A fast algorithm for genome-wide haplotype pattern mining

<p>Abstract</p> <p>Background</p> <p>Identifying the genetic components of common diseases has long been an important area of research. Recently, genotyping technology has reached the level where it is cost effective to genotype single nucleotide polymorphism (SNP) markers covering the entire genome, in thousands of individuals, and analyse such data for markers associated with a diseases. The statistical power to detect association, however, is limited when markers are analysed one at a time. This can be alleviated by considering multiple markers simultaneously. The <it>Haplotype Pattern Mining </it>(HPM) method is a machine learning approach to do exactly this.</p> <p>Results</p> <p>We present a new, faster algorithm for the HPM method. The new approach use patterns of haplotype diversity in the genome: locally in the genome, the number of observed haplotypes is much smaller than the total number of possible haplotypes. We show that the new approach speeds up the HPM method with a factor of 2 on a genome-wide dataset with 5009 individuals typed in 491208 markers using default parameters and more if the pattern length is increased.</p> <p>Conclusion</p> <p>The new algorithm speeds up the HPM method and we show that it is feasible to apply HPM to whole genome association mapping with thousands of individuals and hundreds of thousands of markers.</p

Root exudates associated with the resistance of four chickpea cultivars (Cicer arietinum) to two races of Fusarium oxysporum f.sp. ciceris

The germination of race 1 spores of F. o. f.sp. ciceris was significantly inhibited by the root exudate of the wilt-resistant chickpea cultivars CPS1 and WR315 compared with untreated spores and spores treated with root exudates from susceptible cultivars. The effect was concn dependent, such that the exudate from 1 g of root in 2 ml of water almost completely inhibited spore germination, whereas the exudate from 1 g of root in 20 ml of water did not. The inhibitory effects of the active exudates were negated when the apolar components of the exudates were removed by extraction with ethyl acetate. The root exudates of the susceptible cv. JG62 and the late wilting cv. H208 did not inhibit germination. The hyphal growth of germinated spores was also strongly inhibited by the concentrated exudates of CPS1 and WR315, and diluted exudates were less potent. The highest concn of the exudate of the susceptible cv. JG62 showed some inhibition of hyphal growth, whereas none of the exudates of H208 contained any antifungal activity. The effect of the exudates on the spores of race 2 was similar to that reported for race 1, except that the water-soluble components of the crude root exudate of WR315 after ethyl acetate extraction also significantly inhibited germination. Overall, the spores of race 2 appeared to be more susceptible to the effects of the exudates. The ethyl acetate fractions of the root exudates of CPS1 and WR315 strongly inhibited germination and hyphal growth of both race 1 and race 2, the effect being concn dependent. It is concluded that the resistance of chickpeas to vascular wilt depends, at least in part, on antifungal activity of root exudates. Differences in the expression of resistance in the field could depend upon the concn or rate of production of constitutive antifungal components by the root

Factors Influencing Receipt of Iron Supplementation by Young Children and their Mothers in Rural India: Local and National Cross-Sectional Studies

<p>Abstract</p> <p>Background</p> <p>In India, 55% of women and 69.5% of preschool children are anaemic despite national policies recommending routine iron supplementation. Understanding factors associated with receipt of iron in the field could help optimise implementation of anaemia control policies. Thus, we undertook 1) a cross-sectional study to evaluate iron supplementation to children (and mothers) in rural Karnataka, India, and 2) an analysis of all-India rural data from the National Family Health Study 2005-6 (NFHS-3).</p> <p>Methods</p> <p>All children aged 12-23 months and their mothers served by 6 of 8 randomly selected sub-centres managed by 2 rural Primary Health Centres of rural Karnataka were eligible for the Karnataka Study, conducted between August and October 2008. Socioeconomic and demographic data, access to health services and iron receipt were recorded. Secondly, NFHS-3 rural data were analysed. For both studies, logistic regression was used to evaluate factors associated with receipt of iron.</p> <p>Results</p> <p>The Karnataka Study recruited 405 children and 377 of their mothers. 41.5% of children had received iron, and 11.5% received iron through the public system. By multiple logistic regression, factors associated with children's receipt of iron included: wealth (Odds Ratio (OR) 2.63 [95% CI 1.11, 6.24] for top vs bottom wealth quintile), male sex (OR 2.45 [1.47, 4.10]), mother receiving postnatal iron (OR 2.31 [1.25, 4.28]), mother having undergone antenatal blood test (OR 2.10 [1.09, 4.03]); Muslim religion (OR 0.02 [0.00, 0.27]), attendance at Anganwadi centre (OR 0.23 [0.11, 0.49]), fully vaccinated (OR 0.33 [0.15, 0.75]), or children of mothers with more antenatal health visits (8-9 visits OR 0.25 [0.11, 0.55]) were less likely to receive iron. Nationally, 3.7% of rural children were receiving iron; this was associated with wealth (OR 1.12 [1.02, 1.23] per quintile), maternal education (compared with no education: completed secondary education OR 2.15 [1.17, 3.97], maternal antenatal iron (2.24 [1.56, 3.22]), and child attending an Anganwadi (OR 1.47 [1.20, 1.80]).</p> <p>Conclusion</p> <p>In rural India, public distribution of iron to children is inadequate and disparities exist. Measures to optimize receipt of government supplied iron to all children regardless of wealth and ethnic background could help alleviate anaemia in this population.</p

The Role of Health Systems Factors in Facilitating Access to Psychotropic Medicines: A Cross-Sectional Analysis of the WHO-AIMS in 63 Low- and Middle-Income Countries

In a cross-sectional analysis of WHO-AIMS data, Ryan McBain and colleagues investigate the associations between health system components and access to psychotropic drugs in 63 low and middle income countries

Comparative Expression Profiling of Leishmania: Modulation in Gene Expression between Species and in Different Host Genetic Backgrounds

The single-celled parasite Leishmania, transmitted by sand flies in more than 88 tropical and sub-tropical countries globally, infects man and other mammals, causing a spectrum of diseases called the leishmaniases. Over 12 million people are currently infected worldwide with 2 million new cases reported each year. The type of leishmaniasis that develops in the mammalian host is dependent on the species of infecting parasite and the immune response to infection (that can be influenced by host genetic variation). Our research is focused on identifying parasite factors that contribute to pathogenicity in the host and understanding how these might differ between parasite species that give rise to the different clinical forms of leishmaniasis. Molecules of this type might lead to new therapeutic tools in the longer term. In this paper, we report a comparative analysis of gene expression profiles in three Leishmania species that give rise to different types of disease, focusing on the intracellular stages that reside in mammalian macrophages. Our results show that there are only a small number of differences between these parasite species, with host genetics playing only a minor role in influencing the parasites' response to their intracellular habitat. These small changes may be significant, however, in determining the clinical outcome of infection

Equity in healthcare for coronary heart disease, Wales (UK) 2004–2010: A population-based electronic cohort study

Despite substantial falls in coronary heart disease (CHD) mortality in the United Kingdom (UK), marked socioeconomic inequalities in CHD risk factors and CHD mortality persist. We investigated whether inequity in CHD healthcare in Wales (UK) could contribute to the observed social gradient in CHD mortality. Linking data from primary and secondary care we constructed an electronic cohort of individuals (n = 1199342) with six year follow-up, 2004–2010. We identified indications for recommended CHD interventions, measured time to their delivery, and estimated risk of receiving the interventions for each of five ordered deprivation groups using a time-to-event approach with Cox regression frailty models. Interventions in primary and secondary prevention included risk-factor measurement, smoking management, statins and antihypertensive therapy, and in established CHD included medication and revascularization. For primary prevention, five of the 11 models favoured the more deprived and one favoured the less deprived. For medication in secondary prevention and established CHD, one of the 15 models favoured the more deprived and one the less deprived. In relation to revascularization, six of the 12 models favoured the less deprived and none favoured the more deprived–this evidence of inequity exemplified by a hazard ratio for revascularization in stable angina of 0.79 (95% confidence interval 0.68, 0.92). The main study limitation is the possibility of under-ascertainment or misclassification of clinical indications and treatment from variability in coding. Primary care components of CHD healthcare were equitably delivered. Evidence of inequity was found for revascularization procedures, although this inequity is likely to have only a modest effect on social gradients in CHD mortality. Policymakers should focus on reducing inequalities in CHD risk factors, particularly smoking, as these, rather than inequity in healthcare, are likely to be key drivers of inequalities in CHD mortality

Association of circulating angiotensin converting enzyme activity with respiratory muscle function in infants

<p>Abstract</p> <p>Background</p> <p>Angiotensin converting enzyme (ACE) gene contains a polymorphism, consisting of either the presence (I) or absence (D) of a 287 base pair fragment. Deletion (D) is associated with increased circulating ACE (cACE) activity. It has been suggested that the D-allele of ACE genotype is associated with power-oriented performance and that cACE activity is correlated with muscle strength. Respiratory muscle function may be similarly influenced. Respiratory muscle strength in infants can be assessed specifically by measurement of the maximum inspiratory pressure during crying (Pi_max). Pressure-time index of the respiratory muscles (PTImus) is a non-invasive method, which assesses the load to capacity ratio of the respiratory muscles.</p> <p>The objective of this study was to determine whether increased cACE activity in infants could be related to greater respiratory muscle strength and to investigate the potential association of cACE with PTImus measurements as well as the association of ACE genotypes with cACE activity and respiratory muscle strength in this population.</p> <p>Methods</p> <p>Serum ACE activity was assayed by using a UV-kinetic method. ACE genotyping was performed by polymerase chain reaction amplification, using DNA from peripheral blood. PTImus was calculated as (Pi_mean/Pi_max) × (Ti/Ttot), where Pi_meanwas the mean inspiratory pressure estimated from airway pressure, generated 100 milliseconds after an occlusion (P_0.1), Pi_maxwas the maximum inspiratory pressure and Ti/Ttot was the ratio of the inspiratory time to the total respiratory cycle time. Pi_maxwas the largest pressure generated during brief airway occlusions performed at the end of a spontaneous crying effort.</p> <p>Results</p> <p>A hundred and ten infants were studied. Infants with D/D genotype had significantly higher serum ACE activity than infants with I/I or I/D genotypes. cACE activity was significantly related to Pi_maxand inversely related to PTImus. No association between ACE genotypes and Pdi_maxmeasurements was found.</p> <p>Conclusions</p> <p>These results suggest that a relation in cACE activity and respiratory muscle function may exist in infants. In addition, an association between ACE genotypes and cACE activity, but not respiratory muscle strength, was demonstrated.</p

Randomised trials relevant to mental health conducted in low and middle-income countries: a survey

<p>Abstract</p> <p>Background</p> <p>A substantial proportion of the psychiatric burden of disease falls on the world's poorest nations, yet relatively little is known about randomised trials conducted in these countries. Our aim was to identify and describe a representative sample of mental health trials from low and middle-income countries.</p> <p>Methods</p> <p>6107 electronic records, most with full text copies, were available following extensive searches for randomised or potentially randomised trials from low and middle-income countries published in 1991, 1995 and 2000. These records were searched to identify studies relevant to mental health. Data on study characteristics were extracted from the full text copies.</p> <p>Results</p> <p>Trials relevant to mental health were reported in only 3% of the records. 176 records reporting 177 trials were identified: 25 were published in 1991, 45 in 1995, and 106 in 2000. Participants from China were represented in 46% of trials described. 68% of trials had <100 participants. The method of sequence generation was described in less than 20% of reports and adequate concealment of allocation was described in only 12% of reports. Participants were most frequently adults with unipolar depression (36/177) or schizophrenia (36/177). 80% of studies evaluated pharmacological interventions, a third of which were not listed by WHO as essential drugs. 41% of reports were indexed on PubMed; this proportion decreased from 68% in 1991 to 32% in 2000.</p> <p>Conclusion</p> <p>In terms of overall health burden, trial research activity from low and middle-income countries in mental health appears to be low, and in no area adequately reflects need.</p

From little things, big things grow: trends and fads in 110 years of Australian ornithology

Publishing histories can reveal changes in ornithological effort, focus or direction through time. This study presents a bibliometric content analysis of Emu (1901&ndash;2011) which revealed 115 trends (long-term changes in publication over time) and 18 fads (temporary increases in publication activity) from the classification of 9,039 articles using 128 codes organised into eight categories (author gender, author affiliation, article type, subject, main focus, main method, geographical scale and geographical location). Across 110 years, private authorship declined, while publications involving universities and multiple institutions increased; from 1960, female authorship increased. Over time, question-driven studies and incidental observations increased and decreased in frequency, respectively. Single species and &lsquo;taxonomic group&rsquo; subjects increased while studies of birds at specific places decreased. The focus of articles shifted from species distribution and activities of the host organisation to breeding, foraging and other biological/ecological topics. Site- and Australian-continental-scales slightly decreased over time; non-Australian studies increased from the 1970s. A wide variety of fads occurred (e.g. articles on bird distribution, 1942&ndash;1951, and using museum specimens, 1906&ndash;1913) though the occurrence of fads decreased over time. Changes over time are correlated with technological, theoretical, social and institutional changes, and suggest ornithological priorities, like those of other scientific disciplines, are temporally labil