Landraces indigenous in China formed distinct clades, and some showed admixture in genomes. Conclusions: Analysis of chromosome-scale mango genome sequences reveals photosynthesis and lipid metabolism are preferentially retained after a recent WGD event, and expansion of CHS genes is likely associated with urushiol biosynthesis in mango. Genome resequencing clarifies two groups of mango varieties, discovers allelic admixture in commercial varieties, and shows distinct genetic background of landraces

AaABF3, an Abscisic Acid–Responsive Transcription Factor, Positively Regulates Artemisinin Biosynthesis in Artemisia annua

Artemisinin is well known for its irreplaceable curative effect on the devastating parasitic disease, Malaria. This sesquiterpenoid is specifically produced in Chinese traditional herbal plant Artemisia annua. Earlier studies have shown that phytohormone abscisic acid (ABA) plays an important role in increasing the artemisinin content, but how ABA regulates artemisinin biosynthesis is still poorly understood. In this study, we identified that AaABF3 encoded an ABRE (ABA-responsive elements) binding factor. qRT-PCR analysis showed that AaABF3 was induced by ABA and expressed much higher in trichomes where artemisinin is synthesized and accumulated. To further investigate the mechanism of AaABF3 regulating the artemisinin biosynthesis, we carried out dual-luciferase analysis, yeast one-hybrid assay and electrophoretic mobility shift assay. The results revealed that AaABF3 could directly bind to the promoter of ALDH1 gene, which is a key gene in artemisinin biosynthesis, and activate the expression of ALDH1. Functional analysis revealed that overexpression of AaABF3 in A. annua enhanced the production of artemisinin, while RNA interference of AaABF3 resulted in decreased artemisinin content. Taken together, our results demonstrated that AaABF3 played an important role in ABA-regulated artemisinin biosynthesis through direct regulation of artemisinin biosynthesis gene, ALDH1

Dynamic reversible evolution of solid electrolyte interface in nonflammable triethyl phosphate electrolyte enabling safe and stable potassium-ion batteries

Potassium-ion batteries (PIBs) are a favorable alternative to lithium-ion batteries (LIBs) for the large-scale electrochemical storage devices because of the high natural abundance of potassium resources. However, conventional PIB electrodes usually exhibit low actual capacities and poor cyclic stability due to the large radius of potassium ions (1.39 Å). In addition, the high reactivity of potassium metal raises serious safety concerns. These characteristics seriously inhibit the practical use of PIB electrodes. Here, zinc phosphide composites are rationally designed as PIB anodes for operation in a nonflammable triethyl phosphate (TEP) electrolyte to solve the above-mentioned issues. The optimized zinc phosphide composite with 20 wt% zinc phosphate presents a high specific capacity (571.1 mA h g−1 at 0.1 A g−1) and excellent cycling performance (484.9 mA h g−1 with the capacity retention of 94.5% after 1000 cycles at 0.5 A g−1) in the KFSI-TEP electrolyte. XPS depth profile analysis shows that the improved cycling stability of the composite is closely related to the reversible dynamic evolutions and conversions of the sulfur-containing species in the solid electrolyte interphase (SEI) during the charge/discharge process. This dynamic reversible SEI concept may provide a new strategy for the design of superior electrodes for PIBs

The genome evolution and domestication of tropical fruit mango

Background: Mango is one of the world’s most important tropical fruits. It belongs to the family Anacardiaceae, which includes several other economically important species, notably cashew, sumac and pistachio from other genera. Many species in this family produce family-specific urushiols and related phenols, which can induce contact dermatitis. Results: We generate a chromosome-scale genome assembly of mango, providing a reference genome for the Anacardiaceae family. Our results indicate the occurrence of a recent whole-genome duplication (WGD) event in mango. Duplicated genes preferentially retained include photosynthetic, photorespiration, and lipid metabolic genes that may have provided adaptive advantages to sharp historical decreases in atmospheric carbon dioxide and global temperatures. A notable example of an extended gene family is the chalcone synthase (CHS) family of genes, and particular genes in this family show universally higher expression in peels than in flesh, likely for the biosynthesis of urushiols and related phenols. Genome resequencing reveals two distinct groups of mango varieties, with commercial varieties clustered with India germplasms and demonstrating allelic admixture, and indigenous varieties from Southeast Asia in the second group. Landraces indigenous in China formed distinct clades, and some showed admixture in genomes. Conclusions: Analysis of chromosome-scale mango genome sequences reveals photosynthesis and lipid metabolism are preferentially retained after a recent WGD event, and expansion of CHS genes is likely associated with urushiol biosynthesis in mango. Genome resequencing clarifies two groups of mango varieties, discovers allelic admixture in commercial varieties, and shows distinct genetic background of landraces

An L1 box binding protein, GbML1, interacts with GbMYB25 to control cotton fibre development

Transcription factors play key roles in plant development through their interaction with cis-elements and/or other transcription factors. A HD-Zip IV family transcription factor, Gossypium barbadense Meristem Layer 1 (GbML1) has been identified and characterized here. GbML1 specifically bound to the L1 box and the promoters of GbML1 and GbRDL1. GbML1 physically interacted with a key regulator of cotton fibre development, GbMYB25. Truncated and point mutation assays indicated the START–SAD domain was required for the binding to the C terminal domain (CTD) of GbMYB25. GbML1 overexpression in Arabidopsis increased the number of trichomes on stems and leaves and increased the accumulation of anthocyanin in leaves. Taken together, the L1 box binding protein, GbML1 was identified as the first partner for GbMYB25 and the role of START domain was discovered to be a protein binding domain in plants. Our findings will help the improvement of cotton fibre production and the understanding of the key role of HD-Zip family and MYB family in plants