Development of Techniques for the Automatic Extraction and Grade Detection of Glioma Tumors from Conventional Brain Magnetic Resonant Images

Cerebral glioma is the most prevalent primary brain tumor, which are classified broadly into low and high grades according to the degree of malignancy. High grade gliomas are highly malignant which possess a poor prognosis, and the patients survive less than eighteen months after diagnosis. Low grade gliomas are slow growing, least malignant and has better response to therapy. To date, histological grading is used as the standard technique for diagnosis, treatment planning and survival prediction. The main objective of this thesis is to propose novel methods for automatic extraction of low and high grade glioma and other brain tissues, grade detection techniques for glioma using conventional magnetic resonance imaging (MRI) modalities and 3D modelling of glioma from segmented tumor slices in order to assess the growth rate of tumors. Two new methods are developed for extracting tumor regions, of which the second method, named as Adaptive Gray level Algebraic set Segmentation Algorithm (AGASA) can also extract white matter and grey matter from T1 FLAIR an T2 weighted images. The methods were validated with manual Ground truth images, which showed promising results. The developed methods were compared with widely used Fuzzy c-means clustering technique and the robustness of the algorithm with respect to noise is also checked for different noise levels. Image texture can provide significant information on the (ab)normality of tissue, and this thesis expands this idea to tumour texture grading and detection. Based on the thresholds of discriminant first order and gray level cooccurrence matrix based second order statistical features three feature sets were formulated and a decision system was developed for grade detection of glioma from conventional T2 weighted MRI modality.The quantitative performance analysis using ROC curve showed 99.03% accuracy for distinguishing between advanced (aggressive) and early stage (non-aggressive) malignant glioma. The developed brain texture analysis techniques can improve the physician’s ability to detect and analyse pathologies leading to a more reliable diagnosis and treatment of disease. The segmented tumors were also used for volumetric modelling of tumors which can provide an idea of the growth rate of tumor; this can be used for assessing response to therapy and patient prognosis.

Enhancement of Calcifications in Mammograms using Volterra Series based Quadratic Filter

The paper summarizes the design and implementation of a quadratic edge detection filter, based on Volterra series, for enhancing calcifications in mammograms. The proposed filter can account for much of the polynomial nonlinearities inherent in the input mammogram image and can replace the conventional edge detectors like Laplacian, gaussian etc. The filter gives rise to improved visualization and early detection of microcalcifications, which if left undetected, can lead to breast cancer. The performance of the filter is analyzed and found superior to conventional spatial edge detectors

Primary Prevention and Screening Strategies for Colorectal Cancer: Which Strategy Should Take?

Objective: To explore and define the utility of different strategies for primary prevention (ASA, diet, physical activity) and strategies of screening test (FOBT, sigmoidoscopy, colonoscopy, etc.) for colorectal cancer. Data source: Databases consulted were MEDLINE (1966 to 2006), DARE (1980 to 2006), Cochrane Central Register of Controlled Trials, Cochrane Collaboration’s Registry of Clinical Trials, Cochrane Database of Systematic Reviews and LILACS. Study selection: Studies such clinical trial, cohort and case-control studies of the effectiveness of tests for screening and primary prevention adenoma and colorectal cancer were identified by two reviewers. Data Extraction: The extraction of data and its evaluation is done in most of the process so paired. Limitations: Not strictly complies with the methodology of a systematic review and therefore reproducibility is questionable, the conclusions of this study should be extrapolated with caution. Conclusions: The major strategy of screening on the effectiveness of early detection of premalignant lesions or cancer is colonoscopy every 5 years, however it is necessary to evaluate this measure cost-effectiveness studies. For primary prevention, aspirin and cyclooxygenase-2 inhibitors reduce the incidence of colorectal adenomas. Aspirin can reduce colorectal cancer incidence. However, these medications may be associated with a significant risk of cardiovascular events and gastrointestinal bleeding. The balance between risks and benefits must be evaluated in future studies.

Breast cancer incidence and overdiagnosis in Catalonia (Spain)

Early detection of breast cancer (BC) with mammography may cause overdiagnosis and overtreatment, detecting tumors which would remain undiagnosed during a lifetime. The aims of this study were: first, to model invasive BC incidence trends in Catalonia (Spain) taking into account reproductive and screening data; and second, to quantify the extent of BC overdiagnosis. We modeled the incidence of invasive BC using a Poisson regression model. Explanatory variables were: age at diagnosis and cohort characteristics (completed fertility rate, percentage of women that use mammography at age 50, and year of birth). This model also was used to estimate the background incidence in the absence of screening. We used a probabilistic model to estimate the expected BC incidence if women in the population used mammography as reported in health surveys. The difference between the observed and expected cumulative incidences provided an estimate of overdiagnosis.Incidence of invasive BC increased, especially in cohorts born from 1940 to 1955. The biggest increase was observed in these cohorts between the ages of 50 to 65 years, where the final BC incidence rates more than doubled the initial ones. Dissemination of mammography was significantly associated with BC incidence and overdiagnosis. Our estimates of overdiagnosis ranged from 0.4% to 46.6%, for women born around 1935 and 1950, respectively.Our results support the existence of overdiagnosis in Catalonia attributed to mammography usage, and the limited malignant potential of some tumors may play an important role. Women should be better informed about this risk. Research should be oriented towards personalized screening and risk assessment tools

Chemical composition observed over the mid-Atlantic and the detection of pollution signatures far from source regions

The atmospheric composition of the central North Atlantic region has been sampled using the FAAM BAe146 instrumented aircraft during the Intercontinental Transport of Ozone and Precursors (ITOP) campaign, part of the wider International Consortium for Atmospheric Research on Transport and Transformation (ICARTT). This paper presents an overview of the ITOP campaign. Between late July and early August 2004, twelve flights comprising 72 hours of measurement were made in a region from approximately 20 to 40°W and 33 to 47°N centered on Faial Island, Azores, ranging in altitude from 50 to 9000 m. The vertical profiles of O3 and CO are consistent with previous observations made in this region during 1997 and our knowledge of the seasonal cycles within the region. A cluster analysis technique is used to partition the data set into air mass types with distinct chemical signatures. Six clusters provide a suitable balance between cluster generality and specificity. The clusters are labeled as biomass burning, low level outflow, upper level outflow, moist lower troposphere, marine and upper troposphere. During this summer, boreal forest fire emissions from Alaska and northern Canada were found to provide a major perturbation of tropospheric composition in CO, PAN, organic compounds and aerosol. Anthropogenic influenced air from the continental boundary layer of the USA was clearly observed running above the marine boundary layer right across the mid-Atlantic, retaining high pollution levels in VOCs and sulfate aerosol. Upper level outflow events were found to have far lower sulfate aerosol, resulting from washout on ascent, but much higher PAN associated with the colder temperatures. Lagrangian links with flights of other aircraft over the USA and Europe show that such signatures are maintained many days downwind of emission regions. Some other features of the data set are highlighted, including the strong perturbations to many VOCs and OVOCs in this remote region.

Development and validation of a parent report measure for detection of cognitive delay in infancy

Aim To develop a brief, parent-completed instrument (‘ERIC’) for detection of cognitive delay in 10-24 month-olds born preterm, or with low birth weight, or with perinatal complications, and to establish its diagnostic properties. Method Scores were collected from parents of 317 children meeting ≥1 inclusion criteria (birth weight <1500g; gestational age <34 completed weeks; 5-minute Apgar <7; presence of hypoxic-ischemic encephalopathy) and meeting no exclusion criteria. Children were assessed for cognitive delay using a criterion score on the Bayley Scales of Infant and Toddler Development Cognitive Scale III1 <80. Items were retained according to their individual associations with delay. Sensitivity, specificity, Positive and Negative Predictive Values were estimated and a truncated ERIC was developed for use <14 months. Results ERIC detected 17 out of 18 delayed children in the sample, with 94.4% sensitivity (95% CI [confidence interval] 83.9-100%), 76.9% specificity (72.1-81.7%), 19.8% positive predictive value (11.4-28.2%); 99.6% negative predictive value (98.7-100%); 4.09 likelihood ratio positive; and 0.07 likelihood ratio negative; the associated Area under the Curve was .909 (.829-.960). Interpretation ERIC has potential value as a quickly-administered diagnostic instrument for the absence of early cognitive delay in preterm or premature infants of 10-24 months, and as a screen for cognitive delay. Further research may be needed before ERIC can be recommended for wide-scale use.

It is always on your mind: experiences and perceptions of falling of older people and their carers and the potential of a mobile falls detection device

Background. Falls and fear of falling present a major risk to older people as both can affect their quality of life and independence. Mobile assistive technologies (AT) fall detection devices may maximise the potential for older people to live independently for as long as possible within their own homes by facilitating early detection of falls. Aims. To explore the experiences and perceptions of older people and their carers as to the potential of a mobile falls detection AT device. Methods. Nine focus groups with 47 participants including both older people with a range of health conditions and their carers. Interviews were audio recorded, transcribed verbatim, and thematically analysed. Results. Four key themes were identified relating to participants’ experiences and perceptions of falling and the potential impact of a mobile falls detector: cause of falling, falling as everyday vulnerability, the environmental context of falling, and regaining confidence and independence by having a mobile falls detector. Conclusion. The perceived benefits of a mobile falls detector may differ between older people and their carers. The experience of falling has to be taken into account when designing mobile assistive technology devices as these may influence perceptions of such devices and how older people utilise them.

Detection of Streptococcus agalactiae colonization in pregnant women by using combined swab cultures: cross-sectional prevalence study

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Detection of numerical chromosome anomalies in interphase cells of benign and malignant thyroid lesions using fluorescence in situ hybridization

Benign and malignant thyroid tumors constitute a wide range of neoplasias showing recurrent chromosome abnormalities. In an attempt to characterize specific numerical chromosome abnormalities in thyroid tissues, We present here the findings from a study of archival samples depicted by 10 malignant tumors, 30 benign lesions, and 10 normal thyroid tissues. Fluorescence in situ hybridization was performed on noncultured samples using biotinylated centromere-specific probes for chromosomes 7, 10, and 17. Trisomy or tetrasomy 7 were present in 19 benign and in 7 malignant tumors. Trisomy 10 or 17 were observed in 18 adenomas or goiters and in 9 carcinomas, and monosomy 17 was seen in 2 carcinomas. Our findings suggest that such abnormalities are an in vivo phenomenon and may be important in the neoplastic proliferation of thyroid gland. (C) Elsevier B.V., 2000. All rights reserved.

Fluorescence spectroscopy for the detection of tongue carcinoma - validation in an animal model

The efficacy of fluorescence spectroscopy to detect squamous cell carcinoma is evaluated in an animal model following laser excitation at 442 and 532 nm. Lesions are chemically induced with a topical DMBA application at the left lateral tongue of Golden Syrian hamsters. The animals are investigated every 2 weeks after the 4th week of induction until a total of 26 weeks. The right lateral tongue of each animal is considered as a control site (normal contralateral tissue) and the induced lesions are analyzed as a set of points covering the entire clinically detectable area. Based on fluorescence spectral differences, four indices are determined to discriminate normal and carcinoma tissues, based on intraspectral analysis. The spectral data are also analyzed using a multivariate data analysis and the results are compared with histology as the diagnostic gold standard. The best result achieved is for blue excitation using the KNN (K-nearest neighbor, a interspectral analysis) algorithm with a sensitivity of 95.7% and a specificity of 91.6%. These high indices indicate that fluorescence spectroscopy may constitute a fast noninvasive auxiliary tool for diagnostic of cancer within the oral cavity. (C) 2008 Society of Photo-Optical Instrumentation Engineers.

A label-free immunosensor based on recordable compact disk chip for early diagnostic of the dengue virus infection

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

HPLC-EICD: An Useful Tool for the Pursuit of Novel Analytical Strategies for the Detection of Antioxidant Secondary Metabolites

Living cells are continuously exposed to a variety of challenges that exert oxidative stress and are directly related with senescence and the onset of various pathological conditions such as coronary heart disease, rheumatoid arthritis and cancer. Nevertheless, living organisms have developed a complex antioxidant network to counteract reactive species that are detrimental to life. With the aim of bio-prospecting plant species from the Brazilian Cerrado and Atlantic Forest, we have established a methodology to detect secondary antioxidant metabolites in crude extracts and fractions obtained from plant species. Combining HPLC with an electrochemical detector allowed us to detect micromolecules that showed antioxidant activities in Chimarrhis turbinata (DC) leaf extracts. Comparison with purified flavonoid standards led us to identify the compounds in their natural matrices giving valuable information on their antioxidant capacity.

Fine needle aspirate cell blocks are reliable for detection of hormone receptors and HER-2 by immunohistochemistry in breast carcinoma

Aims: To evaluate the reliability of fine needle aspirate cell blocks in the assessment of oestrogen receptor (ER), progesterone receptor (PR) and HER-2/neu proteins by immunohistochemistry in comparison with surgical specimens. Materials and methods: This is a retrospective study of 62 cases of breast carcinoma diagnosed by fine needle aspiration cytology (FNAC) and confirmed using the surgical specimen. Immunohistochemical tests were performed to assess the presence of oestrogen receptor (ER), progesterone receptor (PR) and HER-2/neu proteins in cell blocks and the corresponding surgical specimens. The cell block method used alcohol prior to formalin fixation. Cases with 10% or more stained cells were considered positive for ER and PR. Positivity for HER-2/neu was assessed on a scale of 0-3+. The criterion for positivity was a score of 3+. Results: Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy of the cell blocks in the investigation of ER, PR and HER-2/neu protein (3+) were (%): ER, 92.7, 85.7, 92.7, 85.7 and 90.3; PR, 92.7, 94.7, 97.4, 87.0 and 93.5; HER-2/neu, 70.0, 100.0, 100.0, 94.5 and 95.2. Discrepancies were seen in cell blocks in the 1+ and 2+ HER-2/neu staining scores: two of 12 cases scoring 2+ and one case of 26 scoring 1+ on cell blocks scored 3+ on surgical specimens. The correlation index between cell block and corresponding surgical specimen varied from 90% to 94%. Conclusion: Cell blocks provide a useful method of assessing ER, PR and HER-2/neu, mainly for inoperable and recurrent cases, but consideration should be given to carrying out FISH analysis on 1+ as well as 2+ HER-2/neu results. © 2012 Blackwell Publishing Ltd.

Detection of determinant genes and diagnostic via Item Response Theory

ABSTRACT: This work presents a method to analyze characteristics of a set of genes that can have an influence in a certain anomaly, such as a particular type of cancer. A measure is proposed with the objective of diagnosing individuals regarding the anomaly under study and some characteristics of the genes are analyzed. Maximum likelihood equations for general and particular cases are presented.

Correlation of clinical, cytological and histological findings in oral squamous cell carcinomas

The present study aimed to investigate the efficiency of exfoliative cytology by correlating the clinical lesions of oral squamous cell carcinoma (OSCC) with exfoliative cytology and histopathological findings. Cases of OSCC diagnosed between 1984 and 2010 were analyzed. The inclusion criteria for the present study were the availability of detailed clinical findings and a diagnosis of the disease through exfoliative cytology and histopathology. The cases were assessed and assigned scores, which were then submitted to modal expression analysis, which considers the higher frequency scores, thus relating the variables. The cytological findings demonstrated that the majority of the cases had malignant potential. Exfoliative cytology should be used as a supplementary tool for the diagnosis of OSCC, as it enables the early detection of these lesions. However, cytology should not be used as a substitute for histopathological examination.