Equivariant Hypergraph Diffusion Neural Operators

Hypergraph neural networks (HNNs) using neural networks to encode hypergraphs provide a promising way to model higher-order relations in data and further solve relevant prediction tasks built upon such higher-order relations. However, higher-order relations in practice contain complex patterns and are often highly irregular. So, it is often challenging to design an HNN that suffices to express those relations while keeping computational efficiency. Inspired by hypergraph diffusion algorithms, this work proposes a new HNN architecture named ED-HNN, which provably represents any continuous equivariant hypergraph diffusion operators that can model a wide range of higher-order relations. ED-HNN can be implemented efficiently by combining star expansions of hypergraphs with standard message passing neural networks. ED-HNN further shows great superiority in processing heterophilic hypergraphs and constructing deep models. We evaluate ED-HNN for node classification on nine real-world hypergraph datasets. ED-HNN uniformly outperforms the best baselines over these nine datasets and achieves more than 2\%$\uparrow$ in prediction accuracy over four datasets therein.Comment: Code: https://github.com/Graph-COM/ED-HN

Inductive Representation Learning in Temporal Networks via Causal Anonymous Walks

Temporal networks serve as abstractions of many real-world dynamic systems. These networks typically evolve according to certain laws, such as the law of triadic closure, which is universal in social networks. Inductive representation learning of temporal networks should be able to capture such laws and further be applied to systems that follow the same laws but have not been unseen during the training stage. Previous works in this area depend on either network node identities or rich edge attributes and typically fail to extract these laws. Here, we propose Causal Anonymous Walks (CAWs) to inductively represent a temporal network. CAWs are extracted by temporal random walks and work as automatic retrieval of temporal network motifs to represent network dynamics while avoiding the time-consuming selection and counting of those motifs. CAWs adopt a novel anonymization strategy that replaces node identities with the hitting counts of the nodes based on a set of sampled walks to keep the method inductive, and simultaneously establish the correlation between motifs. We further propose a neural-network model CAW-N to encode CAWs, and pair it with a CAW sampling strategy with constant memory and time cost to support online training and inference. CAW-N is evaluated to predict links over 6 real temporal networks and uniformly outperforms previous SOTA methods by averaged 10% AUC gain in the inductive setting. CAW-N also outperforms previous methods in 4 out of the 6 networks in the transductive setting.Comment: Published in ICLR 2021. A bug in previous versions is fixe

A systematic investigation of Escherichia coli central carbon metabolism in response to superoxide stress

<p>Abstract</p> <p>Background</p> <p>The cellular responses of bacteria to superoxide stress can be used to model adaptation to severe environmental changes. Superoxide stress promotes the excessive production of reactive oxygen species (ROS) that have detrimental effects on cell metabolic and other physiological activities. To antagonize such effects, the cell needs to regulate a range of metabolic reactions in a coordinated way, so that coherent metabolic responses are generated by the cellular metabolic reaction network as a whole. In the present study, we have used a quantitative metabolic flux analysis approach, together with measurement of gene expression and activity of key enzymes, to investigate changes in central carbon metabolism that occur in <it>Escherichia coli </it>in response to paraquat-induced superoxide stress. The cellular regulatory mechanisms involved in the observed global flux changes are discussed.</p> <p>Results</p> <p>Flux analysis based on nuclear magnetic resonance (NMR) and mass spectroscopy (MS) measurements and computation provided quantitative results on the metabolic fluxes redistribution of the <it>E. coli </it>central carbon network under paraquat-induced oxidative stress. The metabolic fluxes of the glycolytic pathway were redirected to the pentose phosphate pathway (PP pathway). The production of acetate increased significantly, the fluxes associated with the TCA cycle decreased, and the fluxes in the glyoxylate shunt increased in response to oxidative stress. These global flux changes resulted in an increased ratio of NADPH:NADH and in the accumulation of α-ketoglutarate.</p> <p>Conclusions</p> <p>Metabolic flux analysis provided a quantitative and global picture of responses of the <it>E. coli </it>central carbon metabolic network to oxidative stress. Systematic adjustments of cellular physiological state clearly occurred in response to changes in metabolic fluxes induced by oxidative stress. Quantitative flux analysis therefore could reveal the physiological state of the cell at the systems level and is a useful complement to molecular systems approaches, such as proteomics and transcription analyses.</p

Temporal variability in trace metal solubility in a paddy soil not reflected in uptake by rice (Oryza sativa L.)

Alternating flooding and drainage conditions have a strong influence on redox chemistry and the solubility of trace metals in paddy soils. However, current knowledge of how the effects of water management on trace metal solubility are linked to trace metal uptake by rice plants over time is still limited. Here, a field-contaminated paddy soil was subjected to two flooding and drainage cycles in a pot experiment with two rice plant cultivars, exhibiting either high or low Cd accumulation characteristics. Flooding led to a strong vertical gradient in the redox potential (Eh). The pH and Mn, Fe, and dissolved organic carbon concentrations increased with decreasing Eh and vice versa. During flooding, trace metal solubility decreased markedly, probably due to sulfide mineral precipitation. Despite its low solubility, the Cd content in rice grains exceeded the food quality standards for both cultivars. Trace metal contents in different rice plant tissues (roots, stem, and leaves) increased at a constant rate during the first flooding and drainage cycle but decreased after reaching a maximum during the second cycle. As such, the high temporal variability in trace metal solubility was not reflected in trace metal uptake by rice plants over time. This might be due to the presence of aerobic conditions and a consequent higher trace metal solubility near the root surface, even during flooding. Trace metal solubility in the rhizosphere should be considered when linking water management to trace metal uptake by rice over time

Characterization and evaluation of rice blast resistance of Chinese indica hybrid rice parental lines

The development of resistant varieties and hybrid combinations has been the most effective and economical strategy to control blast disease caused by Magnaporthe oryzae. However, the distribution of major R genes and blast resistance characterization in hybrid rice parents has not been well investigated, resulting in their limited use in hybrid rice blast-resistance breeding. In the present study, 88 elite indica hybrid rice parental lines were evaluated with 30 isolates of M. oryzae collected from the main planting area of indica hybrid rice in China and were characterized for the presence of 11 major resistance genes using molecular markers. The pathogenicity assays showed that four types of hybrid rice parent line showed some resistance to M. oryzae. However, the proportions of highly resistant lines and the mean resistance frequency (RF) varied among the four types, with resistance in decreasing order shown by three-line restorer lines, three-line maintainer lines, two-line sterile lines, and two-line restorer lines. All 88 hybrid rice parental lines carried more than one R gene, but none carried the R genes Pi1 and Pi2. Although Pid3 and Pi9 were present only in three-line restorer lines and Pigm only in three-line maintainer lines, the remaining six R genes (Pib, Pid2, Pi5, Pia, Pi54, and Pita) were present in the four types of hybrid rice parent with significantly different distribution frequencies. The correlation between R genes and resistance reactions was investigated. The results are expected to provide useful information for rational utilization of major R genes in hybrid rice breeding programs. Keywords: Hybrid rice parental lines, Magnaporthe oryzae, Pi genes, Resistance evaluation, Molecular marker

Solubility of trace metals in two contaminated paddy soils exposed to alternating flooding and drainage

Uptake of trace metals by crops is determined by the solubility of trace metals. In paddy soils, flooding and drainage influence redox chemistry and consequently trace metal solubility and thus uptake by rice plants. Current knowledge on how the dynamics in redox chemistry affect the solubility of trace metals in contaminated paddy soils is still limited. The objectives of our study were to investigate (i) the effects of flooding and drainage on trace metal solubility in paddy soils and (ii) to what extent a multi-surface modeling approach can predict trace metal solubility under changing redox conditions. We performed a column experiment with two contaminated paddy soils with similar soil properties but contrasting pH. During two successive flooding and drainage cycles, dynamics in Eh, pH and dissolved organic matter concentrations greatly affected trace metal solubility for both soils. Multi-surface model predictions indicate that under aerobic conditions, the higher pH of the alkaline soil leads to a stronger complexation of trace metals by reactive surfaces of the soil and, consequently, to lower dissolved concentrations than in the acidic soil. Under anaerobic conditions, predictions shows that sulfide precipitates control trace metal solubility in both soils, but still the higher pH of the alkaline soil leads to lower trace metal concentrations in soil solution at equilibrium. Furthermore, model calculations showed that stoichiometry and solubility of copper sulfide minerals can substantially affect solubility of other trace metals especially when trace element concentrations exceed soil sulfate concentrations. This stoichiometry and solubility should be considered when predicting the solubility of trace metals under anaerobic conditions. (C) 2015 Elsevier B.V. All rights reserved

Influence of pH on the redox chemistry of metal (hydr)oxides and organic matter in paddy soils

The primary purpose of this study was to determine how flooding and draining cycles affect the redox chemistry of metal (hydr)oxides and organic matter in paddy soils and how the pH influences these processes. Our secondary purpose was to determine to what extent a geochemical thermodynamic equilibrium model can be used to predict the solubility of Mn and Fe during flooding and draining cycles in paddy soils

Combination Patterns of Major <i>R</i> Genes Determine the Level of Resistance to the <i>M</i>. <i>oryzae</i> in Rice (<i>Oryza sativa</i> L.)

<div><p>Rice blast caused by <i>Magnaporthe oryzae</i> is the most devastating disease of rice and poses a serious threat to world food security. In this study, the distribution and effectiveness of 18 <i>R</i> genes in 277 accessions were investigated based on pathogenicity assays and molecular markers. The results showed that most of the accessions exhibited some degree of resistance (resistance frequency, RF >50%). Accordingly, most of the accessions were observed to harbor two or more <i>R</i> genes, and the number of <i>R</i> genes harbored in accessions was significantly positively correlated with RF. Some <i>R</i> genes were demonstrated to be specifically distributed in the genomes of rice sub-species, such as <i>Pigm</i>, <i>Pi9</i>, <i>Pi5</i> and <i>Pi1</i>, which were only detected in <i>indica</i>-type accessions, and <i>Pik</i> and <i>Piz</i>, which were just harbored in <i>japonica</i>-type accessions. By analyzing the relationship between <i>R</i> genes and RF using a multiple stepwise regression model, the <i>R</i> genes <i>Pid3</i>, <i>Pi5</i>, <i>Pi9</i>, <i>Pi54</i>, <i>Pigm </i>and <i>Pit</i> were found to show the main effects against <i>M</i>. <i>oryzae</i> in <i>indica</i>-type accessions, while <i>Pita</i>, <i>Pb1</i>, <i>Pik</i>, <i>Pizt</i> and <i>Pia</i> were indicated to exhibit the main effects against <i>M</i>. <i>oryzae</i> in <i>japonica</i>-type accessions. Principal component analysis (PCA) and cluster analysis revealed that combination patterns of major <i>R</i> genes were the main factors determining the resistance of rice varieties to <i>M</i>. <i>oryzae</i>, such as ‘<i>Pi9</i>+<i>Pi54</i>’, ‘<i>Pid3</i>+<i>Pigm</i>’, ‘<i>Pi5</i>+<i>Pid3</i>+<i>Pigm</i>’, ‘<i>Pi5</i>+<i>Pi54</i>+<i>Pid3</i>+<i>Pigm</i>’, ‘<i>Pi5</i>+<i>Pid3</i>’ and ‘<i>Pi5</i>+<i>Pit</i>+<i>Pid3</i>’ in <i>indica</i>-type accessions and ‘<i>Pik+Pib</i>’, ‘<i>Pik+Pita</i>’, ‘<i>Pik+Pb1</i>’, ‘<i>Pizt+Pia</i>’ and ‘<i>Pizt+Pita</i>’ in <i>japonica</i>-type accessions, which were able to confer effective resistance against <i>M</i>. <i>oryzae</i>. The above results provide good theoretical support for the rational utilization of combinations of major <i>R</i> genes in developing rice cultivars with broad-spectrum resistance.</p></div

Comprehensive evaluation of resistance effects of pyramiding lines with different broad-spectrum resistance genes against Magnaporthe oryzae in rice (Oryza sativa L.)

Abstract Background Broad-spectrum resistance gene pyramiding helps the development of varieties with broad-spectrum and durable resistance to M. oryzae. However, detailed information about how these different sources of broad-spectrum resistance genes act together or what are the best combinations to achieve broad-spectrum and durable resistance is limited. Results Here a set of fifteen different polygene pyramiding lines (PPLs) were constructed using marker-assisted selection (MAS). Using artificial inoculation assays at seedling and heading stage, combined with natural induction identification under multiple field environments, we evaluated systematically the resistance effects of different alleles of Piz locus (Pigm, Pi40, Pi9, Pi2 and Piz) combined with Pi1, Pi33 and Pi54, respectively, and the interaction effects between different R genes. The results showed that the seedling blast and panicle blast resistance levels of PPLs were significantly higher than that of monogenic lines. The main reason was that most of the gene combinations produced transgressive heterosis, and the transgressive heterosis for panicle blast resistance produced by most of PPLs was higher than that of seedling blast resistance. Different gene pyramiding with broad-spectrum R gene produced different interaction effects, among them, the overlapping effect (OE) between R genes could significantly improve the seedling blast resistance level of PPLs, while the panicle blast resistance of PPLs were remarkably correlated with OE and complementary effect (CE). In addition, we found that gene combinations, Pigm/Pi1, Pigm/Pi54 and Pigm/Pi33 displayed broad-spectrum resistance in artificial inoculation at seedling and heading stage, and displayed stable broad-spectrum resistance under different disease nursery. Besides, agronomic traits evaluation also showed PPLs with these three gene combinations were at par to the recurrent parent. Therefore, it would provide elite gene combination model and germplasms for rice blast resistance breeding program. Conclusions The development of PPLs and interaction effect analysis in this study provides valuable theoretical foundation and innovative resources for breeding broad-spectrum and durable resistant varieties