NAFLDkb: A Knowledge Base and Platform for Drug Development against Nonalcoholic Fatty Liver Disease.

Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease with a broad spectrum of histologic manifestations. The rapidly growing prevalence and the complex pathologic mechanisms of NAFLD pose great challenges for treatment development. Despite tremendous efforts devoted to drug development, there are no FDA-approved medicines yet. Here, we present NAFLDkb, a specialized knowledge base and platform for computer-aided drug design against NAFLD. With multiperspective information curated from diverse source materials and public databases, NAFLDkb presents the associations of drug-related entities as individual knowledge graphs. Practical drug discovery tools that facilitate the utilization and expansion of NAFLDkb have also been implemented in the web interface, including chemical structure search, drug-likeness screening, knowledge-based repositioning, and research article annotation. Moreover, case studies of a knowledge graph repositioning model and a generative neural network model are presented herein, where three repositioning drug candidates and 137 novel lead-like compounds were newly established as NAFLD pharmacotherapy options reusing data records and machine learning tools in NAFLDkb, suggesting its clinical reliability and great potential in identifying novel drug-disease associations of NAFLD and generating new insights to accelerate NAFLD drug development. NAFLDkb is freely accessible at https://www.biosino.org/nafldkb and will be updated periodically with the latest findings.

The composition differences between small black beans and big black beans from different habitats and its effects on the processing of Polygonum multiflorum.

INTRODUCTION: The roots of Polygonum multiflorum (PM) serve as a classical traditional Chinese medicine (TCM), which has multiple biological activities. However, many cases of hepatotoxicity in PM have been reported in recent years. Processing PM with black beans decoction is one of the typical processing methods to reduce the hepatotoxicity of PM since ancient times. OBJECTIVES: To find potential effective constituents, as well as the optimal variety and origin of black beans for the processing of PM. METHODS: Based on ultrahigh-performance liquid chromatography Q-Orbitrap mass spectrometry (UHPLC-Q-Orbitrap-MS) analysis, we measured the contents of the two potential toxic compounds (emodin-8-O-glucoside and torachrysone-O-hexose) in raw PM (R-PM), PM processed with big black beans (B-PM) and PM processed with small black beans (S-PM). The flow cytometry method analysed the effects of different processed products of PM on apoptosis of L02 cells in different drug concentration. Proton nuclear magnetic resonance (1 H-NMR) and UHPLC-Q-Orbitrap-MS together with multivariate statistical analysis were used to systematically analyse the different components between small black beans (Small-BB) and big black beans (Big-BB) from 30 different habitats. RESULTS: The toxicity was ranked from small to large: S-PM < B-PM < R-PM. Processing PM with black beans could significantly decrease the apoptosis rate of L02 cells, especially when the drug concentration is 80 µg/mL. Besides, we find five differential compounds (α-arabinose, α-galactose, proline, isomer of daidzein and isomer of genistein) may be potential active ingredients. In terms of the black beans collected from 30 producing areas, we find that Small-BB from Weifang in Shandong province was optimum to processing PM, followed by Shangqiu in Henan province, Jilin and Liaoning province. CONCLUSION: The ingredients that affect the processing of PM may be attributed to α-arabinose, α-galactose, proline, isomer of daidzein and isomer of genistein in black beans. When the drug concentration is higher, the effect of reducing the hepatotoxicity of PM is better. Besides, Small-BB was more effective than Big-BB for reducing the toxicity of PM, especially Small-BB from Weifang in Shandong, Shangqiu in Henan province and northeast China.

Enhanced microbiota profiling in patients with quiescent Crohn's disease through comparison with paired healthy first-degree relatives.

Prior studies indicate no correlation between the gut microbes of healthy first-degree relatives (HFDRs) of patients with Crohn's disease (CD) and the development of CD. Here, we utilize HFDRs as controls to examine the microbiota and metabolome in individuals with active (CD-A) and quiescent (CD-R) CD, thereby minimizing the influence of genetic and environmental factors. When compared to non-relative controls, the use of HFDR controls identifies fewer differential taxa. Faecalibacterium, Dorea, and Fusicatenibacter are decreased in CD-R, independent of inflammation, and correlated with fecal short-chain fatty acids (SCFAs). Validation with a large multi-center cohort confirms decreased Faecalibacterium and other SCFA-producing genera in CD-R. Classification models based on these genera distinguish CD from healthy individuals and demonstrate superior diagnostic power than models constructed with markers identified using unrelated controls. Furthermore, these markers exhibited limited discriminatory capabilities for other diseases. Finally, our results are validated across multiple cohorts, underscoring their robustness and potential for diagnostic and therapeutic applications.

Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder.

Microbial signatures have emerged as promising biomarkers for disease diagnostics and prognostics, yet their variability across different studies calls for a standardized approach to biomarker research. Therefore, we introduce xMarkerFinder, a four-stage computational framework for microbial biomarker identification with comprehensive validations from cross-cohort datasets, including differential signature identification, model construction, model validation and biomarker interpretation. xMarkerFinder enables the identification and validation of reproducible biomarkers for cross-cohort studies, along with the establishment of classification models and potential microbiome-induced mechanisms. Originally developed for gut microbiome research, xMarkerFinder's adaptable design makes it applicable to various microbial habitats and data types. Distinct from existing biomarker research tools that typically concentrate on a singular aspect, xMarkerFinder uniquely incorporates a sophisticated feature selection process, specifically designed to address the heterogeneity between different cohorts, extensive internal and external validations, and detailed specificity assessments. Execution time varies depending on the sample size, selected algorithm and computational resource. Accessible via GitHub ( https://github.com/tjcadd2020/xMarkerFinder ), xMarkerFinder supports users with diverse expertise levels through different execution options, including step-to-step scripts with detailed tutorials and frequently asked questions, a single-command execution script, a ready-to-use Docker image and a user-friendly web server ( https://www.biosino.org/xmarkerfinder ).

Global fungal-host interactome mapping identifies host targets of candidalysin.

Candidalysin, a cytolytic peptide toxin secreted by the human fungal pathogen Candida albicans, is critical for fungal pathogenesis. Yet, its intracellular targets have not been extensively mapped. Here, we performed a high-throughput enhanced yeast two-hybrid (HT-eY2H) screen to map the interactome of all eight Ece1 peptides with their direct human protein targets and identified a list of potential interacting proteins, some of which were shared between the peptides. CCNH, a regulatory subunit of the CDK-activating kinase (CAK) complex involved in DNA damage repair, was identified as one of the host targets of candidalysin. Mechanistic studies revealed that candidalysin triggers a significantly increased double-strand DNA breaks (DSBs), as evidenced by the formation of γ-H2AX foci and colocalization of CCNH and γ-H2AX. Importantly, candidalysin binds directly to CCNH to activate CAK to inhibit DNA damage repair pathway. Loss of CCNH alleviates DSBs formation under candidalysin treatment. Depletion of candidalysin-encoding gene fails to induce DSBs and stimulates CCNH upregulation in a murine model of oropharyngeal candidiasis. Collectively, our study reveals that a secreted fungal toxin acts to hijack the canonical DNA damage repair pathway by targeting CCNH and to promote fungal infection.

Evaluation of Chinese healthcare organizations' innovative performance in the digital health era.

Background: Healthcare workers' relationship with industry is not merely an agent mediating between consumer and vendor, but they are also inventors of the interventions they exist to deliver. Driven by the background of the digital health era, scientific research and technological (Sci-tech) innovation in the medical field are becoming more and more closely integrated. However, scholars shed little light on Sci-tech relevance to evaluate the innovation performance of healthcare organizations, a distinctive feature of healthcare organizations' innovation in the digital health era. Methods: Academic publications and patents are the manifestations of scientific research outputs and technological innovation outcomes, respectively. The study extracted data from publications and patents of 159 hospitals in China to evaluate their innovation performance. A total of 18 indicators were constructed, four of which were based on text similarity match and represented the Sci-tech relevance. We then applied factor analyses, analytical hierarchy process, and logistic regression to construct an evaluation model. We also examined the relationship between hospitals' innovation performance and their geographical locations. Finally, we implemented a mediation analysis to show the influence of digital health on hospital innovation performance. Results: A total of 16 indicators were involved, four of which represented the Sci-tech including the number of articles matched per patent (NAMP), the number of patents matched per article (NPMA), the proportion of highly matched patents (HMP), and the proportion of highly matched articles (HMA). Indicators of HMP (r = 0.52, P = 2.40 × 10-12), NAMP (r = 0.52, P = 2.54 × 10-12), and NPMA (r = 0.51, P = 5.53 × 10-12) showed a strong positive correlation with hospital innovation performance score. The evaluation model in this study was different from other Chinese existing hospital ranking systems. The regional innovation performance index (RIP) of healthcare organizations is highly correlated with per capita disposable income (r = 0.58) and regional GDP (r = 0.60). There was a positive correlation between digital health innovation performance scores and overall hospital innovation performance scores (r = 0.20). In addition, the hospitals' digital health innovation performance affected the hospital's overall innovation score with the mediation of Sci-tech relevance indicators (NPMA and HMA). The hospitals' digital health innovation performance score showed a significant correlation with the number of healthcare workers (r = 0.44). Conclusion: This study constructed an assessment model with four invented indicators focusing on Sci-tech relevance to provide a novel tool for researchers to evaluate the innovation performance of healthcare organizations in the digital health era. The regions with high RIP were concentrated on the eastern coastal areas with a higher level of economic development. Therefore, the promotion of scientific and technological innovation policies could be carried out in advance in areas with better economic development. The innovations in the digital health field by healthcare workers enhance the Sci-tech relevance in hospitals and boost their innovation performance. The development of digital health in hospitals depends on the input of medical personnel.

A Comprehensive Study on the Chemical Constituents and Pharmacokinetics of Erzhi Formula and Jiawei Erzhi Formula Based on Targeted and Untargeted LC-MS Analysis.

BACKGROUND: Erzhi formula (EZF) is a traditional Chinese medicine prescription, which has been widely used in the treatment of osteoporosis and premature ovarian failure. OBJECTIVE: To enhance curative effects, the other two herbal medicines, including Spatholobi Caulis (SC) and Achyranthes bidentata Blume (ABB), were added into the original EZF formula to obtain two new Jiawei-EZF (JW-EZF) preparations. To clarify the effect of the compatibility of herbs for original formulas, the chemical constituents and bioactive compounds in vivo were detected. METHODS: An efficient and sensitive targeted and untargeted UHPLC/ESI-Q-Orbitrap MS method, together with mass defect filter and precursor ion list, was established firstly for the profiling of different EZF formulas. Furthermore, eleven absorbed compounds (apigenin, luteoloside, luteolin, oleuropein, wedelolactone, acteoside, specnuezhenide, 11-methyloleoside, ecliptasaponin A, formononetin, and ß-ecdysone) were simultaneously quantified in rat plasma. RESULTS: A total of 124, 162, and 177 compounds were identified or tentatively identified in EZF, JW-3-EZF (EZF+SC) and JW-4-EZF (EZF+SC+ABB), respectively. 110 compounds were found to be common constituents in the three formulas. Moreover, 66 prototypes were unambiguously identified in the rats' plasma after oral administration of the three formulas using the same strategy. 11 out of the 66 absorbed components were simultaneously quantitated in the pharmacokinetic (PK) study. Compared to the original EZF, the plasma AUC(0-24h) and AUC(0-∞) of apigenin, 11-methyloleoside, luteolin, luteoloside, wedelolactone, and acteoside were found to be significantly increased after oral administration of JW-3-EZF, and plasma AUC(0-24h) and AUC(0-∞) of apigenin, wedelolactone, and acteoside, were also found to be significantly increased after JW-4-EZF administration. CONCLUSION: The combined qualitative and quantitative methods were used to provide a potential approach to the characterization and quality control of the Traditional Chinese Medicine (TCM) and its preparations.

IBD Subtype-Regulators IFNG and GBP5 Identified by Causal Inference Drive More Intense Innate Immunity and Inflammatory Responses in CD Than Those in UC.

Background: The pathological differences between Crohn's disease (CD) and ulcerative colitis (UC) are substantial and unexplained yet. Here, we aimed to identify potential regulators that drive different pathogenesis of CD and UC by causal inference analysis of transcriptome data. Methods: Kruskal-Wallis and Dunnett's tests were performed to identify differentially expressed genes (DEGs) among CD patients, UC patients, and controls. Subsequently, differentially expressed pathways (DEPs) between CD and UC were identified and used to construct the interaction network of DEPs. Causal inference was performed to identify IBD subtype-regulators. The expression of the subtype-regulators and their downstream genes was validated by qRT-PCR with an independent cohort. Results: Compared with the control group, we identified 1,352 and 2,081 DEGs in CD and UC groups, respectively. Multiple DEPs between CD and UC were closely related to inflammation-related pathways, such as NOD-like receptor signaling, IL-17 signaling, and chemokine signaling pathways. Based on the priori interaction network of DEPs, causal inference analysis identified IFNG and GBP5 as IBD subtype-regulators. The results with the discovery cohort showed that the expression level of IFNG, GBP5, and NLRP3 was significantly higher in the CD group than that in the UC group. The regulation relationships among IFNG, GBP5, and NLRP3 were confirmed with transcriptome data from an independent cohort and validated by qRT-PCR. Conclusion: Our study suggests that IFNG and GBP5 were IBD subtype-regulators that trigger more intense innate immunity and inflammatory responses in CD than those in UC. Our findings reveal pathomechanical differences between CD and UC that may contribute to personalized treatment for CD and UC.

Putative Familial Transmissible Bacteria of Various Body Niches Link with Home Environment and Children's Immune Health.

Owing to their significant impact on children's long-term health, familial factors in the microbiomes of children have attracted increasing attention. However, the mechanism underlying microbiome transmission across generations remains unclear. A significantly lower alpha diversity was observed in the gut flora of children than in the gut flora of parents and grandparents; the alpha diversity of oral and skin microbiota was relatively higher in children than in their predecessors. Gut, oral, and skin microbiome was more similar between family members than between unrelated individuals. Meanwhile, 55.05%, 61.09%, and 76.73% of amplicon sequence variants (ASVs) in children's gut, oral, and skin microbiomes, respectively, were transmitted from all family members. Among these, the most transmissible ASVs belonged to Methylophilaceae, Solimonadaceae, Neisseriaceae, and Burkholderiaceae, which were defined as "putative familial transmissible bacteria." Furthermore, we found that the time spent with parents/grandparents and children's dietary preferences were important factors that influenced the proportion of the transmissible microbiome. Moreover, the majority of transmissible ASVs (85.06%), especially those of Ruminococcaceae and Lachnospiraceae, were significantly associated with the immune indices, such as CD3+, CD4+, CD8+, IgG, and IgA. IMPORTANCE Our study revealed that the children's microbiota was partially transmitted from their family members and specific putative transmissible ASVs were associated with the immune system of children. These findings suggest that home life plays a key role in the shaping of young children's microbiomes and has long-term health benefits.

Comparison of heterotrophic and autotrophic denitrification processes for nitrate removal from phosphorus-limited surface water.

Phosphorus (P) limitation has been demonstrated for micro-polluted surface water denitrification treatment in previous study. In this paper, a lab-scale comparative study of autotrophic denitrification (ADN) and heterotrophic denitrification (HDN) in phosphorus-limited surface water was investigated, aiming to find out the optimal nitrogen/phosphorus (N/P) ratio and the mechanism of the effect of P limitation on ADN and HDN. Furthermore, the optimal denitrification process was applied to the West Lake denitrification project, aiming to improve the water quality of the West Lake from worse than grade V to grade IV (GB3838-2006). The lab-scale study showed that the lack of P indeed inhibited HDN more greatly than ADN. The optimal N/P ratio for ADN and HDN was 25 and a 0.15 mg PO43--P L-1 of microbial available phosphorus (MAP) was observed. P additions could greatly enhance the resistance of ADN and HDN to hydraulic loading shock. Besides, The P addition could effectively stimulate the HDN performance via enriching the heterotrophic denitrifiers and the denitrifying phosphate-accumulating organisms (DNPAOs). Additionally, HDN was more effective and cost-effective than ADN for treating P-limited surface water. The study of the full-scale HDBF (heterotrophic denitrification biofilter) indicated that the denitrification performance was periodically impacted by P limitation, particularly at low water temperatures.

[Killing effect of double suicide genes mediated by retroviral vector on k562 cells].

The aim of study was to investigate the killing effect of double suicide gene system mediated by retroviral vector on K562 cells in vivo and ex vivo. CDglyTK gene was transfected into PA317 cells by using lipofectamine. K562 cells were infected with viral supernatant. K562/CDglyTK cells were treated with 5-fluorocytosine (5-FC) and/or ganciclovir (GCV). Mice were randomly divided into three groups: tumor formation, tumor inhibition and tumor therapy. Each mouse was implanted with K562/CDglyTK cells or K562 cells. The results indicated that the killing effect of 5-FC in combination with GCV on K562/CDglyTK was more significant than using 5-FC or GCV alone. In vivo study showed that after being injected subcutaneously with K562 cells and K562/CDglyTK cells, there was not obvious difference in tumor formation rate of mice, 5-FC + GCV could suppress tumor formation of the K562/CDglyTK cells. After being treated with 5-FC and GCV, the median tumor volume of mice implanted with K562/CDglyTK cells decreased obviously, compared with the control group. Their median survival was significantly prolonged. It is concluded that double suicide genes are more effective for killing effect on K562 cells in vivo and in ex vivo. It may be applicable to clinical gene therapy.