Automated Hierarchical Image Segmentation Based on Merging of Quadrilaterals

Proceedings of the 6th WSEAS International Conference on Signal Processing, Computational Geometry & Artifical Vision, 2006, p. 135-140This paper proposes a quadrilateral-based and automated hierarchical segmentation method, in which quadrilaterals are first constructed from an edge map, where neighboring quadrilaterals with similar features of interest are then merged together in a hierarchical mode to form regions. When evaluated qualitatively and quantitatively, the proposed method outperforms three traditional and commonly-used techniques, namely, K-means clustering, seeded region growing and quadrilateral-based segmentation. It is shown by experimental results that our proposed method is robust in both recovering missed important regions while preventing unnecessary over-segmentation, and offers an efficient description of the segmented objects conducive to content-based applications.postprintThe 6th WSEAS International Conference on Signal Processing, Computational Geometry & Artificial Vision (ISCGAV'06), Crete, Greece, August 2006. in Conference Proceedings, 2006, p. 135-14

Development and Validation of the Chinese Attitudes to Starting Insulin Questionnaire (Ch-ASIQ) for Primary Care Patients with Type 2 Diabetes

Objectives: To develop and evaluate the psychometric properties of a Chinese questionnaire which assesses the barriers and enablers to commencing insulin in primary care patients with poorly controlled Type 2 diabetes. Research Design and Method: Questionnaire items were identified using literature review. Content validation was performed and items were further refined using an expert panel. Following translation, back translation and cognitive debriefing, the translated Chinese questionnaire was piloted on target patients. Exploratory factor analysis and item-scale correlations were performed to test the construct validity of the subscales and items. Internal reliability was tested by Cronbach's alpha. Results: Twenty-seven identified items underwent content validation, translation and cognitive debriefing. The translated questionnaire was piloted on 303 insulin naïve (never taken insulin) Type 2 diabetes patients recruited from 10 government-funded primary care clinics across Hong Kong. Sufficient variability in the dataset for factor analysis was confirmed by Bartlett's Test of Sphericity (P 0.4 and Eigenvalues >1. Total variance for the 10 factors was 66.22%. Kaiser-Meyer-Olkin measure was 0.725. Cronbach's alpha coefficients for the first four factors were ≥0.6 identifying four subscales to which 13 items correlated. Remaining sub-scales and items with poor internal reliability were deleted. The final 13-item instrument had a four scale structure addressing: 'Self-image and stigmatization'; 'Factors promoting self-efficacy; 'Fear of pain or needles'; and 'Time and family support'. Conclusion: The Chinese Attitudes to Starting Insulin Questionnaire (Ch-ASIQ) appears to be a reliable and valid measure for assessing barriers to starting insulin. This short instrument is easy to administer and may be used by healthcare providers and researchers as an assessment tool for Chinese diabetic primary care patients, including the elderly, who are unwilling to start insulin. © 2013 Fu et al.published_or_final_versio

Increased entropy of signal transduction in the cancer metastasis phenotype

Studies into the statistical properties of biological networks have led to important biological insights, such as the presence of hubs and hierarchical modularity. There is also a growing interest in studying the statistical properties of networks in the context of cancer genomics. However, relatively little is known as to what network features differ between the cancer and normal cell physiologies, or between different cancer cell phenotypes. Based on the observation that frequent genomic alterations underlie a more aggressive cancer phenotype, we asked if such an effect could be detectable as an increase in the randomness of local gene expression patterns. Using a breast cancer gene expression data set and a model network of protein interactions we derive constrained weighted networks defined by a stochastic information flux matrix reflecting expression correlations between interacting proteins. Based on this stochastic matrix we propose and compute an entropy measure that quantifies the degree of randomness in the local pattern of information flux around single genes. By comparing the local entropies in the non-metastatic versus metastatic breast cancer networks, we here show that breast cancers that metastasize are characterised by a small yet significant increase in the degree of randomness of local expression patterns. We validate this result in three additional breast cancer expression data sets and demonstrate that local entropy better characterises the metastatic phenotype than other non-entropy based measures. We show that increases in entropy can be used to identify genes and signalling pathways implicated in breast cancer metastasis. Further exploration of such integrated cancer expression and protein interaction networks will therefore be a fruitful endeavour.Comment: 5 figures, 2 Supplementary Figures and Table

Genome maps across 26 human populations reveal population-specific patterns of structural variation.

Large structural variants (SVs) in the human genome are difficult to detect and study by conventional sequencing technologies. With long-range genome analysis platforms, such as optical mapping, one can identify large SVs (>2 kb) across the genome in one experiment. Analyzing optical genome maps of 154 individuals from the 26 populations sequenced in the 1000 Genomes Project, we find that phylogenetic population patterns of large SVs are similar to those of single nucleotide variations in 86% of the human genome, while ~2% of the genome has high structural complexity. We are able to characterize SVs in many intractable regions of the genome, including segmental duplications and subtelomeric, pericentromeric, and acrocentric areas. In addition, we discover ~60 Mb of non-redundant genome content missing in the reference genome sequence assembly. Our results highlight the need for a comprehensive set of alternate haplotypes from different populations to represent SV patterns in the genome

A critical evaluation of network and pathway based classifiers for outcome prediction in breast cancer

Recently, several classifiers that combine primary tumor data, like gene expression data, and secondary data sources, such as protein-protein interaction networks, have been proposed for predicting outcome in breast cancer. In these approaches, new composite features are typically constructed by aggregating the expression levels of several genes. The secondary data sources are employed to guide this aggregation. Although many studies claim that these approaches improve classification performance over single gene classifiers, the gain in performance is difficult to assess. This stems mainly from the fact that different breast cancer data sets and validation procedures are employed to assess the performance. Here we address these issues by employing a large cohort of six breast cancer data sets as benchmark set and by performing an unbiased evaluation of the classification accuracies of the different approaches. Contrary to previous claims, we find that composite feature classifiers do not outperform simple single gene classifiers. We investigate the effect of (1) the number of selected features; (2) the specific gene set from which features are selected; (3) the size of the training set and (4) the heterogeneity of the data set on the performance of composite feature and single gene classifiers. Strikingly, we find that randomization of secondary data sources, which destroys all biological information in these sources, does not result in a deterioration in performance of composite feature classifiers. Finally, we show that when a proper correction for gene set size is performed, the stability of single gene sets is similar to the stability of composite feature sets. Based on these results there is currently no reason to prefer prognostic classifiers based on composite features over single gene classifiers for predicting outcome in breast cancer

The breast cancer somatic 'muta-ome': tackling the complexity

Acquired somatic mutations are responsible for approximately 90% of breast tumours. However, only one somatic aberration, amplification of the HER2 locus, is currently used to define a clinical subtype, one that accounts for approximately 10% to 15% of breast tumours. In recent years, a number of mutational profiling studies have attempted to further identify clinically relevant mutations. While these studies have confirmed the oncogenic or tumour suppressor role of many known suspects, they have exposed complexity as a main feature of the breast cancer mutational landscape (the 'muta-ome'). The two defining features of this complexity are (a) a surprising richness of low-frequency mutants contrasting with the relative rarity of high-frequency events and (b) the relatively large number of somatic genomic aberrations (approximately 20 to 50) driving an average tumour. Structural features of this complex landscape have begun to emerge from follow-up studies that have tackled the complexity by integrating the spectrum of genomic mutations with a variety of complementary biological knowledge databases. Among these structural features are the growing links between somatic gene disruptions and those conferring breast cancer risk, mutually exclusive coexistence and synergistic mutational patterns, and a clearly non-random distribution of mutations implicating specific molecular pathways in breast tumour initiation and progression. Recognising that a shift from a gene-centric to a pathway-centric approach is necessary, we envisage that further progress in identifying clinically relevant genomic aberration patterns and associated breast cancer subtypes will require not only multi-dimensional integrative analyses that combine mutational and functional profiles, but also larger profiling studies that use second- and third-generation sequencing technologies in order to fill out the important gaps in the current mutational landscape

Expression, Localization, and Phosphorylation of Akt1 in Benign and Malignant Thyroid Lesions

The serine/threonine protein kinase Akt is a key molecule in the phosphatidyl inositol 3-kinase pathway that is often overactivated in human cancers. Three Akt isoforms (Akt1, Akt2, Akt3) have been identified in human cells and they show different distribution and have non-redundant functions. The aim of this study was to determine whether the expression, phosphorylation, and localization of Akt1 isoform in human thyroid malignant lesions are different from those in benign lesions. Nuclear and cytoplasmic fractions were isolated from tissue samples and Western blot method was used to detect Akt1 presence in both cellular fractions. Akt1 expression was also assessed by ELISA method. To estimate Akt1 phosphorylation, kinase was immunoprecipitated from cell lysates and tested with anti-phospho-Akt antibodies. The Akt1 expression in majority of thyroid cancer samples was significantly higher than in benign lesions (p < 0.05). Akt1 both in differentiated cancers (follicular and papillary) and benign lesions was localized mainly in cytoplasmic fraction. In two of three anaplastic cancer samples Akt1 was predominantly localized in nucleus. The ratio of phosphorylated Akt1 to total Akt1 was lower in cancers than in non-neoplastic lesions and adenomas. Thus, although Akt1 seems to be overexpressed in thyroid neoplasms, its high phosphorylation is not characteristic for thyroid cancers

Pulse wave velocity is associated with increased plasma oxLDL in ageing but not with FGF21 and habitual exercise

Fibroblast growth factor 21 (FGF21) and adiponectin increase expression of genes involved in antioxidant pathways, but their roles in mediating oxidative stress and arterial stiffness with ageing and habitual exercise remain unknown. We explored the role of the FGF21–adiponectin axis in mediating oxidative stress and arterial stiffness with ageing and habitual exercise. Eighty age- and sex-matched healthy individuals were assigned to younger sedentary or active (18–36 years old,n=20 each) and older sedentary or active (45–80 years old,n=20 each) groups. Arterial stiffness was measured indirectly using pulse wave velocity (PWV). Fasted plasma concentrations of FGF21, adiponectin and oxidized low-density lipoprotein (oxLDL) were measured. PWV was 0.2-fold higher and oxLDL concentration was 25.6% higher (both p<0.001) in older than younger adults, despite no difference in FGF21 concentration (p=0.097) between age groups. PWV (p=0.09) and oxLDL concentration (p=0.275) did not differ between activity groups but FGF21 concentration was 9% lower in active than sedentary individuals (p=0.011). Adiponectin concentration did not differ by age (p=0.642) or exercise habits (p=0.821). In conclusion, age, but not habitual exercise, was associated with higher oxidative stress and arterial stiffness. FGF21 and adiponectin did not differ between younger and older adults, unlikely mediating oxidative stress and arterial stiffness in healthy adults. <br

Virtual versus Physical Channel for Sex Networking in Men Having Sex with Men of Sauna Customers in the City of Hong Kong

BACKGROUND: Advances in communication technology may affect networking pattern, thereby influencing the dynamics of sex partnership. The aim of the study is to explore the impacts of partner sourcing through internet and related channels on exposure risk to sexually transmitted infections (STI) including HIV. METHODS: Using venue-based sampling, a cross-sectional questionnaire survey was conducted at saunas frequented by men having sex with men (MSM) in Hong Kong. Comparison was made between MSM sourcing partners through physical venues alone versus concomitant users of physical and virtual channels, the latter referring to internet and smart-phone applications, using bivariate logistic regression. RESULTS: Over a 7-week study period, 299 MSM were recruited from 9 saunas. Three main types of sex partners were distinguished: steady (46.8%), regular (26.4%) and casual (96.0%) partners. Users of sauna (n = 78) were compared with concomitant users of saunas and virtual channels (n = 179) for partner sourcing. Sauna-visiting virtual channel users were younger and inclined to use selected physical venues for sourcing partners. Smart-phone users (n = 90) were not different from other internet-users in terms of age, education level and single/mixed self-identified body appearance. Classifying respondents into high risk and low risk MSM by their frequency of condom use, concomitant use of both sauna and virtual channels accounted for a higher proportion in the high risk category (71.6% vs. 58.2%, OR = 1.81, p<0.05). In virtual channel users, partner sourcing through smart-phone was not associated with a higher practice of unprotected sex. CONCLUSION: MSM sauna customers commonly use virtual channels for sex partner sourcing. Unprotected sex is more prevalent in sauna customers who use virtual channel for sex partner sourcing. While the popularity of smart-phone is rising, its use is not associated with increased behavioural risk for HIV/STI transmission