Use of Hyperspectral Images (HSI) and Convolutional Neural Network (CNN) To Identify Normal, Precancerous and Cancerous Tissues

Cancer detection has been a great topic of research for a long time, as early detection of cancer can help in increasing the survival rate of patients by providing on time better treatment. A robust system is required in order to detect early-stage cancer as its difficult to identify early-stage cancer from the normal clinical process. The computer vision techniques provide a new way to understand the challenges related to the medical image analysis. This thesis presents the medical image analysis using a combination of Convolutional Neural Network and Hyperspectral Images of cancer patient\u27s tissues. The idea behind choosing the CNN is it has been doing really well in image processing and outperformed the other traditional techniques. An attempt is made to distinguish between Normal Tissues, Premature Tissues and Oesophageal adenocarcinoma (OAC) tissues. The dataset used here posses many challenges like less number of instances and most importantly imbalanced data, which means some instances are very few in comparison to others. This thesis focuses on improving the F1 Score of the CNN classifier and the performance is measured after fine-tuning the baseline model. The experiment result shows that fine-tuning the CNN algorithm help in improving the F1 Score a bit though haven\u27t achieved great result due to the limitation of imbalanced data. This work is a contribution towards detection of early-stage cancer through images, which clinical processes are unable to detect

Development of transcriptional amplification systems to target and characterize cancer cells based on gene expression altered during prostate cancer development and treatment

Le cancer de la prostate (CaP) est le cancer dont l’incidence augmente le plus vite parmi les hommes. Selon la Société Canadienne du Cancer, en 2015, 24 000 nouveaux cas de cancer de la prostate seront diagnostiqués et 4 100 patients en décèderont. Bien que des techniques cliniques pour la détection, le diagnostique et le traitement du CaP soient disponibles et importantes dans le traitement actuel de la maladie, elles sont cependant limitées. L’exploitation de plusieurs promoteurs dont l’activité est altérée au cours du développement du cancer est un moyen pour surmonter ces limitations. L’ARN non codant PCA3 est un biomarqueur unique du CaP qui a été largement étudié et dont l’expression est 60 fois plus forte dans les cellules de CaP que dans les cellules bégnines de prostate. Le gène de l’APS (PSEBC) est un marqueur important en clinique, il reflète la réponse au traitement par privation androgénique. Ces études ont pour objectif de développer des systèmes d’amplification transcriptionnel avec les promoteurs PCA3 et PSEBC pour non seulement cibler mais aussi caractériser les cellules cancéreuses de prostate lors de la progression de la maladie. Nous avons générés plusieurs systèmes dans des adénovirus contenant différentes constructions avec le promoteur proximal PCA3 de 152 pb, le système d’amplification TSTA et le gène rapporteur de la luciférase. Nous avons testé leur spécificité pour les cellules du CaP par infection transitoire. Nous avons amélioré le système TSTA et généré le PCA3-3STA. Nous avons ensuite intégré le promoteur PCA3 avec le promoteur PSA pour générer un autre nouveau système d’amplification transcriptionnelle qui se nomme le système «Multiple Promoter Integrated Transcriptional Amplification (MP-ITSTA)». Ces systèmes ont ensuite été exploités avec un microscope à bioluminescence pour cibler des cellules de CaP provenant de biopsies liquides de patients. Dans le chapitre deux, nous avons montré que l’activité de PCA3-3STA était hautement spécifique pour les cellules de CaP. Son activité était de 98,7 à 108 fois plus fortes dans les cellules de CaP que dans les cellules primaires bégnines de prostate ou dans les cellules cancéreuses nonprostatiques. Dans des modèles murins de xénogreffes de lignées cellulaires de CaP, nous avons montré que PCA3-3STA pouvait imager de manière très sensible l’activité du promoteur PCA3. De plus, sur des modèles de cultures primaires de biopsies, nous avons montré que le système PCA3-3STA ciblait spécifiquement les cellules épithéliales de CaP sans affecter les cellules stromales. Dans le chapitre trois, nous avons ensuite développé une technique en combinat la microscopie à bioluminescence avec le système TSTA et le promoteur PSA pour cibler les cellules de CaP purifiées de sang de patients et évaluer, cellule par cellule, l’hétérogénéité de leur réponse aux anti-androgènes. Cette technique a aussi montré que la microscopie à bioluminescence est hautement quantitative et a la capacité de détecter les changements moléculaires à l’échelle de la cellule. Le quatrième chapitre présente le système MP-ITSTA. Le système intègre l’activation combinée de deux promoteurs qui contrôlent l’expression d’un seul gène rapporteur. La combinaison du promoteur PCA3 avec celui de l’APS permet d’évaluer, cellule par cellule, la réponse aux anti-androgènes de cellules de CaP prélevés à partir d’urine de patients. C’est pourquoi, les systèmes PCA3-3STA et MP-ITSTA sont des systèmes d’expression spécifiques au cancer de la prostate avec le potentiel de cibler et détecter avec précision les cellules épithéliales de CaP ainsi que leur réponse aux traitements thérapeutiques in vivo et ex vivo. Ces systèmes peuvent jouer un rôle important pour l’imagerie moléculaire, l’immunothérapie et la thérapie génique.Development Of Transcriptional Amplification Systems To Target and Interrogate Cancer Cells Based On Gene Expression Altered During Cancer Development and Treatment Prostate cancer (PCa) is the fastest rising cancer among the males. According to the Canadian Cancer Society in 2015 it was estimated that 24 000 new cases will be diagnosed with prostate cancer and 4100 patients will die from the disease. Although already available clinical techniques for the detection, prognosis and treatment of PCa play an important role in decision making, they are limited in terms of the ability of detecting PCa cells, prognosis and increasing over all survival of patients. Exploitation of several gene promoters altered during cancer development act as important tool to overcome these limitations. PCA3 noncoding long RNA is a unique PCa biomarker that has been widely studied for its sixty-fold overexpression in PCa cells, compared to benign prostate cells. PSA (PSEBC) gene is of high clinical significance as it can give an account of response to androgen deprivation treatments. These studies aim to develop Transcriptional Amplification Systems that can target as well as characterise cancer cells during disease progression using PCA3 and PSA gene promoters. Various adenovirus constructs incorporating the proximal 152 bp PCA3 promoter, the TSTA system and the Firefly luciferase reporter gene were generated and the specificity of the promoter was tested in PCa cells by transient infection. We have improved the TSTA system and generated the (PCA3-3STA). We further integrated the PCA3 promoter along with the PSA promoter to generate a new transcriptional amplification system that we named the Multiple Promoter Integrated Transcriptional Amplification (MP-ITSTA) system. These systems were further applied to target PCa cells from body fluids of patients using bioluminescence microscopy. In chapter two we show that PCA3-3STA activity was highly specific for PCa cells, ranging between 98.7 and 108.0-fold higher, respectively, than that for benign prostate or non-PCa cells. In PCa cell line mouse xenografts, PCA3-3STA was shown to image PCA3 promoter activity with high sensitivity. Moreover, when primary PCa biopsies were infected with PCA3-3STA, it managed to image PCa epithelial cells but not stromal cells. In chapter three we further developed a bioluminescence microscopy technique using the TSTA system with PSA promoter to target PCa cells from blood of patients and assess heterogeneous single cell response to antiandrogens. This technique also shows that bioluminescence microscopy is highly quantitative and has the ability to detect molecular changes at the cellular level. The fourth chapter presents the MP-ITSTA system. This system integrates the combined activation of two promoters giving a single reporter gene expression. PCA3 when combined with the PSA promoter could assess single cell response to antiandrogens in cells isolated from urine of patients. Hence, PCA3-3STA and MP-ITSTA utilizing the bioluminescence microscopy represent a prostate- and PCa-specific expression systems with the potential to target, with high accuracy, PCa epithelial cells, assess their response to therapy in vivo and ex vivo. This can play an important role for imaging, immunotherapy, or gene therapy

Fiscal Decentralization: Does The Source Of Revenue Matter?

Fiscal Decentralization: does the Source of Revenue Matter? Evidence from Rural India Pallavi Jain Govil Adviser: Professor Timothy J. Goodspeed Is the pattern of expenditures of village governments related to their sources of revenue? Do village governments use own-source revenues more efficiently than transfer grants to provide public services to their constituents? This paper begins with the premise that local governments are more participative, more acceptable, and more accountable and hence, deliver better. I use a policy change introduced in 1997 in province of Madhya Pradesh in India, whereby the power to collect royalty and lease rents on minor mineral mines and fishing tanks was transferred to village governments, as a natural experiment and examine whether expenditure patterns of villages that received such resources differ from those that did not. I find that village governments choose to spend their fiscal resources differently depending on where the money comes from, even if these resources are completely `untied\u27 and could be spent entirely at the discretion of the village governments. I also compare the social outcomes in villages that gained such additional resources to those that didn\u27t, and thus remained more dependent on transfer grants from the state and central government for their development needs. Using village level data, I find evidence to support the hypothesis that fiscal decentralization through assignment of taxation powers is more effective in achieving desired outcomes as compared to a transfer of an equal amount of resources by way of grants

Foreign bodies in upper aero-digestive tract: a clinical study

Background: Foreign-body ingestion and aspiration are common childhood adverse events, hence are commonest causes of morbidity and mortality in infants and children worldwide.Aim of current study was to identify the patients with foreign-body ingestion and aspiration, develop a suitable algorithm for their management and study various complications following their removal.Methods: The present study was carried out in G.R. medical college, Gwalior, M. P. during last one year on hundred patients diagnosed as case of foreign-body in upper aero-digestive tract on the basis of history, examination and investigations.Results: Foreign-bodies in upper aero-digestive tract were seen mostly in children less than 10 years of age (91%). The youngest was 8 months old and the oldest 48 years. Coins were the most common foreign-bodies in oesophagus (90%) while whistle in the upper airway (40%). Right bronchus is the commonest site of impaction in the airway (50%), while cricopharynx is most common in the oesophagus (95.55%). Patients with oesophageal foreign bodies presented mostly with the chief complaint of foreign body sensation (63.4%) in the throat whereas those with airway foreign body presented mostly with dyspnoea and choking sensation (60%). Pooling of saliva was most commonly seen in patients with oesophageal foreign bodies (43.3%). Tachypnoea was the most common sign in cases of trachea-bronchial foreign bodies (80%). Positive radiological evidence was present in 88% of upper aero-digestive foreign-bodies. Only 2.2% cases showed complications following oesophagoscopy. Tracheo-bronchial foreign-bodies were removed by emergency bronchoscopy. 20% cases had complications post-operatively.Conclusion: Early detection by meticulous history, imaging modality & prompt management remains basis for favourable outcome and prevents fatal complications.

Comparative Study Of Relational Database Model and Resource Description Framework(RDF) Model

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A PCA3 gene-based transcriptional amplification system targeting primary prostate cancer.

Targeting specifically primary prostate cancer (PCa) cells for immune therapy, gene therapy or molecular imaging is of high importance. The PCA3 long non-coding RNA is a unique PCa biomarker and oncogene that has been widely studied. This gene has been mainly exploited as an accurate diagnostic urine biomarker for PCa detection. In this study, the PCA3 promoter was introduced into a new transcriptional amplification system named the 3-Step Transcriptional Amplification System (PCA3-3STA) and cloned into type 5 adenovirus. PCA3-3STA activity was highly specific for PCa cells, ranging between 98.7- and 108.0-fold higher than that for benign primary prostate epithelial or non-PCa cells, respectively. In human PCa xenografts, PCA3-3STA displayed robust bioluminescent signals at levels that are sufficient to translate to positron emission tomography (PET)-based reporter imaging. Remarkably, when freshly isolated benign or cancerous prostate biopsies were infected with PCA3-3STA, the optical signal produced from primary PCa biopsies was significantly higher than from benign prostate biopsies (4.4-fold, p < 0.0001). PCA3-3STA therefore represents a PCa-specific expression system with the potential to target, with high accuracy, primary or metastatic PCa epithelial cells for imaging, vaccines, or gene therapy

How to assign volunteers to tasks compatibly ? A graph theoretic and parameterized approach

In this paper we study a resource allocation problem that encodes correlation between items in terms of \conflict and maximizes the minimum utility of the agents under a conflict free allocation. Admittedly, the problem is computationally hard even under stringent restrictions because it encodes a variant of the {\sc Maximum Weight Independent Set} problem which is one of the canonical hard problems in both classical and parameterized complexity. Recently, this subject was explored by Chiarelli et al.~[Algorithmica'22] from the classical complexity perspective to draw the boundary between {\sf NP}-hardness and tractability for a constant number of agents. The problem was shown to be hard even for small constant number of agents and various other restrictions on the underlying graph. Notwithstanding this computational barrier, we notice that there are several parameters that are worth studying: number of agents, number of items, combinatorial structure that defines the conflict among the items, all of which could well be small under specific circumstancs. Our search rules out several parameters (even when taken together) and takes us towards a characterization of families of input instances that are amenable to polynomial time algorithms when the parameters are constant. In addition to this we give a superior 2^{m}|I|^{\Co{O}(1)} algorithm for our problem where $m$ denotes the number of items that significantly beats the exhaustive \Oh(m^{m}) algorithm by cleverly using ideas from FFT based fast polynomial multiplication; and we identify simple graph classes relevant to our problem's motivation that admit efficient algorithms

A retrospective study of intramedullary tibia nailing system intended for tibia fracture

Background: The aim of the study was to investigate the performance of the intramedullary tibia nail in the treatment of tibia fractures, mostly shaft fractures. The objective of this study was to assess the post-operative complication due to the treatment involving tibia nails.Methods: This was a retrospective study to study the results obtained after tibia nail surgery. A total of 32 patients were selected based on inclusion and exclusion criteria (25 males and 7 females; average age- 37 years). The fracture was classified according to AO classification, the nailing device is intended for 41-A1/A2, 42 and 43-A1/A2/A3 types of fractures. The patients with at least three visits within 180 days were selected for data collection.Results: The clinical outcomes include pain scale assessment from the baseline/enrolment to the last follow up which shows no pain (93.7%) and mild pain (6.7%) after 180 days. No implant-related problems like implant loosening.Conclusions: For the treatment of tibia shaft fracture which can either be closed or open, intramedullary tibia nailing devices like KN-2T and KN-5T have been concluded to be the good approach

Self-Supervised Learning for Invariant Representations From Multi-Spectral and SAR Images

Self-Supervised learning (SSL) has become the new state of the art in several domain classification and segmentation tasks. One popular category of SSL are distillation networks such as Bootstrap Your Own Latent (BYOL). This work proposes RS-BYOL, which builds on BYOL in the remote sensing (RS) domain where data are non-trivially different from natural RGB images. Since multi-spectral (MS) and synthetic aperture radar (SAR) sensors provide varied spectral and spatial resolution information, we utilise them as an implicit augmentation to learn invariant feature embeddings. In order to learn RS based invariant features with SSL, we trained RS-BYOL in two ways, i.e. single channel feature learning and three channel feature learning. This work explores the usefulness of single channel feature learning from random 10 MS bands of 10m-20 m resolution and VV-VH of SAR bands compared to the common notion of using three or more bands. In our linear probing evaluation, these single channel features reached a 0.92 F1 score on the EuroSAT classification task and 59.6 mIoU on the IEEE Data Fusion Contest (DFC) segmentation task for certain single bands. We also compare our results with ImageNet weights and show that the RS based SSL model outperforms the supervised ImageNet based model. We further explore the usefulness of multi-modal data compared to single modality data, and it is shown that utilising MS and SAR data allows better invariant representations to be learnt than utilising only MS data

MULTI-MODAL SELF-SUPERVISED REPRESENTATION LEARNING FOR EARTH OBSERVATION

Self-Supervised learning (SSL) has reduced the performance gap between supervised and unsupervised learning, due to its ability to learn invariant representations. This is a boon to the domains like Earth Observation (EO), where labelled data availability is scarce but unlabelled data is freely available. While Transfer Learning from generic RGB pre-trained models is still common-place in EO, we argue that, it is essential to have good EO domain specific pre-trained model in order to use with downstream tasks with limited labelled data. Hence, we explored the applicability of SSL with multi-modal satellite imagery for downstream tasks. For this we utilised the state-of-art SSL architectures i.e. BYOL and SimSiam to train on EO data. Also to obtain better invariant representations, we considered multi-spectral (MS) images and synthetic aperture radar (SAR) images as separate augmented views of an image to maximise their similarity. Our work shows that by learning single channel representations through non-contrastive learning, our approach can outperform ImageNet pre-trained models significantly on a scene classification task. We further explored the usefulness of a momentum encoder by comparing the two architectures i.e. BYOL and SimSiam but did not identify a significant improvement in performance between the models