Browsing by Subject "hierarchical clustering"

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  • Unbiased Biomarkers Prediction Re; Jevnikar, Zala; Östling, Jörgen; Vaarala, Outi (2019)
    Background: Although several studies link high levels of IL-6 and soluble IL-6 receptor (sIL-6R) to asthma severity and decreased lung function, the role of IL-6 trans-signaling (IL-6TS) in asthmatic patients is unclear. Objective: We sought to explore the association between epithelial IL-6TS pathway activation and molecular and clinical phenotypes in asthmatic patients. Methods: An IL-6TS gene signature obtained from air-liquid interface cultures of human bronchial epithelial cells stimulated with IL-6 and sIL-6R was used to stratify lung epithelial transcriptomic data (Unbiased Biomarkers in Prediction of Respiratory Disease Outcomes [U-BIOPRED] cohorts) by means of hierarchical clustering. IL-6TS-specific protein markers were used to stratify sputum biomarker data (Wessex cohort). Molecular phenotyping was based on transcriptional profiling of epithelial brushings, pathway analysis, and immunohistochemical analysis of bronchial biopsy specimens. Results: Activation of IL-6TS in air-liquid interface cultures reduced epithelial integrity and induced a specific gene signature enriched in genes associated with airway remodeling. The IL-6TS signature identified a subset of patients with IL-6TS-high asthma with increased epithelial expression of IL-6TS-inducible genes in the absence of systemic inflammation. The IL-6TS-high subset had an overrepresentation of frequent exacerbators, blood eosinophilia, and submucosal infiltration of T cells and macrophages. In bronchial brushings Toll-like receptor pathway genes were upregulated, whereas expression of cell junction genes was reduced. Sputum sIL-6R and IL-6 levels correlated with sputum markers of remodeling and innate immune activation, in particular YKL-40, matrix metalloproteinase 3, macrophage inflammatory protein 1 beta, IL-8, and IL-1 beta. Conclusions: Local lung epithelial IL-6TS activation in the absence of type 2 airway inflammation defines a novel subset of asthmatic patients and might drive airway inflammation and epithelial dysfunction in these patients.
  • Xu, Xin; Lu, Jiaheng; Wang, Wei (2018)
    It is well-known that the values of symbolic variables may take various forms such as an interval, a set of stochastic measurements of some underlying patterns or qualitative multi-values and so on. However, the majority of existing work in symbolic data analysis still focuses on interval values. Although some pioneering work in stochastic pattern based symbolic data and mixture of symbolic variables has been explored, it still lacks flexibility and computation efficiency to make full use of the distinctive individual symbolic variables. Therefore, we bring forward a novel hierarchical clustering method with weighted general Jaccard distance and effective global pruning strategy for complex symbolic data and apply it to emitter identification. Extensive experiments indicate that our method has outperformed its peers in both computational efficiency and emitter identification accuracy.
  • Roukka, Sulo; Puputti, Sari; Aisala, Heikki; Hoppu, Ulla; Seppä, Laila; Sandell, Mari A. (2021)
    Chemesthesis is a part of the flavor experience of foods. Chemesthetic perception is studied to understand its effect on food-related behavior and health. Thus, the objective of this research was to study individual differences in chemesthetic perception. Our study involved sensory tests of three chemesthetic modalities (astringency, pungency, and cooling). Participants (N = 196) evaluated the intensity of samples in different concentrations using a line scale under sensory laboratory conditions. Aluminum ammonium sulfate, capsaicin, and menthol were used as the prototypic chemesthetic compounds. The participants were divided into sensitivity groups in different chemesthetic modalities by hierarchical clustering based on their intensity ratings. In addition, an oral chemesthesis sensitivity score was determined to represent the generalized chemesthesis sensitivity. The results showed that people can perceive chemesthesis on different intensity levels. There were significantly positive correlations between (1) sensitivity scores for oral chemesthesis and taste as well as (2) each chemesthesis and taste modalities. Moreover, based on the multinomial logistic regression model, significant interactions between oral chemesthesis and taste sensitivity were discovered. Our findings showed that people can be classified into different oral chemesthesis sensitivity groups. The methods and results of this study can be utilized to investigate associations with food-related behavior and health.