Probability Distributions.- Linear Models for Regression.- Linear Models for Classification.- Neural Networks.- Kernel Methods.- Sparse Kernel Machines.- Graphical Models.- Mixture Models and EM.- Approximate Inference.- Sampling Methods.- Continuous Latent Variables.- Sequential Data.- Combining Models.

Pattern Recognition and Machine Learning

Hyperspectral imaging (HSI) is an emerging imaging modality for medical applications, especially in disease diagnosis and image-guided surgery. HSI acquires a three-dimensional dataset called hypercube, with two spatial dimensions and one spectral dimension. Spatially resolved spectral imaging obtained by HSI provides diagnostic information about the tissue physiology, morphology, and composition. This review paper presents an overview of the literature on medical hyperspectral imaging technology and its applications. The aim of the survey is threefold: an introduction for those new to the field, an overview for those working in the field, and a reference for those searching for literature on a specific application.

https://www.spiedigitallibrary.org/journals/journal-of-biomedical-optics/volume-19/issue-1/010901/Medical-hyperspectral-imaging-a-review/10.1117/1.JBO.19.1.010901.pdf

Medical hyperspectral imaging: a review

This article reviews some of the recent advances on FTIR spectroscopy in areas related to natural tissues and cell biology. It is the second review publication resulting from a detailed study on the applications of spectroscopic methods in biological studies and summarizes some of the most widely used peak frequencies and their assignments. The aim of these studies is to prepare a database of molecular fingerprints, which will help researchers in defining the chemical structure of the biological tissues introducing most of the important peaks present in the natural tissues. In spite of applying different methods, there seems to be a considerable similarity in defining the peaks of identical areas of the FTIR spectra. As a result, it is believed that preparing a unique collection of the frequencies encountered in FTIR spectroscopic studies can lead to significant improvements both in the quantity and quality of research and their outcomes. This article is the first review of its kind that provides...

Fourier Transform Infrared (FTIR) Spectroscopy of Biological Tissues

The post-genomics era has brought with it ever increasing demands to observe and characterise variation within biological systems. This variation has been studied at the genomic (gene function), proteomic (protein regulation) and the metabolomic (small molecular weight metabolite) levels. Whilst genomics and proteomics are generally studied using microarrays (genomics) and 2D-gels or mass spectrometry (proteomics), the technique of choice is less obvious in the area of metabolomics. Much work has been published employing mass spectrometry, NMR spectroscopy and vibrational spectroscopic techniques, amongst others, for the study of variations within the metabolome in many animal, plant and microbial systems. This review discusses the advantages and disadvantages of each technique, putting the current status of the field of metabolomics in context, and providing examples of applications for each technique employed.

Measuring the metabolome: current analytical technologies

Fourier Transform Infrared (FTIR) has been developed as a tool for the simultaneous and quantitative determination of organic components, including chemical bond, as well as organic content (e.g. protein, carbohydrate and lipid). However, until now, there is no further information for the detailed information in the FTIR peaks. The objective of this study was to demonstrate how to read and assess chemical bond and structure in the organic material. The analysis was then compared with the literatures. The step-by-step method on how to read the FTIR data was presented, including reviewing simple to the complex organic materials. This study is potential to be used as a standard information on how to read FTIR peaks in the biochemical and organic materials.

/pdf/how-to-read-and-interpret-ftir-spectroscope-of-organic-36wshpk8sv.pdf

How to Read and Interpret FTIR Spectroscope of Organic Material

Colon cancer is the third leading class of cancer causing increased mortality in developed countries. A polyp is one type of lesion observed in a majority of colon cancer patients. Here, we re- port a microscopic Fourier transform infrared (FTIR) study of normal, adenomatous polyp and malignant cells from biopsies of 24 patients. The goal of our study was to differentiate an adenomatous polyp from a malignant cell using FTIR microspectroscopy and artificial neural network (ANN) analysis. FTIR spectra and biological markers such as phosphate, RNA/DNA derived from spectra, were useful in identifying normal cells from abnormal ones that consisted of adenomatous polyp and malignant cells. However, the biological markers failed to differentiate between adenomatous polyp and malignant cases. By employing a combination of wavelet features and an ANN based clas- sifier, we were able to classify the different cells as normal, adenoma- tous polyp and cancerous in a given tissue sample. The percentage of success of classification was 89%, 81%, and 83% for normal, ad- enomatous polyp, and malignant cells, respectively. A comparison of the method proposed with the pathological method is also discussed.

Diagnostic potential of Fourier-transform infrared microspectroscopy and advanced computational methods in colon cancer patients.

Elucidation of the evolution of inflammatory bowel disease (IBD) to cancer by clinical symptoms and histopathology of biopsies is important. Fourier transform infrared microspectroscopy (FTIR-MSP) has shown promise as a diagnostic tool for distinction of normal and cancer cells and tissues. In the present work, FTIR-MSP is used to evaluate IBD cases and to study the IR spectral characteristic with respect to cancer and normal tissues from formalin-fixed colonic biopsies from patients. Specific regions of the spectra were analyzed by statistical tools to study variations in metabolites that signified changes between the two pathological conditions: IBD and cancer. IBD tissues can be grouped with cancer or normal tissue using certain parameters such as phosphate content and RNA/DNA ratio as calculated from the spectra and show intermediate levels with regard to these metabolites. Further classification of the spectra by cluster analysis indicated which cases of Crohn's disease (3 of 10 cases) or ulcerative colitis (7 of 10 cases) were more likely to progress to cancer. The study exhibits that FTIR-MSP can detect gross biochemical changes in morphologically identical IBD and cancer tissues and suggest which cases of IBD may require further evaluation for carcinogenesis.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/bip.20154

Inflamatory bowel diseases as an intermediate stage between normal and cancer: A FTIR-microspectroscopy approach

Bacterial pathogens are one of the primary causes of human morbidity worldwide. Historically, antibiotics have been highly effective against most bacterial pathogens; however, the increasing resistance of bacteria to a broad spectrum of commonly used antibiotics has become a global health-care problem. Early and rapid determination of bacterial susceptibility to antibiotics has become essential in many clinical settings and, sometimes, can save lives. Currently classical procedures require at least 48 h for determining bacterial susceptibility, which can constitute a life-threatening delay for effective treatment. Infrared (IR) microscopy is a rapid and inexpensive technique, which has been used successfully for the detection and identification of various biological samples; nonetheless, its true potential in routine clinical diagnosis has not yet been established. In this study, we evaluated the potential of this technique for rapid identification of bacterial susceptibility to specific antibiotics based...

Using infrared spectroscopy and multivariate analysis to detect antibiotics' resistant Escherichia coli bacteria

Microscopic FTIR spectroscopy was used to investigate the spectral differences between normal cells in culture and cells infected with various members of the herpes family of viruses [Herpes simplex (HSV) and Varicella zoster (VZV)]. The main objective of this study is to evaluate the possibility of developing microscopic FTIR spectroscopy as a sensitive assay for the detection of herpetic infections at their early stages. The advantage of this method over conventional FTIR spectroscopy is that it facilitates inspection of restricted regions of tissue. Our results showed significant and consistent differences between all normal and HSV or VZV infected cells that were tested. Detectable and significant spectral differences between normal and infected cells are seen as early as 24 h postinfection, but the damage of the cells (cytopathic effect), caused by the infecting virus, can be seen by optical microscope observations at only 3 days postinfection. An impressive increase in the levels of vital cellular metabolites was seen in the herpes virus infected cells compared to normal cells. It seems that this spectral behavior is unique for infection with herpes viruses, because when these cells were infected with other viruses from different families like retroviruses, a considerable decrease in the levels of vital cellular metabolites was seen in infected cells compared to normal cells. Cluster analysis performed on FTIR mass chromatography yielded 100% accuracy in classifying control uninfected and VZV or HSV infected cells. Our data strongly support the possibility of developing FTIR microscopy as a diagnostic method for early detection of herpetic infections.

Ahmad Salman

Papers

Diagnostic potential of Fourier-transform infrared microspectroscopy and advanced computational methods in colon cancer patients.

Inflamatory bowel diseases as an intermediate stage between normal and cancer: A FTIR-microspectroscopy approach

Using infrared spectroscopy and multivariate analysis to detect antibiotics' resistant Escherichia coli bacteria

FTIR spectroscopic method for detection of cells infected with herpes viruses.

Novel spectral method for the study of viral carcinogenesis in vitro.