Effectiveness and Efficiency: Label-Aware Hierarchical Subgraph Learning for Protein-Protein Interaction.

The study of protein-protein interactions (PPIs) holds immense significance in understanding various biological activities, as well as in drug discovery and disease diagnosis. Existing deep learning methods for PPI prediction, including graph neural networks (GNNs), have been widely employed as the solutions, while they often experience a decline in performance in the real world. We claim that the topological shortcut is one of the key problems contributing negatively to the performance, according to our analysis. By modeling the PPIs as a graph with protein as nodes and interactions as edge types, the prevailing models tend to learn the pattern of nodes' degrees rather than intrinsic sequence-structure profiles, leading to the problem termed topological shortcut. The huge data growth of PPI leads to intensive computational costs and challenges computing devices, causing infeasibility in practice. To address the discussed problems, we propose a label-aware hierarchical subgraph learning method (laruGL-PPI) that can effectively infer PPIs while being interpretable. Specifically, we introduced edge-based subgraph sampling to effectively alleviate the problems of topological shortcuts and high computing costs. Besides, the inner-outer connections of PPIs are modeled as a hierarchical graph, together with the dependencies between interaction types constructed by a label graph. Extensive experiments conducted across various scales of PPI datasets have conclusively demonstrated that the laruGL-PPI method surpasses the most advanced PPI prediction techniques currently available, particularly in the testing of unseen proteins. Also, our model can recognize crucial sites of proteins, such as surface sites for binding and active sites for catalysis.

Proposal to classify Ralstonia solanacearum phylotype I strains as Ralstonia nicotianae sp. nov., and a genomic comparison between members of the genus Ralstonia.

A Gram-negative, aerobic, rod-shaped, motile bacterium with multi-flagella, strain RST, was isolated from bacterial wilt of tobacco in Yuxi city of Yunnan province, China. The strain contains the major fatty acids of C16:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). The polar lipid profile of strain RST consists of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and unidentified aminophospholipid. Strain RST contains ubiquinones Q-7 and Q-8. 16S rRNA gene sequence (1,407 bp) analysis showed that strain RST is closely related to members of the genus Ralstonia and shares the highest sequence identities with R. pseudosolanacearum LMG 9673T (99.50%), R. syzygii subsp. indonesiensis LMG 27703T (99.50%), R. solanacearum LMG 2299T (99.28%), and R. syzygii subsp. celebesensis LMG 27706T (99.21%). The 16S rRNA gene sequence identities between strain RST and other members of the genus Ralstonia were below 98.00%. Genome sequencing yielded a genome size of 5.61 Mbp and a G + C content of 67.1 mol%. The genomic comparison showed average nucleotide identity (ANIb) values between strain RST and R. pseudosolanacearum LMG 9673T, R. solanacearum LMG 2299T, and R. syzygii subsp. indonesiensis UQRS 627T of 95.23, 89.43, and 91.41%, respectively, and the corresponding digital DNA-DNA hybridization (dDDH) values (yielded by formula 2) were 66.20, 44.80, and 47.50%, respectively. In addition, strains belonging to R. solanacearum phylotype I shared both ANIb and dDDH with strain RST above the species cut-off values of 96 and 70%, respectively. The ANIb and dDDH values between the genome sequences from 12 strains of R. solanacearum phylotype III (Current R. pseudosolanacearum) and those of strain RST were below the species cut-off values. Based on these data, we concluded that strains of phylotype I, including RST, represent a novel species of the genus Ralstonia, for which the name Ralstonia nicotianae sp. nov. is proposed. The type strain of Ralstonia nicotianae sp. nov. is RST (=GDMCC 1.3533T = JCM 35814T).

Effect of Nd Element of Mg-Nd Binary Alloy on the Corrosion Resistance in Sulfate-Reducing Bacteria Solution.

In this paper, the corrosion resistances of Mg-Nd binary alloys with various contents of the neodymium (Nd) element in sulfate-reducing bacteria (SRB) were studied. In the SRB medium, the results of weight loss experiments showed that the increase in the Mg12Nd phase in the alloy increased the galvanic corrosion and the corrosion rate. However, when the continuous network distribution of the second phase formed, the corrosion resistance of the alloy improved. The biofilm was formed by the adhesion of the SRB. Meanwhile, the protection from the corrosion improved due to the corrosion products, which prevent the penetration of corrosive ions. On the other hand, the products of biological metabolism accelerated the corrosion of the matrix.

The Role of Inflammation in Cognitive Impairment of Obstructive Sleep Apnea Syndrome.

Obstructive sleep apnea syndrome (OSAS) has become a major worldwide public health concern, given its global prevalence. It has clear links with multiple comorbidities and mortality. Cognitive impairment is one related comorbidity causing great pressure on individuals and society. The clinical manifestations of cognitive impairment in OSAS include decline in attention/vigilance, verbal-visual memory loss, visuospatial/structural ability impairment, and executive dysfunction. It has been proven that chronic intermittent hypoxia (CIH) may be a main cause of cognitive impairment in OSAS. Inflammation plays important roles in CIH-induced cognitive dysfunction. Furthermore, the nuclear factor kappa B and hypoxia-inducible factor 1 alpha pathways play significant roles in this inflammatory mechanism. Continuous positive airway pressure is an effective therapy for OSAS; however, its effect on cognitive impairment is suboptimal. Therefore, in this review, we address the role inflammation plays in the development of neuro-impairment in OSAS and the association between OSAS and cognitive impairment to provide an overview of its pathophysiology. We believe that furthering the understanding of the inflammatory mechanisms involved in OSAS-associated cognitive impairment could lead to the development of appropriate and effective therapy.

Superstructure MOF as a framework to composite MoS2 with rGO for Li/Na-ion battery storage with high-performance and stability.

Metal sulfides, one kind of electrode material with very high theoretical capacity, have been widely studied for use in lithium and sodium ion batteries. However, there are some problems hindering their applications in electrodes, such as low conductivity and volume expansion. The MOF introduces metals with different coordination strengths into an existing MOF structure, which improves the performance of the electrode to a certain extent. In this paper, Fe/Zn bimetallic MOF rod-like superstructure was prepared based on Ostwald theory. Accompanied by sulfuration, the MOF was effectively combined with MoS2 and GO, and the objective materials Fe7S8-C/ZnS-C@MoS2/rGO composites were successfully prepared. The MOF material provides a good frame and an efficient electron transport path, while the robust rGO wall effectively inhibits the pulverization of materials during the lithium/sodium intercalation/escalation courses. This particular material exhibited excellent cycling and rate capability performance when used in Li/Na-ion batteries. When used in Li-batteries, the electrode material delivered a specific capacity of 1598.3 mA h g-1 at 0.1 A g-1 and remained at 1196.7 mA h g-1 even after about 100 cycles and further exhibited a specific capacity of 368.68 mA h g-1 at the current rate of 5 A g-1 even after 1000 cycles, respectively. As for sodium batteries, these electrode materials exhibited an initial reversible capacity of 1053.6 mA h g-1 at 0.1 A g-1 and the reversible capacity was still as high as 592.2 mA h g-1 after 200 cycles. It is perhaps that this composite material with its particular architecture and composition is greatly beneficial for electron transfer and Li/Na ion diffusion. In the repeated physicochemical/nutrifying process, the appropriate distance between adjacent MOFs is of great help in preventing volume changes and thus improving the electrochemical performance.

Mixed-Halide Perovskite Film-Based Neuromorphic Phototransistors for Mimicking Experience-History-Dependent Sensory Adaptation.

Sensory adaptation is an essential function for humans to live on the earth. Herein, a hybrid synaptic phototransistor based on the mixed-halide perovskite/organic semiconductor film is reported. This hybrid phototransistor achieves photosensitive performance including a high photoresponsivity over 4 × 103 A/W and an excellent specific detectivity of 2.8 × 1016 Jones. Due to the photoinduced halide-ion segregation of the mixed-halide perovskites and their slow recovery properties, the experience-history-dependent sensory adaptation behavior can be mimicked. Moreover, the light pulse width, intensity, light wavelength, and gate bias can be used to regulate the adaptation processes to improve its adaptability and perceptibility in different environments. The CsPbBrxI3-x/organic semiconductor hybrid films produced by spin coating are beneficial to large-scale fabrication. This study fabricates a novel solution-processable light-stimulated synapse based on inorganic perovskites for mimicking the human sensory adaptation that makes it possible to approach artificial neural sensory systems.

Phenolic profile of jujube fruit subjected to gut microbiota fermentation and its antioxidant potential against ethyl carbamate-induced oxidative damage.

OBJECTIVES: To evaluate the composition of bioactive substances and the antioxidant effects of jujube fruit under gut microbiota fermentation (GMF), and the inhibitory effect on cytotoxicity caused by ethyl carbamate (EC). METHODS: Changes in the contents of flavonoids, polyphenols, total sugars, and reducing sugars of jujube fruit after GMF (0, 2, 6, 12, 24, and 48 h) were determined. The oxidation resistance of fermented jujube fruits (from 0 to 48 h fermentation) was evaluated using in vitro 2,2'-azinobis-(3-ethylbenzthiazoline-6-sulphonate) (ABTS) and ferric reducing antioxidant power (FRAP) assays. Inhibitory effects of 48 h-fermented jujube fruit at various concentrations (0.25, 0.50, 1.00, and 2.00 mg/mL) on EC-treated toxicity and DNA damage of Caco-2 cells were estimated using 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) and nuclear staining assays, respectively. Effects of different concentrations of jujube fruit on EC-treated Caco-2 cells' intracellular reactive oxygen species (ROS), glutathione (GSH) levels, and mitochondrial membrane potential (MMP) were also evaluated. RESULTS: Jujube fruit has rich bioactive components after GMF and shows strong antioxidant capacity. Fermented jujube fruit can inhibit the cytotoxicity and DNA damage of Caco-2 cells caused by EC and reduce intracellular ROS generation, as well as restoring GSH and MMP. CONCLUSIONS: Fermented jujube fruit extracts produced by GMF still contain biologically active substances which retain biological activity and antioxidation capabilities.

Progress on the Mechanism for Aspirin's Anti-tumor Effects.

Since its discovery more than 100 years ago, aspirin has been widely used for its antipyretic, analgesic, anti-inflammatory, and anti-rheumatic activities. In addition to these applications, it is increasingly becoming clear that the drug also has great potential in the field of cancer. Here, we briefly review the current insights on aspirin's anti-tumor effects. These are multiple and vary from inhibiting the major cellular mTOR pathways, acting as a calorie-restricted mimetic by inhibition of energy production, suppressing platelet aggregation and granule release, inhibiting the immune escape of tumor cells, to decreasing inflammatory responses. We consider these five mechanisms of action the most significant for aspirin's anti-tumor effects, whereby the anti-tumor effect may ultimately stem from its inhibition of energy metabolism, platelet function, and inflammatory response. As such, aspirin can play an important role to reduce the occurrence, proliferation, and metastasis of various types of tumors. However, most of the collected data are still based on epidemiological investigations. More direct and effective evidence is needed, and the side effects of aspirin intake need to be solved before this drug can be widely applied in cancer treatment.

Long non-coding RNA VIM Antisense RNA 1 (VIM-AS1) sponges microRNA-29 to participate in diabetic retinopathy.

AIMS: Long non-coding RNA (lncRNA) VIM Antisense RNA 1 (VIM-AS1) has been reported to be correlated with type 2 diabetes (T2D) susceptibility, while the roles of this lncRNA in T2D and its complications remain unclear. This study aimed to explore the role of VIM-AS1 in diabetic retinopathy (DR). METHODS: Gene expression levels in both human specimens and in vitro cultivated cells were determined by qPCR and western blot. Overexpression experiments were performed to analyze gene interactions. Cell apoptosis after transfections was detected by cell apoptosis assay. RESULTS: We found that VIM-AS1 was significantly downregulated in T2D patients in comparison with that in healthy controls. Specifically, the expression levels of VIM-AS1 were lowest among T2D patients complicated with DR. Bioinformatics analysis showed that VIM-AS1 can interact with microRNA 29 (miR-29), which is a critical player in high glucose-induced apoptosis of human retinal pigment epithelial cells (RPEs). Dual-luciferase assay also revealed the direct interaction between them. High glucose treatment led to upregulated miR-29 and downregulated VIM-AS1. However, overexpression of VIM-AS1 and miR-29 did not affect the expression of each other. Cell apoptosis analysis showed that overexpression of VIM-AS1 reduced the enhancing effects of miR-29 overexpression on RPEs cell proliferation. CONCLUSIONS: Therefore, VIM-AS1 may sponge miR-29 to participate in DR.

Fructan from Polygonatum cyrtonema Hua as an eco-friendly corrosion inhibitor for mild steel in HCl media.

An effective and biodegradable polygonatum fructan (PF) from Polygonatum cyrtonema Hua was studied as an eco-friendly corrosion inhibitor for mild steel protection in 1 M HCl, whose inhibition performance was studied by weight loss tests, electrochemical techniques, and surface analysis techniques (SECM, FTIR). The experimental results showed that PF has outstanding inhibition performance for mild steel in hydrochloric acid, and the inhibition efficiency increased with the increase of its concentration and temperature. Polarization studies indicated that PF is a mixed-type corrosion inhibitor, and its adsorption mode conforms to Langmuir isotherm, mainly chemisorption. An adsorption-related protective inhibitor film formed on the surface of mild steel was verified and investigated based on its surface analysis and characterization. Quantum chemical analysis showed that the adsorption of PF on the surface of mild steel has obvious chemical properties.

Prognostic value of Epstein-Barr virus DNA level for nasopharyngeal carcinoma: a meta-analysis of 8128 cases.

BACKGROUND: Plasma levels of Epstein-Barr virus (EBV) DNA have been employed to predict survival outcomes of patients with nasopharyngeal carcinoma (NPC). However, the prognostic value of subsequent EBV DNA levels (mid or post treatment) for NPC is needed to identify by a large cohort of patients. We performed a meta-analysis of studies including data from 8128 patients to evaluate the prognostic value of EBV DNA in NPC patients. METHODS: We searched PubMed, Web of Science, and the Cochrane library for prospective and retrospective studies. Hazard ratios (HRs) and confidence intervals (CIs) were extracted from the studies or calculated and pooled to assess the association between EBV DNA levels pre-treatment (pre-DNA), mid-treatment (mid-DNA), and post-treatment (post-DNA) on clinical outcomes. RESULTS: A total of 22 studies with 8128 patients was included for analysis. Pre-DNA levels predicted overall survival, progression-free survival, distant metastasis-free survival, and local-regional failure survival with HRs (95% CIs) of 2.70 (2.06, 3.54), 2.70 (2.12, 3.44), 3.49 (2.35, 5.17), and 2.00 (1.45, 2.76), respectively, and the corresponding HRs for post-DNA levels were 4.86 (3.30, 7.17), 6.29 (3.41, 11.60), 5.68 (2.71,11.93), respectively. Mid-DNA levels predicted overall survival and progression-free survival with an HR (95% CI) of 3.02 (1.54, 5.29) and 3.15 (2.05, 4.83). Subgroup analysis showed that the HR of post-DNA wasn't influenced by different detection time of post-DNA (P = 0.22, I2 = 33.2%). CONCLUSION: The EBV DNA levels have a significant prognostic impact in patients with NPC. The effect of post-treatment EBV DNA level dominated that of pre-DNA and mid-DNA levels.

Heavy metals contamination and accumulation in submerged macrophytes in an urban river in China.

Deteriorating urban water quality has attracted considerable attention in China. We investigated the contamination levels and distribution of heavy metals (As, Cd, Cu, Ni, Pb, and Zn) in Yuxi River water and sediments, and assessed the heavy metal accumulation capability of five species of submerged macrophytes: Vallisneria natans (Lour.) Hara, Potamogeton pectinatus L., Hydrilla verticillata (L. f.) Royle, Myriophyllum spicatum L., and Potamogeton crispus L. Samples were collected from upstream and downstream locations in different season. The results showed that the levels of heavy metals in the downstream areas were higher than in the upstream areas. Heavy metal concentrations in the river water during the dry seasons were higher than those during the rainy seasons, and the opposite results appeared in sediments and submerged macrophytes. In general, the river was slightly contaminated by heavy metals, and the concentrations of Pb and Ni in this river should serve as a warning, while Cd and Zn pollution in the sediments desperately needs to be removed. Furthermore, Potamogeton pectinatus L. showed a higher accumulation capacity for these metals among the five native submerged macrophytes and could be defined as a hyperaccumulator for Cd. Therefore, the potential use of native aquatic plants in contaminated rivers is worth further exploration.

Structure and function of the bacterial communities during rhizoremediation of hexachlorobenzene in constructed wetlands.

Vertical flow constructed wetlands (VF CWs) are considered to be effective for treating organic pollutants. The rhizosphere of macrophytes such as Phragmites sp., Typha sp. serves as an active and dynamic zone for the microbial degradation of organic pollutants. However, it is still not clear how soil bacterial communities respond to macrophytes and pollutants during the process. For this purpose, the seedlings of Phragmites australis and Typha angustifolia were planted respectively in the VF CWs added with HCB at a dose of 2 mg/kg. During 96 days of cultivation, we monitored hexachlorobenzene (HCB) removal efficiency by GC/MS and the structure of the rhizosphere bacterial communities in the different VF CWs by denaturing gradient gel electrophoresis (DGGE), and constructed bacterial clone library based on PCR-amplified 16S rRNA gene. As expected, the rhizosphere bacterial communities also remained insensitive to HCB exposure in the wetland soil. The diversity of these microbes presented two stages, from the varied up and down to equilibrium in the entire experimental period. Molecular analysis revealed that the phylum Firmicutes dominated over the bacterial communities. The genera that increased under HCB stress included the well-known HCB-degrading bacteria (Pseudomonas sp. and Alcaligenes sp.) and other common bacteria found in contaminated soil but with lesser known practical functions (Burkholderia sp., Lysinibacillus fusiformis, and Bacillus cereus). Furthermore, there was a certain variance in the relative abundances of the bacterial phyla and HCB removal efficiency among different VF CW treatments. The degradation of HCB in T. angustifolia microcosms was faster than that in P. australis and unvegetated wetlands, and the highest bacterial diversity and richness was found in the VF CWs comprising T. angustifolia.

An approach to biodegradation of chlorobenzenes: combination of Typha angustifolia and bacterial effects on hexachlorobenzene degradation in water.

Although rhizoremediation is an effective approach to remove organic pollutants from the environment, little is known about the mechanism of hexachlorobenzene (HCB) biodegradation in water. In this study, we used Typha angustifolia (T. angustifolia) grown in sterile Hoagland nutrient solution to determine the rhizosphere effects on the ability of bacteria in water to reduce HCB levels. The results revealed that T. angustifolia could facilitate HCB degradation and that the initial HCB concentration was the major factor responsible for HCB degradation in nutrient solution. Furthermore, HCB biodegradation in low-HCB nutrient solution with T. angustifolia fitted the first-order kinetics, owing to the high concentration of total organic carbon, low HCB toxicity, and unique bacterial community in the T. angustifolia rhizosphere. Denaturing gradient gel electrophoresis indicated that the rhizosphere effects and different dosages of HCB have significant effects on the bacterial communities by repressing and favoring certain populations. The most successful bacteria to adapt to HCB contamination was Bacillus sp., while the dominant bacterial phyla in HCB-polluted water were Proteobacteria and Firmicutes.

[Association of C677T gene polymorphisms of methylenetetrahydrofolate reductase and plasma homocysteine level with hyperlipidemia].

OBJECTIVE: To study the association of methylenetetrahydrofolate reductase (MTHFR) gene C677T mutation and plasma homocysteine (Hcy) levels with hyperlipidemia. METHODS: Blood samples were collected from 1591 adults for detecting MTHFR gene C677T polymorphism with polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), plasma Hcy levels with enzymatic cycling method, and blood lipid levels as well. The patients were divided according to the lipid levels into hyperlipidemia group (n=694) and healthy control group (n=897) and the differences in MTHFR gene C677T polymorphisms and plasma Hcy levels were compared. RESULTS: The hyperlipidemia group and healthy control group showed no significant differences in CC, CT, or TT genotype frequencies or C and T allele frequencies of MTHFR C677T gene, and had comparable plasma Hcy levels (P>0.05). Patients with 3 different MTHFR C677T genotypes had significant differences in plasma Hcy levels (P<0.01) but not in blood lipid levels (P>0.05). Pairwise comparison indicated a significantly higher plasma Hcy level in TT genotype than in CC and CT genotypes (P<0.01), and the latter two genotypes showed no significant difference (P>0.05). CONCLUSION: MTHFR C677T polymorphisms and plasma Hcy levels are closely related but neither of them is associated with hyperlipidemia. The TT genotype is associated with a significantly higher plasma Hcy level than CC and CT genotypes.

Deriving sorption indices for the prediction of potential phosphorus loss from calcareous soils.

The aim of this study was to develop techniques to evaluate soil phosphorus (P) sorption capacity (PSC) and determine critical soil P levels to predict P loss potential for calcareous soils. Seventy-five soils mostly from Northern China were analyzed for soil P using four extraction methods (water, Pw; carbonate, POls; ammonium oxalate, Pox; and Mehlich 3, PM3) as well as PSC derived from single-point (PSC150) and multipoint sorption (S t) isotherms. Strong correlation was found between PSC150 and S t (r (2)=0.89, p<0.001). The sum of αCaM3 and ßMgM3 as an index of PSC (PSC(CaM3 + MgM3)) was most closely related to the maximum amount of P sorbed (S max) as given by the sum of S t and soil initial P setting α=0.039 and ß=0.462 (r (2)=0.80, p<0.001). The degree of P saturation (DPS) was thereafter calculated from PSC(CaM3 + MgM3) (DPS(CaM3 + MgM3)), to which Olsen P (POls) was significantly correlated (r (2)=0.82, p<0.001). In a split-line regression from Pw against DPS(CaM3 + MgM3) (r (2)=0.87, p<0.05), a change point was identified at 28.1% DPS(CaM3 + MgM3), which was equivalent to 49.2 mg kg(-1) POls and corresponded to a Pw concentration of 8.8 mg kg(-1). After the change point, a sharp increase in Pw was observed. Our results reveal a new approach to approximating DPS from CaM3 and MgM3 for calcareous soils without the need to generate a S max. We conclude that in the absence of an environmental soil test criteria for P, the DPS(CaM3 + MgM3) and POls could be used to predict P loss potential from calcareous soils.

Hexachlorobenzene dechlorination in constructed wetland mesocosms.

We studied the dechlorination of hexachlorobenzene (HCB) in wetland mesocosm (MC) trials filled with sediment (well mineralized homogenized peat mixed with mud) from a wastewater treatment wetland located in a floodplain: three MCs were planted with common reed (Phragmites australis) and another three with broad-leaved cattail (Typha latifolia). According to the rootzone development we distinguished between the upper (0-10 cm from the soil surface) and lower layers (20-30 cm). Over 36 days, the initial measured concentration of HCB was reduced to 61%, 51%, 42% and 40% in the lower layer without roots of Phragmites, in the lower layer with roots of Typha, in the upper layer with roots of Typha, and in the upper layer with roots of Phragmites respectively. The 90% degradation time (DT(90)) of the initial measured HCB can be calculated as 192, 121, 110 and 92 days (d) respectively. PeCB, 1, 2, 3, 4-, 1, 2, 3, 5- and 1, 2, 4, 5-TeCB, and 1, 2, 3-, 1, 2, 4- and 1, 3, 5-TCB were the main dechlorination products detected in MC sediment samples. The dechlorination rates of HCB were higher in sediment layers with well-developed root zones. According to the DT(50) of 28-58 days and DT(90) of 92-192 days, HCB can be considered to be a less persistent organic pollutant in constructed wetlands.