Use of CT-derived radiomic features to preoperatively identify invasive mucinous adenocarcinoma in solitary pulmonary nodules ≤3 cm.

Objective: In this study, we aimed to utilize computed tomography (CT)-derived radiomics and various machine learning approaches to differentiate between invasive mucinous adenocarcinoma (IMA) and invasive non-mucinous adenocarcinoma (INMA) preoperatively in solitary pulmonary nodules (SPN) ≤3 cm. Methods: A total of 538 patients with SPNs measuring ≤3 cm were enrolled, categorized into either the IMA group (n = 50) or INMA group (n = 488) based on postoperative pathology. Radiomic features were extracted from non-contrast-enhanced CT scans and identified using the least absolute shrinkage and selection operator (LASSO) algorithm. In constructing radiomics-based models, logistic regression, support vector machines, classification and regression trees, and k-nearest neighbors were employed. Additionally, a clinical model was developed, focusing on CT radiological features. Subsequently, this clinical model was integrated with the most effective radiomic model to create a combined model. Performance assessments of these models were conducted, utilizing metrics such as the area under the receiver operating characteristic curve (AUC), DeLong's test, net reclassification index (NRI), and integrated discrimination improvement (IDI). Results: The support vector machine approach showed superior predictive efficiency, with AUCs of 0.829 and 0.846 in the training and test cohorts, respectively. The clinical model had AUCs of 0.760 and 0.777 in the corresponding cohorts. The combined model had AUCs of 0.847 and 0.857 in the corresponding cohorts. Furthermore, compared to the radiomic model, the combined model significantly improved performance in both the training (DeLong test P = 0.045, NRI 0.206, IDI 0.024) and test cohorts (P = 0.029, NRI 0.125, IDI 0.032), as well as compared to the clinical model in both the training (P = 0.01, NRI 0.310, IDI 0.09) and test cohorts (P = 0.047, NRI 0.382, IDI 0.085). Conclusion: the combined model exhibited excellent performance in distinguishing between IMA and INMA in SPNs ≤3 cm.

Comparing GDF9 in mature follicles and clinical outcomes across different PCOS phenotype.

Background: Polycystic ovary syndrome (PCOS) is main cause of anovulatory infertility in women with gestational age. There are currently four distinct phenotypes associated with individualized endocrinology and metabolism. Growth differentiation factor 9 (GDF9) is a candidate as potential biomarker for the assessment of oocyte competence. The effect on oocyte capacity has not been evaluated and analyzed in PCOS phenotypes. Objective: We aimed to screen the expression levels of GDF9 in mature follicles of women with controlled ovarian hyperstimulation (COS) with different PCOS phenotypes. To determine the correlation between the expression level of GDF9 and oocyte development ability. Methods: In Part 1, we conducted a retrospective study comparing the clinical outcomes and endocrine characteristics of patients with PCOS according to different subgroups (depending on the presence or absence of the main features of polycystic ovarian morphology (PCOM), hyperandrogenism (HA), and oligo-anovulation (OA)) and non-PCOS control group. We stratified PCOS as phenotype A (n = 29), phenotype B (n = 18) and phenotype D (n = 24). In Part 2, the expression of GDF9 in follicular fluid (FF) and cumulus cells (CCs) were detected by enzyme-linked immunosorbent assay (ELISA) and immunohistochemistry, respectively. Results: In Part 1, the baseline clinical, hormonal, and ultrasonographic characteristics of the study population were matched with the presence or absence of the cardinal features of each PCOS phenotypes showed a clear difference. Phenotypes A and D had statistically significant associations with blastocyst formation and clinical pregnancy compared with phenotypes B (p < 0.001). In Part 2, the levels of GDF9 in FF and CCs for phenotype A and B were significantly were higher than those of phenotype D (P = 0.019, P = 0.0015, respectively). Multivariate logistic regression analysis showed that GDF9 was an important independent predictor of blastocyst formation (P＜0.001). The blastocyst formation rate of phenotype A was higher than that of phenotype B and D (P＜0.001). Combining the results of the two parts, GDF9 appears to play a powerful role in the development of embryos into blastocysts. Conclusions: GDF9 expression varies with different PCOS phenotypes. Phenotype A had higher GDF9 levels and blastocyst formation ability.

Effect of Electroacupuncture Combined with Pelvic Floor Muscle Exercise on Urinary Symptoms, Sexual Dysfunction and Pelvic Floor Muscle Strength in Female Patients with Overactive Bladder: A Retrospective Study.

OBJECTIVE: This study aimed to investigate the effect of electroacupuncture combined with pelvic floor muscle exercise in the treatment of female overactive bladder (OAB). METHODS: The clinical data of 134 female patients with OAB admitted to our hospital from April 2022 to June 2023 were retrospectively analysed. The patients were divided into the combination group (n = 74) and the single group (n = 60). The general demographic data, total effective rate, pad weight, female sexual function index (FSFI) score, oxford muscle grading scale and incontinence impact questionnaire short form (IIQ-7) were collected. Propensity score matching (PSM) was used to match the baseline data of the two groups at 1:1 ratio, and t test, chi-square test and analysis of variance were used for calculation. RESULTS: A total of 90 patients were selected after PSM. No significant difference in baseline data was found between the two groups (p > 0.05). Before treatment, no significant difference in FSFI score, oxford muscle grading scale and IIQ-7 score was found between the two groups (p > 0.05). The total effective rate of the combination group was higher than that of the single group (p < 0.05). After 3 weeks and 1 month of treatment, in addition to orgasm and sexual desire, the scores of sexual excitement and sexual satisfaction in the combination group were higher than those in the single group (p < 0.05). The combination group displayed higher oxford muscle grading scale and lower IIQ-7 and pad weight than the single group, and the differences were statistically significant (p < 0.05). CONCLUSIONS: The effect of electroacupuncture stimulation combined with pelvic floor muscle exercise is more significant, which can alleviate urinary symptoms, reduce urine leakage, enhance pelvic floor muscle strength and alleviate sexual dysfunction.

On the mechanism of wogonin against acute monocytic leukemia using network pharmacology and experimental validation.

Wogonin is a natural flavone compound from the plant Scutellaria baicalensis, which has a variety of pharmacological activities such as anti-cancer, anti-virus, anti-inflammatory, and immune regulation. However, the potential mechanism of wogonin remains unknown. This study was to confirm the molecular mechanism of wogonin for acute monocytic leukemia treatment, known as AML-M5. The potential action targets between wogonin and acute monocytic leukemia were predicted from databases. The compound-target-pathway network and protein-protein interaction network (PPI) were constructed. The enrichment analysis of related targets and molecular docking were performed. The network pharmacological results of wogonin for AML-M5 treatment were verified using the THP-1 cell line. 71 target genes of wogonin associated with AML-M5 were found. The key genes TP53, SRC, AKT1, RELA, HSP90AA1, JUN, PIK3R1, and CCND1 were preliminarily found to be the potential central targets of wogonin for AML-M5 treatment. The PPI network analysis, GO analysis and KEGG pathway enrichment analysis demonstrated that the PI3K/AKT signaling pathway was the significant pathway in the wogonin for AML-M5 treatment. The antiproliferative effects of wogonin on THP-1 cells of AML-M5 presented a dose-dependent and time-dependent manner, inducing apoptosis, blocking the cell cycle at the G2/M phase, decreasing the expressions of CCND1, CDK2, and CyclinA2 mRNA, as well as AKT and p-AKT proteins. The mechanisms of wogonin on AML-M5 treatment may be associated with inhibiting cell proliferation and regulating the cell cycle via the PI3K/AKT signaling pathway.

Identification of a novel Providencia species showing multi-drug-resistant in three patients with hospital-acquired infection.

Providencia species are important opportunistic pathogens for humans and are associated with several infectious diseases. In this study, we found three clinical strains belonging to a novel Providencia species, namely Providencia huashanensis, including strains CRE-3FA-0001T, CRE-138-0026, and CRE-138-0111. These strains were recovered from three patients, and all of them were associated with nosocomial infections, including surgical site, urinary tract, and intracranial infections. The three strains showed high-level resistance to many types of antimicrobials, including amikacin, aztreonam, ceftazidime, cefepime, ciprofloxacin, colistin, polymyxin B, imipenem, meropenem, ceftazidime-avibactam, imipenem-relebactam. Investigation of the resistance mechanism revealed that acquired resistance genes such as blaKPC, blaNDM, blaPER, blaOXA, aac, ant, qnrD, etc., played an important role in the multidrug-resistant phenotype for the three strains. The phylogenetic trees were reconstructed based on the 16S rRNA gene sequences, multi-locus sequence analysis, and core SNPs. The genome sequence of the strains had a range of 83.5-85.8% average nucleotide identity (ANI) and 21-25.5% in silico DNA-DNA hybridization (isDDH) score with other Providencia type strains. The ANI&isDDH values and the phylogenetic tree indicated that the strains CRE-3FA-0001T, CRE-138-0026, and CRE-138-0111 strains should be considered as a novel species of the genus Providencia, for which the name P. huashanensis sp. nov. is proposed. The type strain is CRE-3FA-0001T =CCTCC AB 2023186T=KCTC 8373T.

Lead exposure induces neurodysfunction through caspase-1-mediated neuronal pyroptosis.

Chronic lead (Pb) exposure causes neurodysfunction and contributes to the development of neurodegenerative disease. However, the mechanism of Pb-induced neurological dysfunction have yet to be fully elucidated. This study determined the role pyroptosis plays in Pb-induced neurodysfunction in neurons. We used both in vitro and in vivo approaches to explore whether Pb exposure induces caspase-1-mediated pyroptosis in neurons and its relationship to Pb-induced neurological disorders. Our findings showed that caspase-1-mediated pyroptosis in Pb-exposed neurons activated glycogen synthase kinase 3 protease activity by disrupting Ca2+/calmodulin-dependent protein kinase II/cAMP-response element binding protein pathway, leading to neurological disorders. Moreover, the caspase-1 inhibition VX-765 or the non-steroidal anti-inflammatory drug sodium para-aminosalicylic acid (PAS-Na) attenuated the Pb-induced neurological disorders by alleviating caspase-1 mediated neuronal pyroptosis. Our novel studies suggest that caspase-1-mediated pyroptosis in neurons represents a potential mechanism for Pb-induced neurodysfunction, identifying a putative target for attenuating the neurodegenerative effects induced by this metal.

Pancreatic cancer cells hijack tumor suppressive microRNA-26a to promote radioresistance and potentiate tumor repopulation.

Pancreatic cancer is one of the most lethal cancers with significant radioresistance and tumor repopulation after radiotherapy. As a type of short non-coding RNA that regulate various biological and pathological processes, miRNAs might play vital role in radioresistance. We found by miRNA sequencing that microRNA-26a (miR-26a) was upregulated in pancreatic cancer cells after radiation, and returned to normal state after a certain time. miR-26a was defined as a tumor suppressive miRNA by conventional tumor biology experiments. However, transient upregulation of miR-26a after radiation significantly promoted radioresistance, while stable overexpression inhibited radioresistance, highlighting the importance of molecular dynamic changes after treatment. Mechanically, transient upregulation of miR-26a promoted cell cycle arrest and DNA damage repair to promote radioresistance. Further experiments confirmed HMGA2 as the direct functional target, which is an oncogene but enhances radiosensitivity. Moreover, PTGS2 was also the target of miR-26a, which might potentiate tumor repopulation via delaying the synthesis of PGE2. Overall, this study revealed that transient upregulation of miR-26a after radiation promoted radioresistance and potentiated tumor repopulation, highlighting the importance of dynamic changes of molecules upon radiotherapy.

Global burden of non-communicable diseases attributable to kidney dysfunction with projection into 2040.

BACKGROUND: Spatiotemporal disparities exist in the disease burden of non-communicable diseases (NCDs) attributable to kidney dysfunction, which has been poorly assessed. The present study aimed to evaluate the spatiotemporal trends of the global burden of NCDs attributable to kidney dysfunction and to predict future trends. METHODS: Data on NCDs attributable to kidney dysfunction, quantified using deaths and disability-adjusted life-years (DALYs), were extracted from the Global Burden of Diseases Injuries, and Risk Factors (GBD) Study in 2019. Estimated annual percentage change (EAPC) of age-standardized rate (ASR) was calculated with linear regression to assess the changing trend. Pearson's correlation analysis was used to determine the association between ASR and Sociodemographic Index (SDI) for 21 GBD regions. A Bayesian age-period-cohort (BAPC) model was used to predict future trends up to 2040. RESULTS: Between 1990 and 2019, the absolute number of deaths and DALYs from NCDs attributable to kidney dysfunction increased globally. The death cases increased from 1,571,720 (95% uncertainty interval [UI]: 1,344,420-1,805,598) in 1990 to 3,161,552 (95% UI: 2,723,363-3,623,814) in 2019 for both sexes combined. Both the ASR of death and DALYs increased in Andean Latin America, the Caribbean, Central Latin America, Southeast Asia, Oceania, and Southern Sub-Saharan Africa. In contrast, the age-standardized metrics decreased in the high-income Asia Pacific region. The relationship between SDI and ASR of death and DALYs was negatively correlated. The BAPC model indicated that there would be approximately 5,806,780 death cases and 119,013,659 DALY cases in 2040 that could be attributed to kidney dysfunction. Age-standardized death of cardiovascular diseases (CVDs) and CKD attributable to kidney dysfunction were predicted to decrease and increase from 2020 to 2040, respectively. CONCLUSION: NCDs attributable to kidney dysfunction remain a major public health concern worldwide. Efforts are required to attenuate the death and disability burden, particularly in low and low-to-middle SDI regions.

Identification of key genes and biological pathways associated with vascular aging in diabetes based on bioinformatics and machine learning.

Vascular aging exacerbates diabetes-associated vascular damage, a major cause of microvascular and macrovascular complications. This study aimed to elucidate key genes and pathways underlying vascular aging in diabetes using integrated bioinformatics and machine learning approaches. Gene expression datasets related to vascular smooth muscle cell (VSMC) senescence and diabetic vascular aging were analyzed. Differential expression analysis identified 428 genes associated with VSMC senescence. Functional enrichment revealed their involvement in cellular senescence, ECM-receptor interaction, PI3K-Akt and AGE-RAGE signaling pathways. Further analysis of diabetic vascular aging datasets revealed 52 differentially expressed genes, enriched in AMPK signaling, AGE-RAGE signaling, cellular senescence, and VEGF signaling pathways. Machine learning algorithms, including LASSO regression and SVM-RFE, pinpointed six key genes: TFB1M, FOXRED2, LY75, DALRD3, PI4K2B, and NDOR1. Immune cell infiltration analysis demonstrated correlations between diabetic vascular aging, the identified key genes, and infiltration levels of plasma cells, M1 macrophages, CD8+ T cells, eosinophils, and regulatory T cells. In conclusion, this study identified six pivotal genes (TFB1M, FOXRED2, LY75, DALRD3, PI4K2B, and NDOR1) closely associated with diabetic vascular aging through integrative bioinformatics and machine learning approaches. These genes are linked to alterations in the immune microenvironment during diabetic vascular aging. This study provides a reference and basis for molecular mechanism research, biomarker mining, and diagnosis and treatment evaluation of diabetes-related vascular aging.

Streptomyces pratensis S10 inhibits spread of Fusarium graminearum invasive hyphae and toxisome formation in wheat plants.

Fusarium head blight (FHB) of wheat, mainly caused by Fusarium graminearum, leads to severe economic losses worldwide. Effective management measures for controlling FHB are not available, due to a lack of resistant cultivars. Currently, the utilization of biological control is a promising approach that can be used to help manage FHB. Previous studies have confirmed that Streptomyces pratensis S10 harbors excellent inhibitory effects on F. graminearum. However, there is no information regarding invasive hyphae of F. graminearum are inhibited by S10. Thus, we investigated the effects of S10 on F. graminearum strain PH-1 hyphae extension, toxisome formation, and TRI5 gene expression on wheat plants via microscopic observation. The results showed that S10 effectively inhibited spread of F. graminearum hyphae along the rachis, restricting the infection of neighboring florets via the phloem. In the presence of S10, the hyphal growth is impeded by formation of dense cell wall thickenings in the rachis internode surrounding the F. graminearum infection site, avoiding cell plasmolysis and collapse. We further demonstrated that S10 largely prevented cell-to-cell invasion of fungal hyphae inside wheat coleoptiles using a constitutively green fluorescence protein-expressing F. graminearum strain, PH-1. Importantly, S. pratensis S10 inhibited toxisome formation and TRI5 gene expression in wheat plants during infection. Collectively, these findings indicated that S. pratensis S10 prevents spread of F. graminearum invasive hyphae via the rachis.

Green Fabrication of Superhydrophilic/Underwater Superoleophobic Composite Membrane for High-Efficiency Oil/Water Separation in Harsh Environments.

Due to the high oil spill incidence and industrial wastewater discharge including oil and emulsified oil, designing and synthesizing oil-water separation materials which can maintain stability under harsh environmental conditions with high separation efficiencies remains a great challenge. The present work developed an easy, green, cost-effective, and easily scaled-up approach for fabricating cellulose-based membranes. First, we coated polydopamine (PDA) onto fibers of filter membrane (FM). Then, the PDA-FM membrane was immersed into the mixed solution of poly(vinyl alcohol)/poly(acrylic acid) (PVA/PAA) and further thermally cross-linked at 150 °C to create a superhydrophilic/underwater superoleophobic membrane (PVA/PAA@PDA-FM) to separate oil/water mixtures. The simple thermally cross-linking process promotes multiple covalent chemical bonds generation between cellulose filter membrane, PAA, PDA, and PVA, endowing membranes with excellent stability and resistance to acidity, alkalinity, and salinity. The PVA/PAA@PDA-FM membrane not only demonstrates great separation performance (>99.8%) and great flux (>1000 L m-2 h-1) in oil-water immiscible mixtures but also maintains high separation efficiency under conditions of high acidity, alkalinity, and salinity. Additionally, the PVA/PAA@PDA-FM membrane exhibits excellent separation capacity in oil-water emulsions, which can maintain the >99.6% separation efficiency even after 40 cycles in harsh environments, showing outstanding reusability. Thus, due to the multiple cross-linked networks in the membrane, the excellent performance makes the PVA/PAA@PDA-FM membrane a good application prospect in water purification and oily wastewater treatment.

Application and potential value of curcumin in prostate cancer: a meta-analysis based on animal models.

Introduction: Curcumin is gaining recognition as an agent for cancer chemoprevention and is presently administered to humans. However, the limited number of clinical trials conducted for the treatment of prostate cancer is noteworthy. Animal models serve as valuable tools for enhancing our understanding of disease mechanisms and etiology in humans. The objective of this study was to examine the anti-prostate cancer effects of curcumin in vivo for comprehending its current research status and potential clinical applicability. Methods: Our methodology involved a systematic exploration of animal studies pertaining to curcumin and prostate cancer, as documented in PubMed, Web of Science, Embase, Cochrane Library, CNKI, Wanfang database, Vip database, and SinoMed, up to 03 September 2023. Risk of bias was assessed using the SYRCLE Animal Study Risk of Bias tool. The results were combined using the RevMan 5.3. Results: A comprehensive analysis was conducted on 17 studies encompassing 263 mouse transplantation tumor models. The findings of this meta-analysis demonstrated that curcumin exhibited a superior inhibitory effect on the volume of prostate cancer tumors in mice compared to the control group (standardized mean difference [SMD]: 1.16, 95% confidence interval [CI]: 0.52, 1.80, p < 0.001). Additionally, curcumin displayed a more effective inhibition of mice prostate cancer tumor weight (SMD: -3.27, 95% CI: -4.70, -1.83, p < 0.001). Furthermore, in terms of tumor inhibition rate, curcumin exhibited greater efficacy (SMD: 0.25, 95% CI: 0.23, 0.27, p < 0.001). Moreover, curcumin more effectively inhibited PCNA mRNA (SMD: -3.11, 95% CI: -4.60, -1.63, p < 0.001) and MMP2 mRNA (SMD: -3.19, 95% CI: 5.85, -0.53, p < 0.001). Conclusion: Curcumin exhibited inhibitory properties towards prostate tumor growth and demonstrated a beneficial effect on prostate cancer treatment, thereby offering substantiation for further clinical investigations. It is important to acknowledge that the included animal studies exhibited considerable heterogeneity, primarily because of the limited number of studies included. Consequently, additional randomized controlled trials are required to comprehensively assess the efficacy of curcumin in humans. Systematic Review Registration: (https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42023464661), identifier (CRD42023464661).

Interleukin-27 Promotes the Generation of Myeloid-derived Suppressor Cells to Alleviate Graft-versus-host Disease.

BACKGROUND: Stimulation of myeloid-derived suppressor cell (MDSC) formation represents a potential curative therapeutic approach for graft-versus-host disease (GVHD), which significantly impacts the prognosis of allogeneic hematopoietic stem cell transplantation. However, the lack of an effective strategy for inducing MDSC production in vivo has hindered their clinical application. In our previous study, MDSC expansion was observed in interleukin (IL)-27-treated mice. METHODS: In this study, we overexpressed exogenous IL-27 in mice using a recombinant adeno-associated virus vector to investigate its therapeutic and exacerbating effects in murine GVHD models. RESULTS: In our study, we demonstrated that exogenous administration of IL-27 significantly suppressed GVHD development in a mouse model. We found that IL-27 treatment indirectly inhibited the proliferation and activation of donor T cells by rapidly expanding recipient and donor myeloid cells, which act as MDSCs after irradiation or under inflammatory conditions, rather than through regulatory T-cell expansion. Additionally, IL-27 stimulated MDSC expansion by enhancing granulocyte-monocyte progenitor generation. Notably, we verified that IL-27 signaling in donor T cells exerted an antagonistic effect on GVHD prevention and treatment. Further investigation revealed that combination therapy involving IL-27 and T-cell depletion exhibited remarkable preventive effects on GVHD in both mouse and xenogeneic GVHD models. CONCLUSIONS: Collectively, these findings suggest that IL-27 promotes MDSC generation to reduce the incidence of GVHD, whereas targeted activation of IL-27 signaling in myeloid progenitors or its combination with T-cell depletion represents a potential strategy for GVHD therapy.

FOXO3 suppresses lymphoma progression through promoting miR-34b/HSPG2 axis.

BACKGROUND: Diffuse large B-cell lymphoma (DLBCL) is the most common type of lymphoma, which caused many patients to lose their precious lives. FOXO3 was a suppressor in various cancers, however, the role and mechanism of FOXO3 in DLBCL remain unclear. METHODS: Bioinformatics analysis was used to offer information FOXO3 expression and its expression for prognosis of DLBCL patients. The abundance of genes and proteins was evaluated using RT-qPCR and western blot. Cell proliferation and apoptosis was detected by CCK-8 and flow cytometry. The interactions among FOXO3, miR-34b, and HSPG2 were predicted by TransmiR and Starbase and validated using dual luciferase reporter assay, ChIP assay, and RIP assay. RESULTS: Our findings revealed that FOXO3 expression was abnormally declined in DLBCL cells. FOXO3 upregulation restrained cell proliferation and promoted cell apoptosis of DLBCL cells, while miR-34b inhibitor eliminated these influences. Similarly, miR-34b mimic suppressed malignant behaviors of DLBCL cells, which were abolished by HSPG2 overexpression. Mechanically, FOXO3 induced miR-34b expression through interacting with miR-34b promoter and HSPG2 was a targeted gene of miR-34b. CONCLUSION: FOXO3 attenuated the capability of cell proliferation and promoted cell apoptosis rate of DLBCL cells through affecting miR-34b/HSPG2 axis, therefore inhibiting DLBCL progression.

Weighted gene co-expression network analysis reveals hub genes regulating response to salt stress in peanut.

Peanut (Arachis hypogaea L.) is an important oilseed crop worldwide. However, soil salinization becomes one of the main limiting factors of peanut production. Therefore, developing salt-tolerant varieties and understanding the molecular mechanisms of salt tolerance is important to protect peanut yield in saline areas. In this study, we selected four peanut varieties with contrasting response to salt challenges with T1 and T2 being tolerance and S1 and S2 being susceptible. High-throughput RNA sequencing resulted in more than 314.63 Gb of clean data from 48 samples. We identified 12,057 new genes, 7,971of which have functional annotations. KEGG pathway enrichment analysis of uniquely expressed genes in salt-tolerant peanut revealed that upregulated genes in the root are involved in the MAPK signaling pathway, fatty acid degradation, glycolysis/gluconeogenesis, and upregulated genes in the shoot were involved in plant hormone signal transduction and the MAPK signaling pathway. Na+ content, K+ content, K+/ Na+, and dry mass were measured in root and shoot tissues, and two gene co-expression networks were constructed based on weighted gene co-expression network analysis (WGCNA) in root and shoot. In this study, four key modules that are highly related to peanut salt tolerance in root and shoot were identified, plant hormone signal transduction, phenylpropanoid biosynthesis, starch and sucrose metabolism, flavonoid biosynthesis, carbon metabolism were identified as the key biological processes and metabolic pathways for improving peanut salt tolerance. The hub genes include genes encoding ion transport (such as HAK8, CNGCs, NHX, NCL1) protein, aquaporin protein, CIPK11 (CBL-interacting serine/threonine-protein kinase 11), LEA5 (late embryogenesis abundant protein), POD3 (peroxidase 3), transcription factor, and MAPKKK3. There were some new salt-tolerant genes identified in peanut, including cytochrome P450, vinorine synthase, sugar transport protein 13, NPF 4.5, IAA14, zinc finger CCCH domain-containing protein 62, beta-amylase, fatty acyl-CoA reductase 3, MLO-like protein 6, G-type lectin S-receptor-like serine/threonine-protein kinase, and kinesin-like protein KIN-7B. The identification of key modules, biological pathways, and hub genes in this study enhances our understanding of the molecular mechanisms underlying salt tolerance in peanuts. This knowledge lays a theoretical foundation for improving and innovating salt-tolerant peanut germplasm.

CVGAE: A Self-Supervised Generative Method for Gene Regulatory Network Inference Using Single-Cell RNA Sequencing Data.

Gene regulatory network (GRN) inference based on single-cell RNA sequencing data (scRNAseq) plays a crucial role in understanding the regulatory mechanisms between genes. Various computational methods have been employed for GRN inference, but their performance in terms of network accuracy and model generalization is not satisfactory, and their poor performance is caused by high-dimensional data and network sparsity. In this paper, we propose a self-supervised method for gene regulatory network inference using single-cell RNA sequencing data (CVGAE). CVGAE uses graph neural network for inductive representation learning, which merges gene expression data and observed topology into a low-dimensional vector space. The well-trained vectors will be used to calculate mathematical distance of each gene, and further predict interactions between genes. In overall framework, FastICA is implemented to relief computational complexity caused by high dimensional data, and CVGAE adopts multi-stacked GraphSAGE layers as an encoder and an improved decoder to overcome network sparsity. CVGAE is evaluated on several single cell datasets containing four related ground-truth networks, and the result shows that CVGAE achieve better performance than comparative methods. To validate learning and generalization capabilities, CVGAE is applied in few-shot environment by change the ratio of train set and test set. In condition of few-shot, CVGAE obtains comparable or superior performance.

Drugst.One - a plug-and-play solution for online systems medicine and network-based drug repurposing.

In recent decades, the development of new drugs has become increasingly expensive and inefficient, and the molecular mechanisms of most pharmaceuticals remain poorly understood. In response, computational systems and network medicine tools have emerged to identify potential drug repurposing candidates. However, these tools often require complex installation and lack intuitive visual network mining capabilities. To tackle these challenges, we introduce Drugst.One, a platform that assists specialized computational medicine tools in becoming user-friendly, web-based utilities for drug repurposing. With just three lines of code, Drugst.One turns any systems biology software into an interactive web tool for modeling and analyzing complex protein-drug-disease networks. Demonstrating its broad adaptability, Drugst.One has been successfully integrated with 21 computational systems medicine tools. Available at https://drugst.one, Drugst.One has significant potential for streamlining the drug discovery process, allowing researchers to focus on essential aspects of pharmaceutical treatment research.

Ratiometric fluorescence method comprising carbon dots and rhodamine 6G encapsulated in metal-organic framework microcubes for curcumin detection.

A ratiometric fluorescence method comprising carbon dots (CDs) and rhodamine 6G (Rh-6G) encapsulated in the microcubes of metal-organic framework (MOF-5) is introduced for the sensitive detection of curcumin (Cur) in condiments. CDs@MOF-5@Rh-6G, synthesized by the adsorption of Rh-6G on MOF-5 embedded with CDs, showed two distinct emission peaks at 435 and 560 nm under excitation at 335 nm, and could be used for Cur detection by ratiometric fluorescence. In the presence of Cur, the fluorescence of the CDs at 435 nm (F435) was quenched by Cur owing to internal filtering and dynamic quenching effects, whereas the emission of Rh-6G at 560 nm (F560) remained unchanged (335 nm is the excitation wavelength, 435 and 560 nm are the emission wavelengths, in which F435/F560 values are used as the output results). Under optimal conditions, a linear relationship was observed between the Cur concentration (in the range 0.1-5 µmol/L) and F435/F560 value for CDs@MOF-5@Rh-6G, with a detection limit of 15 nmol/L. Notably, the proposed method could accurately detect Cur in mustard, curry, and red pepper powders. Therefore, this study could improve the quality control of food and facilitate the development of sensitive ratiometric fluorescence probes.