高血压性心脏病生物标志物的筛选：基于中国重庆市7家医疗机构的数据分析研究*

目的: 筛选高血压性心脏病（HHD）的影响因素,建立HHD的预测模型,为HHD的发生提供预警。方法: 选取中国重庆市某医科院校数据研究院平台2016年1月1日至2019年12月31日主要诊断为高血压性心脏病和高血压患者。通过单因素分析、多因素分析筛选HHD的影响因素,采用R语言分别构建Logistics模型、随机森林（RF）模型和极限梯度上升（XGBoost）模型。结果: 单因素分析筛选出60项差异指标,多因素分析筛选出18项差异指标（P<0.05）。Logistics模型、RF模型、XGBoost模型曲线下面积（AUC）分别为0.979、0.983和0.990。结论: 本文建立的3种HHD预测模型结果稳定,其中XGBoost模型对于HHD的发生具有良好的诊断效应。     

北部湾茅尾海无瓣海桑红树林地上生物量反演——基于XGBoost机器学习算法

无瓣海桑是广西从自治区外引进的外来红树林树种,采用定量化算法精确估算无瓣海桑地上生物量对红树林生态修复以及海洋蓝碳监测提供经验和方法。论文以广西茅尾海自然保护区无瓣海桑红树林为研究对象,以野外实测无瓣海桑红树林地上生物量数据和Sentinel-1/2卫星提取的后向散射数据、波段数据、植被指数数据和纹理指数数据为数据源,通过分析各遥感因子与实测红树林地上生物量之间的重要性关系,采用极端梯度提升(XGBoost)机器学习算法对比了不同的变量组合对模型精度的影响,最后基于优选的变量组合反演了无瓣海桑红树林的地上生物量。结果表明：(1)研究区无瓣海桑红树林实测树高范围为1.55—13.58m,平均值为8.37m,胸径范围为0.7—41cm,平均值为15.62cm;(2)通过XGBoost算法优选的21个特征变量组合模型拟合效果较好,其模型在测试阶段R²=0.7237,RMSE=21.70Mg/hm²。XGBoost算法反演研究区无瓣海桑地上生物量介于19.14—138.46Mg/hm²之间,平均值为51.92Mg/hm^...     

基于拉曼技术的单细胞生长检测方法

目的 单细胞生长检测可以更加科学地揭示微生物代谢变化的规律,为后期微生物工程应用提供指导。针对微生物生长应用于食品安全期和最佳食用期的精准检测问题,本文提出一种基于拉曼技术的单细胞生长检测方法。方法 首先,通过同步培养实验采集了枯草芽孢杆菌两个批次共900个单细胞拉曼光谱（SCRS）数据,其中600个用于训练和测试,另一批次300个用于模型验证。其次,基于主成分分析的特征关系矩阵,提出CP-SP特征评估方法以筛选SCRS特征用于模型检测。再基于XGBoost构建检测模型,并应用网格搜索和交叉验证对检测模型进行调优。最后,应用混淆矩阵、ROC曲线评估模型对细胞滞后期、对数期和稳定期的检测准确率、敏感性和特异性。结果 选用CP-SP筛选的第一、第二和第四主成分较特征贡献率前3个主成分的分类性能提高了3.1%,调优后的细胞生长检测模型测试准确率为96.0%,验证准确率为92.3%。结论 基于拉曼技术的单细胞生长检测方法能准确识别单细胞生长状态且具有较高的泛化能力,可为食品安全和保鲜制定精准调控机制提供科学指导。     

基于生物信息学的胃癌早期诊断预测模型研究

利用The Cancer Genome Atlas和Genotype-Tissue Expression公共数据检索收集胃癌(Gastric cancer,GC)基因表达数据集,筛选与早期胃癌密切相关的基因并构建胃癌早期诊断预测模型。运用Deseq2软件包筛选早期胃癌差异基因,并对差异基因进行GO和KEGG富集分析。通过STRING数据库建立其蛋白质相互作用网络并利用Cytoscape软件提取关键子网得到候选关键基因,进一步利用MedCalc软件确认胃癌早期诊断关键基因。根据筛选得到的10个关键基因构建基于支持向量机、随机森林、朴素贝叶斯、K-近邻、极限梯度提升和自适应提升等六种算法的胃癌早期诊断预测模型,依据ROC曲线和准确率等评价指标对各个分类器模型进行评估,通过独立测试集验证得到极致梯度提升诊断预测模型为最优模型。本研究成果为提高结胃癌早期诊断的研究提供了新的思路和方法。     

Machine learning algorithms to predict the 1 year unfavourable prognosis for advanced schistosomiasis

Short-term prognosis of advanced schistosomiasis has not been well studied. We aimed to construct prognostic models using machine learning algorithms and to identify the most important predictors by utilising routinely available data under the government medical assistance programme. An established database of advanced schistosomiasis in Hunan, China was utilised for analysis. A total of 9541 patients for the period from January 2008 to December 2018 were enrolled in this study. Candidate predictors were selected from demographics, clinical features, medical examinations and test results. We applied five machine learning algorithms to construct 1 year prognostic models: logistic regression (LR), decision tree (DT), random forest (RF), artificial neural network (ANN) and extreme gradient boosting (XGBoost). An area under the receiver operating characteristic curve (AUC) was used to evaluate the model performance. The important predictors of the optimal model for unfavourable prognosis within 1 year were identified and ranked. There were 1249 (13.1%) cases having unfavourable prognoses within 1 year of discharge. The mean age of all participants was 61.94 years, of whom 70.9% were male. In general, XGBoost showed the best predictive performance with the highest AUC (0.846; 95% confidence interval (CI): 0.821, 0.871), compared with LR (0.798; 95% CI: 0.770, 0.827), DT (0.766; 95% CI: 0.733, 0.800), RF (0.823; 95% CI: 0.796, 0.851), and ANN (0.806; 95% CI: 0.778, 0.835). Five most important predictors identified by XGBoost were ascitic fluid volume, haemoglobin (HB), total bilirubin (TB), albumin (ALB), and platelets (PT). We proposed XGBoost as the best algorithm for the evaluation of a 1 year prognosis of advanced schistosomiasis. It is considered to be a simple and useful tool for the short-term prediction of an unfavourable prognosis for advanced schistosomiasis in clinical settings.     

Machine learning approach to predict terrestrial gross primary productivity using topographical and remote sensing data

Gross Primary Productivity (GPP) is the amount of sequestered CO₂ during plant photosynthesis. GPP is an important indicator of ecosystem health in various ecologies and to assess climate change. The objective of the present work is to propose a machine learning based GPP estimation model using remote sensing (RS) data in combination with meteorological data (MET) and topographical data (TOPO) for prediction of GPP, which can be upscaled in temporal and spatial resolution. Random Forest Regression (RFR) is proposed for this using the Fluxnet2015 GPP dataset for the Australian region. This model has attained a very high accuracy with an R² value of 0.82, as estimated by 10-fold cross-validation. The model has been compared with state-of-the-art machine learning models and found to be performing better than others. Different feature sets like MET-features and TOPO-features were evaluated in combination with RS-features. The results exhibited that the RFR model performed better when MET and TOPO features are combined with RS-features. GPP prediction for the year 2014, in 8 days temporal and 500m  spatial resolution for the Australian region for different plant function types is demonstrated using the proposed model and produced very high value of R² (0.84), when compared to ground truth. Thus, the proposed approach of the RFR model for GPP estimation showed significant improvement in regional carbon cycle studies and can also be employed for simulating GPP for the future under different climate scenarios.     

R package for animal behavior classification from accelerometer data—rabc

Increasingly, animal behavior studies are enhanced through the use of accelerometry. To allow translation of raw accelerometer data to animal behaviors requires the development of classifiers. Here, we present the “rabc” (r for animal behavior classification) package to assist researchers with the interactive development of such animal behavior classifiers in a supervised classification approach. The package uses datasets consisting of accelerometer data with their corresponding animal behaviors (e.g., for triaxial accelerometer data along the x, y and z axes arranged as “x, y, z, x, y, z,…, behavior”). Using an example dataset collected on white stork (Ciconia ciconia), we illustrate the workflow of this package, including accelerometer data visualization, feature calculation, feature selection, feature visualization, extreme gradient boost model training, validation, and, finally, a demonstration of the behavior classification results.     

Multi-omics Biomarker Pipeline Reveals Elevated Levels of Protein-glutamine Gamma-glutamyltransferase 4 in Seminal Plasma of Prostate Cancer Patients

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Highlights

• •Seventy-six most promising proteins were qualified, and 19 proteins were verified by SRM in 219 seminal plasma samples of patients with prostate cancer and negative biopsies.
• •Prostate-specific, secreted and androgen-regulated protein-glutamine gamma-glutamyltransferase 4 (TGM4) was verified by SRM assay and an in-house immunoassay.
• •TGM4 detected prostate cancer on biopsy in seminal plasma (AUC=0.66), but not in blood serum.

     

MagicalRsq: Machine-learning-based genotype imputation quality calibration

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