Wavelet-based noise reduction of cDNA microarray images

The advent of microarray imaging technology has lead to enormous progress in the life sciences by allowing scientists to analyze the expression of thousands of genes at a time. For complementary DNA (cDNA) microarray experiments, the raw data are a pair of red and green channel images corresponding to the treatment and control samples. These images are contaminated by a high level of noise due to the numerous noise sources affecting the image formation. A major challenge of microarray image analysis is the extraction of accurate gene expression measurements from the noisy microarray images. A crucial step in this process is denoising, which consists of reducing the noise in the observed microarray images while preserving the signal information as much as possible. This thesis deals with the problem of developing novel methods for reducing noise in cDNA microarray images for accurate estimation of the gene expression levels. Denoising methods based on the wavelet transform have shown significant success when applied to natural images. However, these methods are not very efficient for reducing noise in cDNA microarray images. An important reason for this is that existing methods are only capable of processing the red and green channel images separately. In doing so. they ignore the signal correlation as well as the noise correlation that exists between the wavelet coefficients of the two channels. The primary objective of this research is to design efficient wavelet-based noise reduction algorithms for cDNA microarray images that take into account these inter-channel dependencies by 'jointly' estimating the noise-free coefficients in both the channels. Denoising algorithms are developed using two types of wavelet transforms, namely, the frequently-used discrete wavelet transform (DWT) and the complex wavelet transform (CWT). The main advantage of using the DWT for denoising is that this transform is computationally very efficient. In order to obtain a better denoising performance for microarray images, however, the CWT is preferred to DWT because the former has good directional selectivity properties that are necessary for better representation of the circular edges of spots. The linear minimum mean squared error and maximum a posteriori estimation techniques are used to develop bivariate estimators for the noise-free coefficients of the two images. These estimators are derived by utilizing appropriate joint probability density functions for the image coefficients as well as the noise coefficients of the two channels. Extensive experimentations are carried out on a large set of cDNA microarray images to evaluate the performance of the proposed denoising methods as compared to the existing ones. Comparisons are made using standard metrics such as the peak signal-to-noise ratio (PSNR) for measuring the amount of noise removed from the pixels of the images, and the mean absolute error for measuring the accuracy of the estimated log-intensity ratios obtained from the denoised version of the images. Results indicate that the proposed denoising methods that are developed specifically for the microarray images do, indeed, lead to more accurate estimation of gene expression levels. Thus, it is expected that the proposed methods will play a significant role in improving the reliability of the results obtained from practical microarray experiments

Assessing power to detect gene-environment interactions using surrogate outcomes : simulation study

The low power of gene-environment (G {604} E) interaction studies is of major concern in genetic-epidemiolgic research. Past research involving binary outcomes has focussed mainly on the development of efficient study designs to address this problem. This thesis explores an alternative strategy that uses quantitative 'surrogates' of the 'clinical' binary outcome to improve power to detect G {604} E interactions. Efficiency of the quantitative 'surrogate' outcome X versus the binary outcome Y is assessed for three hypothetical models of the relationship between the outcomes, and their relationships to genetic susceptibility, exposure, and other risk factors. In the first scenario, X is a risk factor of disease, and a mediator for the effect of G {604} E interaction. In the second scenario, X is considered a marker of disease outcome. Finally, repeated measures of the disease marker X are used to define alternative binary and quantitative outcomes. Simulations are used to estimate the power to detect G {604} E interaction in models using these alternative outcome

Aesthetic implant: A new era of aesthetic dentistry

The dental implant is used to replace the natural tooth system. It requires comprehensive preoperative planning and precise surgical execution. In this case report, a 45 year old male presented with missing upper left maxillary central incisor which was extracted 5 months back. He had discomfort during function and unwillingness to smile. He wanted to replace that edentulous area. The treatment options for replacing the missing tooth were discussed with the patient. Finally, with patient\u27s consent the decision was made to replace that edentulous area with an implant supported porcelain fused to metal prosthesis in an esthetic manner. Recall visits exhibited patient\u27s high-level confidence of smile with optimum satisfaction and successful aesthetic outcome.

Aesthetic implant: A new era of aesthetic dentistry

The dental implant is used to replace the natural tooth system. It requires comprehensive preoperative planning and precise surgical execution. In this case report, a 45 year old male presented with missing upper left maxillary central incisor which was extracted 5 months back. He had discomfort during function and unwillingness to smile. He wanted to replace that edentulous area. The treatment options for replacing the missing tooth were discussed with the patient. Finally, with patient's consent the decision was made to replace that edentulous area with an implant supported porcelain fused to metal prosthesis in an esthetic manner. Recall visits exhibited patient's high-level confidence of smile with optimum satisfaction and successful aesthetic outcome.

Association between malnutrition and anemia in under-five children and women of reproductive age: Evidence from Bangladesh Demographic and Health Survey 2011.

BACKGROUND:Bangladesh is one of the most anemia prone countries in South Asia. Children of age under five years and women of reproductive age are particularly vulnerable in this region. Although several studies have investigated the risk factors of anemia, only few have explored its association with malnutrition, despite its high prevalence in the same group. The objective of this paper is to investigate the association of malnutrition with anemia by conducting separate analyses for under-five children and women of reproductive age using data from the nationally representative 2011 Bangladesh Demographic and Health Survey. METHODS:Two binary outcome variables are considered separately: presence of anemia in children under five years of age (Hb<11.0 g/dl) and presence of anemia in women of childbearing age (Hb<12.0 g/dl). The exposures of interest corresponding to these two outcomes are stunting (low height-for-age) and low BMI (<18.5 kg/m2), respectively. Preliminary analysis involves estimating the association between exposure and outcome while controlling for a single confounder by computing adjusted odds ratios (adjOR) using the Cochran-Mantel-Haenszel approach in stratified analysis. Later, associations between the exposures and outcomes are estimated separately for under-five children and women of reproductive age by fitting multivariable regression models that adjust simultaneously for several confounders. RESULTS:The prevalence of anemia is found to be higher among both the stunted children and women with low BMI compared to their healthy counterparts (Children: 56% vs 48%; women: 50% vs 43%). Furthermore, stunted children and women with low BMI have significantly increased odds of developing anemia, as reflected by the adjusted ORs of 1.76 (95% CI:1.10-2.83) and 1.81 (95% CI: 1.11-3.48), respectively. The association of stunting with anemia in children was modified by their age and socio-economic condition, where risk of being anemic decreases with increasing age but with a lower rate for stunted children from richest family. In addition, stunted children of anemic mothers are at greater risk of being anemic compared to non-stunted children of anemic or non-anemic mothers. Again the association between BMI and anemia in women is modified by the level of education, with risk of anemia being lowest among women with low BMI and higher education. CONCLUSION:Evidence-based policies targeting the vulnerable groups are required to combat anemia and nutritional deficiencies simultaneously under the same program

Association of Low-Birth Weight with Malnutrition in Children under Five Years in Bangladesh: Do Mother's Education, Socio-Economic Status, and Birth Interval Matter?

Malnutrition in children under five years remains a significant problem in Bangladesh, despite substantial socio-economic progress and a decade of interventions aimed at improving it. Although several studies have been conducted to identify the important risk factors of malnutrition, none of them assess the role of low birth weight (LBW) despite its high prevalence (36%). This study examines the association between LBW and malnutrition using data from the Bangladesh Demographic and Health Survey (BDHS) 2011 and provides practical guidelines for improving nutritional status of children.Malnutrition in children is measured in terms of their height-for-age, weight-for-height, and weight-for-age. Children whose Z-scores for either of these indices are below two standard deviations (-2SD) from median of WHO's reference population are considered as stunted, wasted or underweight, respectively. The association between malnutrition and LBW was investigated by calculating adjusted risk-ratio (RR), which controls for potential confounders such as child's age and sex, mother's education and height, length of preceding-birth-interval, access to food, area of residence, household socio-economic status. Adjusted RR was calculated using both Cochran-Mantel-Haenszel approach and multivariable logistic regression models controlling for confounder.The prevalence of malnutrition was markedly higher in children with LBW than those with normal birth-weights (stunting: 51% vs 39%; wasting: 25% vs 14% and underweight: 52% vs 33%). While controlling for the known risk factors, children with LBW had significantly increased risk of becoming malnourished compared to their counter part with RR 1.23 (95% CI:1.16-1.30), 1.71 (95% CI:1.53-1.92) and 1.47 (95% CI: 1.38-1.56) for stunting, wasting and underweight, respectively. The observed associations were not modified by factors known to reduce the prevalence of malnutrition, such as higher education of mother, better household socio-economic conditions and longer birth-interval.Higher education of mother, better household socio-economic conditions and prolonged birth intervals alone are not sufficient in bringing about substantial reductions in prevalence of child malnutrition in Bangladesh. Targeted interventions should be designed to reduce prevalence of LBW in addition to improving mother's education and other socio-demographic conditions

Distribution of children under five years by background characteristics.

<p>Distribution of children under five years by background characteristics.</p