Combination of DROOL rules and Protégé knowledge bases in the ONTO-H annotation tool

ONTO-H is a semi-automatic collaborative tool for the semantic annotation of documents, built as a Protégé 3.0 tab plug-in. Among its multiple functionalities aimed at easing the document annotation process, ONTO-H uses a rule-based system to create cascading annotations out from a single drag and drop operation from a part of a document into an already existing concept or instance of the domain ontology being used for annotation. It also gives support to the detection of name conflicts and instance duplications in the creation of the annotations. The rule system runs on top of the open source rule engine DROOLS and is connected to the domain ontology used for annotation by means of an ad-hoc programmed Java proxy

A search asymmetry for interocular conflict

When two different images are presented to the two eyes, the percept will alternate between the images (a phenomenon called binocular rivalry). In the present study, we investigate the degree to which such interocular conflict is conspicuous. By using a visual search task, we show that search for interocular conflict is near efficient (15 ms/item) and can lead to a search asymmetry, depending on the contrast in the display. We reconcile our findings with those of Wolfe and Franzel (1988), who reported inefficient search for interocular conflict (26 ms/item) and found no evidence for a search asymmetry. In addition, we provide evidence for the suggestion that differences in search for interocular conflict are contingent on the degree of abnormal fusion of the dissimilar images

Measurement of Receptor-Activated Phosphoinositide Turnover in Rat Brain: Nonequivalence of Inositol Phosphate and CDP-Diacylglycerol Formation

Two methods for the measurement of receptor-activated phosphoinositide turnover were evaluated for their degree of correspondence in slices of rat brain; they involved the Li + -dependent accumulations of either [ 3 H]-inositol-labeled inositol phosphates or [ 3 H]cytidine-labeled CDP-diacylglycerol. In contrast to the expectation that the ratio of these two responses would remain approximately constant, varying degrees of correspondence were obtained. The two extremes are exemplified by carbachol, which elicited large increases in both inositol phosphate and CDP-diacylglycerol labeling, and endothelin, which gave a robust inositol phosphate response with little or no accumulation of 3 H-CDP-diacylglycerol. No instance of the presence of the latter response in the absence of 3 H-inositol phosphate accumulation was observed. Measurement of 3 H-CDP-diacylglycerol accumulation thus may add additional insight into the regulation of phosphoinositide turnover and the complex actions of Li + .Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/66135/1/j.1471-4159.1993.tb03258.x.pd

BOLITA, an Arabidopsis AP2/ERF-like transcription factor that affects cell expansion and proliferation/differentiation pathways

The BOLITA (BOL) gene, an AP2/ERF transcription factor, was characterized with the help of an activation tag mutant and overexpression lines in Arabidopsis and tobacco. The leaf size of plants overexpressing BOL was smaller than wild type plants due to a reduction in both cell size and cell number. Moreover, severe overexpressors showed ectopic callus formation in roots. Accordingly, global gene expression analysis using the overexpression mutant reflected the alterations in cell proliferation, differentiation and growth through expression changes in RBR, CYCD, and TCP genes, as well as genes involved in cell expansion (i.e. expansins and the actin remodeling factor ADF5). Furthermore, the expression of hormone signaling (i.e. auxin and cytokinin), biosynthesis (i.e. ethylene and jasmonic acid) and regulatory genes was found to be perturbed in bol-D mutant leave

Socioeconomic inequality in domains of health: results from the World Health Surveys

<p>Abstract</p> <p>Background</p> <p>In all countries people of lower socioeconomic status evaluate their health more poorly. Yet in reporting overall health, individuals consider multiple domains that comprise their perceived health state. Considered alone, overall measures of self-reported health mask differences in the domains of health. The aim of this study is to compare and assess socioeconomic inequalities in each of the individual health domains and in a separate measure of overall health.</p> <p>Methods</p> <p>Data on 247,037 adults aged 18 or older were analyzed from 57 countries, drawn from all national income groups, participating in the World Health Survey 2002-2004. The analysis was repeated for lower- and higher-income countries. Prevalence estimates of poor self-rated health (SRH) were calculated for each domain and for overall health according to wealth quintiles and education levels. Relative socioeconomic inequalities in SRH were measured for each of the eight health domains and for overall health, according to wealth quintiles and education levels, using the relative index of inequality (RII). A RII value greater than one indicated greater prevalence of self-reported poor health among populations of lower socioeconomic status, called pro-rich inequality.</p> <p>Results</p> <p>There was a descending gradient in the prevalence of poor health, moving from the poorest wealth quintile to the richest, and moving from the lowest to the highest educated groups. Inequalities which favor groups who are advantaged either with respect to wealth or education, were consistently statistically significant in each of the individual domains of health, and in health overall. However the size of these inequalities differed between health domains. The prevalence of reporting poor health was higher in the lower-income country group. Relative socioeconomic inequalities in the health domains and overall health were higher in the higher-income country group than the lower-income country group.</p> <p>Conclusions</p> <p>Using a common measurement approach, inequalities in health, favoring the rich and the educated, were evident in overall health as well as in every health domain. Existent differences in averages and inequalities in health domains suggest that monitoring should not be limited only to overall health. This study carries important messages for policy-making in regard to tackling inequalities in specific domains of health. Targeting interventions towards individual domains of health such as mobility, self-care and vision, ought to be considered besides improving overall health.</p

Does Selective Migration Explain the Hispanic Paradox?: A Comparative Analysis of Mexicans in the U.S. and Mexico

Latino immigrants, particularly Mexican, have some health advantages over U.S.-born Mexicans and Whites. Because of their lower socioeconomic status, this phenomenon has been called the epidemiologic “Hispanic Paradox.” While cultural theories have dominated explanations for the Paradox, the role of selective migration has been inadequately addressed. This study is among the few to combine Mexican and U.S. data to examine health selectivity in activity limitation, self-rated health, and chronic conditions among Mexican immigrants, ages 18 and over. Drawing on theories of selective migration, this study tested the “healthy migrant” and “salmon-bias” hypotheses by comparing the health of Mexican immigrants in the U.S. to non-migrants in Mexico, and to return migrants in Mexico. Results suggest that there are both healthy migrant and salmon-bias effects in activity limitation, but not other health aspects. In fact, consistent with prior research, immigrants are negatively selected on self-rated health. Future research should consider the complexities of migrants’ health profiles and examine selection mechanisms alongside other factors such as acculturation

Identification of factors required for meristem function in Arabidopsis using a novel next generation sequencing fast forward genetics approach

<p>Abstract</p> <p>Background</p> <p>Phenotype-driven forward genetic experiments are powerful approaches for linking phenotypes to genomic elements but they still involve a laborious positional cloning process. Although sequencing of complete genomes now becomes available, discriminating causal mutations from the enormous amounts of background variation remains a major challenge.</p> <p>Method</p> <p>To improve this, we developed a universal two-step approach, named 'fast forward genetics', which combines traditional bulk segregant techniques with targeted genomic enrichment and next-generation sequencing technology</p> <p>Results</p> <p>As a proof of principle we successfully applied this approach to two Arabidopsis mutants and identified a novel factor required for stem cell activity.</p> <p>Conclusion</p> <p>We demonstrated that the 'fast forward genetics' procedure efficiently identifies a small number of testable candidate mutations. As the approach is independent of genome size, it can be applied to any model system of interest. Furthermore, we show that experiments can be multiplexed and easily scaled for the identification of multiple individual mutants in a single sequencing run.</p

Simulation of Organ Patterning on the Floral Meristem Using a Polar Auxin Transport Model

An intriguing phenomenon in plant development is the timing and positioning of lateral organ initiation, which is a fundamental aspect of plant architecture. Although important progress has been made in elucidating the role of auxin transport in the vegetative shoot to explain the phyllotaxis of leaf formation in a spiral fashion, a model study of the role of auxin transport in whorled organ patterning in the expanding floral meristem is not available yet. We present an initial simulation approach to study the mechanisms that are expected to play an important role. Starting point is a confocal imaging study of Arabidopsis floral meristems at consecutive time points during flower development. These images reveal auxin accumulation patterns at the positions of the organs, which strongly suggests that the role of auxin in the floral meristem is similar to the role it plays in the shoot apical meristem. This is the basis for a simulation study of auxin transport through a growing floral meristem, which may answer the question whether auxin transport can in itself be responsible for the typical whorled floral pattern. We combined a cellular growth model for the meristem with a polar auxin transport model. The model predicts that sepals are initiated by auxin maxima arising early during meristem outgrowth. These form a pre-pattern relative to which a series of smaller auxin maxima are positioned, which partially overlap with the anlagen of petals, stamens, and carpels. We adjusted the model parameters corresponding to properties of floral mutants and found that the model predictions agree with the observed mutant patterns. The predicted timing of the primordia outgrowth and the timing and positioning of the sepal primordia show remarkable similarities with a developing flower in nature

Genetic architecture of spatial electrical biomarkers for cardiac arrhythmia and relationship with cardiovascular disease

The 3-dimensional spatial and 2-dimensional frontal QRS-T angles are measures derived from the vectorcardiogram. They are independent risk predictors for arrhythmia, but the underlying biology is unknown. Using multi-ancestry genome-wide association studies we identify 61 (58 previously unreported) loci for the spatial QRS-T angle (N = 118,780) and 11 for the frontal QRS-T angle (N = 159,715). Seven out of the 61 spatial QRS-T angle loci have not been reported for other electrocardiographic measures. Enrichments are observed in pathways related to cardiac and vascular development, muscle contraction, and hypertrophy. Pairwise genome-wide association studies with classical ECG traits identify shared genetic influences with PR interval and QRS duration. Phenome-wide scanning indicate associations with atrial fibrillation, atrioventricular block and arterial embolism and genetically determined QRS-T angle measures are associated with fascicular and bundle branch block (and also atrioventricular block for the frontal QRS-T angle). We identify potential biology involved in the QRS-T angle and their genetic relationships with cardiovascular traits and diseases, may inform future research and risk prediction