Comprehensive interrogation of gene lists from genome-scale cancer screens with oncoEnrichR

Genome-scale screening experiments in cancer produce long lists of candidate genes that require extensive interpretation for biological insight and prioritization for follow-up studies. Interrogation of gene lists frequently represents a significant and time-consuming undertaking, in which experimental biologists typically combine results from a variety of bioinformatics resources in an attempt to portray and understand cancer relevance. As a means to simplify and strengthen the support for this endeavor, we have developed oncoEnrichR, a flexible bioinformatics tool that allows cancer researchers to comprehensively interrogate a given gene list along multiple facets of cancer relevance. oncoEnrichR differs from general gene set analysis frameworks through the integration of an extensive set of prior knowledge specifically relevant for cancer, including ranked gene-tumor type associations, literature-supported proto-oncogene and tumor suppressor gene annotations, target druggability data, regulatory interactions, synthetic lethality predictions, as well as prognostic associations, gene aberrations and co-expression patterns across tumor types. The software produces a structured and user-friendly analysis report as its main output, where versions of all underlying data resources are explicitly logged, the latter being a critical component for reproducible science. We demonstrate the usefulness of oncoEnrichR through interrogation of two candidate lists from proteomic and CRISPR screens. oncoEnrichR is freely available as a web-based service hosted by the Galaxy platform ( https://oncotools.elixir.no ), and can also be accessed as a stand-alone R package ( https://github.com/sigven/oncoEnrichR ).     

信息化技术应用于静脉血栓栓塞症护理的研究进展

综述信息化技术在静脉血栓栓塞症护理领域中风险预测、警报接收与上报、抗凝防治管理、医护人员相关继续医学教育、患者疾病预后管理的应用现状，总结其应用阻碍因素，旨在为我国静脉血栓栓塞症护理信息化建设提供参考。     

基于正交试验的肾造瘘管固定方案研究

目的 探讨基于正交试验的肾造瘘管不同固定方案的比较效果。方法 将14Fr硅胶肾造瘘管固定在聚乙烯展板和拉力显示器上，以固定材料、固定方法、面积为3个影响因素，每个因素3个水平，每组进行3次试验再求平均值作为最后拉力值F，共进行9个固定方案共27次试验。利用L9（33）正交试验矩阵研究不同材料（医用橡皮膏、医用透气胶带、医用无纺布胶带）、固定方法（交叉固定法、“工”字固定法和改良“工”字固定法）及面积(16 cm2、24 cm2、32 cm2）对肾造瘘管固定强度的影响。结果 正交试验所选的3种影响因素中，对拉力值影响显著性排序为：材料＞方法＞面积；3种固定材料中，医用橡皮膏固定强度最大。结论 肾造瘘管固定方案中，最佳固定组合为以医用橡皮膏结合改良“工”字法固定，可为临床管道固定方案的选择提供参考。     

童年期不良经历对个体健康影响的研究进展

童年期不良经历(ACEs)作为一项全球性的严峻公共卫生挑战,其对全生命周期的健康影响不容小觑。因此本文从心理健康、生理健康、性传播疾病及危险性行为、健康危险行为4个方面对ACEs的健康影响进行综述,为ACEs及其可能健康结局提供参考。     

基于LDA模型的中医药人工智能领域主题演化分析＊

目的 梳理总结中医药人工智能领域近40年的研究情况，分析该领域研究主题演化过程，发现热点主题和研究前沿。方法 本研究检索了CNKI和WOS中中医药人工智能领域的文献，根据生命周期理论划分不同时间片，将文献摘要作为研究对象，采用LDA主题模型挖掘文本主题，分析主题的演化过程，识别热点主题。结果 纳入中英文文献2750篇，根据生命周期理论划分中医药人工智能领域发展阶段，分别建立全局和各阶段的LDA模型，挖掘出全局热点主题有中医专家系统、中医辅助诊断系统、中医药数据挖掘等，发现主题演化路径并进行可视化展示。结论 中医药与人工智能主要的结合点在中医智能系统、中医药知识组织和中医智能诊疗机器人这3方面，这3个方向的研究均离不开神经网络技术的支持，同时也结合了关联规则发现、复杂网络研究等方法。     

CD19 + CD21lo/neg cells are increased in systemic sclerosis-associated interstitial lung disease

Interstitial lung disease (ILD) represents a significant cause of morbidity and mortality in systemic sclerosis (SSc). The purpose of this study was to examine recirculating lymphocytes from SSc patients for potential biomarkers of interstitial lung disease (ILD). Peripheral blood mononuclear cells (PBMCs) were isolated from patients with SSc and healthy controls enrolled in the Vanderbilt University Myositis and Scleroderma Treatment Initiative Center cohort between 9/2017–6/2019. Clinical phenotyping was performed by chart abstraction. Immunophenotyping was performed using both mass cytometry and fluorescence cytometry combined with t-distributed stochastic neighbor embedding analysis and traditional biaxial gating. This study included 34 patients with SSc-ILD, 14 patients without SSc-ILD, and 25 healthy controls. CD21^lo/neg cells are significantly increased in SSc-ILD but not in SSc without ILD (15.4 ± 13.3% vs. 5.8 ± 0.9%, p = 0.002) or healthy controls (5.0 ± 0.5%, p < 0.0001). While CD21^lo/neg B cells can be identified from a single biaxial gate, tSNE analysis reveals that the biaxial gate is comprised of multiple distinct subsets, all of which are increased in SSc-ILD. CD21^lo/neg cells in both healthy controls and SSc-ILD are predominantly tBET positive and do not have intracellular CD21. Immunohistochemistry staining demonstrated that CD21^lo/neg B cells diffusely infiltrate the lung parenchyma of an SSc-ILD patient. Additional work is needed to validate this biomarker in larger cohorts and longitudinal studies and to understand the role of these cells in SSc-ILD.

     

Validity of the Central Sensitization Inventory (CSI) through Rasch analysis in patients with knee osteoarthritis

Clinical Rheumatology - Central sensitization (CS) is a known contributor to chronic pain in people with knee osteoarthritis (KOA) and is commonly measured by psychophysical testing or...