Robust Topology Optimization Based on Stochastic Collocation Methods under Loading Uncertainties

A robust topology optimization (RTO) approach with consideration of loading uncertainties is developed in this paper. The stochastic collocation method combined with full tensor product grid and Smolyak sparse grid transforms the robust formulation into a weighted multiple loading deterministic problem at the collocation points. The proposed approach is amenable to implementation in existing commercial topology optimization software package and thus feasible to practical engineering problems. Numerical examples of two- and three-dimensional topology optimization problems are provided to demonstrate the proposed RTO approach and its applications. The optimal topologies obtained from deterministic and robust topology optimization designs under tensor product grid and sparse grid with different levels are compared with one another to investigate the pros and cons of optimization algorithm on final topologies, and an extensive Monte Carlo simulation is also performed to verify the proposed approach

MGCN: Semi-supervised Classification in Multi-layer Graphs with Graph Convolutional Networks

Graph embedding is an important approach for graph analysis tasks such as node classification and link prediction. The goal of graph embedding is to find a low dimensional representation of graph nodes that preserves the graph information. Recent methods like Graph Convolutional Network (GCN) try to consider node attributes (if available) besides node relations and learn node embeddings for unsupervised and semi-supervised tasks on graphs. On the other hand, multi-layer graph analysis has been received attention recently. However, the existing methods for multi-layer graph embedding cannot incorporate all available information (like node attributes). Moreover, most of them consider either type of nodes or type of edges, and they do not treat within and between layer edges differently. In this paper, we propose a method called MGCN that utilizes the GCN for multi-layer graphs. MGCN embeds nodes of multi-layer graphs using both within and between layers relations and nodes attributes. We evaluate our method on the semi-supervised node classification task. Experimental results demonstrate the superiority of the proposed method to other multi-layer and single-layer competitors and also show the positive effect of using cross-layer edges

Reliability-Based Topology Optimization Using Stochastic Response Surface Method with Sparse Grid Design

A mathematical framework is developed which integrates the reliability concept into topology optimization to solve reliability-based topology optimization (RBTO) problems under uncertainty. Two typical methodologies have been presented and implemented, including the performance measure approach (PMA) and the sequential optimization and reliability assessment (SORA). To enhance the computational efficiency of reliability analysis, stochastic response surface method (SRSM) is applied to approximate the true limit state function with respect to the normalized random variables, combined with the reasonable design of experiments generated by sparse grid design, which was proven to be an effective and special discretization technique. The uncertainties such as material property and external loads are considered on three numerical examples: a cantilever beam, a loaded knee structure, and a heat conduction problem. Monte-Carlo simulations are also performed to verify the accuracy of the failure probabilities computed by the proposed approach. Based on the results, it is demonstrated that application of SRSM with SGD can produce an efficient reliability analysis in RBTO which enables a more reliable design than that obtained by DTO. It is also found that, under identical accuracy, SORA is superior to PMA in view of computational efficiency

Entailment Tree Explanations via Iterative Retrieval-Generation Reasoner

Large language models have achieved high performance on various question answering (QA) benchmarks, but the explainability of their output remains elusive. Structured explanations, called entailment trees, were recently suggested as a way to explain and inspect a QA system's answer. In order to better generate such entailment trees, we propose an architecture called Iterative Retrieval-Generation Reasoner (IRGR). Our model is able to explain a given hypothesis by systematically generating a step-by-step explanation from textual premises. The IRGR model iteratively searches for suitable premises, constructing a single entailment step at a time. Contrary to previous approaches, our method combines generation steps and retrieval of premises, allowing the model to leverage intermediate conclusions, and mitigating the input size limit of baseline encoder-decoder models. We conduct experiments using the EntailmentBank dataset, where we outperform existing benchmarks on premise retrieval and entailment tree generation, with around 300% gain in overall correctness.Comment: published in NAACL 202

Post-pollination sepal longevity of female flower co-regulated by energy-associated multiple pathways in dioecious spinach

Reproductive growth is a bioenergetic process with high energy consumption. Pollination induces female flower longevity in spinach by accelerating sepal retention and development. Cellular bioenergetics involved in cellular growth is at the foundation of all developmental activities. By contrast, how pollination alter the sepal cells bioenergetics to support energy requirement and anabolic biomass accumulation for development is less well understood. To investigate pollination-induced energy-associated pathway changes in sepal tissues after pollination, we utilized RNA-sequencing to identify transcripts that were differentially expressed between unpollinated (UNP) and pollinated flower sepals at 12, 48, and 96HAP. In total, over 6756 non-redundant DEGs were identified followed by pairwise comparisons (i.e. UNP vs 12HAP, UNP vs 48HAP, and UNP vs 96HAP). KEGG enrichment showed that the central carbon metabolic pathway was significantly activated after pollination and governed by pivotal energy-associated regulation pathways such as glycolysis, the citric acid cycle, oxidative phosphorylation, photosynthesis, and pentose phosphate pathways. Co-expression networks confirmed the synergistically regulation interactions among these pathways. Gene expression changes in these pathways were not observed after fertilization at 12HAP, but started after fertilization at 48HAP, and significant changes in gene expression occurred at 96HAP when there is considerable sepal development. These results were also supported by qPCR validation. Our results suggest that multiple energy-associated pathways may play a pivotal regulatory role in post-pollination sepal longevity for developing the seed coat, and proposed an energy pathway model regulating sepal retention in spinach

The Euscaphis japonica genome and the evolution of malvids

Malvids is one of the largest clades of rosids, includes 58 families and exhibits remarkable morphological and ecological diversity. Here, we report a high-quality chromosome-level genome assembly for Euscaphis japonica, an early-diverging species within malvids. Genome-based phylogenetic analysis suggests that the unstable phylogenetic position of E. japonica may result from incomplete lineage sorting and hybridization event during the diversification of the ancestral population of malvids. Euscaphis japonica experienced two polyploidization events: the ancient whole genome triplication event shared with most eudicots (commonly known as the c event) and a more recent whole genome duplication event, unique to E. japonica. By resequencing 101 samples from 11 populations, we speculate that the temperature has led to the differentiation of the evergreen and deciduous of E. japonica and the completely different population histories of these two groups. In total, 1012 candidate positively selected genes in the evergreen were detected, some of which are involved in flower and fruit development. We found that reddening and dehiscence of the E. japonica pericarp and long fruit-hanging time promoted the reproduction of E. japonica populations, and revealed the expression patterns of genes related to fruit reddening, dehiscence and abscission. The key genes involved in pentacyclic triterpene synthesis in E. japonica were identified, and different expression patterns of these genes may contribute to pentacyclic triterpene diversification. Our work sheds light on the evolution of E. japonica and malvids, particularly on the diversification of E. japonica and the genetic basis for their fruit dehiscence and abscission.DATA AVAILABILITY STATEMENT : All sequences described in this manuscript have been submitted to the National Genomics Data Center (NGDC). The raw whole-genome data of E. japonica have been deposited in BioProject/GSA (https://bigd.big.ac.cn/gsa.) under the accession codes PRJCA005268/CRA004271, and the assembly and annotation data have been deposited at BioProject/GWH (https://bigd.big.ac.cn/gwh) under the accession codes PRJCA005268/GWHBCHS00000000. The raw transcriptomes data of E. japonica have been deposited in BioProject/GSA (https://bigd.big.ac.cn/gsa.) under the accession codes PRJCA005298/CRA004272.SUPPLEMENTARY MATERIAL 1: Supplementary Note 1. Chromosome number assessment. Supplementary Note 2. Whole-genome duplication identification and dating. Supplementary Note 3. Observation of E. japonica seed dispersal. Supplementary Note 4. Determination of pentacyclic triterpene substances. Figure S1. Cytogenetic analysis of E. japonica. Figure S2. Genome size and heterozygosity of E. japonica estimation using 17 k-mer distribution. Figure S3. Interchromosomal of Hi-C chromosome contact map of E. japonica genome. Figure S4. Gene structure prediction results of E. japonica and other species. Figure S5. Venn diagram shows gene families of malvids. Figure S6. Phylogenetic tree constructed by chloroplast genomes from 17 species. Figure S7. Concatenated- and ASTRAL-based phylogenetic trees. Figure S8. Ks distribution in E. japonica. Figure S9. Distributions of synonymous substitutions per synonymous site (Ks) of one-to-one orthologs identified between E. japonica and P. trichocarpa and V. vinifera. Figure S10. Population structure plot. Figure S11. Fixation index (FST) heat map among E. japonica populations. Figure S12. Phylogenetic analysis of MADS-box genes from O. sativa, A. thaliana, E. japonica, and T. cacao. Figure S13. Observation the fruit development. Figure S14. Animal seed dispersal. Figure S15. Anthocyanin biosynthesis in E. japonica fruits. Figure S16. Carotenoid accumulation and the chlorophyll degradation in E. japonica fruits. Figure S17. Expression profile of fruit dehiscence-related genes. Figure S18. Phylogenetic tree of DELLA genes obtained from six malvids species. Figure S19. Phylogenetic tree of CAD genes obtained from seven malvids species. Figure S20. Expression pattern of fruit abscission-related genes. Figure S21. Structure of pentacyclic triterpene compounds separated from Euscaphis. Figure S22. Phylogenetic tree of HMGR gene in plants. Figure S23. Phylogenetic tree of P450s gene family obtained from A. thaliana and E. japonica.SUPPLEMENTARY MATERIAL 2: Table S1. Assembled statistics of E. japonica genome. Table S2. Evaluation of E. japonica genome assembly. Table S3. Chromosome length of E. japonica. Table S4. Prediction of gene structures of the E. japonica genome. Table S5. Statistics on the function annotation of the E. japonica genome. Table S6. Non-coding RNA annotation results of E. japonica genome. Table S7. BUSCO assessment of the E. japonica annotated genome. Table S8. Statistic of repeat sequence in E. japonica genome. Table S9. Gene-clustering statistics for 17 species. Table S10. KEGG enrichment result of unique genes families of E. japonica. Table S11. Gene Ontology (GO) and KEGG enrichment result of significant shared by malvids species gene families. Table S12. Gene Ontology (GO) and KEGG enrichment result of significant expansion of E. japonica gene families. Table S13. Gene Ontology (GO) enrichment result of significant contraction of E. japonica gene families. Table S14. Statistical sampling population information. Table S15. Statistics population resequencing information. Table S16. Statistical nucleotide polymorphisms in the populations. Table S17. Candidate positive selection genes (PSGs) in the evergreen population. Table S18. Candidate positive selection genes (PSGs) in the deciduous population. Table S19. Gene Ontology (GO) enrichment result of significant PSGs in the evergreen population. Table S20. List of MADS-box genes identified in E. japonica. Table S21. Genes involved in anthocyanin biosynthesis, carotenoid biosynthesis, and chlorophyll degradation. Table S22. Identification fruit dehiscence-related genes in E. japonica. Table S23. Genes related to lignin synthesis that are highly expressed during pericarp dehiscence. Table S24. Gene expression levels (FPKMs) of fruit abscission-related genes in pericarp. Table S25. Triterpene compounds separated from Euscaphis. Table S26. Number of putative pentacyclic triterpene-related genes in the malvids species. Table S27. Identified pentacyclic triterpene synthesis-related genes in E. japonica genome. Table S28. Statistical simple sequence repeat.Fund for Excellent Doctoral Dissertation of Fujian Agriculture and Forestry University, China; Fujian Provincial Department of Science E. japonica Evolution and Selection of Ornamental Medicinal Resources, China; the Project of Forestry Peak Discipline at Fujian Agriculture and Forestry University, China; the Collection, Development and Utilization of Eascaphis konlshli Germplasm Resources; the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program and from Ghent University.https://onlinelibrary.wiley.com/journal/1365313xam2022BiochemistryGeneticsMicrobiology and Plant Patholog

The complete plastome of Cymbidium tortisepalum (Orchidaceae) hermaphrodite

We report a complete chloroplast (cp) genome of a Cymbidium tortisepalum hermaphrodite. The cp genome is 149,764 bp in length, with a large single-copy region (LSC) of 85,257 bp and a small single-copy region (SSC) of 13,317 bp, which were separated by a pair of 25,595 bp inverted repeat regions (IRs). The genome contained 130 genes, with 111 unique genes, including 77 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The overall GC content is 37.11% with the values of the LSC, SSC, and IR regions are 34.44%, 29.67%, and 43.49%, respectively. Further, phylogenetic analysis suggested that the plastome of C. tortisepalum hermaphrodite is close to published C. sinense (NC021430.1), C. kanran (KU179435.1), C. tortisepalum (NC021431.1), and C. ensifolium (NC028525.1) plastomes

The complete chloroplast genome of a Cymbidium Tortisepalum (Orchidaceae) male mutant

The chloroplast (cp) genome of natural male mutant Cymbidium tortisepalum ‘Guanshihe’ has been characterized using Illumina pair-end sequencing technology. The complete cp genome was 149,830 bp in length, containing a large single-copy region (LSC) of 85,131 bp and a small single-copy region (SSC) of 13,275 bp, which were separated by a pair of 25,712 bp inverted repeat regions (IRs). The genome contained 130 genes, with 111 unique genes, including 77 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The overall GC content is 37.09% with the values of the LSC, SSC, and IR regions are 34.40%, 29.63%, and 43.45%, respectively. Further, phylogenetic analysis suggested that the plastome of C. tortisepalum male mutant ‘Guanshihe’ is close to sequenced C. sinense, C. kanran, C. tortisepalum, and C. ensifolium plastomes

Synthesis and Characterization of Beta/MCM-41 Composite Zeolite and its Performance for n-Butane Adsorption

A series of beta/MCM-41 composites with different molar ratios of microporous template agent (tetraethylammonium hydroxide or TEAOH) to mesoporous template agent (cetyltrimethylammonium bromide or CTAB) was synthesized using a two-step method. Results of X-ray powder diffraction, scanning electron microscopy and N 2 adsorption confirmed that a proper molar ratio of TEAOH to CTAB benefit the formation of composite structures. The measurements of adsorption of n-butane onto the as-synthesized composites were performed at 308 K. All the experimental data fitted well with the Langmuir model. The results of n-butane adsorption demonstrated that the specific surface area and micropore volume played important roles in determining the adsorption capacity of the composites. The isosteric heat of n-butane adsorption at different coverage was also calculated using Clausius–Clapeyron equation