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Neural network pruning is a popular approach to reducing the computational complexity of deep neural networks. In recent years, as growing evidence shows that conventional network pruning methods employ inappropriate proxy metrics, and as new types of hardware become increasingly available, hardware-aware network pruning that incorporates hardware characteristics in the loop of network pruning has gained growing attention. Both network accuracy and hardware efficiency (latency, memory consumption, etc.) are critical objectives to the success of network pruning, but the conflict between the multiple objectives makes it impossible to find a single optimal solution. Previous studies mostly convert the hardware-aware network pruning to optimization problems with a single objective. In this paper, we propose to solve the hardware-aware network pruning problem with Multi-Objective Evolutionary Algorithms (MOEAs). Specifically, we formulate the problem as a multi-objective optimization problem, and propose a novel memetic MOEA, namely HAMP, that combines an efficient portfolio-based selection and a surrogate-assisted local search, to solve it. Empirical studies demonstrate the potential of MOEAs in providing simultaneously a set of alternative solutions and the superiority of HAMP compared to the state-of-the-art hardware-aware network pruning method.

Amaranthus tricolor is an important vegetable, and its quality is affected by salt stress. Cation/proton antiporters (CPA) contribute to plant development and tolerance to salt stress. In this study, 35 CPA genes were identified from a genome database for A. tricolor, including 9 NHX, 5 KEA, and 21 CPA2 genes. Furthermore, in A. tricolor, the expression levels of most AtrNHX genes were higher at a low salinity level (50 or 100 mM NaCl) than in the control or 200 mM NaCl treatment. Levels of most AtrNHX genes were elevated in the stem. Moreover, AtrNHX8 was homologous to AtNHX4, which is involved in the regulation of sodium homeostasis and salt stress response. After AtrNHX8 overexpression in Arabidopsis thaliana, seed germination was better, and the flowering time was earlier than that of wild-type plants. Additionally, the overexpression of AtrNHX8 in A. thaliana improved salt tolerance. These results reveal the roles of AtrNHX genes under salt stress and provide valuable information on this gene family in amaranth.

IntroductionWRKY TFs (WRKY transcription factors) contribute to the synthesis of secondary metabolites in plants. Betalains are natural pigments that do not coexist with anthocyanins within the same plant. Amaranthus tricolor (‘Suxian No.1’) is an important leaf vegetable rich in betalains. However, the WRKY family members in amaranth and their roles in betalain synthesis and metabolism are still unclear.MethodsTo elucidate the molecular characteristics of the amaranth WRKY gene family and its role in betalain synthesis, WRKY gene family members were screened and identified using amaranth transcriptome data, and their physicochemical properties, conserved domains, phylogenetic relationships, and conserved motifs were analyzed using bioinformatics methods.ResultsIn total, 72 WRKY family members were identified from the amaranth transcriptome. Three WRKY genes involved in betalain synthesis were screened in the phylogenetic analysis of WRKY TFs. RT-qPCR showed that the expression levels of these three genes in red amaranth ‘Suxian No.1’ were higher than those in green amaranth ‘Suxian No.2’ and also showed that the expression level of AtrWRKY42 gene short-spliced transcript AtrWRKY42-2 in Amaranth ‘Suxian No.1’ was higher than that of the complete sequence AtrWRKY42-1, so the short-spliced transcript AtrWRKY42-2 was mainly expressed in ‘Suxian No.2’ amaranth. Moreover, the total expression levels of AtrWRKY42-1 and AtrWRKY42-2 were down-regulated after GA3 treatment, so AtrWRKY42-2 was identified as a candidate gene. Therefore, the short splice variant AtrWRKY42-2 cDNA sequence, gDNA sequence, and promoter sequence of AtrWRKY42 were cloned, and the PRI 101-AN-AtrWRKY42-2-EGFP vector was constructed to evaluate subcellular localization, revealing that AtrWRKY42-2 is located in the nucleus. The overexpression vector pRI 101-AN-AtrWRKY42-2-EGFP and VIGS (virus-induced gene silencing) vector pTRV2-AtrWRKY42-2 were transferred into leaves of ‘Suxian No.1’ by an Agrobacterium-mediated method. The results showed that AtrWRKY42-2 overexpression could promote the expression of AtrCYP76AD1 and increase betalain synthesis. A yeast one-hybrid assay demonstrated that AtrWRKY42-2 could bind to the AtrCYP76AD1 promoter to regulate betalain synthesis.DiscussionThis study lays a foundation for further exploring the function of AtrWRKY42-2 in betalain metabolism.

Amaranth plants contain abundant betalains and flavonoids. Anthocyanins are important flavonoids; however, they cannot coexist in the same plant with betalains. Blue light influences metabolite synthesis and hypocotyl elongation; accordingly, analyses of its effects on betalain and flavonoid biosynthesis in Amaranthus tricolor may provide insight into the distribution of these plant pigments. We analyzed the betalain and flavonoid content and transcriptome profiles in amaranth hypocotyls under blue light and dark conditions. Furthermore, we analyzed the expression patterns of key genes related to betalains and flavonoids. Amaranth hypocotyls were shorter and redder and showed higher betalain and flavonoid content under blue light than in dark conditions. Key genes involved in the synthesis of betalains and flavonoids were upregulated under blue light. The gene encoding DELLA was also upregulated. These results suggest that blue light favors the synthesis of both betalains and flavonoids via the suppression of bioactive gibberellin and the promotion of DELLA protein accumulation, which also suppresses hypocotyl elongation. The metabolite profiles differed between plants under blue light and dark conditions. These findings improve our understanding of the environmental cues and molecular mechanisms underlying pigment variation in Amaranthus.

Amaranth plants contain large amounts of betalains, including betaxanthins and betacyanins. Amaranthin is a betacyanin, and its molecular structure and associated metabolic pathway differ from those of betanin in beet plants. The chlorophyll, carotenoid, betalain, and flavonoid contents in amaranth leaves were analyzed. The abundance of betalain, betacyanin, and betaxanthin was 2-5-fold higher in the red leaf sectors than in the green leaf sectors. Moreover, a transcriptome database was constructed for the red and green sectors of amaranth leaves harvested from 30-day-old seedlings. 22 unigenes were selected to analyze the expression profiles in the two leaf sectors. The RNA-sequencing data indicated that many unigenes are involved in betalain metabolic pathways. The potential relationships between diverse metabolic pathways and betalain metabolism were analyzed. The validation of the expression of 22 selected unigenes in a qRT-PCR assay revealed the genes that were differentially expressed in the two leaf sectors. Betalains were biosynthesized in specific tissues of the red sectors of amaranth leaves. Almost all of the genes related to betalain metabolism were identified in the transcriptome database, and the expression profiles were different between the red sectors and green sectors in the leaf. Amaranth plants consist of diverse metabolic pathways, and the betalain metabolic pathway is linked to a group of other metabolic pathways.

Amaranthus tricolor L. is a C4 plant, which is consumed as a major leafy vegetable in some tropical countries. Under conditions of high temperature and short daylight, Am. tricolor readily bolts and blooms, degrading leaf quality. A preliminary in vitro flowering study demonstrated that the flowering control pathway in Am. tricolor may differ from that of Arabidopsis. Nevertheless, no transcriptome analysis of the flowering process in Amaranthus has been conducted. To study Am. tricolor floral regulatory mechanisms, we conducted a large-scale transcriptome analysis--based on Illumina HiSeq sequencing of cDNA libraries generated from Am. tricolor at young seedling (YSS), adult seedling (ASS), flower bud (FBS), and flowering (FS) stages. A total of 99,312 unigenes were obtained. Using BLASTX, 43,088 unigenes (43.39%) were found to have significant similarity with accessions in Nr, Nt, and Swiss-Prot databases. Of these unigenes, 11,291 were mapped to 266 KEGG pathways. Further analysis of the four digital transcriptomes revealed that 735, 17,184, 274, and 206 unigenes were specifically expressed during YSS, ASS, FBS, and FS, respectively, with 59,517 unigenes expressed throughout the four stages. These unigenes were involved in many metabolic pathways related to in vitro flowering. Among these pathways, 259 unigenes were associated with ubiquitin-mediated proteolysis, indicating its importance for in vitro flowering in Am. tricolor. Other pathways, such as circadian rhythm and cell cycle, also had important roles. Finally, 26 unigenes were validated by qRT-PCR in samples from Am. tricolor at YSS, ASS, FBS, and FS; their differential expressions at the various stages indicate their possible roles in Am. tricolor growth and development, but the results were somewhat similar to Arabidopsis. Because unigenes involved in many metabolic pathways or of unknown function were revealed to regulate in vitro plantlet growth and flowering in Am. tricolor, the process appears to be highly complex in this species.

Amaranth, a green leafy vegetable with high edible value, is rich in flavonoids and carotenoids. Aromatic amino acids are favored to secondary metabolites biosynthesis as precursors. Our previous study showed that flavonoids could be produced using amaranth callus. However, the effects of aromatic amino acids on the callus growth, the accumulation of secondary metabolites, and the expression of related genes in amaranth are still unclear. In this study, the results showed that aromatic amino acids could promote the growth of amaranth callus. Meanwhile, tyrosine and phenylalanine within fitting concentrations were beneficial to flavonoid accumulation and expression regulation of the related gene. In contrast, aromatic amino acids reduced carotenoid accumulation. The results provide a scientific basis and method for callus culture and flavonoid production by the callus of amaranth. [ABSTRACT FROM AUTHOR]

Deep neural networks are vulnerable to adversarial examples, even in the black-box setting where the attacker is only accessible to the model output. Recent studies have devised effective black-box attacks with high query efficiency. However, such performance is often accompanied by compromises in attack imperceptibility, hindering the practical use of these approaches. In this article, we propose to restrict the perturbations to a small salient region to generate adversarial examples that can hardly be perceived. This approach is readily compatible with many existing black-box attacks and can significantly improve their imperceptibility with little degradation in attack success rates. Furthermore, we propose the Saliency Attack, a new black-box attack aiming to refine the perturbations in the salient region to achieve even better imperceptibility. Extensive experiments show that compared to the state-of-the-art black-box attacks, our approach achieves much better imperceptibility scores, including most apparent distortion (MAD), L0 and L2 distances, and also obtains significantly better true success rate and effective query number judged by a human-like threshold on MAD. Importantly, the perturbations generated by our approach are interpretable to some extent. Finally, it is also demonstrated to be robust to different detection-based defenses. [ABSTRACT FROM AUTHOR]

To explore the effects of the combination of auxin and cytokinin on amaranths callus induction, proliferation and the content of flavonoids, Amaranthus spp. was used to carry out the research in this article. The results showed that explants in MS + 3.0 mg·L-1 BAP + 0.5 mg·L-1 2,4-D could promote callus formation and growth. The callus in PI 277269, Ame 18049, and PI 604669 hypocotyl has a high induction rate, but it was compact. The callus in PI 572261 was opposite. The callus proliferation has been maintained for more 3 years, and the proliferation coefficient was up to 25.24 in the medium (MS + 3.0 mg·L-1 BAP + 0.5 mg·L-1 2,4-D). The growth curve of amaranth callus is 'S' curve on the solid medium or in the suspension cell culture. MS + 3.0 mg·L-1 BAP + 0.5 mg·L-1 2,4-D was beneficial for the content and yield of flavonoid in the callus. [ABSTRACT FROM AUTHOR]

Red amaranth is an important fresh vegetable with valuable nutritional properties. Blue light is favorable for the accumulation of many metabolites and inhibits hypocotyl elongation in plants. However, the relation between metabolite induction and the inhibition of hypocotyl elongation by blue light in red amaranth is unclear. Here, we used LC-MS/MS-based widely targeted metabolomics to identify key compounds and to compare the metabolite composition of red amaranth under dark and blue light conditions. A total of 444 metabolites were identified, 37 of which differed between the two conditions. A pathway enrichment analysis also identified significant differences between the two conditions. Fifteen lipids, all up-regulated under the blue light, were significantly different. The amino acid content was lower under the blue light than under the dark condition. We found cyanidin chloride and anthocyanin 3-O-beta-D-glucoside which are the two components involved in the anthocyanin pathway. Our results verify the high nutritional quality of the red amaranth and suggest that blue light influences metabolite synthesis and hypocotyl elongation in the species. [ABSTRACT FROM AUTHOR]

Longan (Dimocarpus longan Lour.), an important subtropical fruit in the family Sapindaceae, is grown in more than 10 countries. Longan is an edible drupe fruit and a source of traditional medicine with polyphenol-rich traits. Tree size, alternate bearing, and witches' broom disease still pose serious problems. To gain insights into the genomic basis of longan traits, a draft genome sequence was assembled. The draft genome (about 471.88 Mb) of a Chinese longan cultivar, "Honghezi," was estimated to contain 31 007 genes and 261.88 Mb of repetitive sequences. No recent whole-genome-wide duplication event was detected in the genome. Whole-genome resequencing and analysis of 13 cultivated D. longan accessions revealed the extent of genetic diversity. Comparative transcriptome studies combined with genome-wide analysis revealed polyphenol-rich and pathogen resistance characteristics. Genes involved in secondary metabolism, especially those from significantly expanded (DHS, SDH, F3'H, ANR, and UFGT) and contracted (PAL, CHS, and F3'5'H) gene families with tissue-specific expression, may be important contributors to the high accumulation levels of polyphenolic compounds observed in longan fruit. The high number of genes encoding nucleotide-binding site leucine-rich repeat (NBS-LRR) and leucine-rich repeat receptor-like kinase proteins, as well as the recent expansion and contraction of the NBS-LRR family, suggested a genomic basis for resistance to insects, fungus, and bacteria in this fruit tree. These data provide insights into the evolution and diversity of the longan genome. The comparative genomic and transcriptome analyses provided information about longan-specific traits, particularly genes involved in its polyphenol-rich and pathogen resistance characteristics. [ABSTRACT FROM AUTHOR]

In this article, we successfully apply the novel model selection method, Bayesian composite model space approach which has been used to map quantitative trait loci (QTL) for allelic substitution model, to map QTL for variance component model. The novel model selection approach has two advantages compared to the reversible jump Markov chain Monte Carlo method. Firstly, it mixes well due to the fixedness of the model dimension; secondly, it can map multiple QTL with higher power especially in genome-wide QTL mapping; finally, in the new method, it is also easy to incorporate our prior information about the variance components, which may bring precise estimate for variance components. A series of simulation experiments were conducted to demonstrate the general characters of the proposed method. The computer program is written in FORTRAN language, which is also built into a software “BayesMapQTL”, and they also can be used for real data analysis and are available for request. [ABSTRACT FROM AUTHOR]

Abstract  Using the data of crosses of multiple of inbred lines for mapping QTL can increase QTL detecting power compared with only cross of two inbred lines. Although many fixed-effect model methods have been proposed to analyze such data, they are largely based on one-QTL model or main effect model, and the interaction effects between QTL are always neglected. However, effectively separating the interaction effects from the residual error can increase the statistical power. In this article, we both extended the novel Bayesian model selection method and Bayesian shrinkage estimation approaches to multiple inbred line crosses. With two extensions, interacting QTL are effectively detected with high solution; in addition, the posterior variances for both main effects and interaction effects are also subjected to full Bayesian estimate, which is more optimal than two step approach involved in maximum-likelihood. A series of simulation experiments have been conducted to demonstrate the performance of the methods. The computer program written in FORTRAN language is freely available on request. [ABSTRACT FROM AUTHOR]