PGCNMDA: Learning node representations along paths with graph convolutional network for predicting miRNA-disease associations.

Identifying miRNA-disease associations (MDAs) is crucial for improving the diagnosis and treatment of various diseases. However, biological experiments can be time-consuming and expensive. To overcome these challenges, computational approaches have been developed, with Graph Convolutional Network (GCN) showing promising results in MDA prediction. The success of GCN-based methods relies on learning a meaningful spatial operator to extract effective node feature representations. To enhance the inference of MDAs, we propose a novel method called PGCNMDA, which employs graph convolutional networks with a learning graph spatial operator from paths. This approach enables the generation of meaningful spatial convolutions from paths in GCN, leading to improved prediction performance. On HMDD v2.0, PGCNMDA obtains a mean AUC of 0.9229 and an AUPRC of 0.9206 under 5-fold cross-validation (5-CV), and a mean AUC of 0.9235 and an AUPRC of 0.9212 under 10-fold cross-validation (10-CV), respectively. Additionally, the AUC of PGCNMDA also reaches 0.9238 under global leave-one-out cross-validation (GLOOCV). On HMDD v3.2, PGCNMDA obtains a mean AUC of 0.9413 and an AUPRC of 0.9417 under 5-CV, and a mean AUC of 0.9419 and an AUPRC of 0.9425 under 10-CV, respectively. Furthermore, the AUC of PGCNMDA also reaches 0.9415 under GLOOCV. The results show that PGCNMDA is superior to other compared methods. In addition, the case studies on pancreatic neoplasms, thyroid neoplasms and leukemia show that 50, 50 and 48 of the top 50 predicted miRNAs linked to these diseases are confirmed, respectively. It further validates the effectiveness and feasibility of PGCNMDA in practical applications.

Nonreciprocal magnon blockade based on nonlinear effects.

We present an alternative scheme to achieve nonreciprocal unconventional magnon blockade (NUMB) in a hybrid system formed by two microwave cavities and one yttrium iron garnet (YIG) sphere, where the pump and signal cavities interact nonlinearly with each other and the signal cavity is coupled to the YIG sphere. It is found that the nonlinear coupling occurs between the pump cavity and magnon modes due to the dispersive interactions among three bosonic modes. Meanwhile, the Kerr nonlinearity is present in the pump cavity. Based on these nonlinear effects, a nonreciprocal magnon blockade could be achieved with the help of the weak parametric driving of the pump cavity. The present work provides an alternative method to prepare single magnon resource, which may be helpful for quantum information processing.

[Discussion on Key Control Points and Common Problems of Molecular Diagnostic Reagents in the Process of Design and Development].

Design and development process of molecular diagnostic reagents is critical to quality management system of in vitro diagnostic reagent. Based on the technical characteristics of molecular diagnostic reagents, the study analyzed the concerned key control points and common problems in the process of design and development from the view of registration quality management system. It aimed at offering technical guidance on design and development process of molecular reagents and registration quality management system to enterprises, thus improving the product development efficiency, optimizing the quality management system, and increasing the efficiency and quality of registration and declaration.

[A Brief Discussion on the in Vitro Diagnostic Reagent Inspection Practice of Self-examination Management Regulations for Medical Device Registration].

On October 21, 2021, the National Medical Products Administration issued and implemented the Self-examination Management Regulations for Medical Device Registration. The regulations clarify the specific requirements of the registration applicants in the process of self-examination, and put forward detailed requirements from the aspects of self-examination ability, self-examination report, declaration materials and responsibility requirements, so as to ensure the orderly development of the self-examination of medical device registration. Based on the actual verification work of in vitro diagnostic reagent, this study briefly discussed the understanding of the relevant contents of the regulations, aiming to provide some reference for enterprises and related supervision departments that have the requirement of registered self-examination.

Towards Monodisperse Star-Shaped Ladder-Type Conjugated Systems: Design, Synthesis, Stabilized Blue Electroluminescence, and Amplified Spontaneous Emission.

A novel series of monodisperse star-shaped ladder-type oligo(p-phenylene)s, named as TrL-n (n=1-3), have been explored. Their thermal and electrochemical properties, fluorescence transients, photoluminescence quantum yields, density functional theory calculations, electroluminescence (EL) and amplified spontaneous emission (ASE) properties have been systematically investigated to unravel the molecular design on optoelectronic properties. The resulting materials showed excellent structural perfection, free of chemical defects, and exhibited great thermal stability (Td : 404-418 °C and Tg : 147-184 °C) and amorphous glassy morphologies. Compared with their corresponding linear counterparts FL-m (m=1-3), TrL-n showed only little bathochromic shifts (5-12 nm) for the absorption maxima λmax in both solution and films. The star-shaped ladder-type compounds exhibited enhanced optical stability and suppressed low-energy emission. Their EL spectra exhibited excellent stability with increasing the driving voltage from 6 to 12 V. Moreover, superior low ASE thresholds were recorded for TrL-n compared with FL-m. Rather low ASE threshold (29 nJ per pulse or 1.60 µJ cm-2 ) was recorded for TrL-3, demonstrating their promising potential as excellent gain media. This study provides a novel design concept to develop monodisperse star-shaped ladder-type materials with excellent structural perfection, which are vital for shedding light on exploring robust organic emitters for optoelectronic applications.

Ursodeoxycholic acid and 4-phenylbutyrate prevent endoplasmic reticulum stress-induced podocyte apoptosis in diabetic nephropathy.

Endoplasmic reticulum (ER) stress, resulting from the accumulation of misfolded and/or unfolded proteins in ER membranes, is involved in the pathogenesis of diabetic nephropathy (DN). The aim of this study was to investigate the role of ER stress inhibitors ursodeoxycholic acid (UDCA) and 4-phenylbutyrate (4-PBA) in the treatment of DN in db/db mice. Findings have revealed that diabetic db/db mice were more hyperglycemic than their non-diabetic controls, and exhibited a marked increase in body weight, water intake, urine volume, fasting plasma glucose, systolic blood pressure, glucose and insulin tolerance. UDCA (40 mg/kg/day) or 4-PBA (100 mg/kg/day) treatment for 12 weeks resulted in an improvement in these biochemical and physical parameters. Moreover, UDCA or 4-PBA intervention markedly decreased urinary albuminuria and attenuated mesangial expansion in diabetic db/db mice, compared with db/db mice treated with vehicle. These beneficial effects of UDCA or 4-PBA on DN were associated with the inhibition of ER stress, as evidenced by the decreased expression of BiP, phospho-IRE1α, phospho-eIF2α, CHOP, ATF-6 and spliced X-box binding protein-1 in vitro and in vivo. UDCA or 4-PBA prevented hyperglycemia-induced or high glucose (HG)-induced apoptosis in podocytes in vivo and in vitro via the inhibition of caspase-3 and caspase-12 activation. Autophagy deficiency was also seen in glomeruli in diabetic mice and HG-incubated podocytes, exhibiting decreased expression of LC3B and Beclin-1, which could be restored by UDCA or 4-PBA treatment. Taken together, our results have revealed an important role of ER stress in the development of DN, and UDCA or 4-PBA treatment may be a potential novel therapeutic approach for the treatment of DN.

Improvement of Huangqi Decoction on Endothelial Dysfunction in 5/6 Nephrectomized Rats.

BACKGROUND/AIMS: Endothelial dysfunction is a major factor in the progression of chronic kidney disease, which correlates with oxidative stress and NO deficiency. Huangqi decoction (HQD) is a potential anti-oxidant ingredient in renoprotection. However, the underlying mechanisms remained identified. Therefore, we investigated whether HQD exhibit improvement in endothelial dysfunction in the 5/6 nephrectomy (Nx) rat model. METHODS: Male Wistar rats (180 - 250 g) were divided into sham, Nx and Nx + HQD (0.05, 0.15 and 0.45 g/kg) group, respectively. Renal function and histology were examined with ELISA and Immunohistochemical analysis. Endothelium-dependent relaxation of rat aortas was investigated by isometric tension recordings. Oxidative stress and NO bioavailability were detected by ELISA, DHE-staining, DAF-2 staining and western blotting. RESULTS: Compared with Nx rats, HQD treatment reversed the functional and structural changes of kidney significantly. Besides, endothelium-dependent relaxation of rat aortas was also improved by HQD treatment. NADPH oxidase and ROS generation were inhibited while NO bioavailability was enhanced. CONCLUSION: HQD can act as a potent prescription for the treatment of endothelium related vascular complications.

Ursodeoxycholic Acid Ameliorated Diabetic Nephropathy by Attenuating Hyperglycemia-Mediated Oxidative Stress.

Oxidative stress has a great role in diabetes and diabetes induced organ damage. Endoplasmic reticulum (ER) stress is involved in the onset of diabetic nephropathy. We hypothesize that ER stress inhibition could protect against kidney injury through anti-oxidative effects. To test whether block ER stress could attenuate oxidative stress and improve diabetic nephropathy in vivo and in vitro, the effect of ursodeoxycholic acid (UDCA), an ER stress inhibitor, on spontaneous diabetic nephropathy db/db mice, ER stress inducer or high glucose-triggered podocytes were studied. Mice were assigned to 3 groups (n=6 per group): control group (treated with vehicle), db/db group (treated with vehicle), and UDCA group (db/db mice treated with 40 mg/kg/d UDCA). After 8 weeks treatment, mice were sacrificed. Blood and kidneys were collected for the assessment of albumin/creatinine ratio, blood urea nitrogen (BUN), serum creatinine (SCr), insulin, total cholesterol, triglyceride, low density lipoprotein cholesterol (LDL-C), oxidized LDL-C, high density lipoprotein cholesterol (HDL-C), non-esterified fatty acid (NEFA), superoxide dismutase (SOD), catalase (CAT), methane dicarboxylic aldehyde (MDA), the expressions of SOD isoforms and glutathione peroxidase 1, as well as histopathological examination. In addition, generation of reactive oxygen species (ROS) was detected by 2'7'-dichlorodihydrofluorescein diacetate (DCFH-DA) fluorescence. The results showed that UDCA alleviated renal ER stress-evoked cell death, oxidative stress, renal dysfunction, ROS production, upregulated the expression of Bcl-2 and suppressed Bax in vivo and in vitro. Hence, inhibition ER stress diminishes oxidative stress and exerts renoprotective effects.

Hederagenin improves Alzheimer's disease through PPARα/TFEB-mediated autophagy.

BACKGROUND: Autophagic flux is coordinated by a network of master regulatory genes, which centered on transcription factor EB (TFEB). The disorders of autophagic flux are closely associated with Alzheimer's disease (AD), and thus restoring autophagic flux to degrade pathogenic proteins has become a hot therapeutic strategy. Hederagenin (HD), a triterpene compound, isolated from a variety food such as Matoa (Pometia pinnata) Fruit, Medicago sativa, Medicago polymorpha L. Previous studies have shown that HD has the neuroprotective effect. However, the effect of HD on AD and underlying mechanisms are unclear. PURPOSE: To determine the effect of HD on AD and whether it promotes autophagy to reduce AD symptoms. STUDY DESIGN: BV2 cells, C. elegans and APP/PS1 transgenic mice were used to explore the alleviative effect of HD on AD and the molecular mechanism in vivo and in vitro. METHODS: The APP/PS1 transgenic mice at 10 months were randomized into 5 groups (n = 10 in each group) and orally administrated with either vehicle (0.5% CMCNa), WY14643 (10 mg/kg/d), low-dose of HD (25 mg/kg/d), high-dose of HD (50 mg/kg/d) or MK-886 (10 mg/kg/d) + HD (50 mg/kg/d) for consecutive 2 months. The behavioral experiments including morris water maze test, object recognition test and Y maze test were performed. The effects of HD on Aß deposition and alleviates Aß pathology in transgenic C. elegans were operated using paralysis assay and fluorescence staining assay. The roles of HD in promoting PPARα/TFEB-dependent autophagy were investigated using the BV2 cells via western blot analysis, real-time quantitative PCR (RT-qPCR), molecular docking, molecular dynamic (MD) simulation, electron microscope assay and immunofluorescence. RESULTS: In this study, we found that HD upregulated mRNA and protein level of TFEB and increased the distribution of TFEB in the nucleus, and the expressions of its target genes. HD also promoted the expressions of LC3BII/LC3BI, LAMP2, etc., and promoted autophagy and the degradation of Aß. HD reduced Aß deposition in the head area of C. elegans and Aß-induced paralysis. HD improved cognitive impairment and pathological changes in APP/PS1 mice by promoting autophagy and activating TFEB. And our results also showed that HD could strongly target PPARα. More importantly, these effects were reversed by treatment of MK-886, a selective PPARα antagonist. CONCLUSION: Our present findings demonstrated that HD attenuated the pathology of AD through inducing autophagy and the underlying mechanism associated with PPARα/TFEB pathway.

[Retarding potential of biochar on antibiotic resistance genes in soil and the mechanisms: A review.] / ç”Ÿç‰©ç‚­å¯¹åœŸå£¤ä¸­æŠ—ç”Ÿç´ æŠ—æ€§åŸºå› çš„é˜»æŽ§æ½œåŠ›åŠæœºåˆ¶ç ”ç©¶è¿›å±•.

Antibiotic resistance genes (ARGs) in soil pose a major challenge to global environment and health. The development of effective technologies to reduce their negative effects has implications for maintaining soil health and human health. Biochar would be a suitable control material due to its characteristics of high carbon content, large surface area, excellent adsorption capacity, and economic advantages. There are three mechanisms underlying its negative effects on the abundance of ARGs: 1) adsorption of certain pollutants (e.g., antibiotics and heavy metals) to reduce the co-selective pressure of ARGs; 2) alteration of microbial composition through altering soil physico-chemical properties, and thereby limiting the ability of bacteria to undergo horizontal transfer of ARGs; 3) direct impairment of horizontal gene transfer by the adsorption of horizontal transfer vectors such as plasmids, transposons, and integrons. However, the negative effect of biochar depends on the source of material, pyrolysis process, and its amount added. Furthermore, field aging of biochar may reduce its ability to block ARGs. Endogenous contaminants of biochar, such as polycyclic aromatic hydrocarbons and heavy metals, may cause the enrichment of specific antibiotic-resistant bacteria in the environment or induce horizontal gene transfer. In further studies, suitable biochar should be selected according to soil environments, and biochar aging control measures should be taken to improve its retarding effect on ARGs.

Astragaloside IV prevents endothelial dysfunction by improving oxidative stress in streptozotocin-induced diabetic mouse aortas.

Oxidative stress serves a role in endothelial dysfunction exhibited by patients with diabetes mellitus. Astragaloside IV (AS-IV) is a major active ingredient of Radix Astragali, which is considered to exhibit vasoprotective effects through unknown mechanisms. Thus, the current study was performed to investigate the protective effects of AS-IV in streptozotocin (STZ)-induced endothelial dysfunction and to explore whether antioxidant mechanisms were involved. The protective effects of AS-IV on the endothelium-dependent relaxation and contraction of aortic rings were determined by isometric tension recordings. NADPH subunits and endothelial nitric oxide synthase (eNOS) expression was identified via western blotting. Superoxide dismutase and malondialdehyde levels were assayed using ELISA. Furthermore, the generation of reactive oxygen species (ROS) and nitric oxide (NO) was detected via dihydroethidium and 4,5-diaminofluorescein diacetate staining, respectively. The results revealed that STZ-injected mice exhibited increased aortic endothelium-dependent vasoconstriction and decreased vasorelaxation to acetylcholine. However, AS-IV treatment reversed these effects. NG-nitro-L-arginine was subsequently used to completely inhibit impaired relaxation. Accordingly, impaired NO generation was restored following AS-IV treatment by increasing eNOS phosphorylation levels. Furthermore, ROS formation was also depressed following AS-IV treatment compared with that in STZ-injected mice. AS-IV also decreased the expression of various NADPH subunits, including human neutrophil cytochrome b light chain, neutrophil cytosolic factor 1, NADPH oxidase (NOX)2, NOX4 and Rac-1. The results of the current study may provide novel evidence that diabetes-induced vascular injury arises from either the inhibition of eNOS or the activation of NOX-derived ROS generation. In addition, the results warrant further investigation into the application of AS-IV treatment, leading to the improvement of oxidative stress, in patients with diabetes exhibiting endothelial dysfunction.

[Effects of sewage sludge compost on the growth and element uptake of Neolamarckia cadamba seedlings]. / æ±¡æ³¥å †è‚¥å¯¹é»„æ¢æœ¨å¹¼è‹—ç”Ÿé•¿å’Œå ƒç´ å¸æ”¶çš„å½±å“.

Sewage sludge compost (SSC) is rich in organic matter and nutrient elements indispensable to plant growth. Utilizing SSC as seedling growing substrate is generally recognized as a new ecological method for utilization of sewage sludge. We investigated impacts of SSC treatments including 0% (CK), 25% (T1), 50% (T2), 75% (T3), and 100% (T4) on the growth and nutrient uptake of Neolamarckia cadamba seedlings in a 7-month pot experiment. The changes in element contents in substrate after pot experiment were also addressed. Results showed the SSC treatments had significant impacts on the growth of N. cadamba seedlings. The seedlings in T4 treatment grew abnormally and all died in two weeks after transplanting. Seedling height, ground diameter and biomass in T1, T2 and T3 treatments were significantly higher than CK, with those in T2 being the best among all treatments. Seedlings in T2 and T3 treatments took up significantly more N, P, K, Cu, Zn, Pb and Cd, while those in T1 treatment absorbed significantly more N and Pb than CK. The heavy metal uptake amount of each treatment exhibited the order of Zn＞Cu＞Pb＞Cd. At the end of the pot experiment, the contents of organic matter, N, P and K in growing substrate were still relatively high, and a certain portion of heavy metals still remained in the substrate, but with lower contents than the standards set for agricultural usage-oriented sewage sludge, indicating that the post-experiment substrate may be reused.

Indoxyl sulfate potentiates endothelial dysfunction via reciprocal role for reactive oxygen species and RhoA/ROCK signaling in 5/6 nephrectomized rats.

Accumulative indoxyl sulfate (IS) retained in chronic kidney disease (CKD) can potentiate vascular endothelial dysfunction, and herein, we aim at elucidating the underlying mechanisms from the perspective of possible association between reactive oxygen species (ROS) and RhoA/ROCK pathway. IS-treated nephrectomized rats are administered with antioxidants including NADPH oxidase inhibitor apocynin, SOD analog tempol, and mitochondrion-targeted SOD mimetic mito-TEMPO to scavenge ROS, or ROCK inhibitor fasudil to obstruct RhoA/ROCK pathway. First, we find in response to IS stimulation, antioxidants treatments suppress increased aortic ROCK activity and expression levels. Additionally, ROCK blockade prevent IS-induced increased NADPH oxidase expression (mainly p22phox and p47phox), mitochondrial and intracellular ROS (superoxide and hydrogen peroxide) generation, and decreased Cu/Zn-SOD expression in thoracic aortas. Apocynin, mito-TEMPO, and tempol also reverse these markers of oxidative stress. These results suggest that IS induces excessive ROS production and ROCK activation involving a circuitous relationship in which ROS activate ROCK and ROCK promotes ROS overproduction. Finally, ROS and ROCK depletion attenuate IS-induced decrease in nitric oxide (NO) production and eNOS expression levels, and alleviate impaired vasomotor responses including increased vasocontraction to phenylephrine and decreased vasorelaxation to acetylcholine, thereby preventing cardiovascular complications accompanied by CKD. Taken together, excessive ROS derived from NADPH oxidase and mitochondria coordinate with RhoA/ROCK activation in a form of positive reciprocal relationship to induce endothelial dysfunction through disturbing endothelium-dependent NO signaling upon IS stimulation in CKD status.

Effects of Huang Qi Decoction on Endothelial Dysfunction Induced by Homocysteine.

Vascular endothelial dysfunction can be induced by homocysteine (Hcy) through promoted oxidative stress. Huang Qi decoction (HQD) is a traditional Chinese medical formula and its components possess antioxidant effect. The study herein was therefore designed to investigate the effects of HQD at different dosage on endothelial dysfunction induced by Hcy. Tempol and apocynin were used to investigate whether antioxidant mechanisms were involved. Endothelium-dependent relaxation of rat aortas was investigated by isometric tension recordings. Reactive oxygen species (ROS) in human umbilical vein endothelial cells (HUVECs) was determined by DHE staining. The assessment related to oxidative stress and NO bioavailability was performed by assay kits and western blot. In isometric tension experiment, HQD at the dose of 30 or 100 µg/mL, tempol, or apocynin prevented impaired endothelium-dependent relaxation in isolated aortas elicited by Hcy. In cellular experiments, substantial enhancement in NADPH oxidase and ROS generation and reduction in NO bioavailability triggered by Hcy were reversed by pretreatment of HQD at the dose of 100 µg/mL, tempol, or apocynin. The results proved that HQD at an appropriate dosage presented favorable effects on endothelial dysfunction initiated by Hcy through antioxidant mechanisms. HQD can act as a potent prescription for the treatment of endothelium related vascular complications.

Astragaloside IV Attenuates Podocyte Apoptosis Mediated by Endoplasmic Reticulum Stress through Upregulating Sarco/Endoplasmic Reticulum Ca2+-ATPase 2 Expression in Diabetic Nephropathy.

Sarco/endoplasmic reticulum Ca2+-ATPase (SERCA) plays a central role in the pathogenesis of diabetes. This protein has been recognized as a potential target for diabetic therapy. In this study, we identified astragaloside IV (AS-IV) as a potent modulator of SERCA inhibiting renal injury in diabetic status. Increasing doses of AS-IV (2, 6, and 18 mg kg-1 day-1) were administered intragastrically to db/db mice for 8 weeks. Biochemical and histopathological approaches were conducted to evaluate the therapeutic effects of AS-IV. Cultured mouse podocytes were used to further explore the underlying mechanism in vitro. AS-IV dose-dependently increased SERCA activity and SERCA2 expression, and suppressed ER stress-mediated and mitochondria-mediated apoptosis in db/db mouse kidney. AS-IV also normalized glucose tolerance and insulin sensitivity, improved renal function, and ameliorated glomerulosclerosis and renal inflammation in db/db mice. In palmitate stimulated podocytes, AS-IV markedly improved inhibitions of SERCA activity and SERCA2 expression, restored intracellular Ca2+ homeostasis, and attenuated podocyte apoptosis in a dose-dependent manner with a concomitant abrogation of ER stress as evidenced by the downregulation of GRP78, cleaved ATF6, phospho-IRE1α and phospho-PERK, and the inactivation of both ER stress-mediated and mitochondria-mediated apoptotic pathways. Furthermore, SERCA2b knockdown eliminated the effect of AS-IV on ER stress and ER stress-mediated apoptotic pathway, whereas its overexpression exhibited an anti-apoptotic effect. Our data obtained from in vivo and in vitro studies demonstrate that AS-IV attenuates renal injury in diabetes subsequent to inhibiting ER stress-induced podocyte apoptosis through restoring SERCA activity and SERCA2 expression.

Effects of mannose density on in vitro and in vivo cellular uptake and RNAi efficiency of polymeric nanoparticles.

To evaluate the effects of mannose density on in vitro and in vivo cellular uptake and RNA interference (RNAi) efficiency of polymeric nanoparticles (NPs) in macrophages, mannose-modified trimethyl chitosan-cysteine (MTC) conjugates with mannose densities of 4%, 13%, and 21% (MTC-4, MTC-13, and MTC-21) were synthesized. Tumor necrosis factor-alpha (TNF-α) siRNA loaded MTC NPs with particle sizes of ∼150 nm exhibited desired structural stability and effectively protected siRNA from enzymatic degradation. Generally, cellular uptake and RNAi efficiency were affected by mannose density. As expected, MTC-21 NPs presented the maximum in vitro uptake and RNAi efficacy in Raw 264.7 cells among all NPs tested. However, MTC-4 NPs exhibited the optimal in vivo uptake by peritoneal exudate cell macrophages (PECs). In the inflammation model of acute hepatic injury, orally delivered MTC-4 and MTC-13 NPs worked better in silencing TNF-α expression and alleviating liver damage than MTC-21 NPs. As for the ulcerative colitis model, MTC-4 NPs outperformed MTC-13 and MTC-21 NPs with respect to TNF-α knockdown and therapeutic efficacy following oral administration. These results highlighted the importance of ligand density in cellular uptake and RNAi efficiency, which could serve as a guideline in the rational design of targeted nanocarriers for anti-inflammation therapy.