Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine

DNA cytosine-5 methylation is a well-studied epigenetic pathway implicated in gene expression control and disease pathogenesis. Different technologies have been developed to examine the distribution of 5-methylcytosine (5mC) in specific sequences of the genome. Recently, substantial amounts of 5-hydroxymethylcytosine (5hmC), most likely derived from enzymatic oxidation of 5mC by TET1, have been detected in certain mammalian tissues. Here, we have examined the ability of several commonly used DNA methylation profiling methods to distinguish between 5mC and 5hmC. We show that techniques based on sodium bisulfite treatment of DNA are incapable of distinguishing between the two modified bases. In contrast, techniques based on immunoprecipitation with anti-5mC antibody (methylated DNA immunoprecipitation, MeDIP) or those based on proteins that bind to methylated CpG sequences (e.g. methylated-CpG island recovery assay, MIRA) do not detect 5hmC and are specific for 5mC unless both modified bases occur in the same DNA fragment. We also report that several methyl-CpG binding proteins including MBD1, MBD2 and MBD4 do not bind to sequences containing 5hmC. Selective mapping of 5hmC will require the development of unique tools for the detection of this modified base

The QCD phase diagram at nonzero quark density

We determine the phase diagram of QCD on the \mu-T plane for small to moderate chemical potentials. Two transition lines are defined with two quantities, the chiral condensate and the strange quark number susceptibility. The calculations are carried out on N_t =6,8 and 10 lattices generated with a Symanzik improved gauge and stout-link improved 2+1 flavor staggered fermion action using physical quark masses. After carrying out the continuum extrapolation we find that both quantities result in a similar curvature of the transition line. Furthermore, our results indicate that in leading order the width of the transition region remains essentially the same as the chemical potential is increased.Comment: 12 pages, 6 figure

Get screened: a pragmatic randomized controlled trial to increase mammography and colorectal cancer screening in a large, safety net practice

Abstract Background Most randomized controlled trials of interventions designed to promote cancer screening, particularly those targeting poor and minority patients, enroll selected patients. Relatively little is known about the benefits of these interventions among unselected patients. Methods/Design "Get Screened" is an American Cancer Society-sponsored randomized controlled trial designed to promote mammography and colorectal cancer screening in a primary care practice serving low-income patients. Eligible patients who are past due for mammography or colorectal cancer screening are entered into a tracking registry and randomly assigned to early or delayed intervention. This 6-month intervention is multimodal, involving patient prompts, clinician prompts, and outreach. At the time of the patient visit, eligible patients receive a low-literacy patient education tool. At the same time, clinicians receive a prompt to remind them to order the test and, when appropriate, a tool designed to simplify colorectal cancer screening decision-making. Patient outreach consists of personalized letters, automated telephone reminders, assistance with scheduling, and linkage of uninsured patients to the local National Breast and Cervical Cancer Early Detection program. Interventions are repeated for patients who fail to respond to early interventions. We will compare rates of screening between randomized groups, as well as planned secondary analyses of minority patients and uninsured patients. Data from the pilot phase show that this multimodal intervention triples rates of cancer screening (adjusted odds ratio 3.63; 95% CI 2.35 - 5.61). Discussion This study protocol is designed to assess a multimodal approach to promotion of breast and colorectal cancer screening among underserved patients. We hypothesize that a multimodal approach will significantly improve cancer screening rates. The trial was registered at Clinical Trials.gov NCT00818857http://deepblue.lib.umich.edu/bitstream/2027.42/78264/1/1472-6963-10-280.xmlhttp://deepblue.lib.umich.edu/bitstream/2027.42/78264/2/1472-6963-10-280.pdfPeer Reviewe

Population genomics of domestic and wild yeasts

The natural genetics of an organism is determined by the distribution of sequences of its genome. Here we present one- to four-fold, with some deeper, coverage of the genome sequences of over seventy isolates of the domesticated baker's yeast, _Saccharomyces cerevisiae_, and its closest relative, the wild _S. paradoxus_, which has never been associated with human activity. These were collected from numerous geographic locations and sources (including wild, clinical, baking, wine, laboratory and food spoilage). These sequences provide an unprecedented view of the population structure, natural (and artificial) selection and genome evolution in these species. Variation in gene content, SNPs, indels, copy numbers and transposable elements provide insights into the evolution of different lineages. Phenotypic variation broadly correlates with global genome-wide phylogenetic relationships however there is no correlation with source. _S. paradoxus_ populations are well delineated along geographic boundaries while the variation among worldwide _S. cerevisiae_ isolates show less differentiation and is comparable to a single _S. paradoxus_ population. Rather than one or two domestication events leading to the extant baker's yeasts, the population structure of _S. cerevisiae_ shows a few well defined geographically isolated lineages and many different mosaics of these lineages, supporting the notion that human influence provided the opportunity for outbreeding and production of new combinations of pre-existing variation

Evaluation of a self-management programme for congestive heart failure patients: design of a randomised controlled trial

BACKGROUND: Congestive heart failure (CHF) has a substantial impact on care utilisation and quality of life. It is crucial for patients to cope with CHF adequately, if they are to live an acceptable life. Self-management may play an important role in this regard. Previous studies have shown the effectiveness of the 'Chronic Disease Self-Management Program' (CDSMP), a group-based cognitive behavioural programme for patients with various chronic conditions. However, the programme's effectiveness has not yet been studied specifically among CHF patients. This paper presents the design of a randomised controlled trial to evaluate the effects of the CDSMP on psychosocial attributes, health behaviour, quality of life, and health care utilisation of CHF patients. METHODS/DESIGN: The programme is being evaluated in a two-group randomised controlled trial. Patients were eligible if they had been diagnosed with CHF and experienced slight to marked limitation of physical activity. They were selected from the Heart Failure and/or Cardiology Outpatient Clinics of six hospitals. Eligible patients underwent a baseline assessment and were subsequently allocated to the intervention or control group. Patients allocated to the intervention group were invited to attend the self-management programme consisting of six weekly sessions, led by a CHF nurse specialist and a CHF patient. Those allocated to the control group received care as usual. Follow-up measurements are being carried out immediately after the intervention period, and six and twelve months after the start of the intervention. An effect evaluation and a process evaluation are being conducted. The primary outcomes of the effect evaluation are self-efficacy expectancies, perceived control, and cognitive symptom management. The secondary outcome measures are smoking and drinking behaviour, Body Mass Index (BMI), physical activity level, self-care behaviour, health-related quality of life, perceived autonomy, symptoms of anxiety and depression, and health care utilisation. The programme's feasibility is assessed by measuring compliance with the protocol, patients' attendance and adherence, and the opinions about the programme. DISCUSSION: A total number of 318 patients were included in the trial. At present, follow-up data are being collected. The results of the trial become clear after completion of the data collection in January 2007. TRIAL REGISTRATION: Trialregister () ISRCTN88363287

Medical image colorization for better visualization and segmentation

Medical images contain precious anatomical information for clinical procedures. Improved understanding of medical modality may contribute significantly in arena of medical image analysis. This paper investigates enhancement of monochromatic medical modality into colorized images. Improving the contrast of anatomical structures facilitates precise segmentation. The proposed framework starts with pre-processing to remove noise and improve edge information. Then colour information is embedded to each pixel of a subject image. A resulting image has a potential to portray better anatomical information than a conventional monochromatic image. To evaluate the performance of colorized medical modality, the structural similarity index and the peak signal to noise ratio are computed. Supremacy of proposed colorization is validated by segmentation experiments and compared with greyscale monochromatic images

Alcohol use and abuse in training conscripts of the Hellenic navy

OBJECTIVES: Alcohol abuse and addiction are big current problems of the developed world having multivariate causality and multiple effects. Alcohol abuse in young people is a matter of central importance due to its wide range long lasting effects, especially so in Greece where the problem has only recently started growing. The Hellenic Navy is interested in the complications of alcohol abuse in training conscripts. Because young conscripts will be placed in demanding positions, but also because in Greece the military service is obligatory and represents an important period for the socialization of young men. METHODS: In the present study, levels of alcohol use and abuse were measured in a sample of 650 male training conscripts of the Hellenic Navy. The tools used are: (a) two questionnaires measuring frequency and quantity of alcohol consumption and psychosocial variables, (b) the CAGE test, which is a questionnaire measuring hidden alcoholism. RESULTS: 38,1% conscripts were characterized problematic drinkers according the adolescents criteria. Additional psychological complications were related to alcohol use. Using the stricter criterion for adults (plus psychological complications) 8.9% were found to be problematic drinkers. The use of CAGE questionnaire which is measuring hidden alcoholism, identified 16% of the total sample as hidden alcoholics. DISCUSSION: The findings regarding unregular levels of alcohol use and abuse are presented as well as their relation to psychosocial complications and to demographic characteristics. The results are discussed in the light of Creek and international bibliography