Browsing by Author "Hu, Jie"

Now showing 1 - 2 of 2
  • Thumbnail Image
    Item
    Ensuring sample quality for blood biomarker studies in clinical trials: a multicenter international study for plasma and serum sample preparation
    (2017-12) Kong, Feng-Ming (Spring); Zhao, Lujun; Wang, Luhua; Chen, Yuhchyau; Hu, Jie; Fu, Xiaolong; Bai, Chunxue; Wang, Li; Lawrence, Theodore S.; Anscher, Mitchell S.; Dicker, Adam; Okunieff, Paul; Radiation Oncology, School of Medicine
    Background Sample quality is critical for biomarker detection in oncology, and platelet degradation and contamination in plasma have a remarkable impact on the ability to accurately quantify many blood-based biomarkers. Platelet factor 4 (PF4) can be used as an indicator to monitor sample quality. This multicenter study aimed to determine the impact of critical components of the blood sample handling process on platelet degradation/contamination and to establish an optimal method for collecting platelet-poor plasma samples. Methods At each of six participating centers, blood samples were drawn from 12–13 healthy volunteers. Serum and plasma samples were prepared from whole blood samples using nine different methods that have been commonly used in ongoing multicenter trials. PF4 levels in the prepared samples were measured by enzyme-linked immunosorbent assay (ELISA). Paired t-tests were used for statistical analysis. Results Blood samples were collected from 74 subjects enrolled in six centers. PF4 levels were significantly higher in serum samples than in plasma samples (P<0.001), in plasma samples from blood that sat at room temperature for 5 minutes (P=0.021), in plasma samples prepared at an insufficient centrifugal force (P<0.001), and in plasma samples prepared from blood that sat for longer than 4 hours on ice (P=0.001). For each method, the PF4 levels did not differ significantly among the centers or between Chinese and American subjects. The methods that resulted in normal levels of PF4 involved keeping blood samples on ice for 30 minutes to <4 hours and centrifugation at 2,500–3,000 ×g for 30 min. Conclusions This multicenter study evaluated multiple blood sample handling conditions for minimizing platelet degradation during plasma serum preparation and determined an optimal method for preparing platelet-poor plasma. The findings of this study can be applied in future blood biomarker studies.
  • Thumbnail Image
    Item
    Information Theory in Computational Biology: Where We Stand Today
    (MDPI, 2020-06) Chanda, Pritam; Costa, Eduardo; Hu, Jie; Sukumar, Shravan; Van Hemert, John; Walia, Rasna; Computer and Information Science, School of Science
    "A Mathematical Theory of Communication" was published in 1948 by Claude Shannon to address the problems in the field of data compression and communication over (noisy) communication channels. Since then, the concepts and ideas developed in Shannon's work have formed the basis of information theory, a cornerstone of statistical learning and inference, and has been playing a key role in disciplines such as physics and thermodynamics, probability and statistics, computational sciences and biological sciences. In this article we review the basic information theory based concepts and describe their key applications in multiple major areas of research in computational biology-gene expression and transcriptomics, alignment-free sequence comparison, sequencing and error correction, genome-wide disease-gene association mapping, metabolic networks and metabolomics, and protein sequence, structure and interaction analysis.