Improving cancer subtype diagnosis and grading using clinical decision support system based on computer-aided tissue image analysis

This research focuses towards the development of a clinical decision support system (CDSS) based on cellular and tissue image analysis and classification system that improves consistency and facilitates the clinical decision making process. In a typical cancer examination, pathologists make diagnosis by manually reading morphological features in patient biopsy images, in which cancer biomarkers are highlighted by using different staining techniques. This process is subjected to pathologist's training and experience, especially when the same cancer has several subtypes (i.e. benign tumor subtype vs. malignant subtype) and the same cancer tissue biopsy contains heterogeneous morphologies in different locations. The variability in pathologist's manual reading may result in varying cancer diagnosis and treatment. This Ph.D. research aims to reduce the subjectivity and variation existing in traditional histo-pathological reading of patient tissue biopsy slides through Computer-Aided Diagnosis (CAD). Using the CAD, quantitative molecular profiling of cancer biomarkers of stained biopsy images are obtained by extracting and analyzing texture and cellular structure features. In addition, cancer sub-type classification and a semi-automatic grade scoring (i.e. clinical decision making) for improved consistency over a large number of cancer subtype images can be performed. The CAD tools do have their own limitations and in certain cases the clinicians, however, prefer systems which are flexible and take into account their individuality when necessary by providing some control rather than fully automated system. Therefore, to be able to introduce CDSS in health care, we need to understand users' perspectives and preferences on the new information technology. This forms as the basis for this research where we target to present the quantitative information acquired through the image analysis, annotate the images and provide suitable visualization which can facilitate the process of decision making in a clinical setting.PhDCommittee Chair: Dr. May D. Wang; Committee Member: Dr. Andrew N. Young; Committee Member: Dr. Anthony J. Yezzi; Committee Member: Dr. Edward J. Coyle; Committee Member: Dr. Paul Benkese

An Investigation of the Diagnostic Potential of Autofluorescence Lifetime Spectroscopy and Imaging for Label-Free Contrast of Disease

The work presented in this thesis aimed to study the application of fluorescence lifetime spectroscopy (FLS) and fluorescence lifetime imaging microscopy (FLIM) to investigate their potential for diagnostic contrast of diseased tissue with a particular emphasis on autofluorescence (AF) measurements of gastrointestinal (GI) disease. Initially, an ex vivo study utilising confocal FLIM was undertaken with 420 nm excitation to characterise the fluorescence lifetime (FL) images obtained from 71 GI samples from 35 patients. A significant decrease in FL was observed between normal colon and polyps (p = 0.024), and normal colon and inflammatory bowel disease (IBD) (p = 0.015). Confocal FLIM was also performed on 23 bladder samples. A longer, although not significant, FL for cancer was observed, in paired specimens (n = 5) instilled with a photosensitizer. The first in vivo study was a clinical investigation of skin cancer using a fibre-optic FL spectrofluorometer and involved the interrogation of 27 lesions from 25 patients. A significant decrease in the FL of basal cell carcinomas compared to healthy tissue was observed (p = 0.002) with 445 nm excitation. A novel clinically viable FLS fibre-optic probe was then applied ex vivo to measure 60 samples collected from 23 patients. In a paired analysis of neoplastic polyps and normal colon obtained from the same region of the colon in the same patient (n = 12), a significant decrease in FL was observed (p = 0.021) with 435 nm excitation. In contrast, with 375 nm excitation, the mean FL of IBD specimens (n = 4) was found to be longer than that of normal tissue, although not statistically significant. Finally, the FLS system was applied in vivo in 17 patients, with initial data indicating that 435 nm excitation results in AF lifetimes that are broadly consistent with ex vivo studies, although no diagnostically significant differences were observed in the signals obtained in vivo.Open Acces

Endoscopic Fluorescence Imaging:Spectral Optimization and in vivo Characterization of Positive Sites by Magnifying Vascular Imaging

Since several decades, the physicians are able to access hollow organs with endoscopic methods, which serve both as diagnostic and surgical means in a wide range of disciplines of the modern medicine (e.g. urology, pneumology, gastroenterology). Unfortunately, white light (WL) endoscopy displays a limited sensitivity to early pre-cancerous lesions. Hence, several endoscopic methods based on fluorescence imaging have been developed to overcome this limitation. Both endogenous and exogenously-induced fluorescence have been investigated, leading to commercial products. Indeed, autofluorescence bronchoscopy, as well as porphyrin-based fluorescence cystoscopy, are now on the market. As a matter of fact, fluorescence-based endoscopic detection methods show very high sensitivity to pre-cancerous lesions, which are often overlooked in WL endoscopy, but they still lack specificity mainly due to the high false-positive rate. Although most of these false positives can easily be rejected under WL observation, tissue abnormalities such as inflammations, hyperplasia, and metaplasia are more difficult to identify, often resulting in supplementary biopsies. Therefore, the purpose of this thesis is to study novel, fast, and convenient method to characterize fluorescence positive spots in situ during fluorescence endoscopy and, more generally, to optimize the existing endoscopic setup. In this thesis, several clinical evaluations were conducted either in the tracheo-bronchial tree and the urinary bladder. In the urinary bladder, fluorescence imaging for detection of non-muscle invasive bladder cancer is based on the selective production and accumulation of fluorescing porphyrins, mainly protoporphyrin IX (PpIX), in cancerous tissues after the instillation of Hexvix® during one hour. In this thesis, we adapted a rigid cystoscope to perform high magnification (HM) cystoscopy in order to discriminate false from true fluorescence positive findings. Both white light and fluorescence modes are possible with the magnification cystoscope, allowing observation of the bladder wall with magnification ranging between 30× – for standard observation – and 650×. The optical zooming setup allows adjusting the magnification continuously in situ. In the high magnification regime, the smallest diameter of the field of view is 600 microns and the resolution is 2.5 microns, when in contact with the bladder wall. With this HM cystoscope, we characterized the superficial vascularization of the fluorescing sites in WL (370–700 nm) reflectance imaging in order to discriminate cancerous from non-cancerous tissues. This procedure allowed us to establish a classification based on observed vascular patterns. 72 patients subject to Hexvix® f luorescence cystoscopy were included in the study. Comparison of HM cystoscopy classification with histopathology results confirmed 32/33 (97%) cancerous biopsies, and rejected 17/20 (85%) non-cancerous lesions. No vascular alteration could be observed on the only positive lesion that was negative in HM mode, probably because this sarcomatoid carcinoma was not originating in the bladder mucosa. We established with this study that a magnification ranging between 80× and 100× is an optimal tradeoff to perform both macroscopic PDD and HM reflectance imaging. In order to make this approach more quantitative, different algorithms of image processing (vessel segmentation and skeletonisation, global information extraction) were also implemented in this thesis. In order to better visualize the vessels, we improved their contrast with respect to the background. Since hemoglobin is a very strong absorber, we targeted the two hemoglobin absorption peaks by placing appropriate bandpass filters (blue 405±50 nm, green 550±50 nm) in the light source. HM cystoscopy was then performed sequentially with WL, blue and green illumination. The two latter showed higher vessel-to-background contrast, identifying different layers of vascularization due to the light penetration depth. During fluorescence cystoscopy, we often observed that the images are somehow "blurred" by a greenish screen between endoscope tip and bladder mucosa. Since this effect is enhanced by the urine production, it is more visible with flexible scopes (lower flushing capabilities) and imaging systems that collect only autofluorescence as background. Indeed, when the bladder is not flushed regularly, greenish flows coming out of the ureters can easily be observed. For this reason, it is supposed that some fluorophores contained in the urine are excited by the photodetection excitation light, and appear greenish on the screen. This effect may impair the visualization of the bladder mucosa, and thus cancerous lesions, and lowers sensitivity of the fluorescence cystoscopy. In this thesis, we identified the main metabolites responsible for the liquid fluorescence, and optimized the spectral design accordingly. In the tracheo-bronchial tree, the fluorescence contrast is based on the sharp autofluorescence (AF) decrease on early cancerous lesions in the green spectral region (around 500 nm) and a relatively less important decrease in the red spectral region (> 600 nm) when excited with blue-violet light (around 410 nm). It has been shown over the last years, that this contrast may be attributed to a combined effect of epithelium thickening and higher concentration of hemoglobin in the tissues underneath the (pre-)cancerous lesions. In this thesis, we contributed to the definition of the input design of several new prototypes, that were subsequently tested in the clinical environment. We first showed that narrow-band excitation in the blue-violet could increase the tumor-to-normal spectral contrast in the green spectral region. Then, we quantified the intra- and inter-patient variations in the AF intensities in order to optimize the spectral response of the endoscopic fluorescence imaging system. For this purpose, we developed an endoscopic reference to be placed close to the bronchial mucosa during bronchoscopy. Finally, we evaluated a novel AF bronchoscope with blue-backscattered light on 144 patients. This new device showed increased sensitivity for pre-neoplastic lesions. Similar to what we observed in the bladder, it is likely that developing new imaging capabilities (including vascular imaging) will facilitate discriminating true from false positive in AF bronchoscopy. Here, we demonstrated that this magnification allowed us to resolve vessels with a diameter of about 30 µm. This resolution is likely to be sufficient to identify Shibuya's vascular criteria (loops, meshes, dotted vessels) on AF positive lesions. This criteria allow him to recognize pre-cancerous lesions, and thus can potentially decrease the false-positive rate with our AF imaging system. This magnification was also showed to be better for routine bronchoscopy, since it delivers sharper and more structured images to the operator

Dictionary of Invertebrate Zoology

An exhaustive dictionary of over 13,000 terms relating to invertebrate zoology, including etymologies, word derivations and taxonomic classification. Entries cover parasitology, nematology, marine invertebrates, insects, and anatomy, biology, and reproductive processes for the following phyla: Acanthocephala Annelida Arthropoda Brachiopoda Bryozoa Chaetognatha Cnidaria Ctenophora Echinodermata Echiura Entoprocta Gastrotricha Gnathostomulida Kinorhyncha Loricifera Mesozoa Mollusca Nemata Nematomorpha Nemertea Onychophora Pentastoma Phoronida Placozoa Platyhelminthes Pogonophora Porifera Priapula Rotifera Sipuncula Tardigrada.https://digitalcommons.unl.edu/zeabook/1061/thumbnail.jp

Fluorescence Methods for Investigation of Living Cells and Microorganisms

Fluorescence methods play a leading role in the investigation of biological objects. They are the only non-destructive methods for investigating living cells and microorganisms in vivo. Using intrinsic and artificial fluorescence methods provides deep insight into mechanisms underlying physiological and biochemical processes. This book covers a wide range of modern methods involved in experimental biology. It illustrates the use of fluorescence microscopy and spectroscopy, confocal laser scanning microscopy, flow cytometry, delayed fluorescence, pulse-amplitude-modulation fluorometry, and fluorescent dye staining protocols. This book provides an overview of practical and theoretical aspects of fluorescence methods and their successful application in the investigation of static and dynamic processes in living cells and microorganisms

Environmental taphonomic processes and their effects on skeletal trauma analysis

In recent years there has been extensive research focusing on skeletal trauma as a result of different types of weapons inflicted on bone. However, an important factor that has not been investigated in depth is the potential modification to the observed dimensions and morphology of trauma marks after environmental exposure. Detailed information derived from traumatic lesions to bone is highly valuable in forensic anthropological casework. It is important to understand how taphonomic variables, namely the outdoor environment or fire, may alter trauma morphology. Therefore, the aim of this study is to evaluate the influence of different environmental taphonomic agents on fresh and burned bone trauma that have been inflicted by either blunt or sharp instruments. This research used blunt and sharp weapons to inflict trauma on manually macerated porcine ribs (n=364) and femurs (n=60). Subsequently each specimen was examined, analysed, and photographed. Qualitative and quantitative analyses were undertaken using macroscopic, microscopic and radiological techniques to investigate specific traumatic lesions, such as cut and chop marks, as well as bluntinflicted fractures. The traumatised bones were subsequently deposited on the surface or in a buried environment for a pre-determined length of time (6, 12 and 18 months). In addition, sharp force trauma was inflicted on ribs which were then burned at 850°C in a furnace prior to being buried or placed on the surface for 1 month. The samples were then re-examined and the trauma evidence was compared between pre- and post-environmental exposure. The results showed several trends. Surface colour and taphonomic alterations were linked to macro- and micro-environmental factors, and were also dependent on the duration of environmental exposure. Surface-deposited samples underwent higher degrees of degradation than buried samples. In addition, perimortem blunt and sharp force traumatic lesions on the ribs and femurs were still clearly identifiable after 18-month environmental exposure. This study also illustrated that taphonomic modifications of blunt and sharp injuries were different depending on the interaction between bone, the type of trauma and the surrounding environment. Fractures from different types of weapon showed dissimilar responses to environmental variables. ii Pre-exposure bone and different types of depositional environment had an effect on the rate and pattern of taphonomic modifications on dimensions and morphology of the traumatic lesion. The results of this study should enable an improved determination of skeletal trauma analysis after environmental exposure. Moreover, this study has emphasised the need for a combination of macroscopic, microscopic and radiological techniques to analyse taphonomic phenomena. As environmental factors have the potential to conceal perimortem skeletal trauma, this study advises that when carefully examining traumatic lesions on ribs and femurs as an alteration of their dimensions and morphology is likely to have occurred after prolonged environmental exposure

Capsaicin - Sensitive Neural Afferentation and the Gastrointestinal Tract

The capsaicin, a component of paprika, has been used in the culinary practice of every day nutritional practice. This agent is known to cause a variety of actions in the body through activating capsaicin-sensitive afferent neurons. A recently launched book entitled, Capsaicin-Sensitive Neural Afferentation and the Gastrointestinal Tract: from Bench to Bedside, is attractive for several reasons. First, Prof. Mozsik, a chief editor of this book, is known internationally as an expert in capsaicin pharmacology. Since he has worked for many years as a head of internal medicine, taking care of patients with various GI diseases, he is able to make a correct interpretation of various findings obtained in basic researches to clinical events. Second, although there are many articles about capsaicin, they mostly deal with basic research and finding but do not include much about clinical finding. Third, this book encompassed review articles written by internationally accepted scientists leading the field of capsaicin research, who highlighted the current state of knowledge on pharmacology, physiology and clinical phathophysiology of capsaicin-sensitive afferent neurons, and discussed directions for future research. Overall, this book is for people who are interested in the capsaicin action in body