Graph Neural Networks for Natural Language Processing: A Survey

Deep learning has become the dominant approach in coping with various tasks in Natural LanguageProcessing (NLP). Although text inputs are typically represented as a sequence of tokens, there isa rich variety of NLP problems that can be best expressed with a graph structure. As a result, thereis a surge of interests in developing new deep learning techniques on graphs for a large numberof NLP tasks. In this survey, we present a comprehensive overview onGraph Neural Networks(GNNs) for Natural Language Processing. We propose a new taxonomy of GNNs for NLP, whichsystematically organizes existing research of GNNs for NLP along three axes: graph construction,graph representation learning, and graph based encoder-decoder models. We further introducea large number of NLP applications that are exploiting the power of GNNs and summarize thecorresponding benchmark datasets, evaluation metrics, and open-source codes. Finally, we discussvarious outstanding challenges for making the full use of GNNs for NLP as well as future researchdirections. To the best of our knowledge, this is the first comprehensive overview of Graph NeuralNetworks for Natural Language Processing.Comment: 127 page

Combined antioxidant formulation of ascorbic acid with resveratrol ameliorates isoproterenol-induced myocardial infarction in rats

The current investigation was proposed to assess the effectiveness of the combination of resveratrol and ascorbic acid against Isoproterenol (ISO)-induced myocardial infarction in rats. The experimental model was divided into six groups (n = 6 in each group). Group I: control, Group 2: isoproterenol (ISO)-100 mg/kg b.wt, Group 3: ISO+Resveratrol (RES) (20 mg/kg b.wt) treated, Group 4: ISO+ Ascorbic acid (AA) (80 mg/kg b.wt) treated, Group 5: ISO+RES (20 mg/kg b.wt)+AA (80 mg/kg b.wt) treated and Group 6: RES (20 mg/kg b.wt)+ AA (80 mg/kg b.wt) alone treated. The study showed an increase in lipid peroxides and cardiac markers in the serum samples of experimental animals administered with ISO. Treatment with RES and AA individually and a combinational formulation brought a significant decrease in lipid peroxides and cardiac markers. They increased the level of enzymatic antioxidants and non-enzymatic antioxidant levels. Histopathological results showed the distortion of heart architecture among the experimental groups administered with ISO and significant recovery when treated with RES and AA individually and in their combination. The study presents the effective combination of RES and AA in combating ISO-induced myocardial infarction and protection against ROS-mediated oxidative stress

Molecular and morphological evidence support a new species of Rosaceae Prunus subg. Cerasus from Wuyishan National Park, southeast China

Prunus tongmuensis, a new species of cherry blossom, is described and illustrated from Wuyishan National Park, southeast China. This species is characterized by its tubular to nearly bottle-shaped receptacles and dark purple drupes. It can be distinguished from other wild cherry trees by its flowers and leaves, reddish brown young leaves, presence of 1–2 glands at the base of leaves, petioles densely covered with yellowish brown villi, longer pedicels (0.6–2.5 cm), villous pistil, and dark purple drupes. In the present study, we conducted a comprehensive morphological study based on specimens of the new species and its morphologically close species, field observations, and examination of pollen morphology. In addition, our phylogenetic analysis based on the complete plastid genome sequences further confirms the status of the new species and indicates that it is closely related to Prunus clarofolia, however, it notably differs in leaf shape, size, petiole villus color, gland location, timing of flower and leaf openings, and reflexed or spread sepals, as well as drupe color

A Hybrid Josephson Transmission Line and Passive Transmission Line Routing Framework for Single Flux Quantum Logic

The Single Flux Quantum (SFQ) logic family is a novel digital logic as it provides ultra-fast and energy-efficient circuits. For large-scale SFQ circuit design, specialized electronic design automation (EDA) tools are required due to the differences in logic type, timing constraints and circuit architecture, in contrast to the CMOS logic. In order to improve the overall performance of an SFQ circuit, an efficient routing algorithm should be applied during the layout design to perform accurate timing adjustment for fixing hold violations and optimizing critical paths. Thus, a hybrid Josephson transmission line and passive transmission line routing framework is proposed. It consists of four main modules and an exploration of the potential timing performance based on the given layout placement. The proposed routing tool is demonstrated on seven testbench circuits. The obtained results demonstrate that the operating frequency is greatly improved, and all the hold violations are eliminated for each circuit

Elongated magma plumbing system beneath the Coso volcanic field, California, constrained by seismic reflection tomography

The magma plumbing in the lower crust beneath the Coso volcanic field (CVF) remains controversial, largely because of the absence of high-resolution lower crustal velocity models. For the first time, we develop a high-resolution crustal P-wave velocity model for the Coso-Ridgecrest region by jointly inverting 137,992 first P and 8,636 PmP travel-time data using an eikonal equation-based seismic reflection tomography method. More than half of the PmP travel times are picked from earthquakes after the 2019 Mw 7.1 Ridgecrest earthquake. Such abundant PmP travel times significantly improve the resolution of the lower crust. Our final velocity model reveals a prominent low-velocity body sitting right beneath the CVF at 5–20 km depths, which we interpret as a rhyolite magma reservoir that supplies heat flux to the hot springs and also feeds the volcanic activities at Coso. We find that the upper-middle crustal low-velocity body dips southwards into the lower crust, extending to regions beneath the Indian Wells Valley and the Garlock Fault at depth greater than 20 km. We ascribe the lower crustal low-velocity body (more than 4% Vp reduction) to a basaltic magma reservoir that connects the melts in the uppermost mantle with the eruptible rhyolitic reservoir at shallower depths. The basaltic magma reservoir constitutes an important part of a continuous N-S elongated crustal magma plumbing system beneath the CVF, formed as a combined result of local extension, faulting, and stress distribution.Ministry of Education (MOE)National Research Foundation (NRF)Published versionThis study is supported by the National Research Foundation Singapore and the Singapore Ministry of Education under the Research Centers of Excellence Initiative (04MNS001913A620 and 04MNS001953A620). This study is also supported by the National Natural Science Foundation of China (42174084) and Fundamental Research Funds for the central Universities (JZ2021HGPB0058). The authors gratefully appreciate the financial support from China Scholarship Council (201906690020)

Insight into the microorganisms, quality, and protein structure of golden pompano (Trachinotus ovatus) treated with cold plasma at different voltages

Cold plasma (CP) is a non-thermal novel technology for the processing of heat-sensitive food products, but there is concern regarding its impact on food quality. Voltage is one of the most direct factors affecting the bacteriostatic effect of CP. Golden pompano (Trachinotus ovatus) was treated with CP at different voltages (10, 20, and 30 kV). The total viable count decreased as the CP voltage increased, reaching a maximum reduction of 1.54 lg CFU/g on golden pompano treated at 30 kV. No effects on water-holding capacity, pH, total volatile base nitrogen, and T2b relaxation time were observed, indicating that all CP treatments retained the freshness and bound water of the samples. However, as the CP voltage increased, peroxide value and thiobarbituric acid-reactive substances of golden pompano gradually increased, the protein tertiary structure unfolded, and α-helices converted to β-sheets, indicating inevitable lipid and protein oxidation caused by excessive CP voltage. Therefore, a suitable voltage of CP should be selected to inhibits the growth of microorganisms, which avoids deterioration of sea-foods quality

Comparison of Different Methods for RNA Extraction from Floral Buds of Tree Peony (<i>Paeonia suffruticosa</i> Andr.)

Tree peony (Paeonia suffruticosa Andr.), a species native to China, is one of the most important ornamental and medicinal plants. Like other tree species in temperate and boreal zones, the dormancy-activity transition of floral buds is critical for blooming time and fruit production. However, floral buds contain high levels of secondary metabolites, making the isolation of high quality RNA difficult. To obtain a method suitable for extracting RNA from floral buds of tree peony, we evaluated five different methods, including the cetyltrimethylammonium bromide (CTAB) and Sodium dodecyl sulfate (SDS)-based methods, a modified SDS-TRNzol protocol, and two commercial kits (TRNzol and Qiagen RNeasy Plant Mini Kit). The modified SDS-TRNzol method was capable of efficiently removing polyphenols and other metabolites in floral buds. The isolated RNA was of high purity and integrity, as demonstrated by the the A260/280 ratio of approximately 2.0, and RIN values of more than 9.0. Gel electrophoresis analysis indicated that the extracted RNA had clear 28S and 18S ribosomal RNA bands without DNA contamination. The RNA isolated by this protocol was successfully used for downstream manipulations, such as RT-PCR, RACE, and real-time PCR. Together, the modified SDS-TRNzol protocol is an easy, efficient, and highly reproducible method for RNA isolation from floral buds rich in secondary metabolites

Bactericidal efficacy of plasma-activated water against Vibrio parahaemolyticus on Litopenaeus vannamei

In this study, the antimicrobial mechanism of plasma-activated water (PAW) against Vibrio parahaemolyticus and the effectiveness of PAW in artificially contaminated Litopenaeus vannamei were investigated. The results demonstrated a significant reduction (p &lt; 0.05) in viable counts of V. parahaemolyticus with increasing plasma discharge time (5, 10, 20, and 30 min) and PAW immersion time (3, 5, 10, 20, and 30 s). Specifically, the count of V. parahaemolyticus decreased by 2.1, 2.7, 3.3, and 4.4 log CFU/mL after exposed to PAW 5, PAW 10, PAW 20, and PAW 30 for 30 s, respectively. Significant cell surface wrinkling, accompanied by notable nucleic acid and protein leakage were observed after treatment with PAW. The permeability of the inner and outer cell membranes was significantly increased (p &lt; 0.05), along with an increase in electrical conductivity (p &lt; 0.05). The reactive oxygen species (ROS) within V. parahaemolyticus cells were significantly increased (p &lt; 0.05), while superoxide dismutase (SOD) activity, and the relative expression of the ompW, emrD, and luxS genes were significantly decreased (p &lt; 0.05). A reduction number of 1.3, 1.8, 2.1, and 2.2 log CFU/g of V. parahaemolyticus in artificially contaminated L. vannamei was obtained with PAW for 5 min. The study elucidated that PAW could destroy cell membranes, leading to cell death. The findings would strengthen strategies for V. parahaemolyticus control and provide a potential application of PAW for preserving aquatic products

Calycosin Alleviates Injury in Airway Epithelial Cells Caused by PM 2.5 Exposure via Activation of AMPK Signalling

Introdution. Calycosin, a major active component in Astragali radix, has antitumour and anti-inflammation properties, but its effects on PM 2.5-induced injury in vitro and in vivo have not been clarified. Methods. Phospho-AMP-activated protein kinase (p-AMPK) and AMP-activated protein kinase (AMPK) were detected by western blot. Immunofluorescence staining was used to validate changes in the levels of nuclear factor kappa B (NF-кB) p65 nuclear translocation. Mice were administered intraperitoneally with calycosin one hour before anaesthesia and endotracheal instillation of PM 2.5. The extent of lung injury was evaluated in the H&E-stained lung sections. Apoptotic cells were detected by TUNEL staining. Results. Administration of calycosin was increased in PM 2.5-treated B2B cells in a dose-dependent manner in vitro. Fluorescence signals from anti-NF-кB p65 were increased in nuclei of cells pretreated with calycosin. The level of p-AMPK was increased by calycosin in vitro and in vivo. After pretreatment with compound C, the inhibitory effects of calycosin on cytotoxicity, levels of inflammatory cytokines and p-AMPK, and levels of NF-кB p65 nuclear translocation were not significantly decreased in vitro or in vivo. Conclusions. Calycosin effectively decreased the release of inflammatory cytokines and alleviated injury caused by PM 2.5. These effects were mediated through activation of AMPK to suppress NF-κB signalling

Production forecasting methods for different types of gas reservoirs

Hydrocarbon production in oil and gas fields generally progresses through stages of production ramp-up, plateau (peak), and decline during field development, with the whole process primarily modeled and forecasted using lifecycle models. SINOPEC's conventional gas reservoirs are dominated by carbonates, low-permeability tight sandstone, condensate, volcanic rocks, and medium-to-high-permeability sandstone. This study identifies the optimal production forecasting models by comparing the fitting coefficients of different models and calculating the relative errors in technically recoverable reserves. To improve forecast precision, it suggests substituting exponential smoothing method-derived predictions for anomalous data caused by subjective influences like market dynamics and maintenance activities. The preferred models for carbonate gas reservoir production forecasts are the generalized Weng's, Beta, Class-I generalized mathematical, and Hu-Chen models. The Vapor pressure and Beta models are optimal for forecasting the annual productivity of wells (APW) from gas-bearing low-permeability tight sandstone reservoirs. The Wang-Li, Beta, and Yu QT tb models are apt for moderate-to-small-reserves, single low-permeability tight sandstone gas reservoirs. The Rayleigh, Hu-Chen, and generalized Weng's models are suitable for condensate gas reservoirs. For medium-to-high-permeability sandstone gas reservoirs, the lognormal, generalized gamma, and Beta models are recommended