Vortexing-generated high throughput single-cell droplets for facile analysis of multiplexed microRNA dynamic secretion.

Discriminating secretory phenotypes provides a direct, intact, and dynamic way to evaluate the heterogeneity in cell states and activation, which is significant for dissecting non-genetic heterogeneity for human health studies and disease diagnostics. In particular, secreted microRNAs, soluble signaling molecules released by various cells, are increasingly recognized as a critical mediator for cell-cell communication and the circulating biomarkers for disease diagnosis. However, single-cell analysis of secreted miRNAs is still lacking due to the limited available tools. Herein, we realized three-plexed miRNA secretion analysis over four time points from single cells encapsulated in picoliter droplets with extreme simplicity, coupling vortexing-generated single-cell droplets with multiplexed molecular beacons. Notably, our platform only requires pipetting and vortexing steps to finish the assay setup within 5 min with minimal training, and customized software was developed for automatic data quantification. Applying the platform to human cancer cell lines and primary cells revealed previously undifferentiated heterogeneity and paracrine signaling underlying miRNA secretion. This platform can be used to dissect secretion heterogeneity and cell-cell interactions and has the potential to become a widely used tool in biomedical research.

Cinnamaldehyde: an effective component of Cinnamomum cassia inhibiting Helicobacter pylori.

ETHNOPHARMACOLOGICAL RELEVANCE: Cinnamomum cassia Presl (Cinnamomum cassia) is a common traditional Chinese medicine, which can promote the secretion and digestion of gastric juice, improve the function of gastrointestinal tract. Cinnamaldehyde (CA) is a synthetic food flavoring in the Chinese Pharmacopoeia. AIM OF THE STUDY: This study aimed to search for the active ingredient (CA) of inhibiting H. pylori from Cinnamomum cassia, and elucidate mechanism of action, so as to provide the experimental basis for the treatment of H. pylori infection with Cinnamomum cassia. MATERIALS AND METHODS: It's in vitro and in vivo pharmacological properties were evaluated based on minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), and an acute gastric inflammation model in mice infected with H. pylori. Drug safety was evaluated using the CCK8 method and high-dose administration in mice. The advantageous characteristics of CA in inhibiting H. pylori were confirmed using acidic conditions and in combination with the antibiotics. The mechanism underlying the action of CA on H. pylori was explored using scanning electron microscopy (SEM), adhesion experiments, biofilm inhibition tests, ATP and ROS release experiments, and drug affinity responsive target stability (DARTS) screening of target proteins. The protein function and target genes were verified by molecular docking and Real-Time quantitative reverse transcription PCR (qRT-PCR). RESULTS: The results demonstrated that CA was found to be the main active ingredient against H. pylori in Cinnamomum cassia in-vitro tests, with a MIC of 8-16 µg/mL. Moreover, CA effectively inhibited both sensitive and resistant H. pylori strains. The dual therapy of PPI + CA exhibited remarkable in vivo efficacy in the acute gastritis mouse model, superior to the standard triple therapy. DARTS, molecular docking, and qRT-PCR results suggested that the target sites of action were closely associated with GyrA, GyrB, AtpA, and TopA, which made DNA replication and transcription impossible, then leading to inhibition of bacterial adhesion and colonization, suppression of biofilm formation, and inhibition ATP and enhancing ROS. CONCLUSIONS: This study demonstrated the suitability of CA as a promising lead drug against H. pylori, The main mechanisms can target GyrA ect, leading to reduce ATP and produce ROS, which induces the apoptosis of bacterial.

The extracellular vesicles in HIV infection and progression: mechanisms, and theranostic implications.

Extracellular vesicles (EVs), these minute yet mighty cellular messengers are redefining our understanding of a spectrum of diseases, from cancer to cardiovascular ailments, neurodegenerative disorders, and even infectious diseases like HIV. Central to cellular communication, EVs emerge as both potent facilitators and insightful biomarkers in immune response and the trajectory of disease progression. This review ventures deep into the realm of EVs in HIV-unraveling their pivotal roles in diagnosis, disease mechanism unravelling, and therapeutic innovation. With a focus on HIV, we will highlights the transformative potential of EVs in both diagnosing and treating this formidable virus. Unveiling the intricate dance between EVs and HIV, the review aims to shed light on novel therapeutic strategies that could significantly benefit HIV therapy, potentially even leading to the eradication of HIV.

Pathologically successful conversion hepatectomy for advanced giant hepatocellular carcinoma after multidisciplinary therapy: A case report and review of literature.

BACKGROUND: Hepatocellular carcinoma (HCC) is one of the leading causes of death due to its complexity, heterogeneity, rapid metastasis and easy recurrence after surgical resection. We demonstrated that combination therapy with transcatheter arterial chemoembolization (TACE), hepatic arterial infusion chemotherapy (HAIC), Epclusa, Lenvatinib and Sintilimab is useful for patients with advanced HCC. CASE SUMMARY: A 69-year-old man who was infected with hepatitis C virus (HCV) 30 years previously was admitted to the hospital with abdominal pain. Enhanced computed tomography (CT) revealed a low-density mass in the right lobe of the liver, with a volume of 12.9 cm × 9.4 cm × 15 cm, and the mass exhibited a "fast-in/fast-out" pattern, with extensive filling defect areas in the right branch of the portal vein and an alpha-fetoprotein level as high as 657 ng/mL. Therefore, he was judged to have advanced HCC. During treatment, the patient received three months of Epclusa, three TACE treatments, two HAIC treatments, three courses of sintilimab, and twenty-one months of lenvatinib. In the third month of treatment, the patient developed severe side effects and had to stop immunotherapy, and the Lenvatinib dose had to be halved. Postoperative pathological diagnosis indicated a complete response. The patient recovered well after the operation, and no tumor recurrence was found. CONCLUSION: Multidisciplinary conversion therapy for advanced enormous HCC caused by HCV infection has a significant effect. Individualized drug adjustments should be made during any treatment according to the patient's tolerance to treatment.

Evolution of a Filling Paste Cementitious System and Impact Patterns of Sulfate Mine Water Erosion on Filling Paste Performance.

To assess the impact of sulfate mine water on filling material performance, an accelerated sulfate erosion process was used to analyze the effects of various erosion concentrations, aging periods, and cation types on the macroscopic properties of the filling paste. These properties encompassed apparent phenomena, mass changes, and alterations in the uniaxial compressive strength. Observations revealed sulfate erosion, causing the formation of white substances and salt crystals on specimen surfaces. Initially, all solution-eroded specimens exhibited increased mass and strength. Over time, specimens in 5 and 10% MgSO4 solutions displayed the first signs of decline, while variations in other solutions were relatively small. Increasing the erosion concentration led to greater variations in mass and strength during the initial erosion phase. Specimens in 5 and 10% MgSO4 solutions initially peaked in mass and compressive strength, followed by a decline, while other filling paste specimens continued slow increases. Under equivalent conditions, the MgSO4 solution exhibited stronger erosion than the Na2SO4 solution. Composite erosion by Na2SO4 and MgSO4 involved initial strengthening and gel pore filling, intermediate expansion and crystallization, and late-stage substantial degradation, with MgSO4 exhibiting a more pronounced and complex impact. Gray relational analysis ranked factors affecting mass and uniaxial compressive strength variations as erosion concentration > erosion ion type > erosion aging period. Correlation degrees for factors influencing mass variations were 0.8822, 0.8714, and 0.4754, while for factors influencing uniaxial compressive strength variations, the correlation degrees were 0.8336, 0.7943, and 0.6125, respectively.

ISTR: Mask-Embedding-Based Instance Segmentation Transformer.

Transformer-based instance-level recognition has attracted increasing research attention recently due to the superior performance. However, although attempts have been made to encode masks as embeddings into Transformer-based frameworks, how to combine mask embeddings and spatial information for a transformer-based approach is still not fully explored. In this paper, we revisit the design of mask-embedding-based pipelines and propose an Instance Segmentation TRansformer (ISTR) with Mask Meta-Embeddings (MME), leveraging the strengths of transformer models in encoding embedding information and incorporating spatial information from mask embeddings. ISTR incorporates a recurrent refining head that consists of a Dynamic Box Predictor (DBP), a Mask Information Generator (MIG), and a Mask Meta-Decoder (MMD). To improve the quality of mask embeddings, MME interprets the mask encoding-decoding processes as a mutual information maximization problem, which unifies the objective functions of different decoding schemes such as Principal Component Analysis (PCA) and Discrete Cosine Transform (DCT) with a meta-formulation. Under the meta-formulation, a learnable Spatial Mask Tuner (SMT) is further proposed, which fuses the spatial and embedding information produced from MIG and can significantly boost the segmentation performance. The resulting varieties, i.e., ISTR-PCA, ISTR-DCT, and ISTR-SMT, demonstrate the effectiveness and efficiency of incorporating mask embeddings with the query-based instance segmentation pipelines. On the COCO dataset, ISTR surpasses all predominant mask-embedding-based models by a large margin, and achieves competitive performance compared to concurrent state-of-the-art models. On the Cityscapes dataset, ISTR also outperforms several strong baselines. Our code has been made available at: https://github.com/hujiecpp/ISTR.

The role of Rab GTPase in Plant development and stress.

Small GTPase is a type of crucial regulator in eukaryotes. It acts as a molecular switch by binding with GTP and GDP in cytoplasm, affecting various cellular processes. Small GTPase were divided into five subfamilies based on sequence, structure and function: Ras, Rho, Rab, Arf/Sar and Ran, with Rab being the largest subfamily. Members of the Rab subfamily play an important role in regulating complex vesicle transport and microtubule system activity. Plant cells are composed of various membrane-bound organelles, and vesicle trafficking is fundamental to the existence of plants. At present, the function of some Rab members, such as RabA1a, RabD2b/c and RabF2, has been well characterized in plants. This review summarizes the role of Rab GTPase in regulating plant tip growth, morphogenesis, fruit ripening and stress response, and briefly describes the regulatory mechanisms involved. It provides a reference for further alleviating environmental stress, improving plant resistance and even improving fruit quality.

Transient cavity-cavity strong coupling at terahertz frequency on LiNbO3 chips.

Terahertz (THz) microcavities have garnered considerable attention for their ability to localize and confine THz waves, allowing for strong coupling to remarkably enhance the light-matter interaction. These properties hold great promise for advancing THz science and technology, particularly for high-speed integrated THz chips where transient interaction between THz waves and matter is critical. However, experimental study of these transient time-domain processes requires high temporal and spatial resolution since these processes, such as THz strong coupling, occur in several picoseconds and microns. Thus, most literature studies rarely cover temporal and spatial processes at the same time. In this work, we thoroughly investigate the transient cavity-cavity strong-coupling phenomena at THz frequency and find a Rabi-like oscillation in the microcavities, manifested by direct observation of a periodic energy exchange process via a phase-contrast time-resolved imaging system. Our explanation, based on the Jaynes-Cummings model, provides theoretical insight into this transient strong-coupling process. This work provides an opportunity to deeply understand the transient strong-coupling process between THz microcavities, which sheds light on the potential of THz microcavities for high-speed THz sensor and THz chip design.

Monolithically integrated micro-supercapacitors with high areal number density produced by surface adhesive-directed electrolyte assembly.

Accurately placing very small amounts of electrolyte on tiny micro-supercapacitors (MSCs) arrays in close proximity is a major challenge. This difficulty hinders the development of densely-compact monolithically integrated MSCs (MIMSCs). To overcome this grand challenge, we demonstrate a controllable electrolyte directed assembly strategy for precise isolation of densely-packed MSCs at micron scale, achieving scalable production of MIMSCs with ultrahigh areal number density and output voltage. We fabricate a patterned adhesive surface across MIMSCs, that induce electrolyte directed assembly on 10,000 highly adhesive MSC regions, achieving a 100 µm-scale spatial separation between each electrolyte droplet within seconds. The resultant MIMSCs achieve an areal number density of 210 cells cm-2 and a high areal voltage of 555 V cm-2. Further, cycling the MIMSCs at 190 V over 9000 times manifests no performance degradation. A seamlessly integrated system of ultracompact wirelessly-chargeable MIMSCs is also demonstrated to show its practicality and versatile applicability.

Confined growth of Ultrathin, nanometer-sized FeOOH/CoP heterojunction nanosheet arrays as efficient self-supported electrode for oxygen evolution reaction.

Self-supported electrodes, featuring abundant active species and rapid mass transfer, are promising for practical applications in water electrolysis. However, constructing efficient self-supported electrodes with a strong affinity between the catalytic components and the substrate is of great challenge. In this study, by combining the ideas of in-situ construction and space-confined growth, we designed a novel self-supported FeOOH/cobalt phosphide (CoP) heterojunctions grown on a carefully modified commercial Ni foam (NF) with three-dimensional (3D) hierarchically porous Ni skeleton (FeOOH/CoP/3D NF). The specific porous structure of 3D NF directs the confined growth of FeOOH/CoP catalyst into ultra-thin and small-sized nanosheet arrays with abundant edge active sites. The active FeOOH/CoP component is stably anchored on the rough pore wall of 3D NF support, leading to superior stability and improved conductivity. These structural advantages contributed to a highly facilitated oxygen evolution reaction (OER) activity and enhanced durability of the FeOOH/CoP/3D NF electrode. Herein, the FeOOH/CoP/3D NF electrode afforded a low overpotential of 234 mV at 10 mA cm-2 (41 mV smaller than FeOOH/CoP grown on unmodified Ni foam) and high stability for over 90 h, which is among the top reported OER catalysts. Our study provides an effective idea and technique for the construction of active and robust self-supported electrodes for water electrolysis.

[Visualization of mitochondrial dynamics in tomato based on green fluorescent protein].

This study aimed to visualize the morphological features and dynamic changes of tomato mitochondria to provide a basis for the study of its mitochondrial functions. In this study, transgenic tomatoes expressing mitochondria-localized green fluorescent protein (mitochondria-GFP, Mt-GFP) were obtained by Agrobacterium-mediated genetic transformation. The color, hardness, soluble solids, acidity content, respiration rate, and ethylene production of the transgenic Mt-GFP tomato fruits were determined at the stage of mature green, breaker, and 3, 6, 9 days after breaker, while the wild-type tomato fruits were used as a control. As expected, Mt-GFP recombinant protein did not affect the ripening process, but induced the increased acidity of tomato fruits. The accumulations of Mt-GFP protein in tomato leaves and fruits were successfully verified by Western blotting. The morphological characteristics of mitochondria in flower, leaf and fruit cells as well as the dynamic changes of mitochondria in flower cells were clearly observed and studied under confocal laser microscope. The development of transgenic Mt-GFP tomato plants helps the visualization of tomato mitochondria and provides good research materials for the study of mitochondrial function during tomato development and fruit ripening.

In biased and soft-walled channels: Insights into transport phenomena and damped modulation.

The motion of a particle along a channel of finite width is known to be affected by either the presence of energy barriers or changes in the bias forces along the channel direction. By using the lateral equilibrium hypothesis, we have successfully derived the effective diffusion coefficient for soft-walled channels, and the diffusion is found to be influenced by the curvature profile of the potential. A typical phenomenon of diffusion enhancement is observed under the appropriate parameter conditions. We first discovered an anomalous phenomenon of quasi-periodic enhancement of oscillations, which cannot be captured by the one-dimensional effective potential, under the combination of sub-Ohmic damping with two-dimensional restricted channels. We innovatively develop the effective potential and the formation mechanism of velocity variance under super-Ohmic and ballistic damping, and meanwhile, ergodicity is of concern. The theoretical framework of a ballistic system can be reinterpreted through the folding acceleration theory. This comprehensive analysis significantly enhances our understanding of diffusion processes in constrained geometries.

Direct Oxidation of Methane to Methanol over Transition-Metal-Free Ferrierite Zeolite Catalysts.

Direct oxidation of methane to methanol was reported to be highly dependent on the transition- or noble-metal-loading catalysts in the past decades. Here, we show that the transition-metal-free aluminosilicate ferrierite (FER) zeolite effectively catalyzed methane and N2O to methanol for the first time. The distorted tetracoordinated Al in the framework and pentacoordinated Al on the extra framework formed during calcination, activation, and reaction processes were confirmed as the potential active centers. The possible reaction pathway similar to the Fe-containing zeolites was advocated based on the reaction results using different oxidants, N2O adsorption FTIR spectra, and 27Al MAS NMR spectra. The stable and efficient methanol production capacity of FER zeolite was ascribed to the two-dimensional straight channels and its distinctive Al distribution of FER zeolite (CP914C) from Zeolyst. The transition-metal-free FER zeolite performed better than the record in the literature and our recent results using transition-metal-containing catalysts in terms of selectivity and formation rate of methanol and stability. This work has great significance and prospects for utilizing CH4 and N2O as resources and will open new avenues for methane oxidation.

Caffeic-Acid-Functionalized MWCNTs and PEDOT:PSS Formed Composite Flexible Films with "Reinforced Concrete" Structure for Electrical Heating and EMI Shielding.

Nowadays, flexible multifunctional composites are attracting much attention and are practically being used in various emerging electronic devices. However, most composites suffer from the disadvantages of high loadings of conductive fillers, complicated preparation processes, and low energy conversion efficiency. In this article, Caffeic acid-modified multiwalled carbon nanotubes (C-MWCNTs)/poly(3,4-ethylene dioxythiophene):polystyrene sulfonic acid (PEDOT:PSS)/polyimide (PI) composite films (CPFs) were prepared using a simple layer-by-layer deposition method. The "reinforced concrete" structure of the C-MWCNTs/PEDOT:PSS layer ensures high electrical conductivity of the film, while the PI layer provides excellent mechanical properties (72.69 MPa). The composite film exhibits excellent electrothermal response and thermal stability up to approximately 125 °C at 5 V. In addition, the good conductivity of the film provides its electromagnetic shielding effectiveness (32.69 dB). With these advantages, we expect that flexible CPFs will be widely utilized in wearable devices, electromagnetic interference (EMI) shielding applications, and thermal management of personal or electronic devices.

Observations of the effectiveness, dosage, and prognosis of intensity-modulated radiation therapy under ultrasonic guidance for cervical cancer patients.

BACKGROUND: Volumetric modulated arc therapy (VMAT) guided by ultrasound is a novel radiation therapy technique that facilitates the delineation of the tumor target area under image guidance, enhancing the precision of radiation therapy and maximizing the protection of surrounding tissues. OBJECTIVE: The objective of this paper is to investigate the effectiveness of VMAT under ultrasonic guidance for cervical cancer patients and its impact on radiotherapy dosage and prognosis. METHODS: A retrospective analysis encompassed 128 instances of cervical cancer patients who were admitted to our medical facility between April 2019 and April 2021. The patients were categorized into an observation cohort and a control cohort, depending on variations in treatment modalities post-admission. The control group underwent conventional radiotherapy, whereas the observation group received VMAT guided by ultrasound. Clinical efficacy, average radiation dosages (in the radiotherapy target area, rectum, and bladder), radiotherapy-related toxicities during treatment, and one-year survival rates were compared between the two groups. Additionally, variances in pre- and post-treatment serum levels of squamous cell carcinoma antigen (SCC-Ag), carcinoembryonic antigen (CEA), and carbohydrate antigen 724 (CA724) were subjected to assessment. RESULTS: When compared to the control group (64.52%), the observation cohort's comprehensive effectiveness rate was considerably greater (80.30%). The observation group saw lower average radiation exposures and a reduction in the post-treatment concentrations of CEA, SCC-Ag, and CA724. The overall incidence of adverse effects from radiation treatment also declined. The observation group had a greater one-year survival rate (90.48%) than the control group (73.33%). When comparing the observation cohort to the control group, Kaplan-Meier survival analysis showed a significantly higher one-year survival rate (Log-Rank = 6.530, P= 0.011). CONCLUSION: VMAT guided by ultrasound for patients with cervical cancer demonstrates promising short- and long-term treatment outcomes. It also leads to improvements in serum CEA, SCC-Ag, and CA724 levels, as well as reductions in the average radiation dosages to the radiotherapy target area, rectum, and bladder. This approach warrants attention from clinicians in clinical practice.

Integration of transcriptome, gut microbiota, and physiology reveals toxic responses of the red claw crayfish (Cherax quadricarinatus) to imidacloprid.

Imidacloprid enters the water environment through rainfall and causes harm to aquatic crustaceans. However, the potential chronic toxicity mechanism of imidacloprid in crayfish has not been comprehensively studied. In this study, red claw crayfish (Cherax quadricarinatus) were exposed to 11.76, 35.27, or 88.17 µg/L imidacloprid for 30 days, and changes in the physiology and biochemistry, gut microbiota, and transcriptome of C. quadricarinatus and the interaction between imidacloprid, gut microbiota, and genes were studied. Imidacloprid induced oxidative stress and decreased growth performance in crayfish. Imidacloprid exposure caused hepatopancreas damage and decreased serum immune enzyme activity. Hepatopancreatic and plasma acetylcholine decreased significantly in the 88.17 µg/L group. Imidacloprid reduced the diversity of the intestinal flora, increased the abundance of harmful flora, and disrupted the microbiota function. Transcriptomic analysis showed that the number of up-and-down-regulated differentially expressed genes (DEGs) increased significantly with increasing concentrations of imidacloprid. DEG enrichment analyses indicated that imidacloprid inhibits neurotransmitter transduction and immune responses and disrupts energy metabolic processes. Crayfish could alleviate imidacloprid stress by regulating antioxidant and detoxification-related genes. A high correlation was revealed between GST, HSPA1s, and HSP90 and the composition of gut microorganisms in crayfish under imidacloprid stress. This study highlights the negative effects and provides detailed sequencing data from transcriptome and gut microbiota to enhance our understanding of the molecular toxicity of imidacloprid in crustaceans.

Knockdown of circXPO1 inhibits the development of oral squamous cell carcinoma cells.

BACKGROUND: Circular RNAs (circRNAs) have emerged as pivotal regulators of cellular processes in human malignancies, including oral squamous cell carcinoma (OSCC). METHODS: Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to detect RNA expression levels of circXPO1, miR-524-5p and cyclin D1 (CCND1). Colony formation assay and 5-Ethynyl-2'-deoxyuridine (EdU) assay were performed to analyze cell proliferation, while transwell assay was carried out to investigate the cell migration and invasion. Cell apoptosis was assessed by flow cytometry. Protein expression analysis was implemented by Western blot assay. Additionally, lactate production and glucose consumption were investigated using a lactate assay kit and glucose assay kit, respectively. The in vivo tumorigenic potential of circXPO1 was evaluated using a xenograft mouse model assay. RESULTS: Elevated levels of circXPO1 and CCND1, alongside reduced miR-524-5p expression were decreased in OSCC tissues and cells. Knockdown of circXPO1 in OSCC cells inhibited their proliferative, migratory and invasive capacities, as well as glycolysis, prompting apoptosis. Moreover, circXPO1 silencing hindered tumor growth in vivo. MiR-524-5p could be sequestered by circXPO1, and its inhibition could counteract the beneficial effects of circXPO1 knockdown on OSCC progression. CONCLUSION: Knockdown of circXPO1 inhibited OSCC progression by up-regulating miR-524-5p and down-regulating CCND1 expression, which might provide potential targets for OSCC treatment.

Relationship between Phenotypic Changes of Dendritic Cell Subsets and the Onset of Plateau Phase during Intermittent Interferon Therapy in Patients with CHB.

Objective: This study aimed to evaluate whether the onset of the plateau phase of slow hepatitis B surface antigen decline in patients with chronic hepatitis B treated with intermittent interferon therapy is related to the frequency of dendritic cell subsets and expression of the costimulatory molecules CD40, CD80, CD83, and CD86. Method: This was a cross-sectional study in which patients were divided into a natural history group (namely NH group), a long-term oral nucleoside analogs treatment group (namely NA group), and a plateau-arriving group (namely P group). The percentage of plasmacytoid dendritic cell and myeloid dendritic cell subsets in peripheral blood lymphocytes and monocytes and the mean fluorescence intensity of their surface costimulatory molecules were detected using a flow cytometer. Results: In total, 143 patients were enrolled (NH group, n = 49; NA group, n = 47; P group, n = 47). The results demonstrated that CD141/CD1c double negative myeloid dendritic cell (DNmDC)/lymphocytes and monocytes (%) in P group (0.041 [0.024, 0.069]) was significantly lower than that in NH group (0.270 [0.135, 0.407]) and NA group (0.273 [0.150, 0.443]), and CD86 mean fluorescence intensity of DNmDCs in P group (1832.0 [1484.0, 2793.0]) was significantly lower than that in NH group (4316.0 [2958.0, 5169.0]) and NA group (3299.0 [2534.0, 4371.0]), Adjusted P all < 0.001. Conclusion: Reduced DNmDCs and impaired maturation may be associated with the onset of the plateau phase during intermittent interferon therapy in patients with chronic hepatitis B.

MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation.

We introduce MetaboAnalyst version 6.0 as a unified platform for processing, analyzing, and interpreting data from targeted as well as untargeted metabolomics studies using liquid chromatography - mass spectrometry (LC-MS). The two main objectives in developing version 6.0 are to support tandem MS (MS2) data processing and annotation, as well as to support the analysis of data from exposomics studies and related experiments. Key features of MetaboAnalyst 6.0 include: (i) a significantly enhanced Spectra Processing module with support for MS2 data and the asari algorithm; (ii) a MS2 Peak Annotation module based on comprehensive MS2 reference databases with fragment-level annotation; (iii) a new Statistical Analysis module dedicated for handling complex study design with multiple factors or phenotypic descriptors; (iv) a Causal Analysis module for estimating metabolite - phenotype causal relations based on two-sample Mendelian randomization, and (v) a Dose-Response Analysis module for benchmark dose calculations. In addition, we have also improved MetaboAnalyst's visualization functions, updated its compound database and metabolite sets, and significantly expanded its pathway analysis support to around 130 species. MetaboAnalyst 6.0 is freely available at https://www.metaboanalyst.ca.

Development and experimental validation of an energy metabolism-related gene signature for diagnosing of osteoporosis.

Osteoporosis is usually caused by excessive bone resorption and energy metabolism plays a critical role in the development of osteoporosis. However, little is known about the role of energy metabolism-related genes in osteoporosis. This study aimed to explore the important energy metabolism-related genes involved in the development of osteoporosis and develop a diagnosis signature for osteoporosis. The GSE56814, GSE62402, and GSE7158 datasets were downloaded from the NCBI Gene Expression Omnibus. The intersection of differentially expressed genes between high and low levels of body mineral density (BMD) and genes related to energy metabolism were screened as differentially expressed energy metabolism genes (DE-EMGs). Subsequently, a DE-EMG-based diagnostic model was constructed and differential expression of genes in the model was validated by RT-qPCR. Furthermore, a receiver operating characteristic curve and nomogram model were constructed to evaluate the predictive ability of the diagnostic model. Finally, the immune cell types in the merged samples and networks associated with the selected optimal DE-EMGs were constructed. A total of 72 overlapped genes were selected as DE-EMGs, and a five DE-EMG based diagnostic model consisting B4GALT4, ADH4, ACAD11, B4GALT2, and PPP1R3C was established. The areas under the curve of the five genes in the merged training dataset and B4GALT2 in the validation dataset were 0.784 and 0.790, respectively. Moreover, good prognostic prediction ability was observed using the nomogram model (C index = 0.9201; P = 5.507e-14). Significant differences were observed in five immune cell types between the high- and low-BMD groups. These included central memory, effector memory, and activated CD8 T cells, as well as regulatory T cells and activated B cells. A network related to DE-EMGs was constructed, including hsa-miR-23b-3p, DANCR, 17 small-molecule drugs, and two Kyoto Encyclopedia of Genes and Genomes pathways, including metabolic pathways and pyruvate metabolism. Our findings highlighted the important roles of DE-EMGs in the development of osteoporosis. Furthermore, the DANCR/hsa-miR-23b-3p/B4GALT4 axis might provide novel molecular insights into the process of osteoporosis development.