Discrimination of inflammatory bowel disease using Raman spectroscopy and linear discriminant analysis methods

2016 ◽  
Author(s):  
Hao Ding ◽  
Ming Cao ◽  
Andrew W. DuPont ◽  
Larry D. Scott ◽  
Sushovan Guha ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
Raman Spectroscopy ◽  
Discriminant Analysis ◽  
Linear Discriminant Analysis ◽  
Bowel Disease ◽  
Linear Discriminant ◽  
Analysis Methods ◽  
Inflammatory Bowel

Parameterized Discriminant Analysis Methods

2011 ◽  
pp. 78-105
Author(s):  
David Zhang ◽  
Fengxi Song ◽  
Yong Xu ◽  
Zhizhen Liang
Keyword(s):  
Discriminant Analysis ◽  
Linear Discriminant Analysis ◽  
Scatter Matrix ◽  
Linear Discriminant ◽  
Analysis Methods

In this chapter, we mainly present three kinds of weighted LDA methods. In Sections 5.1, 5.2 and 5.3, we respectively present parameterized direct linear discriminant analysis, weighted nullspace linear discriminant analysis and weighted LDA in the range of within-class scatter matrix. We offer a brief summery of the chapter in Section 5.4.

scholarly journals Clinical characterization of in vivo inflammatory bowel disease with Raman spectroscopy

2017 ◽  
Vol 8 (2) ◽  
pp. 524 ◽  
Author(s):  
Isaac J. Pence ◽  
Dawn B. Beaulieu ◽  
Sara N. Horst ◽  
Xiaohong Bi ◽  
Alan J. Herline ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
Raman Spectroscopy ◽  
Bowel Disease ◽  
Inflammatory Bowel

scholarly journals Single Cell Raman Spectroscopy to Identify Different Stages of Proliferating Human Hepatocytes for Cell Therapy

2021 ◽  
Author(s):  
Chen Ma ◽  
Ludi Zhang ◽  
Ting He ◽  
Huiying Cao ◽  
Chenhui Ma ◽  
...  
Keyword(s):  
Machine Learning ◽  
Raman Spectroscopy ◽  
Discriminant Analysis ◽  
Cell Therapy ◽  
Linear Discriminant Analysis ◽  
Learning Model ◽  
Human Hepatocytes ◽  
Linear Discriminant ◽  
Analytical Technique ◽  
Machine Learning Model

Abstract Background: Cell therapy provides hope for treatment of advanced liver failure. Proliferating human hepatocytes (ProliHHs) were derived from primary human hepatocytes (PHH) and as potential alternative for cell therapy in liver diseases. Due to the continuous decline of mature hepatic genes and increase of progenitor like genes during ProliHHs expanding, it is challenge to monitor the critical changes of the whole process. Raman microspectroscopy is a noninvasive, label free analytical technique with high sensitivity capacity. In this study, we evaluated the potential and feasibility to identify ProliHHs from PHH with Raman spectroscopy.Methods: Raman spectra were collected at least 600 single spectrum for PHH and ProliHHs at different stages (Passage 1 to Passage 4). Linear discriminant analysis and a two-layer machine learning model were used to analyze the Raman spectroscopy data. Significant differences in Raman bands were validated by the associated conventional kits.Results: Linear discriminant analysis successfully classified ProliHHs at different stages and PHH. A two-layer machine learning model was established and the overall accuracy was at 84.6%. Significant differences in Raman bands have been found within different ProliHHs cell groups, especially changes at 1003 cm-1, 1206 cm-1 and 1300 cm-1. These changes were linked with reactive oxygen species, hydroxyproline and triglyceride levels in ProliHHs, and the hypothesis were consistent with the corresponding assay results. Conclusions: In brief, Raman spectroscopy was successfully employed to identify different stages of ProliHHs during dedifferentiation process. The approach can simultaneously trace multiple changes of cellular components from somatic cells to progenitor cells.

scholarly journals Population Structure Discovery in Meta-Analyzed Microbial Communities and Inflammatory Bowel Disease

2020 ◽  
Author(s):  
Siyuan Ma ◽  
Dmitry Shungin ◽  
Himel Mallick ◽  
Melanie Schirmer ◽  
Long H. Nguyen ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
Population Structure ◽  
Microbial Community ◽  
Bowel Disease ◽  
Gut Microbiome ◽  
Large Scale ◽  
Meta Analysis ◽  
Disease Etiology ◽  
Analysis Methods ◽  
Inflammatory Bowel

AbstractMicrobial community studies in general, and of the human microbiome in inflammatory bowel disease (IBD) in particular, have now achieved a scale at which it is practical to associate features of the microbiome with environmental exposures and health outcomes across multiple large-scale populations. This permits the development of rigorous meta-analysis methods, of particular importance in IBD as a means by which the heterogeneity of disease etiology and treatment response might be explained. We have thus developed MMUPHin (Meta-analysis Methods with a Uniform Pipeline for Heterogeneity in microbiome studies) for joint normalization, meta-analysis, and population structure discovery using microbial community taxonomic and functional profiles. Applying this method to ten IBD cohorts (5,151 total samples), we identified a single consistent axis of microbial associations among studies, including newly associated taxa such as Acinetobacter and Turicibacter detected due to the sensitivity of meta-analysis. Linear random effects models further revealed associations with medications, disease location, and interaction effects consistent within and between studies. Finally, multiple unsupervised clustering metrics and dissimilarity measures agreed on a lack of discrete microbiome “types” in the IBD gut microbiome. These results thus provide a benchmark for consistent characterization of the IBD gut microbiome and a general framework applicable to meta-analysis of any microbial community types.

scholarly journals OP10 IgA coating of intestinal microbiota is associated with inflammatory bowel disease in twin pairs discordant for inflammatory bowel disease

2020 ◽  
Vol 14 (Supplement_1) ◽  
pp. S010-S011
Author(s):  
E Brand ◽  
Y Laenen ◽  
F van Wijk ◽  
M de Zoete ◽  
B Oldenburg
Keyword(s):  
Ulcerative Colitis ◽  
Inflammatory Bowel Disease ◽  
Immune System ◽  
Intestinal Microbiota ◽  
Bowel Disease ◽  
Microbial Composition ◽  
Linear Discriminant ◽  
Starting Point ◽  
Inflammatory Bowel ◽  
The Impact

Abstract Background The pathogenesis of inflammatory bowel disease (IBD) is thought to result from an interplay between microbiota, the immune system and the environment in genetically susceptible hosts. Immunoglobulin A (IgA) produced by the immune system can be specifically directed against bacteria. The IgA-coating pattern of intestinal bacteria thus reflects interactions between the immune system and specific bacteria. Studying IBD in twins, concordant and discordant for IBD, reduces the impact of genetic predisposition and childhood exposures and therefore offers the unique opportunity to focus on other factors such as intestinal microbiota composition and immune-interactions in IBD. Methods Faecal samples from twin pairs discordant for Crohn’s disease (CD) or ulcerative colitis (UC) were collected. Employing fluorescence-activated cell sorting, IgA+ and IgA− bacteria from the intestinal microbiota were sorted. Subsequently, (1) the total, (2) IgA+ and (3) IgA− microbial composition was determined by 16S rRNA sequencing (IgA-SEQ). We estimated the relative IgA coating per bacterial species by dividing the abundance of that species in the IgA+ fraction over the abundance in the IgA- fraction, representing the IgA coating index. Linear discriminant analyses were performed with LefSE. Results We included 31 twin pairs (62 individuals) discordant for IBD (CD: 15, UC: 16). 15/32 twin pairs were monozygotic, 43/62 of participants were female, the median age was 47 years (interquartile range: 34–58.5). Of 31 participants with IBD, 7 had signs of active inflammation based on endoscopy, Harvey–Bradshaw index or short clinical colitis activity index. Differences (log-linear discriminant analysis score >3) in the microbial composition of IgA-coated bacteria were observed between CD patients and their twin-siblings not affected by IBD: Dorea formicigenerans (increased in IgA coating), Parabacteroides sp., Christensenellaceae sp., Clostridium sp. and Mollicutes RF39 sp. (decreased in IgA coating). In ulcerative colitis patients, an increase in IgA-coating was observed for Ruminococcus gnavus and Dorea formicigenerans, while Turicibacter sp., Barnesiellaceae sp. and an unclassified Clostridiales sp. were decreased in IgA-coating compared with their twin-siblings not affected by IBD. Conclusion In twins affected by IBD, the pattern of IgA-coated bacteria differs between IBD and non-IBD affected individuals. These data on immune-bacteria interactions could serve as a starting point for the elucidation of the immune-responses triggered by specific bacteria in IBD.

scholarly journals 47 RAMAN SPECTROSCOPY CAN DIFFERENTIATE MUCOSAL HEALING FROM NON-HEALING IN INFLAMMATORY BOWEL DISEASE

2020 ◽  
Vol 91 (6) ◽  
pp. AB1-AB2
Author(s):  
Samuel C. Smith ◽  
Carl Banbury ◽  
Davide Zardo ◽  
Rosanna Cannatelli ◽  
Olga Maria Nardone ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
Raman Spectroscopy ◽  
Bowel Disease ◽  
Mucosal Healing ◽  
Inflammatory Bowel
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