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

Semiparametric Regression for Spatial Data via Deep Learning

In this work, we propose a deep learning-based method to perform semiparametric regression analysis for spatially dependent data. To be specific, we use a sparsely connected deep neural network with rectified linear unit (ReLU) activation function to estimate the unknown regression function that describes the relationship between response and covariates in the presence of spatial dependence. Under some mild conditions, the estimator is proven to be consistent, and the rate of convergence is determined by three factors: (1) the architecture of neural network class, (2) the smoothness and (intrinsic) dimension of true mean function, and (3) the magnitude of spatial dependence. Our method can handle well large data set owing to the stochastic gradient descent optimization algorithm. Simulation studies on synthetic data are conducted to assess the finite sample performance, the results of which indicate that the proposed method is capable of picking up the intricate relationship between response and covariates. Finally, a real data analysis is provided to demonstrate the validity and effectiveness of the proposed method

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

Assessing the efficacy of natural soil biotin on soil quality, microbial diversity, and Rhododendron simsii growth for sustainable landscape architecture

Fertilization significantly influences soil quality and its sustainable use in urban garden maintenance. The widespread application of inorganic fertilizers has raised ecological concerns due to their potential environmental impacts. Organic fertilizers, while beneficial, often have slow effects and are costly. Biofertilizers, with their eco-friendly nature and low carbon footprint, are gaining attention for their multifaceted role in supporting plant growth. Despite the focus on fruit trees, vegetables, and medicinal plants, ornamental plants have been understudied. This study aims to evaluate the efficacy of a novel microbial fertilizer, ‘natural soil biotin’, on Rhododendron plants, specifically the Azalea hybrid ‘Carnation’. The study employed a comparative approach to assess the impact of different fertilization strategies on soil properties, microbial diversity, enzyme activity, plant morphology, and physiological parameters. The application of ‘natural soil biotin’ was compared with the use of inorganic and organic fertilizers. The combined application of ‘natural soil biotin’ was found to effectively enhance soil properties and mitigate the impact of other fertilizers on soil pH. It also improved the relative abundance of beneficial microbial groups such as Proteobacteria, Ascomycota, and Basidiomycota. Furthermore, the mixed application significantly increased the activities of urease and sucrase in Rhododendron plants, which promoted their growth, development, and stress resistance. The results indicate that the mixed application of ‘natural soil biotin’ with inorganic and organic fertilizers not only improved the soil quality but also enhanced the efficiency of fertilizer utilization. This approach led to increased economic and environmental benefits in Rhododendron cultivation. The findings contribute to the foundation for soil improvement and ecological restoration, suggesting that ‘natural soil biotin’ could be a promising alternative or supplement to traditional fertilization methods in sustainable landscape architecture

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

Isolation and characterization of Hc-targeting chimeric heavy chain antibodies neutralizing botulinum neurotoxin type B

BackgroundBotulinum neurotoxin (BoNT) produced by Clostridium botulinum is one of the most potent known toxins. Moreover, BoNT is classified as one of the most important biological warfare agents that threatens the biosafety of the world. Currently, the approved treatment for botulism in humans is the use of polyvalent horse serum antitoxins. However, they are greatly limited because of insufficient supply and adverse reactions. Thus, treatment of human botulism requires the development of effective toxin-neutralizing antibodies. Considering their advantages, neutralizing nanobodies will play an increasing role as BoNTs therapeutics.MethodsHerein, neutralizing nanobodies binding to the heavy chain (Hc) domain of BoNT/B (BHc) were screened from a phage display library. Then, BoNT/B-specific clones were identified and fused with the human Fc fragment (hFc) to form chimeric heavy chain antibodies. Finally, the affinity, specificity, and neutralizing activity of antibodies against BoNT/B in vivo were evaluated.ResultsThe B5-hFc, B9-hFc and B12-hFc antibodies demonstrated high affinity for BHc in the nanomolar range. The three antibodies were proven to have potent neutralizing activity against BoNT/B in vivo.ConclusionThe results demonstrate that inhibiting toxin binding to the host receptor is an efficient strategy and the three antibodies could be used as candidates for the further development of drugs to prevent and treat botulism