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1.
Food Sci Nutr ; 12(5): 3177-3187, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38726456

RESUMO

The demand for identification of maize varieties has increased dramatically due to the phenomenon of mixed seeds and inferior varieties pretending to be high-quality varieties continuing to occur. It is urgent to solve the problem of efficient and accurate identification of maize varieties. A hyperspectral image acquisition system was used to acquire images of maize seeds. Regions of interest (ROI) with an embryo size of 10 × 10 pixel were extracted, and the average spectral information in the range of 949.43-1709.49 nm was intercepted for the subsequent study in order to eliminate random noise at both ends. Savitzky-Golay (SG) smoothing algorithm and multiple scattering correction (MSC) were used to pretreat the full-band spectrum. The feature wavelengths were screened by successive projection algorithms (SPA), competitive adaptive reweighted sampling (CARS) single screening, and two combinations of CARS-SPA and CARS + SPA, respectively. Support vector machines (SVMs) and models optimized based on genetic algorithm (GA), particle swarm optimization (PSO) were established by using full bands (FB) and feature bands as the model input. The results showed that the MSC-(CARS-SPA)-GA-SVM model had the best performance with 93.00% of the test set accuracy, 8 feature variables, and a running time of 24.45 s. MSC pretreatment can effectively eliminate the scattering effect of spectral data, and the feature wavelengths extracted by CARS-SPA can represent all wavelength information. The study proved that hyperspectral imaging combined with GA-SVM can realize the identification of maize varieties, which provided a theoretical basis for maize variety classification and authenticity identification.

2.
Cell Death Discov ; 10(1): 214, 2024 May 02.
Artigo em Inglês | MEDLINE | ID: mdl-38697992

RESUMO

Neutrophil extracellular traps (NETs) are reticular structures composed of neutrophil elastase (NE), cathepsin G (CG) and DNA-histone enzyme complexes. Accumulating evidence has revealed that NETs play important roles in tumor progression, metastasis, and thrombosis. However, our understanding of its clinical value and mechanism of action in oral squamous cell carcinoma (OSCC) is limited and has not yet been systematically described. Here, we aimed to investigate the clinical significance of NETs in OSCC and the mechanisms by which they affect its invasive and metastatic capacity. Our results demonstrated that high enrichment of NETs is associated with poor prognosis in OSCC, and mechanistic studies have shown that NE in NETs promotes invasion and metastasis via NLRP3-mediated inhibition of pyroptosis in OSCC. These findings may provide a new therapeutic approach for OSCC.

3.
J Cancer Res Clin Oncol ; 150(5): 240, 2024 May 07.
Artigo em Inglês | MEDLINE | ID: mdl-38713284

RESUMO

PURPOSE: Head and neck cancer is the sixth most common type of cancer worldwide, wherein the immune responses are closely associated with disease occurrence, development, and prognosis. Investigation of the role of immunogenic cell death-related genes (ICDGs) in adaptive immune response activation may provide cues into the mechanism underlying the outcome of HNSCC immunotherapy. METHODS: ICDGs expression patterns in HNSCC were analyzed, after which consensus clustering in HNSCC cohort conducted. A 4-gene prognostic model was constructed through LASSO and Cox regression analyses to analyze the prognostic index using the TCGA dataset, followed by validation with two GEO datasets. The distribution of immune cells and the response to immunotherapy were compared between different risk subtypes through multiple algorithms. Moreover, immunohistochemical (IHC) analyses were conducted to validate the prognostic value of HSP90AA1 as a predictor of HNSCC patient prognosis. In vitro assays were performed to further detect the effect of HSP90AA1 in the development of HNSCC. RESULTS: A novel prognostic index based on four ICDGs was constructed and proved to be useful as an independent factor of HNSCC prognosis. The risk score derived from this model grouped patients into high- and low-risk subtypes, wherein the high-risk subtype had worse survival outcomes and poorer immunotherapy response. IHC analysis validated the applicability of HSP90AA1 as a predictor of prognosis of HNSCC patients. HSP90AA1 expression in tumor cells promotes the progression of HNSCC. CONCLUSIONS: Together, these results highlight a novel four-gene prognostic signature as a valuable tool to assess survival status and prognosis of HNSCC patients.


Assuntos
Proteínas de Choque Térmico HSP90 , Neoplasias de Cabeça e Pescoço , Carcinoma de Células Escamosas de Cabeça e Pescoço , Humanos , Carcinoma de Células Escamosas de Cabeça e Pescoço/imunologia , Carcinoma de Células Escamosas de Cabeça e Pescoço/genética , Carcinoma de Células Escamosas de Cabeça e Pescoço/patologia , Carcinoma de Células Escamosas de Cabeça e Pescoço/metabolismo , Prognóstico , Proteínas de Choque Térmico HSP90/genética , Proteínas de Choque Térmico HSP90/metabolismo , Neoplasias de Cabeça e Pescoço/imunologia , Neoplasias de Cabeça e Pescoço/patologia , Neoplasias de Cabeça e Pescoço/genética , Neoplasias de Cabeça e Pescoço/metabolismo , Feminino , Masculino , Morte Celular Imunogênica , Biomarcadores Tumorais/genética , Biomarcadores Tumorais/metabolismo , Pessoa de Meia-Idade , Imunoterapia/métodos , Regulação Neoplásica da Expressão Gênica
4.
Comput Methods Programs Biomed ; 252: 108235, 2024 May 18.
Artigo em Inglês | MEDLINE | ID: mdl-38776830

RESUMO

BACKGROUND AND OBJECTIVE: Computer-based biomedical image segmentation plays a crucial role in planning of assisted diagnostics and therapy. However, due to the variable size and irregular shape of the segmentation target, it is still a challenge to construct an effective medical image segmentation structure. Recently, hybrid architectures based on convolutional neural networks (CNNs) and transformers were proposed. However, most current backbones directly replace one or all convolutional layers with transformer blocks, regardless of the semantic gap between features. Thus, how to sufficiently and effectively eliminate the semantic gap as well as combine the global and local information is a critical challenge. METHODS: To address the challenge, we propose a novel structure, called BiU-Net, which integrates CNNs and transformers with a two-stage fusion strategy. In the first fusion stage, called Single-Scale Fusion (SSF) stage, the encoding layers of the CNNs and transformers are coupled, with both having the same feature map size. The SSF stage aims to reconstruct local features based on CNNs and long-range information based on transformers in each encoding block. In the second stage, Multi-Scale Fusion (MSF), BiU-Net interacts with multi-scale features from various encoding layers to eliminate the semantic gap between deep and shallow layers. Furthermore, a Context-Aware Block (CAB) is embedded in the bottleneck to reinforce multi-scale features in the decoder. RESULTS: Experiments on four public datasets were conducted. On the BUSI dataset, our BiU-Net achieved 85.50 % on Dice coefficient (Dice), 76.73 % on intersection over union (IoU), and 97.23 % on accuracy (ACC). Compared to the state-of-the-art method, BiU-Net improves Dice by 1.17 %. For the Monuseg dataset, the proposed method attained the highest scores, reaching 80.27 % and 67.22 % for Dice and IoU. The BiU-Net achieves 95.33 % and 81.22 % Dice on the PH2 and DRIVE datasets. CONCLUSIONS: The results of our experiments showed that BiU-Net transcends existing state-of-the-art methods on four publicly available biomedical datasets. Due to the powerful multi-scale feature extraction ability, our proposed BiU-Net is a versatile medical image segmentation framework for various types of medical images. The source code is released on (https://github.com/ZYLandy/BiU-Net).

5.
Res Sq ; 2024 Apr 19.
Artigo em Inglês | MEDLINE | ID: mdl-38699335

RESUMO

Background: Epigenome-wide association studies have revealed multiple DNA methylation sites (CpGs) associated with alcohol consumption, an important lifestyle risk factor for cardiovascular diseases. Results: We generated an alcohol consumption epigenetic risk score (ERS) based on previously reported 144 alcohol-associated CpGs and examined the association of the ERS with systolic blood pressure (SBP), diastolic blood pressure (DBP), and hypertension (HTN) in 3,898 Framingham Heart Study (FHS) participants. We found an association of alcohol intake with the ERS in the meta-analysis with 0.09 units higher ERS per drink consumed per day (p < 0.0001). Cross-sectional analyses in FHS revealed that a one-unit increment of the ERS was associated with 1.93 mm Hg higher SBP (p = 4.64E-07), 0.68 mm Hg higher DBP (p = 0.006), and an odds ratio of 1.78 for HTN (p < 2E-16). Meta-analysis of the cross-sectional association of the ERS with BP traits in eight independent external cohorts (n = 11,544) showed similar relationships with blood pressure levels, i.e., a one-unit increase in ERS was associated with 0.74 (p = 0.002) and 0.50 (p = 0.0006) mm Hg higher SBP and DBP, but could not confirm the association with hypertension. Longitudinal analyses in FHS (n = 3,260) and five independent external cohorts (n = 4,021) showed that the baseline ERS was not associated with a change in blood pressure over time or with incident HTN. Conclusions: Our findings provide proof-of-concept that utilizing an ERS is a useful approach to capture the recent health consequences of lifestyle behaviors such as alcohol consumption.

6.
J Agric Food Chem ; 72(18): 10655-10664, 2024 May 08.
Artigo em Inglês | MEDLINE | ID: mdl-38661642

RESUMO

Authenticating whole wheat foods poses a significant challenge for both the grain industry and consumers. Alkylresorcinols (ARs), serving as biomarkers of whole wheat, play a crucial role in assessing the authenticity of whole wheat foods. Herein, we introduce a novel molecularly imprinted electrochemical sensor with modifications involving a molecularly imprinted polymer (MIP) and MXene nanosheets, enabling highly sensitive and selective detection of ARs. Notably, we specifically chose 5-heneicosylresorcinol (AR21), the predominant homologue in whole wheat, as the template molecule. α-Cyclodextrin and acrylamide served as dual functional monomers, establishing a robust multiple interaction between the MIP and AR21. As a result, the sensor exhibited a wide linear range of 0.005 to 100 µg·mL-1 and a low detection limit of 2.52 ng·mL-1, demonstrating exceptional selectivity and stability. When applied to commercial whole wheat foods, the assay achieved satisfactory recoveries and accuracy, strongly validating the practicality and effectiveness of this analytical technique.


Assuntos
Técnicas Eletroquímicas , Contaminação de Alimentos , Impressão Molecular , Resorcinóis , Triticum , alfa-Ciclodextrinas , Resorcinóis/química , Resorcinóis/análise , Triticum/química , alfa-Ciclodextrinas/química , Técnicas Eletroquímicas/métodos , Técnicas Eletroquímicas/instrumentação , Contaminação de Alimentos/análise , Limite de Detecção
7.
Spectrochim Acta A Mol Biomol Spectrosc ; 316: 124344, 2024 Aug 05.
Artigo em Inglês | MEDLINE | ID: mdl-38688212

RESUMO

In this work, visible and near-infrared 'point' (Vis-NIR) spectroscopy and hyperspectral imaging (Vis-NIR-HSI) techniques were applied on three different apple cultivars to compare their firmness prediction performances based on a large intra-variability of individual fruit, and develop rapid and simple models to visualize the variability of apple firmness on three apple cultivars. Apples with high degree of intra-variability can strongly affect the prediction model performances. The apple firmness prediction accuracy can be improved based on the large intra-variability samples with the coefficient variation (CV) values over 10%. The least squares-support vector machine (LS-SVM) models based on Vis-NIR-HSI spectra had better performances for firmness prediction than that of Vis-NIR spectroscopy, with the with the Rc2 over 0.84. Finally, The Vis-NIR-HSI technique combined with least squares-support vector machine (LS-SVM) models were successfully applied to visualize the spatial the variability of apple firmness.


Assuntos
Frutas , Imageamento Hiperespectral , Malus , Espectroscopia de Luz Próxima ao Infravermelho , Máquina de Vetores de Suporte , Malus/química , Espectroscopia de Luz Próxima ao Infravermelho/métodos , Imageamento Hiperespectral/métodos , Análise dos Mínimos Quadrados , Frutas/química
8.
J Chromatogr A ; 1724: 464915, 2024 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-38663319

RESUMO

Efficient enrichment of trace zearalenone (ZEN) from the complex traditional Chinese medicine (TCM) samples is quite difficult, but of great significance for TCM quality control. Herein, we reported a novel magnetic solid phase extraction (MSPE) strategy for ZEN enrichment using the amino- and hydroxyl dual-functionalized magnetic microporous organic network (Fe3O4@MON-NH2-OH) as an advanced adsorbent combined with the high-performance liquid chromatography (HPLC) determination. Efficient extraction of ZEN was achieved via the possible hydrogen bonding, hydrophobic, and π-π interactions between Fe3O4@MON-NH2-OH and ZEN. The adsorption capacity of Fe3O4@MON-NH2-OH for ZEN was 215.0 mg g-1 at the room temperature, which was much higher than most of the reported adsorbents. Under the optimal condition, the developed Fe3O4@MON-NH2-OH-MSPE-HPLC method exhibited wide linear range (5-2500 µg L-1), low limits of detection (1.4-35 µg L-1), less adsorbent consumption (5 mg), and large enhancement factor (95) for ZEN. The proposed method was successfully applied to detect trace ZEN from 10 kinds of real TCM samples. Conclusively, this work demonstrates the Fe3O4@MON-NH2-OH can effectively extract trace ZEN from the complex TCM matrices, which may open up a new way for the application of MONs in the enrichment and extraction of trace contaminants or active constituents from the complex TCM samples.


Assuntos
Medicamentos de Ervas Chinesas , Limite de Detecção , Extração em Fase Sólida , Zearalenona , Cromatografia Líquida de Alta Pressão/métodos , Zearalenona/análise , Zearalenona/química , Zearalenona/isolamento & purificação , Extração em Fase Sólida/métodos , Adsorção , Medicamentos de Ervas Chinesas/química , Medicamentos de Ervas Chinesas/isolamento & purificação , Medicina Tradicional Chinesa , Porosidade , Nanopartículas de Magnetita/química
9.
Environ Sci Pollut Res Int ; 31(20): 29434-29448, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38575820

RESUMO

Microplastics (MPs) migrate by adsorbing heavy metals in aquatic environments and act as their carriers. However, the aging mechanisms of MPs in the environment and the interactions between MPs and heavy metals in aquatic environments require further study. In this study, two kinds of materials, polyamide (PA) and polylactic acid (PLA) were used as target MPs, and the effects of UV irradiation on the physical and chemical properties of the MPs and the adsorption behavior of Cu(II) were investigated. The results showed that after UV irradiation, pits, folds and pores appeared on the surface of aged MPs, the specific surface area (SSA) increased, the content of oxygen-containing functional groups increased, and the crystallinity decreased. These changes enhanced the adsorption capacity of aged MPs for Cu(II) pollutants. The adsorption behavior of the PA and PLA MPs for Cu(II) conformed to the pseudo-second-order model and Langmuir isotherm model, indicating that the monolayer chemical adsorption was dominant. The maximum amounts of aged PA and PLA reached 1.415 and 1.398 mg/g, respectively, which were 1.59 and 1.76 times of virgin MPs, respectively. The effects of pH and salinity on the adsorption of Cu(II) by the MPs were significant. Moreover, factors such as pH, salinity and dosage had significant effects on the adsorption of Cu(II) by MPs. Oxidative complexation between the oxygen-containing groups of the MPs and Cu(II) is an important adsorption mechanism. These findings reveal that the UV irradiation aging of MPs can enhance the adsorption of Cu(II) and increase their role as pollutant carriers, which is crucial for assessing the ecological risk of MPs and heavy metals coexisting in aquatic environments.


Assuntos
Cobre , Microplásticos , Poluentes Químicos da Água , Adsorção , Cobre/química , Poluentes Químicos da Água/química , Microplásticos/química , Poliésteres/química
10.
Mol Med ; 30(1): 46, 2024 Apr 08.
Artigo em Inglês | MEDLINE | ID: mdl-38584262

RESUMO

Effective therapeutic targets and early diagnosis are major challenges in the treatment of gastrointestinal tract (GIT) cancers. SALL4 is a well-known transcription factor that is involved in organogenesis during embryonic development. Previous studies have revealed that SALL4 regulates cell proliferation, survival, and migration and maintains stem cell function in mature cells. Additionally, SALL4 overexpression is associated with tumorigenesis. Despite its characterization as a biomarker in various cancers, the role of SALL4 in GIT cancers and the underlying mechanisms are unclear. We describe the functions of SALL4 in GIT cancers and discuss its upstream/downstream genes and pathways associated with each cancer. We also consider the possibility of targeting these genes or pathways as potential therapeutic options for GIT cancers.


Assuntos
Neoplasias Gastrointestinais , Fatores de Transcrição , Humanos , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Neoplasias Gastrointestinais/genética , Células-Tronco/metabolismo , Desenvolvimento Embrionário , Linhagem Celular Tumoral
11.
Oncol Res ; 32(4): 753-768, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38560563

RESUMO

Multiple myeloma (MM) is a hematologic malignancy notorious for its high relapse rate and development of drug resistance, in which cell adhesion-mediated drug resistance plays a critical role. This study integrated four RNA sequencing datasets (CoMMpass, GSE136337, GSE9782, and GSE2658) and focused on analyzing 1706 adhesion-related genes. Rigorous univariate Cox regression analysis identified 18 key prognosis-related genes, including KIF14, TROAP, FLNA, MSN, LGALS1, PECAM1, and ALCAM, which demonstrated the strongest associations with poor overall survival (OS) in MM patients. To comprehensively evaluate the impact of cell adhesion on MM prognosis, an adhesion-related risk score (ARRS) model was constructed using Lasso Cox regression analysis. The ARRS model emerged as an independent prognostic factor for predicting OS. Furthermore, our findings revealed that a heightened cell adhesion effect correlated with tumor resistance to DNA-damaging drugs, protein kinase inhibitors, and drugs targeting the PI3K/Akt/mTOR signaling pathway. Nevertheless, we identified promising drug candidates, such as tirofiban, pirenzepine, erlotinib, and bosutinib, which exhibit potential in reversing this resistance. In vitro, experiments employing NCIH929, RPMI8226, and AMO1 cell lines confirmed that MM cell lines with high ARRS exhibited poor sensitivity to the aforementioned candidate drugs. By employing siRNA-mediated knockdown of the key ARRS model gene KIF14, we observed suppressed proliferation of NCIH929 cells, along with decreased adhesion to BMSCs and fibronectin. This study presents compelling evidence establishing cell adhesion as a significant prognostic factor in MM. Additionally, potential molecular mechanisms underlying adhesion-related resistance are proposed, along with viable strategies to overcome such resistance. These findings provide a solid scientific foundation for facilitating clinically stratified treatment of MM.


Assuntos
Mieloma Múltiplo , Humanos , Mieloma Múltiplo/tratamento farmacológico , Mieloma Múltiplo/genética , Mieloma Múltiplo/patologia , Adesão Celular/genética , Fosfatidilinositol 3-Quinases/metabolismo , Prognóstico , Resistencia a Medicamentos Antineoplásicos/genética , Linhagem Celular Tumoral , Recidiva Local de Neoplasia
12.
Neurophotonics ; 11(2): 025001, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38660382

RESUMO

Significance: Early diagnosis of depression is crucial for effective treatment. Our study utilizes functional near-infrared spectroscopy (fNIRS) and machine learning to accurately classify mild and severe depression, providing an objective auxiliary diagnostic tool for mental health workers. Aim: Develop prediction models to distinguish between severe and mild depression using fNIRS data. Approach: We collected the fNIRS data from 140 subjects and applied a complete ensemble empirical mode decomposition with an adaptive noise-wavelet threshold combined denoising method (CEEMDAN-WPT) to remove noise during the verbal fluency task. The temporal features (TF) and correlation features (CF) from 18 prefrontal lobe channels of subjects were extracted as predictors. Using recursive feature elimination with cross-validation, we identified optimal TF or CF and examined their role in distinguishing between severe and mild depression. Machine learning algorithms were used for classification. Results: The combination of TF and CF as inputs for the prediction model yielded higher classification accuracy than using either TF or CF alone. Among the prediction models, the SVM-based model demonstrates excellent performance in nested cross-validation, achieving an accuracy rate of 92.8%. Conclusions: The proposed model can effectively distinguish mild depression from severe depression.

13.
Front Immunol ; 15: 1298471, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38633263

RESUMO

Introduction: In light of the public health burden of the COVID-19 pandemic, boosting the safety and immunogenicity of COVID-19 vaccines is of great concern. Numerous Traditional Chinese medicine (TCM) preparations have shown to beneficially modulate immunity. Based on pilot experiments in mice that showed that supplementation with Huoxiang Suling Shuanghua Decoction (HSSD) significantly enhances serum anti-RBD IgG titers after inoculation with recombinant SARS-CoV-2 S-RBD protein, we conducted this randomized, double-blind, placebo-controlled clinical trial aimed to evaluate the potential immunogenicity boosting effect of oral HSSD after a third homologous immunization with Sinovac's CoronaVac SARS-CoV-2 (CVS) inactivated vaccine. Methods: A total of 70 participants were randomly assigned (1:1 ratio) to receive a third dose of CVS vaccination and either oral placebo or oral HSSD for 7 days. Safety aspects were assessed by recording local and systemic adverse events, and by blood and urine biochemistry and liver and kidney function tests. Main outcomes evaluated included serum anti-RBD IgG titer, T lymphocyte subsets, serum IgG and IgM levels, complement components (C3 and C4), and serum cytokines (IL-6 and IFN-γ). In addition, metabolomics technology was used to analyze differential metabolite expression after supplementation with HSSD. Results: Following a third CVS vaccination, significantly increased serum anti-RBD IgG titer, reduced serum IL-6 levels, increased serum IgG, IgM, and C3 and C4 levels, and improved cellular immunity, evidenced by reduce balance deviations in the distribution of lymphocyte subsets, was observed in the HSSD group compared with the placebo group. No serious adverse events were recorded in either group. Serum metabolomics results suggested that the mechanisms by which HSSD boosted the immunogenicity of the CVS vaccine are related to differential regulation of purine metabolism, vitamin B6 metabolism, folate biosynthesis, arginine and proline metabolism, and steroid hormone biosynthesis. Conclusion: Oral HSSD boosts the immunogenicity of the CVS vaccine in young and adult individuals. This trial provides clinical reference for evaluation of TCM immunomodulators to improve the immune response to COVID-19 vaccines.


Assuntos
Vacinas contra COVID-19 , COVID-19 , Medicamentos de Ervas Chinesas , Vacinas de Produtos Inativados , Adulto , Humanos , Animais , Camundongos , Interleucina-6 , Pandemias , SARS-CoV-2 , Imunoglobulina G , Imunoglobulina M
14.
ACS Appl Mater Interfaces ; 16(15): 18400-18410, 2024 Apr 17.
Artigo em Inglês | MEDLINE | ID: mdl-38576193

RESUMO

Drug-resistant bacterial infection and biofilm formation are the key inhibitors of wound healing, and new strategies are urgently needed to address these issues. In this study, we designed a pH-responsive co-assembled peptide hydrogel to inhibit Methicillin-resistant Staphylococcus aureus (MRSA) infection and promote wound healing. We synthesized a cationic short peptide (Nap-FFKKK) and a co-assembled hydrogel with curcumin at pH ∼ 7.8. The loaded curcumin was continuously released in a weak acid environment (pH ∼ 5.5). The lysine-rich cationic peptide inhibited biofilm formation in MRSA via electrostatic interaction with the negatively charged bacterial cell surface and, thus, provided a reinforcing antibacterial effect with curcumin. In vitro antibacterial experiments showed that the co-assembled system considerably reduced the minimum inhibitory concentration of curcumin against MRSA by 10-fold and promoted wound healing in a mouse model of MRSA-infected wounds. This study provides a simple and promising strategy to treat drug-resistant bacterial infections in wounds.


Assuntos
Infecções Bacterianas , Curcumina , Staphylococcus aureus Resistente à Meticilina , Infecção dos Ferimentos , Animais , Camundongos , Hidrogéis , Antibacterianos , Peptídeos , Cicatrização , Concentração de Íons de Hidrogênio
15.
Sci China Life Sci ; 2024 Mar 29.
Artigo em Inglês | MEDLINE | ID: mdl-38568343

RESUMO

Detecting genes that affect specific traits (such as human diseases and crop yields) is important for treating complex diseases and improving crop quality. A genome-wide association study (GWAS) provides new insights and directions for understanding complex traits by identifying important single nucleotide polymorphisms. Many GWAS summary statistics data related to various complex traits have been gathered recently. Studies have shown that GWAS risk loci and expression quantitative trait loci (eQTLs) often have a lot of overlaps, which makes gene expression gradually become an important intermediary to reveal the regulatory role of GWAS. In this review, we review three types of gene-trait association detection methods of integrating GWAS summary statistics and eQTLs data, namely colocalization methods, transcriptome-wide association study-oriented approaches, and Mendelian randomization-related methods. At the theoretical level, we discussed the differences, relationships, advantages, and disadvantages of various algorithms in the three kinds of gene-trait association detection methods. To further discuss the performance of various methods, we summarize the significant gene sets that influence high-density lipoprotein, low-density lipoprotein, total cholesterol, and triglyceride reported in 16 studies. We discuss the performance of various algorithms using the datasets of the four lipid traits. The advantages and limitations of various algorithms are analyzed based on experimental results, and we suggest directions for follow-up studies on detecting gene-trait associations.

16.
J Fluoresc ; 2024 Apr 03.
Artigo em Inglês | MEDLINE | ID: mdl-38568408

RESUMO

Tuning fork, consisting of two fork arms and a fork handle, has a stable and rigid structure. Inspired by this structure, a tuning fork-shaped DNA (TF-DNA) fluorescence aptasensor was constructed to detect ochratoxin A (OTA) and aflatoxin B1 (AFB1). A TF-DNA double-stranded structure capable of attaching both OTA aptamer labeled with the FAM fluorescent group (FAM-Apt) and AFB1 aptamer labeled with the ROX fluorescent group (ROX-Apt) was designed and linked to magnetic beads. This TF-DNA double-stranded structure can provide a stable platform for dual-target detection. In the presence of OTA and AFB1, FAM-Apt and ROX-Apt preferentially bound to them and detached from the TF-DNA double-stranded structure. Dual-signal fluorescent probes were collected from the supernatant by magnetic separation, and achieved fluorescence enhancement at 520 nm and 607 nm, respectively. The linear ranges are 0.05 ng/mL to 100 ng/mL for OTA and 0.1 ng/mL to 100 ng/mL for AFB1, and the detection limits are 0.015 ng/mL and 0.045 ng/mL, respectively. The developed sensor has the advantages of simple and fast preparation, good specificity and reproducibility, which is promising for the simultaneous determination of multiple hazardous substances in food.

17.
Wei Sheng Yan Jiu ; 53(2): 229-236, 2024 Mar.
Artigo em Chinês | MEDLINE | ID: mdl-38604958

RESUMO

OBJECTIVE: To investigate the association of polymorphisms in SEC16B rs633715, DNAJC27 rs713586, FTO rs11642015 and MC4R rs6567160 with overweight and obesity in Han Chinese preschool children. METHODS: A total of 749 Han Chinese preschool children from Henan and Guizhou Province of Long-term Health Effects Assessment Project of Infants and Toddlers Nutritional Pack were selected for the study and divided into an overweight and obese group and a normal control group in 2022. rs633715, rs713586, rs11642015 and rs6567160 were genotyped using Kompetitive allele-specific PCR(KASP) technology. The distribution of genotypic polymorphisms was compared using the χ~2 test. The association between the four loci and overweight and obesity in preschool children was analyzed using a multifactorial logistic regression model. RESULTS: The statistical analysis revealed a significant disparity(P<0.05) in the distribution of genotypic polymorphisms of rs633715 and rs6567160 among preschoolers in Henan and Guizhou Province. CC heterozygous mutant and recessive models at rs633715 locus were associated with susceptibility to overweight and obesity in preschool children [OR and 95% CI 2.915(1.163-7.305), and 2.997(1.226-7.323), respectively, both P<0.05]. TC heterozygous mutant and dominant models at rs713586 locus were also associated susceptibility to overweight and obesity in preschool children(OR and 95% CI were 2.362(1.054-5.289)and 2.362(1.054-5.289), respectively, both P<0.05). rs11642015 and rs6567160 loci were not associated with susceptibility to overweight and obesity in preschool children(P>0.05). The result of the analysis of the cumulative effect of rs633715 and rs713586 showed that the number of genotypes carrying the risk genotype was positively associated with the risk of overweight and obesity in preschool children(P_(trend)<0.01). CONCLUSION: Among Han Chinese preschool children, SEC16B rs633715 and DNAJC27 rs713586 were associated with susceptibility to overweight and obesity in preschool children. Moreover, rs633715 and rs713586 had a cumulative effect on susceptibility to overweight and obesity in preschool children, the number of risk genotypes carried was positively associated with childhood overweight and obesity risk.


Assuntos
Dioxigenase FTO Dependente de alfa-Cetoglutarato , Sobrepeso , Obesidade Infantil , Receptor Tipo 4 de Melanocortina , Pré-Escolar , Humanos , Alelos , Dioxigenase FTO Dependente de alfa-Cetoglutarato/genética , Predisposição Genética para Doença , Genótipo , Sobrepeso/genética , Obesidade Infantil/genética , Polimorfismo de Nucleotídeo Único , Receptor Tipo 4 de Melanocortina/genética
18.
Br J Nutr ; : 1-10, 2024 Apr 12.
Artigo em Inglês | MEDLINE | ID: mdl-38606596

RESUMO

Machine learning methods have been used in identifying omics markers for a variety of phenotypes. We aimed to examine whether a supervised machine learning algorithm can improve identification of alcohol-associated transcriptomic markers. In this study, we analysed array-based, whole-blood derived expression data for 17 873 gene transcripts in 5508 Framingham Heart Study participants. By using the Boruta algorithm, a supervised random forest (RF)-based feature selection method, we selected twenty-five alcohol-associated transcripts. In a testing set (30 % of entire study participants), AUC (area under the receiver operating characteristics curve) of these twenty-five transcripts were 0·73, 0·69 and 0·66 for non-drinkers v. moderate drinkers, non-drinkers v. heavy drinkers and moderate drinkers v. heavy drinkers, respectively. The AUC of the selected transcripts by the Boruta method were comparable to those identified using conventional linear regression models, for example, AUC of 1958 transcripts identified by conventional linear regression models (false discovery rate < 0·2) were 0·74, 0·66 and 0·65, respectively. With Bonferroni correction for the twenty-five Boruta method-selected transcripts and three CVD risk factors (i.e. at P < 6·7e-4), we observed thirteen transcripts were associated with obesity, three transcripts with type 2 diabetes and one transcript with hypertension. For example, we observed that alcohol consumption was inversely associated with the expression of DOCK4, IL4R, and SORT1, and DOCK4 and SORT1 were positively associated with obesity, and IL4R was inversely associated with hypertension. In conclusion, using a supervised machine learning method, the RF-based Boruta algorithm, we identified novel alcohol-associated gene transcripts.

19.
World J Gastroenterol ; 30(12): 1655-1662, 2024 Mar 28.
Artigo em Inglês | MEDLINE | ID: mdl-38617735

RESUMO

The gut microbiota is recognized as an endocrine organ with the capacity to influence distant organs and associated biological pathways. Recent advancements underscore the critical role of gut microbial homeostasis in female health; with dysbiosis potentially leading to diseases among women such as polycystic ovarian syndrome, endometriosis, breast cancer, cervical cancer, and ovarian cancer etc. Despite this, there has been limited discussion on the underlying mechanisms. This editorial explores the three potential mechanisms through which gut microbiota dysbiosis may impact the development of diseases among women, namely, the immune system, the gut microbiota-estrogen axis, and the metabolite pathway. We focused on approaches for treating diseases in women by addressing gut microbiota imbalances through probiotics, prebiotics supplementation, and fecal microbiota transplantation (FMT). Future studies should focus on determining the molecular mechanisms underlying associations between dysbiosis of gut microbiota and female diseases to realize precision medicine, with FMT emerging as a promising intervention.


Assuntos
Neoplasias da Mama , Endometriose , Microbioma Gastrointestinal , Feminino , Humanos , Disbiose , Estrogênios
20.
Entropy (Basel) ; 26(3)2024 Feb 28.
Artigo em Inglês | MEDLINE | ID: mdl-38539726

RESUMO

The echo state network (ESN) is a recurrent neural network that has yielded state-of-the-art results in many areas owing to its rapid learning ability and the fact that the weights of input neurons and hidden neurons are fixed throughout the learning process. However, the setting procedure for initializing the ESN's recurrent structure may lead to difficulties in designing a sound reservoir that matches a specific task. This paper proposes an improved pre-training method to adjust the model's parameters and topology to obtain an adaptive reservoir for a given application. Two strategies, namely global random selection and ensemble training, are introduced to pre-train the randomly initialized ESN model. Specifically, particle swarm optimization is applied to optimize chosen fixed and global weight values within the network, and the reliability and stability of the pre-trained model are enhanced by employing the ensemble training strategy. In addition, we test the feasibility of the model for time series prediction on six benchmarks and two real-life datasets. The experimental results show a clear enhancement in the ESN learning results. Furthermore, the proposed global random selection and ensemble training strategies are also applied to pre-train the extreme learning machine (ELM), which has a similar training process to the ESN model. Numerical experiments are subsequently carried out on the above-mentioned eight datasets. The experimental findings consistently show that the performance of the proposed pre-trained ELM model is also improved significantly. The suggested two strategies can thus enhance the ESN and ELM models' prediction accuracy and adaptability.

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