Saliency-Aware Regularized Graph Neural Network

The crux of graph classification lies in the effective representation learning for the entire graph. Typical graph neural networks focus on modeling the local dependencies when aggregating features of neighboring nodes, and obtain the representation for the entire graph by aggregating node features. Such methods have two potential limitations: 1) the global node saliency w.r.t. graph classification is not explicitly modeled, which is crucial since different nodes may have different semantic relevance to graph classification; 2) the graph representation directly aggregated from node features may have limited effectiveness to reflect graph-level information. In this work, we propose the Saliency-Aware Regularized Graph Neural Network (SAR-GNN) for graph classification, which consists of two core modules: 1) a traditional graph neural network serving as the backbone for learning node features and 2) the Graph Neural Memory designed to distill a compact graph representation from node features of the backbone. We first estimate the global node saliency by measuring the semantic similarity between the compact graph representation and node features. Then the learned saliency distribution is leveraged to regularize the neighborhood aggregation of the backbone, which facilitates the message passing of features for salient nodes and suppresses the less relevant nodes. Thus, our model can learn more effective graph representation. We demonstrate the merits of SAR-GNN by extensive experiments on seven datasets across various types of graph data. Code will be released.Comment: Accepted by Artificial Intelligence Journal with minor revisio

A Comparison of Molecular Biology Mechanism of Shewanella putrefaciens between Fresh and Terrestrial Sewage Wastewater

Municipal and industrial wastewater is often discharged into the environment without appropriate treatment, especially in developing countries. As a result, many rivers and oceans are contaminated. It is urgent to control and administer treatments to these contaminated rivers and oceans. However, most mechanisms of bacterial colonization in contaminated rivers and oceans were unknown, especially in sewage outlets. We found Shewanella putrefaciens to be the primary bacteria in the terrestrial sewage wastewater outlets around Ningbo City, China. Therefore, in this study, we applied a combination of differential proteomics, metabolomics, and real-time fluorescent quantitative PCR techniques to identify bacteria intracellular metabolites. We found S. putrefaciens had 12 different proteins differentially expressed in freshwater culture than when grown in wastewater, referring to the formation of biological membranes (Omp35, OmpW), energy metabolism (SOD, deoxyribose-phosphate pyrophosphokinase), fatty acid metabolism (beta-ketoacyl synthase), secondary metabolism, TCA cycle, lysine degradation (2-oxoglutarate reductase), and propionic acid metabolism (succinyl coenzyme A synthetase). The sequences of these 12 differentially expressed proteins were aligned with sequences downloaded from NCBI. There are also 27 differentially concentrated metabolites detected by NMR, including alcohols (ethanol, isopropanol), amines (dimethylamine, ethanolamine), amino acids (alanine, leucine), amine compounds (bilinerurine), nucleic acid compounds (nucleosides, inosines), organic acids (formate, acetate). Formate and ethanolamine show significant difference between the two environments and are possibly involved in energy metabolism, glycerophospholipid and ether lipids metabolism to provide energy supply and material basis for engraftment in sewage. Because understanding S. putrefaciens’s biological mechanism of colonization (protein, gene express and metabolites) in terrestrial sewage outlets is so important to administering and improving contaminated river and to predicting and steering performance, we delved into the biological mechanism that sheds light on the effect of environmental conditions on metabolic pathways

Cloning and Phylogenetic Analysis of Sid-1-Like Genes from Aphids

The sid-1 (systemic interference defective) gene encodes a transmembrane protein that is an important participator in the systemic RNAi pathway and has been reported in several organisms. In insects, sid-1-like genes were described from Tribolium castaneum, Apis mellifera, Bombyx mori and Schistocerca americana, but were not found in Drosophila melanogaster and Anopheles gambiae. To investigate whether this gene occurs in aphid species, RT-PCRs were performed using degenerate primers designed using the conserved motif of sid-1-like genes. An sid-1-like full-length transcript was amplified from the cotton/melon aphid, Aphis gossypii Glover (Homopera: Aphididae), and a fragment was amplified from the grain aphid, Sitobion avenae (F.). The trancript from A. gossypii was 3067 bp long, with an open reading frame encoding 766 amino acids. Sequence analysis indicated that this transcript shares highest similarity with the reported sid-1-like gene in Schistocerca americana (53%, fragment), followed by A. mellifera (44%), T. castaneum (32–44%), B. mori (38–42%) and Caenorhabditis elegans (25%). Analysis of the transmembrane protein topological structure indicated that the protein encoded by this gene has a similar structure to SID-1 of C. elegans. A phylogenetic tree with all available sid-1-like genes suggests that sid-1-like genes may have had a long evolutionary history. Considering its importance in the RNAi pathway, the absence of a sid-1-like gene in D. melanogaster and A. gambiae is worthy of further investigation

Special Libraries, January 1925

Volume 16, Issue 1https://scholarworks.sjsu.edu/sla_sl_1925/1000/thumbnail.jp

Weaning Induced Hepatic Oxidative Stress, Apoptosis, and Aminotransferases through MAPK Signaling Pathways in Piglets

This study investigated the effects of weaning on the hepatic redox status, apoptosis, function, and the mitogen-activated protein kinase (MAPK) signaling pathways during the first week after weaning in piglets. A total of 12 litters of piglets were weaned at d 21 and divided into the weaning group (WG) and the control group (CG). Six piglets from each group were slaughtered at d 0 (d 20, referred to weaning), d 1, d 4, and d 7 after weaning. Results showed that weaning significantly increased the concentrations of hepatic free radicals H2O2 and NO, malondialdehyde (MDA), and 8-hydroxy-2′-deoxyguanosine (8-OHdG), while significantly decreasing the inhibitory hydroxyl ability (IHA) and glutathione peroxidase (GSH-Px), and altered the level of superoxide dismutase (SOD). The apoptosis results showed that weaning increased the concentrations of caspase-3, caspase-8, caspase-9 and the ratio of Bax/Bcl-2. In addition, aspartate aminotransferase transaminase (AST) and alanine aminotransferase (ALT) in liver homogenates increased after weaning. The phosphorylated JNK and ERK1/2 increased, while the activated p38 initially decreased and then increased. Our results suggested that weaning increased the hepatic oxidative stress and aminotransferases and initiated apoptosis, which may be related to the activated MAPK pathways in postweaning piglets

Can proline dehydrogenase—a key enzyme involved in proline metabolism—be a novel target for cancer therapy?

Emerging evidence suggests that proline metabolism is important for regulating the survival and death of different types of cancer cells. Proline dehydrogenase (PRODH), an enzyme catalyzing proline catabolism, and the degradation products of proline by PRODH, such as ATP and ROS, are known to play critical roles in cancer progression. Notably, the role of PRODH in cancer is still complicated and unclear, and primarily depends on the cancer type and tumor microenvironment. For instance, PRODH induces apoptosis and senescence through ROS signaling in different types of cancers, while as a protumor factor, PRODH promotes malignant phenotypes of certain tumors under stresses such as hypoxia. In order to assess whether PRODH can serve as a novel target for cancer therapy, we will provide an overview of the biological functions of PRODH and its double-edged role in cancer in this article

Causal relationships exist between polycystic ovary syndrome and adverse pregnancy and perinatal outcomes: a Mendelian randomization study

IntroductionPrevious observational studies have shown that polycystic ovary syndrome (PCOS) was associated with adverse pregnancy and perinatal outcomes. However, it remains controversial whether PCOS is an essential risk factor for these adverse pregnancy and perinatal outcomes. We aimed to use instrumental variables in a two-sample Mendelian randomization (MR) study to determine causality between PCOS and adverse pregnancy and perinatal outcomes.Materials and methodsSummary statistics were extracted from a recent genome-wide association study (GWAS) meta-analysis conducted in PCOS, which included 10,074 cases and 103,164 controls of European ancestry. Data on Adverse pregnancy and perinatal outcomes were summarized from the FinnGen database of European ancestry, which included more than 180,000 samples. The inverse variance weighted (IVW) method of MR was applied for the main outcome. To assess heterogeneity and pleiotropy, we conducted sensitivity analyses, including leave-one-out analysis, weighted median, MR-PRESSO (Mendelian Randomization Pleiotropy RESidual Sum and Outlier), and MR-Egger regression.ResultsTwo-sample MR analysis with the IVW method suggested that PCOS exerted causal effects on the risk of hypertensive disorders of pregnancy [odds ratio (OR) 1.170, 95% confidence interval (CI) 1.051–1.302, p = 0.004], in particular gestational hypertension (OR 1.083, 95% CI 1.007–1.164, p = 0.031), but not other pregnancy and perinatal diseases (all p > 0.05). Sensitivity analyses demonstrated pleiotropy only in pre-eclampsia or eclampsia (p = 0.0004), but not in other pregnancy and perinatal diseases (all p > 0.05). The results remained consistent after excluding two outliers (all p > 0.05).ConclusionsWe confirmed a causal relationship between PCOS and hypertensive disorders of pregnancy, in particular gestational hypertension, but no association with any other adverse pregnancy or perinatal outcome. Therefore, we suggest that women with PCOS who are pregnant should have their blood pressure closely monitored

Characterizing the Penumbras of White Matter Hyperintensities and Their Associations With Cognitive Function in Patients With Subcortical Vascular Mild Cognitive Impairment

Normal-appearing white matter (NAWM) surrounding white matter hyperintensities (WMHs), frequently known as the WMH penumbra, is associated with subtle white matter injury and has a high risk for future conversion to WMHs. The goal of this study was to define WMH penumbras and to further explore whether the diffusion and perfusion parameters of these penumbras could better reflect cognitive function alterations than WMHs in subjects with subcortical vascular mild cognitive impairment (svMCI). Seventy-three svMCI subjects underwent neuropsychological assessments and 3T MRI scans, including diffusion tensor imaging (DTI) and arterial spin labeling (ASL). To determine the extent of cerebral blood flow (CBF) and DTI penumbras. A NAWM layer mask was generated for periventricular WMHs (PVWMHs) and deep WMHs (DWMHs) separately. Mean values of CBF, fractional anisotropy (FA), mean diffusivity (MD) within the WMHs and their corresponding NAWM layer masks were computed and compared using paired t-tests. Pearson's partial correlations were used to assess the relations of the mean CBF, FA, and MD values within the corresponding penumbras with composite z-scores of global cognition and four cognitive domains controlling for age, sex, and education. For both PVWMHs and DWMHs, the CBF penumbras were wider than the DTI penumbras. Only the mean FA value of the PVWMH-FA penumbra was correlated with the composite z-scores of global cognition before correction (r = 0.268, p = 0.024), but that correlation did not survive after correcting the p-value for multiple comparisons. Our findings showed extensive white matter perfusion disturbances including white matter tissue, both with and without microstructural alterations. The imaging parameters investigated, however, did not correlate to cognition