Open Domain Knowledge Extraction for Knowledge Graphs

The quality of a knowledge graph directly impacts the quality of downstream applications (e.g. the number of answerable questions using the graph). One ongoing challenge when building a knowledge graph is to ensure completeness and freshness of the graph's entities and facts. In this paper, we introduce ODKE, a scalable and extensible framework that sources high-quality entities and facts from open web at scale. ODKE utilizes a wide range of extraction models and supports both streaming and batch processing at different latency. We reflect on the challenges and design decisions made and share lessons learned when building and deploying ODKE to grow an industry-scale open domain knowledge graph.Comment: 7 pages, 7 figures, 5 tables, preprint technical report, no code or data is release

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Multiple primary lung cancer versus intrapulmonary metastatic cancer: A case of multiple pulmonary nodules

A preoperative chest computed tomography examination of the right breast in a 52‐year‐old woman with breast cancer revealed multiple nodules in both lungs. The nodule in the apical segment of the upper lobe of the right lung was larger, at a diameter of approximately 2.1 cm. The patient underwent resection of the right breast, followed by thoracoscopic wedge resection of four pulmonary nodules. Hematoxylin and eosin staining and immunohistochemistry showed that the nodules in the apical and anterior segments of the upper lobe and the paravertebral nodule in the lower lobe of the right lung were primary adenocarcinoma, and the subpleural nodule in the lower lobe of the right lung was infiltrated with inflammatory cells. Exon sequencing was conducted in the resected tissue samples and blood specimens. According to the characteristics of the somatic mutations, the nodule in the apical segment of the upper lobe of the right lung was primary lung adenocarcinoma, the nodule in the anterior segment of the upper lobe and the paravertebral nodule in the lower lobe of the right lung were intrapulmonary metastatic cancer, and the subpleural nodule in the lower lobe of the right lung indicated early stage tumor progression. This case provides new evidence that conducting gene detection in multiple tissue samples from patients who have undergone resection may assist to determine the relationship among multiple nodules in the lung to exclude lung metastasis of breast cancer