Data Compression Concepts and Algorithms and Their Applications to Bioinformatics

Data compression at its base is concerned with how information is organized in data. Understanding this organization can lead to efficient ways of representing the information and hence data compression. In this paper we review the ways in which ideas and approaches fundamental to the theory and practice of data compression have been used in the area of bioinformatics. We look at how basic theoretical ideas from data compression, such as the notions of entropy, mutual information, and complexity have been used for analyzing biological sequences in order to discover hidden patterns, infer phylogenetic relationships between organisms and study viral populations. Finally, we look at how inferred grammars for biological sequences have been used to uncover structure in biological sequences

Data Compression Concepts and Algorithms and Their Applications to Bioinformatics

Data compression at its base is concerned with how information is organized in data. Understanding this organization can lead to efficient ways of representing the information and hence data compression. In this paper we review the ways in which ideas and approaches fundamental to the theory and practice of data compression have been used in the area of bioinformatics. We look at how basic theoretical ideas from data compression, such as the notions of entropy, mutual information, and complexity have been used for analyzing biological sequences in order to discover hidden patterns, infer phylogenetic relationships between organisms and study viral populations. Finally, we look at how inferred grammars for biological sequences have been used to uncover structure in biological sequences

Book Review

Reviewing Frank E. Cooper, Living the Law, Bobbs-Merrill Company, Inc., 195

Early time-locked gamma response and gender specificity

Cataloged from PDF version of article.The aim was to investigate whether gender is a causative factor in the gamma status according to which some individuals respond with time-locked, early gamma response, G+, while the others do not show this response, G-. The sample consisted of 42 volunteer participants (between 19 and 37 years of age with at least 9 years of education). There were 22 females and 20 males. Data were collected under the oddball paradigm. Auditory stimulation (10 ms r/f time, 50 ms duration, 65 dB SPL) consisted of target (2000 Hz; p = .20) stimuli that occurred randomly within a series of standard stimuli (1000 Hz; p = .80). Gamma responses were studied in the amplitude frequency characteristics, in the digitally filtered event-related potentials (f-ERPs) and in the distributions which were obtained using the recently developed time-frequency component analysis (TFCA) technique. Participants were classified into G+ and G- groups with a criterion of full agreement between the results of an automated gamma detection technique and expert opinion. The 2 × 2 × 2 ANOVA on f-ERPs and 2 × 2 × 2 multivariate ANOVA on TFCA distributions showed the main effect of gamma status and gender as significant, and the interaction between gamma status and gender as nonsignificant. Accordingly, individual difference in gamma status is a reliable phenomenon, but this does not depend on gender. There are conflicting findings in the literature concerning the effect of gender on ERP components (N100, P300). The present study showed that if the gamma status is not included in research designs, it may produce a confounding effect on ERP parameters. © 2005 Elsevier B.V. All rights reserved

(Il)Legitimisation of the role of the nation state: Understanding of and reactions to Internet censorship in Turkey

This study aims to explore Turkish citizen-consumers' understanding of and reactions to censorship of websites in Turkey by using in-depth interviews and online ethnography. In an environment where sites such as YouTube and others are increasingly being banned, the citizen-consumers' macro-level understanding is that such censorship is part of a wider ideological plan and their micro-level understanding is that their relationship with the wider global network is reduced, in the sense that they have trouble accessing full information on products, services and experiences. The study revealed that citizen-consumers engage in two types of resistance strategies against such domination by the state: using irony as passive resistance, and using the very same technology used by the state to resist its domination

Risk factors of nasopharyngeal carcinoma in Turkey - an epidemiological survey of the anatolian society of medical oncology

Background: Nasopharyngeal carcinoma is a rare disease in most parts of the world with a multifactorial etiology involving an interaction of genetic, viral, environmental and dietary risk factors. This is the first epidemiologic study aimed to evaluate the risk factors of nasopharyngeal carcinoma in the Turkish population. Methods: We conducted a multicentric, retrospective, case-control study using a standardized questionnaire which captured age, sex, occupation, household type, blood group, dietary habits, smoking, alcohol consumption and oral hygiene. The study included 183 cases and 183 healthy controls matched by sex and age. Multiple logistic regression and univariate analysis were employed. Results: The peak age incidence was 40-50 years and the male to female ratio was 2:1. We observed significant associations between elevated nasopharyngeal carcinoma risk and low socioeconomic status, rural household type (OR:3.95, p0.05); furthermore salty foods had a borderline p value (OR:2.14, p=0.053). Blood type A increased the risk (OR:2.03, p=0.002) while blood type 0 was a protective factor (OR:0.53, p=0.009). Rare habit of teeth brushing (OR:6.17, p<0.001) and ≥10 decayed teeth before diagnosis (OR:2.17, p<0.001) increased the risk. Conclusions: The nasopharyngeal carcinoma risk factors described in the literature are also applicable for the Turkish population. People with type A blood are at risk in Turkey. Salted foods have also a border risk out of the endemic regions. This is the only study showing that poor oral hygene is a serious risk factor for nasopharyngeal carcinoma

New semiquantitative ultrasonographic score for peripheral arterial disease assessment and its association with cardiovascular risk factors

The data concerning the distribution, extent and progression of peripheral arterial disease (PAD), as well as its association with traditional cardiovascular (CV) risk factors, have generally been obtained from studies of patients in advanced stages of the disease undergoing surgical or endovascular treatment. In this study, we have introduced a new semiquantitative ultrasonographic score (ultrasonographic lower limb atherosclerosis (ULLA) score) that is able to categorize lower limb atherosclerotic lesions at all stages of PAD. We then associated these ultrasonographic categories with a CV risk profile. We enrolled 320 consecutive subjects with symptoms suggestive of PAD or with known CV risk factors referring to our angiology unit between 1 July 2014 and 30 June 2015 for ultrasonographic evaluation of the lower limb arteries. Femoropopliteal and run-off segments were categorized together and separately based on their ultrasonographic characteristics. In univariate and multivariate analyses, the ULLA scores were significantly associated with the main CV risk factors, that is, age, male gender, cigarette smoking, arterial hypertension, diabetes, dyslipidemia, sedentary lifestyle, previous CV events and family history of CV disease, and also confirming the specific association of single risk factors with different segments of lower limb arteries. The proposed ULLA score enables a complete evaluation of the entire lower limb atherosclerotic burden, extending the results concerning the association of PAD with CV risk factors to all stages of the disease, including the early stages. It can be feasible that this new score will facilitate better evaluation of the progression of PAD and its prospective role in CV risk stratification

Motives for corporate cash holdings:the CEO optimism effect

We examine the chief executive officer (CEO) optimism effect on managerial motives for cash holdings and find that optimistic and non-optimistic managers have significantly dissimilar purposes for holding more cash. This is consistent with both theory and evidence that optimistic managers are reluctant to use external funds. Optimistic managers hoard cash for growth opportunities, use relatively more cash for capital expenditure and acquisitions, and save more cash in adverse conditions. By contrast, they hold fewer inventories and receivables and their precautionary demand for cash holdings is less than that of non-optimistic managers. In addition, we consider debt conservatism in our model and find no evidence that optimistic managers’ cash hoarding is related to their preference to use debt conservatively. We also document that optimistic managers hold more cash in bad times than non-optimistic managers do. Our work highlights the crucial role that CEO characteristics play in shaping corporate cash holding policy

Glycosaminoglycan and Proteoglycan Biotherapeutics in Articular Cartilage Protection and Repair Strategies: Novel Approaches to Visco?supplementation in Orthobiologics

The aim of this study is to review developments in glycosaminoglycan and proteoglycan research relevant to cartilage repair biology and in particular the treatment of osteoarthritis (OA). Glycosaminoglycans decorate a diverse range of extracellular matrix and cell associated proteoglycans conveying structural organization and physico‐chemical properties to tissues. They play key roles mediating cellular interactions with bioactive growth factors, cytokines, and morphogenetic proteins, and structural fibrillar collagens, cell interactive and extracellular matrix proteoglycans, and glycoproteins which define tissue function. Proteoglycan degradation detrimentally affects tissue functional properties. Therapeutic strategies have been developed to counter these degenerative changes. Neo‐proteoglycans prepared from chondroitin sulfate or hyaluronan and hyaluronan or collagen‐binding peptides emulate the interactive, water imbibing, weight bearing, and surface lubricative properties of native proteoglycans. Many neo‐proteoglycans outperform native proteoglycans in terms of water imbibition, matrix stabilization, and resistance to proteolytic degradation. The biospecificity of recombinant proteoglycans however, provides precise attachment to native target molecules. Visco‐supplements augmented with growth factors/therapeutic cells, hyaluronan, and lubricin (orthobiologicals) have the capacity to lubricate and protect cartilage, control inflammation, and promote cartilage repair and regeneration of early cartilage lesions and may represent a more effective therapeutic approach to the treatment of mild to moderate OA and deserve further study