NAPG: Non-Autoregressive Program Generation for Hybrid Tabular-Textual Question Answering

Hybrid tabular-textual question answering (QA) requires reasoning from heterogeneous information, and the types of reasoning are mainly divided into numerical reasoning and span extraction. Despite being the main challenge of the task compared to extractive QA, current numerical reasoning method simply uses LSTM to autoregressively decode program sequences, and each decoding step produces either an operator or an operand. However, the step-by-step decoding suffers from exposure bias, and the accuracy of program generation drops sharply with progressive decoding. In this paper, we propose a non-autoregressive program generation framework, which facilitates program generation in parallel. Our framework, which independently generates complete program tuples containing both operators and operands, can significantly boost the speed of program generation while addressing the error accumulation issue. Our experiments on the MultiHiertt dataset shows that our model can bring about large improvements (+7.97 EM and +6.38 F1 points) over the strong baseline, establishing the new state-of-the-art performance, while being much faster (21x) in program generation. The performance drop of our method is also significantly smaller than the baseline with increasing numbers of numerical reasoning steps

Genome-wide identification, characterization, expression and enzyme activity analysis of coniferyl alcohol acetyltransferase genes involved in eugenol biosynthesis in Prunus mume.

Prunus mume, a traditional Chinese flower, is the only species of Prunus known to produce a strong floral fragrance, of which eugenol is one of the principal components. To explore the molecular mechanism of eugenol biosynthesis in P. mume, patterns of dynamic, spatial and temporal variation in eugenol were analysed using GC-MS. Coniferyl alcohol acetyltransferase (CFAT), a member of the BAHD acyltransferase family, catalyses the substrate of coniferyl alcohol to coniferyl acetate, which is an important substrate for synthesizing eugenol. In a genome-wide analysis, we found 90 PmBAHD genes that were phylogenetically clustered into five major groups with motif compositions relatively conserved in each cluster. The phylogenetic tree showed that the PmBAHD67-70 proteins were close to the functional CFATs identified in other species, indicating that these four proteins might function as CFATs. In this work, 2 PmCFAT genes, named PmCFAT1 and PmCFAT2, were cloned from P. mume 'Sanlunyudie', which has a strong fragrance. Multiple sequences indicated that PmCFAT1 contained two conserved domains, HxxxD and DFGWG, whereas DFGWG in PmCFAT2 was changed to DFGFG. The expression levels of PmCFAT1 and PmCFAT2 were examined in different flower organs and during the flowering stages of P. mume 'Sanlunyudie'. The results showed that PmCFAT1 was highly expressed in petals and stamens, and this expression increased from the budding stage to the full bloom stage and decreased in the withering stage, consistent with the patterns of eugenol synthesis and emission. However, the peak of gene expression appeared earlier than those of eugenol synthesis and emission. In addition, the expression level of PmCFAT2 was higher in pistils and sepals than in other organs and decreased from the budding stage to the blooming stage and then increased in the withering stage, which was not consistent with eugenol synthesis. Subcellular localization analysis indicated that PmCFAT1 and PmCFAT2 were located in the cytoplasm and nucleus, while enzyme activity assays showed that PmCFAT1 is involved in eugenol biosynthesis in vitro. Overall, the results suggested that PmCFAT1, but not PmCFAT2, contributed to eugenol synthesis in P. mume

An APETALA2 Homolog, RcAP2, Regulates the Number of Rose Petals Derived From Stamens and Response to Temperature Fluctuations

Rosa chinensis, which is a famous traditional flower in China, is a major ornamental plant worldwide. Long-term cultivation and breeding have resulted in considerable changes in the number of rose petals, while most wild Rosaceae plants have only one whorl consisting of five petals. The petals of double flowers reportedly originate from stamens, but the underlying molecular mechanism has not been fully characterized. In this study, we observed that the number of petals of R. chinensis ‘Old Blush’ flowers increased and decreased in response to low- and high-temperature treatments, respectively, similar to previous reports. We characterized these variations in further detail and found that the number of stamens exhibited the opposite trend. We cloned an APETALA2 homolog, RcAP2. A detailed analysis of gene structure and promoter cis-acting elements as well as RcAP2 temporospatial expression patterns and responses to temperature changes suggested that RcAP2 expression may be related to the number of petals from stamen origin. The overexpression of RcAP2 in Arabidopsis thaliana transgenic plants may induce the transformation of stamens to petals, thereby increasing the number of petals. Moreover, silencing RcAP2 in ‘Old Blush’ plants decreased the number of petals. Our results may be useful for clarifying the temperature-responsive mechanism involved in petaloid stamen production, which may be relevant for the breeding of new rose varieties with enhanced flower traits

Protective Effects and Mechanism of a Novel Probiotic Strain <i>Ligilactobacillus salivarius</i> YL20 against <i>Cronobacter sakazakii</i>-Induced Necrotizing Enterocolitis In Vitro and In Vivo

Exposure to probiotics in early life contributes to host intestinal development and prevention of necrotizing enterocolitis (NEC). Cronobacter sakazakii (C. sakazakii), an opportunistic pathogen, can cause NEC, bacteremia, and meningitis in neonates, but the research of probiotics against C. sakazakii is limited relative to other enteropathogens. Here, the protective effect and mechanism of a novel probiotic Ligilactobacillus salivarius (L. salivarius) YL20 isolated from breast milk on C. sakazakii-induced intestinal injury were explored by using two in vitro models, including an C. sakazakii-infected intestinal organoid model and intestinal barrier model, as well as an in vivo experimental animal model. Our results revealed that L. salivarius YL20 could promote epithelial cell proliferation in intestinal organoids, rescue budding-impaired organoids, prevent the decrease of mRNA levels of leucine-rich repeat containing G protein-coupled receptor 5 (Lgr5), zonula occludens-1 (Zo-1) and Occludin, and reverse C. sakazakii-induced low level of Mucin 2 (MUC2) in intestinal organoids. Additionally, YL20 could inhibit C. sakazakii invasion, increase the expression of ZO-1 and occludin in C. sakazakii-infected HT-29 cells, and reverse TEER decrease and corresponding permeability increase across C. sakazakii-infected Caco-2 monolayers. Furthermore, YL20 administration could alleviate NEC in C. sakazakii-infected neonatal mice by increasing the mice survival ratio, decreasing pathology scores, and downregulating pro-inflammatory cytokines. Meanwhile, YL20 could also enhance intestinal barrier function in vivo by increasing the number of goblet cells, the level of MUC-2 and the expression of ZO-1. Our overall findings demonstrated for the first time the beneficial effects of L. salivarius YL20 against C. sakazakii-induced NEC by improving intestinal stem cell function and enhancing intestinal barrier integrity

Top 20 enriched KEGG pathways among DEGs from ‘ST3 vs ST0’, ‘ST9 vs ST3’, and ‘ST9 vs ST0’.

<p>The number of DEGs in each pathway is positively related to the size of the plots. The padj values shown in red are positive.</p

qRT-PCR analysis of 12 DEGs during periods of salt stress.

<p>Twelve unigenes used for verification by qRT-PCR were randomly selected from among salt-response-related genes. The qRT-PCR results are the means ± standard deviations (± SDs) of three replicates.</p

Expression of DEGs in salt-responsive KEGG pathways.

<p>Expression of DEGs in salt-responsive KEGG pathways.</p

Transcriptome analysis of <i>Crossostephium chinensis</i> provides insight into the molecular basis of salinity stress responses

<div><p>Soil salinization is becoming a limitation to the utilization of ornamental plants worldwide. <i>Crossostephium chinensis</i> (Linnaeus) Makino is often cultivated along the southeast coast of China for its desirable ornamental qualities and high salt tolerance. However, little is known about the genomic background of the salt tolerance mechanism in <i>C</i>. <i>chinensis</i>. In the present study, we used Illumina paired-end sequencing to systematically investigate leaf transcriptomes derived from <i>C</i>. <i>chinensis</i> seedlings grown under normal conditions and under salt stress. A total of 105,473,004 bp of reads were assembled into 163,046 unigenes, of which 65,839 (40.38% of the total) and 54,342 (33.32% of the total) were aligned in Swiss-Prot and Nr protein, respectively. A total of 11,331 (6.95%) differentially expressed genes (DEGs) were identified among three comparisons, including 2,239 in ‘ST3 vs ST0’, 5,880 in ‘ST9 vs ST3’ and 9,718 in ‘ST9 vs ST0’, and they were generally classified into 26 Gene Ontology terms and 58 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway terms. Many genes encoding important transcription factors (e.g., <i>WRKY</i>, <i>MYB</i>, and <i>AP2/EREBP</i>) and proteins involved in starch and sucrose metabolism, arginine and proline metabolism, plant hormone signal transduction, amino acid biosynthesis, plant-pathogen interactions and carbohydrate metabolism, among others, were substantially up-regulated under salt stress. These genes represent important candidates for studying the salt-response mechanism and molecular biology of <i>C</i>. <i>chinensis</i> and its relatives. Our findings provide a genomic sequence resource for functional genetic assignments in <i>C</i>. <i>chinensis</i>. These transcriptome datasets will help elucidate the molecular mechanisms responsible for salt-stress tolerance in <i>C</i>. <i>chinensis</i> and facilitate the breeding of new stress-tolerant cultivars for high-saline areas using this valuable genetic resource.</p></div

Expression of salt-responsive gene families.

<p>Expression of salt-responsive gene families.</p