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1.
Front Immunol ; 15: 1393852, 2024.
Article En | MEDLINE | ID: mdl-38711526

Different eukaryotic cell organelles (e.g., mitochondria, endoplasmic reticulum, lysosome) are involved in various cancer processes, by dominating specific cellular activities. Organelles cooperate, such as through contact points, in complex biological activities that help the cell regulate energy metabolism, signal transduction, and membrane dynamics, which influence survival process. Herein, we review the current studies of mechanisms by which mitochondria, endoplasmic reticulum, and lysosome are related to the three major malignant gynecological cancers, and their possible therapeutic interventions and drug targets. We also discuss the similarities and differences of independent organelle and organelle-organelle interactions, and their applications to the respective gynecological cancers; mitochondrial dynamics and energy metabolism, endoplasmic reticulum dysfunction, lysosomal regulation and autophagy, organelle interactions, and organelle regulatory mechanisms of cell death play crucial roles in cancer tumorigenesis, progression, and response to therapy. Finally, we discuss the value of organelle research, its current problems, and its future directions.


Genital Neoplasms, Female , Mitochondria , Organelles , Humans , Female , Genital Neoplasms, Female/pathology , Genital Neoplasms, Female/metabolism , Mitochondria/metabolism , Mitochondria/pathology , Organelles/metabolism , Cell Survival , Animals , Lysosomes/metabolism , Endoplasmic Reticulum/metabolism , Autophagy , Energy Metabolism , Signal Transduction
2.
Adv Mater ; : e2403876, 2024 May 13.
Article En | MEDLINE | ID: mdl-38739951

Sorption-based atmospheric water harvesting is an attractive technology for exploiting unconventional water sources. A critical challenge is how to facilitate fast and continuous collection of potable water from air. Here, a bio-based gel (CAL gel), resulting from the integration of a whole biomass-derived polymer network with lithium chloride is reported. A fast adsorption/desorption kinetics, with a water capture rate of 1.74 kg kg-1 h-1 at 30% relative humidity and a desorption rate of 1.98 kg kg-1 h-1, was simultaneously realized in one piece of CAL gel, because of its strong hygroscopicity, hydrophilic network, abundant water transport channels, photothermal conversion ability, and ∼200-µm-thick self-supporting bulky structure caused by multicomponent synergy. A solar-driven, drum-type, tunable, and portable harvester is designed that can harvest atmospheric water within a brief time. Under outdoor conditions, the harvester with CAL gels operates 36 switches (180°) per day realizes a water yield of 8.96 kg kggel -1 (18.87 g kgdevice -1). This portable harvester highlights the potential for fast and scalable atmospheric water harvesting in extreme environments. This article is protected by copyright. All rights reserved.

3.
Article En | MEDLINE | ID: mdl-38742455

BACKGROUND: Error analysis plays a crucial role in clinical concept extraction, a fundamental subtask within clinical natural language processing (NLP). The process typically involves a manual review of error types, such as contextual and linguistic factors contributing to their occurrence, and the identification of underlying causes to refine the NLP model and improve its performance. Conducting error analysis can be complex, requiring a combination of NLP expertise and domain-specific knowledge. Due to the high heterogeneity of electronic health record (EHR) settings across different institutions, challenges may arise when attempting to standardize and reproduce the error analysis process. OBJECTIVES: This study aims to facilitate a collaborative effort to establish common definitions and taxonomies for capturing diverse error types, fostering community consensus on error analysis for clinical concept extraction tasks. MATERIALS AND METHODS: We iteratively developed and evaluated an error taxonomy based on existing literature, standards, real-world data, multisite case evaluations, and community feedback. The finalized taxonomy was released in both .dtd and .owl formats at the Open Health Natural Language Processing Consortium. The taxonomy is compatible with several different open-source annotation tools, including MAE, Brat, and MedTator. RESULTS: The resulting error taxonomy comprises 43 distinct error classes, organized into 6 error dimensions and 4 properties, including model type (symbolic and statistical machine learning), evaluation subject (model and human), evaluation level (patient, document, sentence, and concept), and annotation examples. Internal and external evaluations revealed strong variations in error types across methodological approaches, tasks, and EHR settings. Key points emerged from community feedback, including the need to enhancing clarity, generalizability, and usability of the taxonomy, along with dissemination strategies. CONCLUSION: The proposed taxonomy can facilitate the acceleration and standardization of the error analysis process in multi-site settings, thus improving the provenance, interpretability, and portability of NLP models. Future researchers could explore the potential direction of developing automated or semi-automated methods to assist in the classification and standardization of error analysis.

4.
J Colloid Interface Sci ; 668: 426-436, 2024 Aug 15.
Article En | MEDLINE | ID: mdl-38688181

Reactive radicals are crucial for activating inert and low-polarity C(sp3)-H bonds for the fabrication of high value-added products. Herein, novel single-crystal oxygen-rich bismuth oxybromide nanosheets (Bi4O5Br2 SCNs) with more than 85 % {10-1} facets exposure and oxygen defects were synthesized via a facile solvothermal route. The Bi4O5Br2 SCNs demonstrated excellent photocatalytic performance in the selective oxidation of toluene under blue light. The yield of benzaldehyde was 1876.66 µmol g-1 h-1, with a selectivity of approximately 90 %. Compared to that of polycrystalline Bi4O5Br2 nanosheets (Bi4O5Br2 PCNs), the activity of Bi4O5Br2 SCNs exhibit a 21-fold increase. Experimental studies and density functional theory (DFT) calculations have demonstrated that the defect Bi4O5Br2 (10-1) facets exhibits exceptional adsorption properties for O2 molecules. In addition, the single-crystal structure in the presence of surface defects significantly increases the separation and transport of photogenerated carriers, resulting in the effective activation of adsorbed O2 into superoxide radicals (•O2-). Subsequently, the positively charged phenylmethyl H is readily linked to the negatively charged superoxide radical anion, thereby activating the CH bond. This study offers a fresh perspective and valuable insights into the development of efficient molecular oxygen-activated photocatalysts and their application in the selective catalytic conversion of aromatic C(sp3)-H bonds.

5.
Blood ; 2024 Apr 24.
Article En | MEDLINE | ID: mdl-38657197

Thrombotic microangiopathy (TMA) is characterized by immunothrombosis and life-threatening organ failure, but the precise underlying mechanism driving its pathogenesis remains elusive. In this study, we hypothesized that gasdermin D (GSDMD), a pore-forming protein serving as the final downstream effector of pyroptosis/interleukin (IL)-1pathway, contributes to TMA and its consequences by amplifying neutrophil maturation and subsequent necrosis. Using a murine model of focal crystalline TMA, we found that Gsdmd-deficiency ameliorated immunothrombosis, acute tissue injury and failure. Gsdmd-/- mice exhibited a decrease in mature IL-1, as well as in neutrophil maturation, 2 integrin activation, and recruitment to TMA lesions, where they formed reduced neutrophil extracellular traps both in arteries and interstitial tissue. The GSDMD inhibitor disulfiram dose-dependently suppressed human neutrophil pyroptosis in response to cholesterol crystals. Experiments with GSDMD-deficient human induced pluripotent stem cell-derived neutrophils confirmed the involvement of GSDMD in neutrophil 2 integrin activation, maturation as well as pyroptosis. Both prophylactic and therapeutic administration of disulfiram protected mice from focal TMA, acute tissue injury and failure. Our data identify GSDMD as a key mediator of focal crystalline TMA and its consequences: ischemic tissue infarction and organ failure. GSDMD could potentially serve as a therapeutic target for systemic forms of TMA.

6.
Gels ; 10(4)2024 Apr 01.
Article En | MEDLINE | ID: mdl-38667659

Antibacterial hydrogels have attracted significant attention due to their diverse applications, efficient antimicrobial properties, and adaptability to various environments and requirements. However, their relatively fragile structure, coupled with the potential for environmental toxicity when exposed to their surroundings for extended periods, may significantly limit their practical application potential. In this work, a composite hydrogel was synthesized with outstanding mechanical features and antibacterial capability. The hydrogel was developed through the combination of the eco-friendly and enduring antibacterial agent, lignin silver nanoparticles (Lig-Ag NPs), with polyvinyl alcohol (PVA) and sodium alginate (SA), in varying proportions. The successful synthesis of the hydrogel and the dispersed distribution of Lig-Ag NPs within the hydrogel were confirmed by various analytical techniques, including field emission scanning electron microscopy (SEM), energy-dispersive spectroscopy (EDS), mercury intrusion porosimetry (MIP), Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS). The formation of multiple hydrogen bonds between Lig-Ag NPs and the composites contributed to a more stable and dense network structure of the hydrogel, consequently enhancing its mechanical properties. Rheological tests revealed that the hydrogel exhibited an elastic response and demonstrated outstanding self-recovery properties. Significantly, the antibacterial hydrogel demonstrated effectiveness against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus), achieving a <5% survival of bacteria within 12 h. This study presented a green and straightforward synthetic strategy for the application of antibacterial composite hydrogels in various fields.

7.
Nanoscale ; 16(18): 9068-9074, 2024 May 09.
Article En | MEDLINE | ID: mdl-38639481

Active terahertz metasurface devices have been widely used in communication technology, optical computing and biosensing. However, numerous dynamically tunable metasurfaces are only operating at a single frequency point or in a narrow range, limiting the further possibility of the devices to meet contemporary broad-spectrum biosensing requirements. In this paper, a novel compact biosensor is proposed with an ultrawide resonance frequency agile channel shifted from 0.82 to 1.85 THz, with a tuning functionality up to 55.7%. In addition, under optical pumping irradiation, the modulator with ultra-fast response is able to complete the ultra-wideband resonant mode conversion from the Fano mode to the electromagnetically induced transparency (EIT) mode within 4 ps, and achieves a frequency shift sensitivity of 118 GHz RIU-1 and 247 GHz RIU-1 at 0.82 and 1.85 THz, respectively. This mechanism implements both refractive index and conductivity sensing functions, which provide a wealth of sensing information. Thus, this work presents the possibility of realising the detection of ultra-wide fingerprint spectra and can be extended to a wider range of optical fields.

8.
Cells ; 13(7)2024 Apr 05.
Article En | MEDLINE | ID: mdl-38607075

GDF15, also known as MIC1, is a member of the TGF-beta superfamily. Previous studies reported elevated serum levels of GDF15 in patients with kidney disorder, and its association with kidney disease progression, while other studies identified GDF15 to have protective effects. To investigate the potential protective role of GDF15 on podocytes, we first performed in vitro studies using a Gdf15-deficient podocyte cell line. The lack of GDF15 intensified puromycin aminonucleoside (PAN)-triggered endoplasmic reticulum stress and induced cell death in cultivated podocytes. This was evidenced by elevated expressions of Xbp1 and ER-associated chaperones, alongside AnnexinV/PI staining and LDH release. Additionally, we subjected mice to nephrotoxic PAN treatment. Our observations revealed a noteworthy increase in both GDF15 expression and secretion subsequent to PAN administration. Gdf15 knockout mice displayed a moderate loss of WT1+ cells (podocytes) in the glomeruli compared to wild-type controls. However, this finding could not be substantiated through digital evaluation. The parameters of kidney function, including serum BUN, creatinine, and albumin-creatinine ratio (ACR), were increased in Gdf15 knockout mice as compared to wild-type mice upon PAN treatment. This was associated with an increase in the number of glomerular macrophages, neutrophils, inflammatory cytokines, and chemokines in Gdf15-deficient mice. In summary, our findings unveil a novel renoprotective effect of GDF15 during kidney injury and inflammation by promoting podocyte survival and regulating endoplasmic reticulum stress in podocytes, and, subsequently, the infiltration of inflammatory cells via paracrine effects on surrounding glomerular cells.


Kidney Diseases , Podocytes , Humans , Mice , Animals , Podocytes/metabolism , Puromycin Aminonucleoside/adverse effects , Puromycin Aminonucleoside/metabolism , Growth Differentiation Factor 15/genetics , Growth Differentiation Factor 15/metabolism , Creatinine/metabolism , Kidney Diseases/metabolism , Inflammation/metabolism , Mice, Knockout
9.
J Mater Chem B ; 12(16): 4039-4052, 2024 Apr 24.
Article En | MEDLINE | ID: mdl-38591157

Clear cell renal cell carcinoma (ccRCC) is a disease with high incidence and poor prognosis. The conventional treatment involves radiotherapy and chemotherapy, but chemotherapeutic agents are often associated with side effects, i.e., cytotoxicity to nontumor cells. Therefore, there is an urgent need for the development of novel therapeutic strategies for ccRCC. We synthesized spherical P/TiO2 nanoparticles (P/TiO2 NPs) by vaporization phosphorization (VP). X-ray photoelectron spectroscopy (XPS) and ultraviolet-visible diffuse reflectance spectroscopy (UV-Vis DRS) analyses confirmed that the anatase TiO2 surface was successfully doped with phosphorus and produced a large number of oxygen vacancies (OV). Serving as a photosensitizer, P/TiO2 NPs not only extended the photoresponse range to the near-infrared II region (NIR II) but also introduced a donor energy level lower than the TiO2 conduction band, narrowing the band gap, which could facilitate the migration of photogenerated charges and trigger the synergistic treatment of photodynamic therapy (PDT) and photothermal therapy (PTT). During NIR irradiation in vitro, the P/TiO2 NPs generated local heat and various oxygen radicals, including 1O2, ˙O2-, H2O2, and ˙OH, which damaged the ccRCC cells. In vivo, administration of the P/TiO2 NPs + NIR reduced the tumor volume by 80%, and had the potential to inhibit tumor metastasis by suppressing intratumor neoangiogenesis. The P/TiO2 NPs showed superior safety and efficacy relative to the conventional chemotherapeutic agent used in ccRCC treatment. This study introduced an innovative paradigm for renal cancer treatment, highlighting the potential of P/TiO2 NPs as safe and effective nanomaterials and presenting a compelling new option for clinical applications in anticancer therapy.


Carcinoma, Renal Cell , Kidney Neoplasms , Nanocomposites , Phosphorus , Photochemotherapy , Photothermal Therapy , Titanium , Titanium/chemistry , Titanium/pharmacology , Phosphorus/chemistry , Humans , Animals , Nanocomposites/chemistry , Kidney Neoplasms/drug therapy , Kidney Neoplasms/pathology , Kidney Neoplasms/therapy , Mice , Carcinoma, Renal Cell/drug therapy , Carcinoma, Renal Cell/pathology , Carcinoma, Renal Cell/therapy , Photosensitizing Agents/chemistry , Photosensitizing Agents/pharmacology , Photosensitizing Agents/chemical synthesis , Antineoplastic Agents/chemistry , Antineoplastic Agents/pharmacology , Antineoplastic Agents/chemical synthesis , Cell Survival/drug effects , Cell Proliferation/drug effects , Mice, Nude , Mice, Inbred BALB C , Drug Screening Assays, Antitumor , Particle Size , Cell Line, Tumor
10.
Food Chem X ; 22: 101301, 2024 Jun 30.
Article En | MEDLINE | ID: mdl-38559440

In this study, liquid chromatography tandem mass spectrometry (LC-MS/MS) was employed to analyze the prevalence of 10 mycotoxins in 140 samples from the Chinese market, aiming to assess the exposure of Chinese individuals to these mycotoxins through the consumption of wine, baijiu, and huangjiu. Mycotoxins were detected in 98% of the samples, with fumonisins (FBs), deoxynivalenol (DON), and zearalenone (ZEN) exhibiting positive rates exceeding 50%. Regarding the exposure of the Chinese population to mycotoxins resulting from alcoholic beverage consumption, fruit wine intake made a relatively significant contribution to aflatoxin exposure, while baijiu showed a relatively significant contribution to ZEN exposure (1.84%). The analysis of the correlation between grape variety, wine region, and mycotoxin content demonstrated that FBs, ZEN, and DON were significantly influenced by grape variety and wine region. This research holds great significance in protecting human life and health, as well as in the production of safer alcoholic beverages.

11.
Article En | MEDLINE | ID: mdl-38568772

The foundation model has recently garnered significant attention due to its potential to revolutionize the field of visual representation learning in a self-supervised manner. While most foundation models are tailored to effectively process RGB images for various visual tasks, there is a noticeable gap in research focused on spectral data, which offers valuable information for scene understanding, especially in remote sensing (RS) applications. To fill this gap, we created for the first time a universal RS foundation model, named SpectralGPT, which is purpose-built to handle spectral RS images using a novel 3D generative pretrained transformer (GPT). Compared to existing foundation models, SpectralGPT 1) accommodates input images with varying sizes, resolutions, time series, and regions in a progressive training fashion, enabling full utilization of extensive RS Big Data; 2) leverages 3D token generation for spatial-spectral coupling; 3) captures spectrally sequential patterns via multi-target reconstruction; 4) trains on one million spectral RS images, yielding models with over 600 million parameters. Our evaluation highlights significant performance improvements with pretrained SpectralGPT models, signifying substantial potential in advancing spectral RS Big Data applications within the field of geoscience across four downstream tasks: single/multi-label scene classification, semantic segmentation, and change detection.

12.
Ecotoxicol Environ Saf ; 276: 116288, 2024 May.
Article En | MEDLINE | ID: mdl-38581909

Cylindrospermopsin (CYN), a cyanobacterial toxin, has been detected in the global water environment. However, information concerning the potential environmental risk of CYN is limited, since the majority of previous studies have mainly focused on the adverse health effects of CYN through contaminated drinking water. The present study reported that CYN at environmentally relevant levels (0.1-100 µg/L) can significantly enhance the conjugative transfer of RP4 plasmid in Escherichia coli genera, wherein application of 10 µg/L of CYN led to maximum fold change of ∼6.5- fold at 16 h of exposure. Meanwhile, evaluation of underlying mechanisms revealed that environmental concentration of CYN exposure could increase oxidative stress in the bacterial cells, resulting in ROS overproduction. In turn, this led to an upregulation of antioxidant enzyme-related genes to avoid ROS attack. Further, inhibition of the synthesis of glutathione (GSH) was also detected, which led to the rapid depletion of GSH in cells and thus triggered the SOS response and promoted the conjugative transfer process. Increase in cell membrane permeability, upregulation of expression of genes related to pilus generation, ATP synthesis, and RP4 gene expression were also observed. These results highlight the potential impact on the spread of antimicrobial resistance in water environments.


Alkaloids , Bacterial Toxins , Cyanobacteria Toxins , Escherichia coli , Glutathione , Plasmids , Uracil , Plasmids/genetics , Glutathione/metabolism , Escherichia coli/drug effects , Escherichia coli/genetics , Bacterial Toxins/toxicity , Uracil/analogs & derivatives , Uracil/toxicity , Oxidative Stress/drug effects , Reactive Oxygen Species/metabolism , Conjugation, Genetic , Drug Resistance, Multiple, Bacterial/drug effects , Drug Resistance, Multiple, Bacterial/genetics
13.
Food Res Int ; 184: 114256, 2024 May.
Article En | MEDLINE | ID: mdl-38609234

Mycotoxins are important risk factors in beer. In this study, a liquid chromatography tandem mass spectrometry (LC-MS/MS) method was developed to determine 10 mycotoxins in beer within 6 min. The method is fast, efficient, and has a simple and quick sample preparation. Validation was conducted based on the performance standards specified in Commission Decision 657/2002/EC, and the results demonstrated excellent linearity (R2 > 0.99), repeatability (RSD < 5 %), quantification limits (0.005-20.246 µg/L), and recovery rates (77 %-118 %). The prevalence of the 10 mycotoxins in 96 beers purchased from the Chinese market was analyzed, and the exposure of the Chinese population to mycotoxins through beer consumption was assessed. Deoxynivalenol (DON) was detected in 93.75 % of the beers, and the incidence of fumonisins (FBs) and zearalenone (ZEN) exceeded 50 %. Beer intake contributed significantly to the exposure of aflatoxins (AFs) and DON, especially in males. Correlation analysis between mycotoxin content in beer, raw materials, and the brewing process revealed that the brewing process significantly affected the content of DON (P < 0.001), while auxiliary materials also had a significant impact on the content of FBs and DON (P < 0.001). This study holds great significance in producing higher quality and safer beer.


Aflatoxins , Mycotoxins , Male , Humans , Beer , Chromatography, Liquid , Tandem Mass Spectrometry
14.
J Am Chem Soc ; 146(11): 7400-7407, 2024 Mar 20.
Article En | MEDLINE | ID: mdl-38456799

Peptidoglycan (PG), an essential exoskeletal polymer in bacteria, is a well-known antibiotic target. PG polymerization requires the action of bacterial transglycosylases (TGases), which couple the incoming glycosyl acceptor to the donor. Interfering with the TGase activity can interrupt the PG assembly. Existing TGase inhibitors like moenomycin and Lipid II analogues always occupy the TGase active sites; other strategies to interfere with proper PG elongation have not been widely exploited. Inspired by the natural 1,6-anhydro-MurNAc termini that mark the ends of PG strands in bacteria, we hypothesized that the incorporation of an anhydromuramyl-containing glycosyl acceptor by TGase into the growing PG may effectively inhibit PG elongation. To explore this possibility, we synthesized 4-O-(N-acetyl-ß-d-glucosaminyl)-1,6-anhydro-N-acetyl-ß-d-muramyl-l-Ala-γ-d-Glu-l-Lys-d-Ala-d-Ala, 1, within 15 steps, and demonstrated that this anhydromuropeptide and its analogue lacking the peptide, 1-deAA, were both utilized by bacterial TGase as noncanonical anhydro glycosyl acceptors in vitro. The incorporation of an anhydromuramyl moiety into PG strands by TGases afforded efficient termination of glycan chain extension. Moreover, the preliminary in vitro studies of 1-deAA against Staphylococcus aureus showed that 1-deAA served as a reasonable antimicrobial adjunct of vancomycin. These insights imply the potential application of such anhydromuropeptides as novel classes of PG-terminating inhibitors, pointing toward novel strategies in antibacterial agent development.


Anti-Bacterial Agents , Peptidoglycan , Peptidoglycan/chemistry , Anti-Bacterial Agents/pharmacology , Bacteria/metabolism , Glycosyltransferases/metabolism
15.
Sleep Med ; 117: 123-130, 2024 May.
Article En | MEDLINE | ID: mdl-38531167

STUDY OBJECTIVES: To systemically describe the clinical features, polysomnography (PSG) finding, laboratory tests and single-nucleotide polymorphisms (SNPs) in a clinic based Chinese primary restless legs syndrome (RLS) population. METHODS: This observational study, conducted from January 2020 to October 2021 across 22 sleep labs in China, recruited 771 patients diagnosed with RLS following the 2014 RLSSG criteria. Clinical data, PSG testing, and laboratory examination and SNPs of patients with RLS were collected. A total of 32 SNPs in 24 loci were replicated using the Asian Screening Array chip, employing data from the Han Chinese Genomes Initiative as controls. RESULTS: In this study with 771 RLS patients, 645 had primary RLS, and 617 has DNA available for SNP study. Among the 645 primary RLS, 59.7% were women. 33% had a family history of RLS, with stronger familial influence in early-onset cases. Clinical evaluations showed 10.4% had discomfort in body parts other than legs. PSG showed that 57.1% of RLS patients had periodic leg movement index (PLMI) of >5/h and 39.1% had PLMI >15/h, respectively; 73.8% of RLS patients had an Apnea-Hypopnea Index (AHI) > 5/h, and 45.3% had an AHI >15/h. The laboratory examinations revealed serum ferritin levels <75 ng/ml in 31.6%, and transferrin saturation (TSAT) of <45% in 88.7% of RLS patients. Seven new SNPs in 5 genes showed a significant allelic association with Chinese primary RLS, with one previously reported (BTBD9) and four new findings (TOX3, PRMT6, DCDC2C, NOS1). CONCLUSIONS: Chinese RLS patients has specific characters in many aspects. A high family history with RLS not only indicates strong genetic influence, but also reminds us to consider the familial effect in the epidemiological study. Newly developed sequencing technique with large samples remains to be done.


Restless Legs Syndrome , Humans , Female , Male , Polysomnography , Restless Legs Syndrome/epidemiology , Sleep , Leg , China , Nuclear Proteins , Protein-Arginine N-Methyltransferases
16.
Brief Bioinform ; 25(3)2024 Mar 27.
Article En | MEDLINE | ID: mdl-38555472

Predicting interactions between microbes and hosts plays critical roles in microbiome population genetics and microbial ecology and evolution. How to systematically characterize the sophisticated mechanisms and signal interplay between microbes and hosts is a significant challenge for global health risks. Identifying microbe-host interactions (MHIs) can not only provide helpful insights into their fundamental regulatory mechanisms, but also facilitate the development of targeted therapies for microbial infections. In recent years, computational methods have become an appealing alternative due to the high risk and cost of wet-lab experiments. Therefore, in this study, we utilized rich microbial metagenomic information to construct a novel heterogeneous microbial network (HMN)-based model named KGVHI to predict candidate microbes for target hosts. Specifically, KGVHI first built a HMN by integrating human proteins, viruses and pathogenic bacteria with their biological attributes. Then KGVHI adopted a knowledge graph embedding strategy to capture the global topological structure information of the whole network. A natural language processing algorithm is used to extract the local biological attribute information from the nodes in HMN. Finally, we combined the local and global information and fed it into a blended deep neural network (DNN) for training and prediction. Compared to state-of-the-art methods, the comprehensive experimental results show that our model can obtain excellent results on the corresponding three MHI datasets. Furthermore, we also conducted two pathogenic bacteria case studies to further indicate that KGVHI has excellent predictive capabilities for potential MHI pairs.


Deep Learning , Humans , Pattern Recognition, Automated , Neural Networks, Computer , Algorithms , Bacteria
17.
Microb Cell Fact ; 23(1): 94, 2024 Mar 27.
Article En | MEDLINE | ID: mdl-38539197

BACKGROUND: Surfactin, a green lipopeptide bio-surfactant, exhibits excellent surface, hemolytic, antibacterial, and emulsifying activities. However, a lack of clear understanding of the synthesis regulation mechanism of surfactin homologue components has hindered the customized production of surfactin products with different biological activities. RESULTS: In this study, exogenous valine and 2-methylbutyric acid supplementation significantly facilitated the production of C14-C15 surfactin proportions (up to 75% or more), with a positive correlation between the homologue proportion and fortified concentration. Subsequently, the branched-chain amino acid degradation pathway and the glutamate synthesis pathway are identified as critical pathways in regulating C14-C15 surfactin synthesis by transcriptome analysis. Overexpression of genes bkdAB and glnA resulted in a 1.4-fold and 1.3-fold increase in C14 surfactin, respectively. Finally, the C14-rich surfactin was observed to significantly enhance emulsification activity, achieving an EI24 exceeding 60% against hexadecane, while simultaneously reducing hemolytic activity. Conversely, the C15-rich surfactin demonstrated an increase in both hemolytic and antibacterial activities. CONCLUSION: This study presents the first evidence of a potential connection between surfactin homologue synthesis and the conversion of glutamate and glutamine, providing a theoretical basis for targeting the synthesis regulation and structure-activity relationships of surfactin and other lipopeptide compounds.


Fatty Acids , Surface-Active Agents , Fatty Acids/metabolism , Surface-Active Agents/metabolism , Glutamic Acid/metabolism , Lipopeptides , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/metabolism , Peptides, Cyclic/chemistry , Bacillus subtilis/genetics
18.
medRxiv ; 2024 Feb 06.
Article En | MEDLINE | ID: mdl-38370703

Background: Social determinants of health (SDoH) like socioeconomics and neighborhoods strongly influence outcomes, yet standardized SDoH data is lacking in electronic health records (EHR), limiting research and care quality. Methods: We searched PubMed using keywords "SDOH" and "EHR", underwent title/abstract and full-text screening. Included records were analyzed under five domains: 1) SDoH screening and assessment approaches, 2) SDoH data collection and documentation, 3) Use of natural language processing (NLP) for extracting SDoH, 4) SDoH data and health outcomes, and 5) SDoH-driven interventions. Results: We identified 685 articles, of which 324 underwent full review. Key findings include tailored screening instruments implemented across settings, census and claims data linkage providing contextual SDoH profiles, rule-based and neural network systems extracting SDoH from notes using NLP, connections found between SDoH data and healthcare utilization/chronic disease control, and integrated care management programs executed. However, considerable variability persists across data sources, tools, and outcomes. Discussion: Despite progress identifying patient social needs, further development of standards, predictive models, and coordinated interventions is critical to fulfill the potential of SDoH-EHR integration. Additional database searches could strengthen this scoping review. Ultimately widespread capture, analysis, and translation of multidimensional SDoH data into clinical care is essential for promoting health equity.

19.
Int Wound J ; 21(2): e14733, 2024 Feb.
Article En | MEDLINE | ID: mdl-38339798

Keloids, pathological scars resulting from skin trauma, have traditionally posed significant clinical management challenges due to their persistence and high recurrence rates. Our research elucidates the pivotal roles of lipids and their derivatives in keloid development, driven by underlying mechanisms of abnormal cell proliferation, apoptosis, and extracellular matrix deposition. Key findings suggest that abnormalities in arachidonic acid (AA) synthesis and non-essential fatty acid synthesis are integral to keloid formation. Further, a complex interplay exists between lipid derivatives, notably butyric acid (BA), prostaglandin E2 (PGE2), prostaglandin D2 (PGD2), and the regulation of hyperfibrosis. Additionally, combinations of docosahexaenoic acid (DHA) with BA and 15-deoxy-Δ12,14-Prostaglandin J2 have exhibited pronounced cytotoxic effects. Among sphingolipids, ceramide (Cer) displayed limited pro-apoptotic effects in keloid fibroblasts (KFBs), whereas sphingosine 1-phosphate (S1P) was found to promote keloid hyperfibrosis, with its analogue, FTY720, demonstrating contrasting benefits. Both Vitamin D and hexadecylphosphorylcholine (HePC) showed potential antifibrotic and antiproliferative properties, suggesting their utility in keloid management. While keloids remain a prevalent concern in clinical practice, this study underscores the promising potential of targeting specific lipid molecules for the advancement of keloid therapeutic strategies.


Keloid , Humans , Keloid/drug therapy , Keloid/pathology , Extracellular Matrix , Fibrosis , Apoptosis , Lipids/pharmacology , Lipids/therapeutic use , Fibroblasts
20.
Bioact Mater ; 35: 534-548, 2024 May.
Article En | MEDLINE | ID: mdl-38414842

Rehabilitation and regenerative medicine are two promising approaches for spinal cord injury (SCI) recovery, but their combination has been limited. Conductive biomaterials could bridge regenerative scaffolds with electrical stimulation by inducing axon regeneration and supporting physiological electrical signal transmission. Here, we developed aligned conductive hydrogel fibers by incorporating carbon nanotubes (CNTs) into methacrylate acylated gelatin (GelMA) hydrogel via rotating liquid bath electrospinning. The electrospun CNT/GelMA hydrogel fibers mimicked the micro-scale aligned structure, conductivity, and soft mechanical properties of neural axons. For in vitro studies, CNT/GelMA hydrogel fibers supported PC12 cell proliferation and aligned adhesion, which was enhanced by electrical stimulation (ES). Similarly, the combination of aligned CNT/GelMA hydrogel fibers and ES promoted neuronal differentiation and axon-like neurite sprouting in neural stem cells (NSCs). Furthermore, CNT/GelMA hydrogel fibers were transplanted into a T9 transection rat spinal cord injury model for in vivo studies. The results showed that the incorporating CNTs could remain at the injury site with the GelMA fibers biodegraded and improve the conductivity of regenerative tissue. The aligned structure of the hydrogel could induce the neural fibers regeneration, and the ES enhanced the remyelination and axonal regeneration. Behavioral assessments and electrophysiological results suggest that the combination of aligned CNT/GelMA hydrogel fibers and ES could significantly restore motor function in rats. This study demonstrates that conductive aligned CNT/GelMA hydrogel fibers can not only induce neural regeneration as a scaffold but also support ESto promote spinal cord injury recovery. The conductive hydrogel fibers enable merging regenerative medicine and rehabilitation, showing great potential for satisfactory locomotor recovery after SCI.

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