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  • Frontiers Media SA  (5)
  • 1
    In: Frontiers in Genetics, Frontiers Media SA, Vol. 13 ( 2022-9-2)
    Abstract: Background: Linking genotypic changes to phenotypic traits based on machine learning methods has various challenges. In this study, we developed a workflow based on bioinformatics and machine learning methods using transcriptomic data for sepsis obtained at the first clinical presentation for predicting the risk of sepsis. By combining bioinformatics with machine learning methods, we have attempted to overcome current challenges in predicting disease risk using transcriptomic data. Methods: High-throughput sequencing transcriptomic data processing and gene annotation were performed using R software. Machine learning models were constructed, and model performance was evaluated by machine learning methods in Python. The models were visualized and interpreted using the Shapley Additive explanation (SHAP) method. Results: Based on the preset parameters and using recursive feature elimination implemented via machine learning, the top 10 optimal genes were screened for the establishment of the machine learning models. In a comparison of model performance, CatBoost was selected as the optimal model. We explored the significance of each gene in the model and the interaction between each gene through SHAP analysis. Conclusion: The combination of CatBoost and SHAP may serve as the best-performing machine learning model for predicting transcriptomic and sepsis risks. The workflow outlined may provide a new approach and direction in exploring the mechanisms associated with genes and sepsis risk.
    Type of Medium: Online Resource
    ISSN: 1664-8021
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2606823-0
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  • 2
    In: Frontiers in Genetics, Frontiers Media SA, Vol. 11 ( 2020-11-4)
    Type of Medium: Online Resource
    ISSN: 1664-8021
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2020
    detail.hit.zdb_id: 2606823-0
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  • 3
    Online Resource
    Online Resource
    Frontiers Media SA ; 2021
    In:  Frontiers in Endocrinology Vol. 12 ( 2021-11-16)
    In: Frontiers in Endocrinology, Frontiers Media SA, Vol. 12 ( 2021-11-16)
    Abstract: An increasing number of studies have related the mitochondrial DNA (mtDNA) content to embryo viability and transfer outcomes. However, previous studies have focused more on the relationship between mtDNA and embryo implantation, few studies have studied the effect of the mtDNA content on live birth. In the study, we investigated whether mtDNA content is a reliable screening biomarker for live birth after single blastocyst transfer. A total of 233 couples with 316 blastocyst stage embryos undergoing in vitro fertilization treatment and pre-implantation genetic testing analysis were included in the study. All embryos were chromosomally normal and had undergone single-embryo transfers. There was no significant difference observed in the blastocyst mtDNA content among the live birth, miscarriage and non-implanted groups (p=0.999), and the mtDNA content in blastocysts from the miscarriage and live birth groups was similar [median (interquartile range), 1.00*10 8 (7.59*10 7 - 1.39*10 8 ) vs 1.01*10 8 (7.37*10 7 - 1.32*10 8 )]. Similarly, no significant association was observed between mtDNA content and embryo implantation potential (p=0.965). After adjusting for multiple confounders in a logistic regression analysis with generalized estimating equations, no associations between mtDNA content and live birth were observed in all blastocysts, Day-5 and Day-6 blastocysts (p=0.567, p=0.673, p=0.165, respectively). The live birth rate was not significantly different between blastocysts with an elevated mtDNA content and blastocysts with a normal mtDNA content (26.7% vs 33.6% p=0.780). Additionally, there was no linear correlation between the mtDNA content and maternal age (p=0.570). In conclusion, the mtDNA content does not seem to be a potential biomarker for embryo transfer outcomes (i.e., implantation and live birth) based on the existing testing tools. Embryos with an elevated mtDNA content also have development potential for successful live birth.
    Type of Medium: Online Resource
    ISSN: 1664-2392
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2021
    detail.hit.zdb_id: 2592084-4
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  • 4
    In: Frontiers in Medicine, Frontiers Media SA, Vol. 9 ( 2022-2-7)
    Abstract: Microalbuminuria (MAU) occurs due to universal endothelial damage, which is strongly associated with kidney disease, stroke, myocardial infarction, and coronary artery disease. Screening patients at high risk for MAU may aid in the early identification of individuals with an increased risk of cardiovascular events and mortality. Hence, the present study aimed to establish a risk model for MAU by applying machine learning algorithms. Methods This cross-sectional study included 3,294 participants ranging in age from 16 to 93 years. R software was used to analyze missing values and to perform multiple imputation. The observed population was divided into a training set and a validation set according to a ratio of 7:3. The first risk model was constructed using the prepared data, following which variables with P & lt;0.1 were extracted to build the second risk model. The second-stage model was then analyzed using a chi-square test, in which a P ≥ 0.05 was considered to indicate no difference in the fit of the models. Variables with P & lt;0.05 in the second-stage model were considered important features related to the prevalence of MAU. A confusion matrix and calibration curve were used to evaluate the validity and reliability of the model. A series of risk prediction scores were established based on machine learning algorithms. Results Systolic blood pressure (SBP), diastolic blood pressure (DBP), fasting blood glucose (FBG), triglyceride (TG) levels, sex, age, and smoking were identified as predictors of MAU prevalence. Verification using a chi-square test, confusion matrix, and calibration curve indicated that the risk of MAU could be predicted based on the risk score. Conclusion Based on the ability of our machine learning algorithm to establish an effective risk score, we propose that comprehensive assessments of SBP, DBP, FBG, TG, gender, age, and smoking should be included in the screening process for MAU.
    Type of Medium: Online Resource
    ISSN: 2296-858X
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2775999-4
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  • 5
    Online Resource
    Online Resource
    Frontiers Media SA ; 2022
    In:  Frontiers in Physiology Vol. 13 ( 2022-8-5)
    In: Frontiers in Physiology, Frontiers Media SA, Vol. 13 ( 2022-8-5)
    Abstract: Recurrent pregnancy loss (RPL) is a major type of pathological pregnancy that still lacks reliable early diagnosis and effective treatment. The placenta is critical to fetal development and pregnancy success because it participates in critical processes such as early embryo implantation, vascular remodeling, and immunological tolerance. RPL is associated with abnormalities in the biological behavior of placental villous trophoblasts, resulting in aberrant placental function. MicroRNAs (miRNAs) are increasingly being recognized as essential regulators of placental development, as well as potential biomarkers. In this study, plasma miRNAs and placental messenger RNAs (mRNAs) from RPL patients and normal pregnant (NP) controls were sequenced and analyzed. Compared to those in NP controls, 108 circulating miRNAs and 1199 placental mRNAs were differentially expressed in RPL samples. A total of 140 overlapping genes (overlapping between plasma miRNA target genes and actual placental disorder genes) were identified, and functional enrichment analysis showed that these genes were mainly related to cell proliferation, angiogenesis, and cell migration. The regulatory network among miRNAs, overlapping genes, and downstream biological processes was analyzed by protein–protein interactions and Cytoscape. Moreover, enriched mRNAs, which were predictive targets of the differentially expressed plasma miRNAs miR-766-5p, miR-1285-3p, and miR-520a-3p, were accordingly altered in the placenta. These results suggest that circulating miRNAs may be involved in the pathogenesis of RPL and are potential noninvasive biomarkers for RPL.
    Type of Medium: Online Resource
    ISSN: 1664-042X
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2564217-0
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