SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access

<p>Abstract</p> <p>Background</p> <p>In the last five years large online resources of human variability have appeared, notably HapMap, Perlegen and the CEPH foundation. These databases of genotypes with population information act as catalogues of human diversity, and are widely used as reference sources for population genetics studies. Although many useful conclusions may be extracted by querying databases individually, the lack of flexibility for combining data from within and between each database does not allow the calculation of key population variability statistics.</p> <p>Results</p> <p>We have developed a novel tool for accessing and combining large-scale genomic databases of single nucleotide polymorphisms (SNPs) in widespread use in human population genetics: SPSmart (SNPs for Population Studies). A fast pipeline creates and maintains a data mart from the most commonly accessed databases of genotypes containing population information: data is mined, summarized into the standard statistical reference indices, and stored into a relational database that currently handles as many as 4 × 10⁹genotypes and that can be easily extended to new database initiatives. We have also built a web interface to the data mart that allows the browsing of underlying data indexed by population and the combining of populations, allowing intuitive and straightforward comparison of population groups. All the information served is optimized for web display, and most of the computations are already pre-processed in the data mart to speed up the data browsing and any computational treatment requested.</p> <p>Conclusion</p> <p>In practice, SPSmart allows populations to be combined into user-defined groups, while multiple databases can be accessed and compared in a few simple steps from a single query. It performs the queries rapidly and gives straightforward graphical summaries of SNP population variability through visual inspection of allele frequencies outlined in standard pie-chart format. In addition, full numerical description of the data is output in statistical results panels that include common population genetics metrics such as heterozygosity, <it>Fst </it>and <it>In</it>.</p

New Experimental Limits on Macroscopic Forces Below 100 Microns

Results of an experimental search for new macroscopic forces with Yukawa range between 5 and 500 microns are presented. The experiment uses 1 kHz mechanical oscillators as test masses with a stiff conducting shield between them to suppress backgrounds. No signal is observed above the instrumental thermal noise after 22 hours of integration time. These results provide the strongest limits to date between 10 and 100 microns, improve on previous limits by as much as three orders of magnitude, and rule out half of the remaining parameter space for predictions of string-inspired models with low-energy supersymmetry breaking. New forces of four times gravitational strength or greater are excluded at the 95% confidence level for interaction ranges between 200 and 500 microns.Comment: 25 Pages, 7 Figures: Minor Correction

Decision and Discovery in Defining “Disease”

This version (May 17, 2005) was published in its final form as: Schwartz PH. Decision and discovery in defining 'disease'. In: Kincaid H, McKitrick J, editors. Establishing medical reality: essays in the metaphysics and epistemology of biomedical science. Dordrecht: Springer; 2007. p. 47-63. http://dx.doi.org/10.1007/1-4020-5216-2_5The debate over how to analyze the concept of disease has often centered on the question of whether to include a reference to values, in particular the ‘disvalue’of diseases, or whether to avoid such notions. ‘Normativists,’such as King ([1954], 1981) and Culver and Gert (1982) emphasize the undesirability of diseases, while ‘Naturalists,’ most prominently Christopher Boorse (1977, 1987, 1997), instead require just the presence of biological dysfunction. The debate between normativism and naturalism often deteriorates into stalemate, with each side able to point out significant problems with the other. It starts to look as if neither approach can work. In this paper, I argue that the standoff stems from deeply questionable assumptions that have been used to formulate the opposing positions and guide the debate. In the end, I propose an alternative set of guidelines that offer a more constructive way to devise and compare theories

Relationship between site of oesophageal cancer and areca chewing and smoking in Taiwan

Among 309 male patients, those who had heavily consumed betel and tobacco were more likely than nonchewers (OR = 2. 91; 95% CI = 1.36-6.25) and nonsmokers (OR = 2.49; 95% CI = 1.02-6.08) to develop cancer in the upper and middle third of the oesophagus, respectively; the effects of alcohol did not dominate in any third

Effective connectivity reveals strategy differences in an expert calculator

Mathematical reasoning is a core component of cognition and the study of experts defines the upper limits of human cognitive abilities, which is why we are fascinated by peak performers, such as chess masters and mental calculators. Here, we investigated the neural bases of calendrical skills, i.e. the ability to rapidly identify the weekday of a particular date, in a gifted mental calculator who does not fall in the autistic spectrum, using functional MRI. Graph-based mapping of effective connectivity, but not univariate analysis, revealed distinct anatomical location of “cortical hubs” supporting the processing of well-practiced close dates and less-practiced remote dates: the former engaged predominantly occipital and medial temporal areas, whereas the latter were associated mainly with prefrontal, orbitofrontal and anterior cingulate connectivity. These results point to the effect of extensive practice on the development of expertise and long term working memory, and demonstrate the role of frontal networks in supporting performance on less practiced calculations, which incur additional processing demands. Through the example of calendrical skills, our results demonstrate that the ability to perform complex calculations is initially supported by extensive attentional and strategic resources, which, as expertise develops, are gradually replaced by access to long term working memory for familiar material

Prevalence of anopheline species and their Plasmodium infection status in epidemic-prone border areas of Bangladesh

<p>Abstract</p> <p>Background</p> <p>Information related to malaria vectors is very limited in Bangladesh. In the changing environment and various <it>Anopheles </it>species may be incriminated and play role in the transmission cycle. This study was designed with an intention to identify anopheline species and possible malaria vectors in the border belt areas, where the malaria is endemic in Bangladesh.</p> <p>Methods</p> <p><it>Anopheles </it>mosquitoes were collected from three border belt areas (Lengura, Deorgachh and Matiranga) during the peak malaria transmission season (May to August). Three different methods were used: human landing catches, resting collecting by mouth aspirator and CDC light traps. Enzyme-linked immunosorbent assay (ELISA) was done to detect <it>Plasmodium falciparum</it>, <it>Plasmodium vivax</it>-210 and <it>Plasmodium vivax</it>-247 circumsporozoite proteins (CSP) from the collected female species.</p> <p>Results</p> <p>A total of 634 female <it>Anopheles </it>mosquitoes belonging to 17 species were collected. <it>Anopheles vagus </it>(was the dominant species (18.6%) followed by <it>Anopheles nigerrimus </it>(14.5%) and <it>Anopheles philippinensis </it>(11.0%). Infection rate was found 2.6% within 622 mosquitoes tested with CSP-ELISA. Eight (1.3%) mosquitoes belonging to five species were positive for <it>P. falciparum</it>, seven (1.1%) mosquitoes belonging to five species were positive for <it>P. vivax </it>-210 and a single mosquito (0.2%) identified as <it>Anopheles maculatus </it>was positive for <it>P. vivax</it>-247. No mixed infection was found. Highest infection rate was found in <it>Anopheles karwari </it>(22.2%) followed by <it>An. maculatus </it>(14.3%) and <it>Anopheles barbirostris </it>(9.5%). Other positive species were <it>An. nigerrimus </it>(4.4%), <it>An. vagus </it>(4.3%), <it>Anopheles subpictus </it>(1.5%) and <it>An. philippinensis </it>(1.4%). <it>Anopheles vagus </it>and <it>An. philippinensis </it>were previously incriminated as malaria vector in Bangladesh. In contrast, <it>An. karwari</it>, <it>An. maculatus</it>, <it>An. barbirostris</it>, <it>An. nigerrimus </it>and <it>An. subpictus </it>had never previously been incriminated in Bangladesh.</p> <p>Conclusion</p> <p>Findings of this study suggested that in absence of major malaria vectors there is a possibility that other <it>Anopheles </it>species may have been playing role in malaria transmission in Bangladesh. Therefore, further studies are required with the positive mosquito species found in this study to investigate their possible role in malaria transmission in Bangladesh.</p

Having a lot of a good thing: multiple important group memberships as a source of self-esteem.

Copyright: © 2015 Jetten et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are creditedMembership in important social groups can promote a positive identity. We propose and test an identity resource model in which personal self-esteem is boosted by membership in additional important social groups. Belonging to multiple important group memberships predicts personal self-esteem in children (Study 1a), older adults (Study 1b), and former residents of a homeless shelter (Study 1c). Study 2 shows that the effects of multiple important group memberships on personal self-esteem are not reducible to number of interpersonal ties. Studies 3a and 3b provide longitudinal evidence that multiple important group memberships predict personal self-esteem over time. Studies 4 and 5 show that collective self-esteem mediates this effect, suggesting that membership in multiple important groups boosts personal self-esteem because people take pride in, and derive meaning from, important group memberships. Discussion focuses on when and why important group memberships act as a social resource that fuels personal self-esteem.This study was supported by 1. Australian Research Council Future Fellowship (FT110100238) awarded to Jolanda Jetten (see http://www.arc.gov.au) 2. Australian Research Council Linkage Grant (LP110200437) to Jolanda Jetten and Genevieve Dingle (see http://www.arc.gov.au) 3. support from the Canadian Institute for Advanced Research Social Interactions, Identity and Well-Being Program to Nyla Branscombe, S. Alexander Haslam, and Catherine Haslam (see http://www.cifar.ca)

Equilibrium Contrast-enhanced CT Imaging to Evaluate Hepatic Fibrosis: Initial Validation by Comparison with Histopathologic Sampling

Purpose To prospectively evaluate hepatic extracellular volume (ECV) fraction measurement at equilibrium computed tomographic (CT) imaging compared with both fibrosis quantified with histologic analysis and the enhanced liver fibrosis panel (ELF) in a cohort of patients with chronic hepatitis. Materials and Methods This prospective study was approved by the regional ethics committee. All patients gave fully informed written consent. Forty patients with a clinical indication for liver biopsy were prospectively recruited for liver ECV quantitation at equilibrium CT imaging. Biopsy samples underwent digital image analysis and assessment of collagen content expressed as the collagen-proportionate area (CPA). Spearman correlation was used to evaluate association between ECV, ELF, and CPA. Multiple regression analysis was used to test prediction of CPA by a model that combined ECV and ELF. ECV, ELF score, and CPA were compared with Ishak stage by using the Kruskal-Wallis test. Results Complete ECV, ELF, and CPA were available in 33 patients. Liver ECV, CPA, and ELF had a median of 0.26 (interquartile range [IQR], 0.24-0.29), 5.0 (IQR, 3.0-15.0), and 9.71 (IQR, 8.14-10.92), respectively. Hepatic ECV demonstrated good association with CPA (r = 0.64; P < .001) and ELF score (r = 0.38; P < .027), with no significant difference in strength of correlation (P = .177). The regression model that combined ELF and ECV achieved good prediction of CPA (R(2) = 0.67; P < .001). Significant variation in ECV and ELF was seen between fibrosis stage groups. Conclusion Hepatic ECV measured with equilibrium CT imaging is associated with biopsy-derived CPA and serum ELF-validated markers of liver fibrosis. This suggests that equilibrium CT imaging can quantify diffuse fibrosis in chronic liver disease. (©) RSNA, 2014