Docking Score ML: Target-Specific Machine Learning Models Improving Docking-Based Virtual Screening in 155 Targets.

In drug discovery, molecular docking methods face challenges in accurately predicting energy. Scoring functions used in molecular docking often fail to simulate complex protein-ligand interactions fully and accurately leading to biases and inaccuracies in virtual screening and target predictions. We introduce the "Docking Score ML", developed from an analysis of over 200,000 docked complexes from 155 known targets for cancer treatments. The scoring functions used are founded on bioactivity data sourced from ChEMBL and have been fine-tuned using both supervised machine learning and deep learning techniques. We validated our approach extensively using multiple data sets such as validation of selectivity mechanism, the DUDE, DUD-AD, and LIT-PCBA data sets, and performed a multitarget analysis on drugs like sunitinib. To enhance prediction accuracy, feature fusion techniques were explored. By merging the capabilities of the Graph Convolutional Network (GCN) with multiple docking functions, our results indicated a clear superiority of our methodologies over conventional approaches. These advantages demonstrate that Docking Score ML is an efficient and accurate tool for virtual screening and reverse docking.

FaissMolLib: An efficient and easy deployable tool for ligand-based virtual screening.

Virtual screening-based molecular similarity and fingerprint are crucial in drug design, target prediction, and ADMET prediction, aiding in identifying potential hits and optimizing lead compounds. However, challenges such as lack of comprehensive open-source molecular fingerprint databases and efficient search methods for virtual screening are prevalent. To address these issues, we introduce FaissMolLib, an open-source virtual screening tool that integrates 2.8 million compounds from ChEMBL and ZINC databases. Notably, FaissMolLib employs the highly efficient Faiss search algorithm, outperforming the Tanimoto algorithm in identifying similar molecules with its tighter clustering in scatter plots and lower mean, standard deviation, and variance in key molecular properties. This feature enables FaissMolLib to screen 2.8 million compounds in just 0.05 seconds, offering researchers an efficient, easily deployable solution for virtual screening on laptops and building unique compound databases. This significant advancement holds great potential for accelerating drug discovery efforts and enhancing chemical data analysis. FaissMolLib is freely available at http://liuhaihan.gnway.cc:80. The code and dataset of FaissMolLib are freely available at https://github.com/Superhaihan/FiassMolLib.

Uncovering the microbiome landscape in sashimi delicacies.

It is widely believed that a significant portion of the gut microbiota, which play crucial roles in overall health and disease, originates from the food we consume. Sashimi is a type of popular raw seafood cuisine. Its microbiome, however, remained to be thoroughly explored. The objective of this study is to explore the microbiome composition in sashimi at the time when it is served and ready to be eaten. Specifically, our tasks include investigating the diversity and characteristics of microbial profiles in sashimi with respect to the fish types. We utilized the Sanger-sequencing based DNA barcoding technology for fish species authentication and next-generation sequencing for sashimi microbiome profiling. We investigated the microbiome profiles of amberjack, cobia, salmon, tuna and tilapia sashimi, which were all identified using the MT-CO1 DNA sequences regardless of their menu offering names. Chao1 and Shannon indexes, as well as Bray-Curtis dissimilarity index were used to evaluate the alpha and beta diversities of sashimi microbiome. We successfully validated our previous observation that tilapia sashimi has a significantly higher proportions of Pseudomonas compared to other fish sashimi, using independent samples (P = 0.0010). Salmon sashimi exhibited a notably higher Chao1 index in its microbiome in contrast to other fish species (P = 0.0031), indicating a richer and more diverse microbial ecosystem. Non-Metric Multidimensional Scaling (NMDS) based on Bray-Curtis dissimilarity index revealed distinct clusters of microbiome profiles with respect to fish types. Microbiome similarity was notably observed between amberjack and tuna, as well as cobia and salmon. The relationship of microbiome similarity can be depicted as a tree which resembles partly the phylogenetic tree of host species, emphasizing the close relationship between host evolution and microbial composition. Moreover, salmon exhibited a pronounced relative abundance of the Photobacterium genus, significantly surpassing tuna (P = 0.0079), observed consistently across various restaurant sources. In conclusion, microbiome composition of Pseudomonas is significantly higher in tilapia sashimi than in other fish sashimi. Salmon sashimi has the highest diversity of microbiome among all fish sashimi that we analyzed. The level of Photobacterium is significantly higher in salmon than in tuna across all the restaurants we surveyed. These findings provide critical insights into the intricate relationship between the host evolution and the microbial composition. These discoveries deepen our understanding of sashimi microbiota, facilitating our decision in selecting raw seafood.

The basic leucine zipper transcription factor MeaB is critical for biofilm formation, cell wall integrity, and virulence in Aspergillus fumigatus.

The regulation of fungal cell wall biosynthesis is crucial for cell wall integrity maintenance and directly impacts fungal pathogen virulence. Although numerous genes are involved in fungal cell wall polysaccharide biosynthesis through multiple pathways, the underlying regulatory mechanism is still not fully understood. In this study, we identified and functionally characterized a direct downstream target of SomA, the basic-region leucine zipper transcription factor MeaB, playing a certain role in Aspergillus fumigatus cell wall integrity. Loss of meaB reduces hyphal growth, causes severe defects in galactosaminogalactan-mediated biofilm formation, and attenuates virulence in a Galleria mellonella infection model. Furthermore, the meaB null mutant strain exhibited hypersensitivity to cell wall-perturbing agents and significantly alters the cell wall structure. Transcriptional profile analysis revealed that MeaB positively regulates the expression of the galactosaminogalactan biosynthesis and ß-1,3-glucanosyltransferase genes uge3, agd3, and sph3 and gel1, gel5, and gel7, respectively, as well as genes involved in amino sugar and nucleotide sugar metabolism. Further study demonstrated that MeaB could respond to cell wall stress and contribute to the proper expression of mitogen-activated protein kinase genes mpkA and mpkC in the presence of different concentrations of congo red. In conclusion, A. fumigatus MeaB plays a critical role in cell wall integrity by governing the expression of genes encoding cell wall-related proteins, thus impacting the virulence of this fungus.IMPORTANCEAspergillus fumigatus is a common opportunistic mold that causes life-threatening infections in immunosuppressed patients. The fungal cell wall is a complex and dynamic organelle essential for the development of pathogenic fungi. Genes involved in cell wall polysaccharide biosynthesis and remodeling are crucial for fungal pathogen virulence. However, the potential regulatory mechanism for cell wall integrity remains to be fully defined in A. fumigatus. In the present study, we identify basic-region leucine zipper transcription factor MeaB as an important regulator of cell wall galactosaminogalactan biosynthesis and ß-1,3-glucan remodeling that consequently impacts stress response and virulence of fungal pathogens. Thus, we illuminate a mechanism of transcriptional control fungal cell wall polysaccharide biosynthesis and stress response. As these cell wall components are promising therapeutic targets for fungal infections, understanding the regulatory mechanism of such polysaccharides will provide new therapeutic opportunities.

Topological properties analysis and identification of mild cognitive impairment based on individual morphological brain network connectome.

Mild cognitive impairment is considered the prodromal stage of Alzheimer's disease. Accurate diagnosis and the exploration of the pathological mechanism of mild cognitive impairment are extremely valuable for targeted Alzheimer's disease prevention and early intervention. In all, 100 mild cognitive impairment patients and 86 normal controls were recruited in this study. We innovatively constructed the individual morphological brain networks and derived multiple brain connectome features based on 3D-T1 structural magnetic resonance imaging with the Jensen-Shannon divergence similarity estimation method. Our results showed that the most distinguishing morphological brain connectome features in mild cognitive impairment patients were consensus connections and nodal graph metrics, mainly located in the frontal, occipital, limbic lobes, and subcortical gray matter nuclei, corresponding to the default mode network. Topological properties analysis revealed that mild cognitive impairment patients exhibited compensatory changes in the frontal lobe, while abnormal cortical-subcortical circuits associated with cognition were present. Moreover, the combination of multidimensional brain connectome features using multiple kernel-support vector machine achieved the best classification performance in distinguishing mild cognitive impairment patients and normal controls, with an accuracy of 84.21%. Therefore, our findings are of significant importance for developing potential brain imaging biomarkers for early detection of Alzheimer's disease and understanding the neuroimaging mechanisms of the disease.

Cellulose cryogels from herbal residues for oily wastewater purification.

Recycling herbal residues for oily wastewater purification is a potential way to use the wastes to treat wastes. Cellulose extracted from herbal residues is a fine material for cryogel fabrication. However, the cellulose cryogels were not suitable for oily wastewater treatment due to their amphiphilicity. To address this issue, the cryogels were modified with methyltrimethoxysilane (MTMS), which made them hydrophobic and reduced their surface energy. In this study, the herbal residues (Ficus microcarpa L. f) were used in cryogel preparation for the first time. The cryogels exhibit super lightweight and low density. The modified cryogels show excellent sorption capacity for free oils, especially silicone oil (51.22 g/g), and outperformed some recent sorbents. They also effectively separated water-in-toluene emulsion stabilized by Span 80, with a separation efficiency of 98.57 % and a flux of 1474.67 L/m2h. This study demonstrated a novel application of waste herbal residues in the field of environmental remediation.

Changes in fatigue among cancer patients before, during, and after radiation therapy: A meta-analysis.

BACKGROUND: Fatigue is a common symptom in cancer patients receiving radiotherapy. However, previous studies report inconsistent patterns of fatigue change. AIM: The aim of this study was to estimate changes in fatigue among patients with cancer before, during, and after radiotherapy. METHODS: Five databases (PubMed, SDOL, CINAHL Plus with Full Text, Medline [ProQuest], and ProQuest Dissertations) were searched for studies published from January 2006 to May 2021. Three effect sizes of fatigue change (immediate, short-term, and long-term) were calculated for each primary study using standardized mean difference. A random-effect model was used to combine effect sizes across studies. Subgroup analyses and meta-regression were performed to identify potential categorical and continuous moderators, respectively. RESULTS: Sixty-five studies were included in this meta-analysis. The weighted mean effect size for immediate, short-term, and long-term effects was 0.409 (p < .001; 95% CI [0.280, 0.537]), 0.303 (p < .001; 95% CI [0.189, 0.417]), and 0.201 (p = .05; 95% CI [-0.001, 0.404]), respectively. Studies with prostate cancer patients had a significantly higher short-term (0.588) and long-term weight mean effect size (0.531) than studies with breast (0.128, -0.072) or other cancers (0.287, 0.215). Higher radiotherapy dosage was significantly associated with a higher effect size for both immediate (ß = .0002, p < .05) and short-term (ß = .0002, p < .05) effect. LINKING EVIDENCE TO ACTION: Findings from this meta-analysis indicated that radiotherapy-induced fatigue (RIF) exist for more than 3 months after the completion of treatment. Assessment of radiation-induced fatigue in cancer patients should extend long after treatment completion, especially for patients with prostate cancer and patients receiving a higher radiation dose. Interventions to reduce fatigue tailored for different treatment phases may be developed.

Characterizing an Uncertainty Diagram and Kirkwood-Dirac Nonclassicality Based on Discrete Fourier Transform.

In this paper, we investigate an uncertainty diagram and Kirkwood-Dirac (KD) nonclassicality based on discrete Fourier transform (DFT) in a d-dimensional system. We first consider the uncertainty diagram of the DFT matrix, which is a transition matrix from basis A to basis B. Here, the bases A, B are not necessarily completely incompatible. We show that for the uncertainty diagram of the DFT matrix, there is no "hole" in the region of the (nA,nB) plane above and on the line nA+nB=d+1. Then, we present where the holes are in the region strictly below the line and above the hyperbola nAnB=d. Finally, we provide an alternative proof of the conjecture about KD nonclassicality based on DFT.

Structural insights into the transcription activation mechanism of the global regulator GlnR from actinobacteria.

In actinobacteria, an OmpR/PhoB subfamily protein called GlnR acts as an orphan response regulator and globally coordinates the expression of genes responsible for nitrogen, carbon, and phosphate metabolism in actinobacteria. Although many researchers have attempted to elucidate the mechanisms of GlnR-dependent transcription activation, progress is impeded by lacking of an overall structure of GlnR-dependent transcription activation complex (GlnR-TAC). Here, we report a co-crystal structure of the C-terminal DNA-binding domain of GlnR (GlnR_DBD) in complex with its regulatory cis-element DNA and a cryo-EM structure of GlnR-TAC which comprises Mycobacterium tuberculosis RNA polymerase, GlnR, and a promoter containing four well-characterized conserved GlnR binding sites. These structures illustrate how four GlnR protomers coordinate to engage promoter DNA in a head-to-tail manner, with four N-terminal receiver domains of GlnR (GlnR-RECs) bridging GlnR_DBDs and the RNAP core enzyme. Structural analysis also unravels that GlnR-TAC is stabilized by complex protein-protein interactions between GlnR and the conserved ß flap, σAR4, αCTD, and αNTD domains of RNAP, which are further confirmed by our biochemical assays. Taken together, these results reveal a global transcription activation mechanism for the master regulator GlnR and other OmpR/PhoB subfamily proteins and present a unique mode of bacterial transcription regulation.

In vitro antifungal and antibiofilm activities of auranofin against itraconazole-resistant Aspergillus fumigatus.

BACKGROUND: Infections caused by azole-resistant Aspergillus are a rising public health threat with high mortality rates, high treatment costs and limited available antifungals, indicating an urgent need for new antifungals or strategies. Our aim was to investigate antifungal and antibiofilm activities of auranofin, an FDA-approved anti-antirheumatic drug. METHODS: Fungal susceptibility testing for auranofin was carried out by the broth-based microdilution methods. Cell viability treated by auranofin was tested by resazurin dye testing. The synergistic effect of auranofin and antifungal drugs was evaluated using checkboard assay. The inhibitory of biofilms were measured by crystal violet staining. Gene expression level analysis and enzyme activity was investigated with qRT-PCR analysis and DTNB assay. The key amino acid residues in the binding of auranofin with A. fumigatus thioredoxin reductase (AfTrxR) were indicated by structural analyses, site-directed mutagenesis, and microscale thermophoresis (MST) assays. RESULTS: Auranofin has fungicidal activity and in vitro antifungal spectrum including Aspergillus flavus, Aspergillus fumigatus, Aspergillus terreus, Aspergillus niger, even itraconazole (ITC)-resistant A. fumigatus. Additionally, it has antibiofilm activities against ITC-resistant A. fumigatus by reducing the expression level of SomA and MedA. Moreover, we discovered a synergistic effect of auranofin and ITC or amphotericin B against ITC-resistant A. fumigatus. Auranofin downregulated the gene transcription of AfTrxR, and strongly inhibited the enzyme activity of AfTrxR through interacting with residues C145 and C148. CONCLUSIONS: Auranofin has fungicidal and antibiofilm activities in Aspergillus spp. and is also a potentiator of ITC or amphotericin B in vitro.

Comparison of puncture methods in patients with hemodialysis: A randomized controlled trial.

INTRODUCTION: Arteriovenous fistula or arteriovenous graft is essential to long-term survival and quality of life in patients receiving hemodialysis. To date, no research has examined the clinical impacts of different puncture methods. This study compared the rope ladder and area puncture techniques in terms of vascular patency, pain, and quality of life among patients receiving hemodialysis. METHODS: A prospective longitudinal study was performed with 6-month follow-up. A total of 98 participants recruited from a hemodialysis center in Taiwan were randomly assigned to receive the rope ladder technique (experimental group) or the area puncture technique (control group). Vascular patency was assessed by examining access flow and percutaneous transluminal angioplasty rate. Pain and quality of life were measured using the Numerical Pain Rating Scale (NPRS) and Kidney Disease Quality of Life Instrument (KDQOL-36™), respectively. All outcome variables were measured repeatedly and analyzed using a generalized estimating equation. RESULTS: Overall, quality of life was significantly better for the experimental group than for the control group (ß = 47.23, p < 0.001). The percutaneous transluminal angioplasty rate was lower for the experimental group than for the control group (12.0% vs. 18.8%). However, no significant differences were found in access flow and pain level between the two groups over time. CONCLUSION: Hemodialysis patients who received the rope ladder puncture technique had a lower percutaneous angioplasty rate and better quality of life than patients who received the area puncture technique, suggesting that the rope ladder technique could be implemented as a routine cannulation method in hemodialysis clinics.

bHLH transcription factor EcdR controls conidia production, pigmentation and virulence in Aspergillus fumigatus.

Invasive Aspergillus fumigatus infection is a disease with high morbidity and mortality rates. Abnormalities in sporulation and pigmentation can significantly alter the pathogenicity of A. fumigatus, thus the mechanisms of conidiation and pigment biosynthesis have gained increasing attention. In Aspergillus oryzae, a novel predicted bHLH protein-encoding gene, ecdR, plays a role in asexual development, and its ortholog has also been characterized in A. nidulans. Herein, we determined its role in A. fumigatus by testing whether ecdR deletion affects asexual development, melanin synthesis, and regulation of virulence in this fungus. Our study shows that EcdR controls conidia and melanin production in A. fumigatus. In addition, we found that virulence in the ΔecdR strain was significantly reduced in the infection model of immunodeficiency mice.

Investigations into the antibacterial effects and potential mechanism of gambogic acid and neogambogic acid.

The growing threat of antibiotic-resistant bacterial infections to public health necessitates the development of novel antibacterial agents. Inhibiting bacterial cell wall synthesis has remained a key focus for antibiotic development. Our search for inhibitors of undecaprenyl diphosphate synthase (UPPS), an essential enzyme required for bacterial cell wall formation, revealed that two primary components of gamboge, gambogic acid (GA) and neogambogic acid (NGA), significantly inhibited the activity of Enterococcus faecalis UPPS (EfaUPPS) with the half maximal inhibitory concentrations (IC50) of 3.08 µM and 3.07 µM, respectively. In the in vitro antibacterial assay, both GA and NGA also exhibited inhibitory activities against E. faecalis with the minimal inhibitory concentrations (MICs) of 2 µg/mL. Using microscale thermophoresis, molecular docking, and enzymatic assays, we further confirmed that GA and NGA occupy the substrate binding pocket of EfaUPPS with micro-molar binding affinity, preventing the natural substrates farnesyl diphosphate (FPP) from entering. Mutagenesis analysis revealed that L91 and L146 are two key residues in the binding between GA/NGA and UPPS. Furthermore, we also demonstrated that GA and NGA can improve E. faecalis-induced undesirable inflammation in a mouse infection model. Taken together, our findings provide a basis for structural optimization of GA/NGA to develop improved antibiotic leads and enhance treatment success rates in clinical practice.

The relationship between parenting engagement and academic performance.

Gender differences in research productivity have been well documented. One frequent explanation of these differences is disproportionate child-related responsibilities for women. However, changing social dynamics around parenting has led to fathers taking an increasingly active role in parenting. This demands a more nuanced approach to understanding the relationship between parenting and productivity for both men and women. To gain insight into associations between parent roles, partner type, research productivity, and research impact, we conducted a global survey that targeted 1.5 million active scientists; we received viable responses from 10,445 parents (< 1% response rate), thus providing a basis for exploratory analyses that shed light on associations between parenting models and research outcomes, across men and women. Results suggest that the gendered effect observed in production may be related by differential engagement in parenting: men who serve in lead roles suffer similar penalties for parenting engagement, but women are more likely to serve in lead roles and to be more engaged across time and tasks, therefore suffering a higher penalty. Taking a period of parental leave is associated with higher levels of productivity; however, the productivity advantage dissipates after six months for the US-sample, and at 12-months for the non-US sample. These results suggest that parental engagement is a more powerful variable to explain gender differences in academic productivity than the mere existence of children, and that policies should factor these labor differentials into account.

Altered pattern analysis and identification of subjective cognitive decline based on morphological brain network.

Subjective cognitive decline (SCD) is considered the first stage of Alzheimer's disease (AD). Accurate diagnosis and the exploration of the pathological mechanism of SCD are extremely valuable for targeted AD prevention. However, there is little knowledge of the specific altered morphological network patterns in SCD individuals. In this present study, 36 SCD cases and 34 paired-matched normal controls (NCs) were recruited. The Jensen-Shannon distance-based similarity (JSS) method was implemented to construct and derive the attributes of multiple brain connectomes (i.e., morphological brain connections and global and nodal graph metrics) of individual morphological brain networks. A t-test was used to discriminate between the selected nodal graph metrics, while the leave-one-out cross-validation (LOOCV) was used to obtain consensus connections. Comparisons were performed to explore the altered patterns of connectome features. Further, the multiple kernel support vector machine (MK-SVM) was used for combining brain connectomes and differentiating SCD from NCs. We showed that the consensus connections and nodal graph metrics with the most discriminative ability were mostly found in the frontal, limbic, and parietal lobes, corresponding to the default mode network (DMN) and frontoparietal task control (FTC) network. Altered pattern analysis demonstrated that SCD cases had a tendency for modularity and local efficiency enhancement. Additionally, using the MK-SVM to combine the features of multiple brain connectomes was associated with optimal classification performance [area under the curve (AUC): 0.9510, sensitivity: 97.22%, specificity: 85.29%, and accuracy: 91.43%]. Therefore, our study highlighted the combination of multiple connectome attributes based on morphological brain networks and offered a valuable method for distinguishing SCD individuals from NCs. Moreover, the altered patterns of multidimensional connectome attributes provided a promising insight into the neuroimaging mechanism and early intervention in SCD subjects.

Deletion of cox7c Results in Pan-Azole Resistance in Aspergillus fumigatus.

In Aspergillus fumigatus, the most prevalent resistance to azoles results from mutational modifications of the azole target protein Cyp51A, but there are non-cyp51A mutants resistant to azoles, and the mechanisms underlying the resistance of these strains remain to be explored. Here, we identified a novel cytochrome c oxidase, cox7c (W56*), nonsense mutation in the laboratory and found that it caused reduced colony growth and resistance to multiantifungal agents. Meanwhile, we revealed that cold storage is responsible for increased tolerance of conidia to itraconazole (ITC) stress, which further advances azole-resistant mutations (cryopreservation→ITC tolerance→azole resistance). The deletion or mutation of cox7c results explicitly in resistance to antifungal-targeting enzymes, including triazoles, polyenes, and allylamines, required for ergosterol synthesis, or resistance to fungal ergosterol. A high-performance liquid chromatography (HPLC) assay showed that the cox7c knockout strain decreased intracellular itraconazole concentration. In addition, the lack of Cox7c resulted in the accumulation of intracellular heme B. We validated that an endogenous increase in, or the exogenous addition of, heme B was capable of eliciting azole resistance, which was in good accordance with the phenotypic resistance analysis of cox7c mutants. Furthermore, RNA sequencing verified the elevated transcriptional expression levels of multidrug transport genes. Additionally, lower itraconazole-induced reactive oxygen species generation in mycelia of a cox7c-deletion strain suggested that this reduction may, in part, contribute to drug resistance. These findings increase our understanding of how A. fumigatus's direct responses to azoles promote fungal survival in the environment and address genetic mutations that arise from patients or environments.

Foveal hypoplasia and characteristics of optical components in patients with familial exudative vitreoretinopathy and retinopathy of prematurity.

There has been limited research regarding the status of foveal hypoplasia and the characteristics of the optical components of the eye in patients with familial exudative vitreoretinopathy (FEVR) and retinopathy of prematurity (ROP). In this retrospective cohort study, patients were classified into five groups: patients with stage 1 and 2 FEVR (FEVR group), patients with ROP who received treatment (treated ROP group), patients with ROP who did not receive treatment (untreated ROP group), patients without ROP who had been born preterm (preterm group), and healthy patients who had been born at term (full-term group). Visual acuity, refractive error, characteristics of the optical components, and features of the fovea were compared. In total, 179 eyes from 100 patients were included. Patients in the FEVR group had the highest degrees of myopia (p < 0.001). The axial length of patients in the FEVR group was significantly longer than that of patients in the treated and untreated ROP, preterm, and full-term groups (p < 0.001, p < 0.001, p = 0.001, and p = 0.003, respectively). Patients in the FEVR group had a higher proportion of grade 4 foveal hypoplasia and thinner foveae than those in the other groups (p < 0.001). Patients with FEVR had significantly greater myopic change than patients with ROP; the significantly longer axial length of the FEVR group might be the reason for the greater myopic change and lesser macular thickness. Patients in the FEVR group had more foveal hypoplasia than those in the other groups.

Gut microbiota: a potential target for traditional Chinese medicine intervention in coronary heart disease.

Coronary heart disease (CHD) is a common ischaemic heart disease whose pathological mechanism has not been fully elucidated. Single target drugs, such as antiplatelet aggregation, coronary artery dilation and lipid-lowering medicines, can relieve some symptoms clinically but cannot effectively prevent and treat CHD. Accumulating evidence has revealed that alterations in GM composition, diversity, and richness are associated with the risk of CHD. The metabolites of the gut microbiota (GM), including trimethylamine N-oxide (TMAO), short-chain fatty acids (SCFAs) and bile acids (BAs), affect human physiology by activating numerous signalling pathways. Due to the advantage of multiple components and multiple targets, traditional Chinese medicine (TCM) can intervene in CHD by regulating the composition of the GM, reducing TMAO, increasing SCFAs and other CHD interventions. We have searched PubMed, Web of science, Google Scholar Science Direct, and China National Knowledge Infrastructure (CNKI), with the use of the keywords "gut microbiota, gut flora, traditional Chinese medicine, herbal medicine, coronary heart disease". This review investigated the relationship between GM and CHD, as well as the intervention of TCM in CHD and GM, and aims to provide valuable insights for the treatments of CHD by TCM.

Neuroprotective Effect of Danggui Shaoyao San via the Mitophagy-Apoptosis Pathway in a Rat Model of Alzheimer's Disease.

Alzheimer's disease (AD) is a serious neurodegenerative disease. While the main pathological characteristic of AD is widely believed to be the accumulation of amyloid-beta (Aß) in neurons around neurofibrillary plaques, the molecular mechanism of pathological changes is not clear. Traditional Chinese medicine offers many treatments for AD. Among these, Danggui Shaoyao San (DSS) is a classic prescription. In this study, an AD model was established by injecting Aß 1-42 into the brains of rats, which were then treated with different concentrations of Danggui Shaoyao San (sham operation; model; and Danggui Shaoyao San high-dose, medium-dose, and low-dose intervention groups). The Morris water maze test was used to assess the learning and memory abilities of the animals in each group. Nissl staining was used to detect neurons. Mitophagy was evaluated by transmission electron microscopy and immunofluorescence colocalization. Apoptosis was assessed by terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay. The expression levels of autophagy- and apoptosis-related proteins were measured by western blot. Compared to the model group, the groups of AD rats administered medium and high doses of Danggui Shaoyao San showed significantly increased learning and memory abilities (P < 0.05), as well as significantly increased autophagosomes in the hippocampus. Moreover, the expression of PTEN-induced kinase 1 (PINK1), Parkin, and microtubule-associated protein light chain 3 (LC3-I/LC3-II) was increased, while that of p62 was significantly decreased (P < 0.05). The neuronal apoptosis rate was also significantly decreased, the Bcl-2/Bax ratio was significantly increased, and the cleaved caspase-3 protein expression was significantly decreased (P < 0.05). Therefore, Danggui Shaoyao San inhibited neuronal apoptosis in AD rats via a mechanism that may be related to the activation of the PINK1-Parkin-mediated mitophagy signaling pathway.

Differences in the Quantity and Composition of Extracellular Vesicles in the Aqueous Humor of Patients with Retinal Neovascular Diseases.

Extracellular vesicles (EVs) are secreted by various cells in the body fluid system and have been found to influence vessel formation and inflammatory responses in a variety of diseases. However, which EVs and their subtypes are involved in vascular retinal diseases is still unclear. Therefore, the aim of this study was to explore the particle distribution of EVs in retinal neovascular diseases, including age-related macular degeneration, polypoidal choroidal vasculopathy, and central retinal vein occlusion. The aqueous humor was harvested from 20 patients with different retinal neovascular diseases and six patients with cataracts as the control group. The particle distribution was analyzed using nanoparticle tracking analysis (NTA) and transmitting electron microscopy (TEM). The results revealed that the disease groups had large amounts of EVs and their subtypes compared to the control group. After isolating exosomes, a higher expression of CD81+ exosomes was shown in the disease groups using flow cytometry. The exosomes were then further classified into three subtypes of exomeres, small exosomes, and large exosomes, and their amounts were shown to differ depending on the disease type. To the best of our knowledge, this is the first study to elucidate the dynamics of EVs in retinal neovascular diseases using clinical cases. Our findings demonstrated the possible functionality of microvesicles and exosomes, indicating the potential of exosomes in the diagnosis and therapy of retinal neovascular diseases.