SigWinR; the SigWin-detector updated and ported to R

<p>Abstract</p> <p>Background</p> <p>Our SigWin-detector discovers significantly enriched windows of (genomic) elements in any sequence of values (genes or other genomic elements in a DNA sequence) in a fast and reproducible way. However, since it is grid based, only (life) scientists with access to the grid can use this tool. Therefore and on request, we have developed the SigWinR package which makes the SigWin-detector available to a much wider audience. At the same time, we have introduced several improvements to its algorithm as well as its functionality, based on the feedback of SigWin-detector end users.</p> <p>Findings</p> <p>To allow usage of the SigWin-detector on a desktop computer, we have rewritten it as a package for R: SigWinR. R is a free and widely used multi platform software environment for statistical computing and graphics. The package can be installed and used on all platforms for which R is available. The improvements involve: a visualization of the input-sequence values supporting the interpretation of Ridgeograms; a visualization allowing for an easy interpretation of enriched or depleted regions in the sequence using windows of pre-defined size; an option that allows the analysis of circular sequences, which results in rectangular Ridgeograms; an application to identify regions of co-altered gene expression (ROCAGEs) with a real-life biological use-case; adaptation of the algorithm to allow analysis of non-regularly sampled data using a constant window size in physical space without resampling the data. To achieve this, support for analysis of windows with an even number of elements was added.</p> <p>Conclusion</p> <p>By porting the SigWin-detector as an R package, SigWinR, improving its algorithm and functionality combined with adequate performance, we have made SigWin-detector more useful as well as more easily accessible to scientists without a grid infrastructure.</p

Delayed presentation of symptomatic breast cancers in Hong Kong: Experience in a public cancer centre

Objective Delayed presentation is an important obstacle to improving cancer treatment outcomes. We aimed to study the magnitude of this problem in Hong Kong and the factors associated with delayed presentation of patients with symptomatic breast cancers. Design Retrospective study using self-administered questionnaires. Setting Clinical Oncology Department in a regional public hospital in Hong Kong. Patients A total of 158 Chinese women with breast cancer referred to our hospital between October 2006 and December 2007 consented to participate in this study. Among these, 59 (37%) patients were referred after having surgery in private sector. Results The mean total delay (from first symptom to treatment) was 22 weeks. The mean patient delay (from first symptom to first consultation) was 13 weeks, constituting the largest component (60%) of the total delay. After symptom onset, the delay exceeded 12 weeks for consulting a doctor in 29%, and for receipt of treatment in 52% of them. Low family income (<HK$5000 per month; P<0.001) and surgery in public hospitals (P=0.013) were both independent predictors of patient delay. Surgery in public hospitals (P=0.006) and low family income (P=0.005) were the only predictors of doctor/system delay and total delay, respectively. Conclusions Delayed presentation and treatment of symptomatic breast cancer remains an important issue in Hong Kong. Apart from socio-economic factors, limited access to public medical care was likely an important contributing factor in delays related to patients as well as to doctor/system.published_or_final_versio

Carbon stocks and pools in relation to the texture of kaolinitic soils from the Brazilian East Coast.

Extremely kaolinitic soils of Tertiary age elevations on the Brazilian east coast present a wide range of texture, which is recognized as one of the main factors controlling the soil organic matter contents. This study aimed to investigate the organic C storage of different compartments of kaolinitic soils. The studied soils had a wide particle size gradient, were under native forest vegetation, and located on Brazil?s eastern coast (Coruripe - CF, Umbaúba - UF, Nova Viçosa - VF, Sooretama - SF, and Itaboraí - IF). The forest cover of all sites allows to record soil properties reference values for a land use condition closer to that of the original sites. We determined soil organic C (SOC) content and SOC stock up to a depth of 1 m, C of topsoil (0.00-0.08 m), aggregate size classes, and dissolved organic carbon (DOC) of the soil surface horizon (A horizon). Soil C stocks at the 0.00-1.00 m depth ranged from 105 to 137 Mg ha-1 and were not regulated by soil texture. The SF soils stored more C up to a depth of 1 m, while lower mean C stocks were found for UF and CF soils. Soil texture was not a reliable index to predict the C contents of the aggregate size classes of the 0.00-0.08 m layer (within each class and in total, using equivalent soil mass of the classes). The most clayey soils had a high percentage of 2-4 mm aggregates and, as a consequence, high aggregate stability indices, which are positively correlated to silt plus clay contents of the soil surface horizon. The proportion of DOC in relation to the total organic C of the surface soil horizon was high for IF and UF areas, which are the less preserved forest fragments among all studied fragments

Student perceptions of teaching quality in five countries: A partial credit model approach to assess measurement invariance

This study examines measurement invariance of student perceptions of teaching quality collected in five countries: Indonesia (n students = 6,331), the Netherlands (n students = 6,738), South Africa (n students = 3,422), South Korea (n students = 6,997) and Spain (n students = 4,676). The administered questionnaire was the My Teacher Questionnaire (MTQ). Student perceived teachers’ teaching quality was estimated using the partial credit model (PCM). Tests for differential item functioning (DIF) were used to assess measurement invariance. Furthermore, if DIF was found, it was explored whether an application of a quasi-international calibration, which estimates country-unique parameters for DIF items, can provide more valid estimates for between-country comparisons. Results indicate the absence of non-uniform DIF, but presence of uniform DIF among most items. This suggests that direct comparisons of raw mean or sum scores between countries is not advisable. Details of the set of invariant items are provided. Furthermore, results suggest that the quasi-international calibration is promising, but also that this approach needs further exploration in the context of student perceptions of teaching quality

Proliferación celular y expresión del VEGF en un carcinoma mamario murino

El objetivo del presente trabajo es analizar la síntesis de ADN (ADNs) y la expresión del VEGF en un carcinoma mamario, el TN60, abarcando un ritmo circadiano.Facultad de Ciencias Médica

Proliferación celular y expresión del VEGF en un carcinoma mamario murino

El objetivo del presente trabajo es analizar la síntesis de ADN (ADNs) y la expresión del VEGF en un carcinoma mamario, el TN60, abarcando un ritmo circadiano.Facultad de Ciencias Médica

Adensamento subsuperficial em solos de tabuleiro do semi-arido do Brasil.

O objetivo do trabalho foi de investigar os processos de formação responsáveis pela diferenciação textural e alterações no horizonte A e B, que possam identificar e caracterizar adensamento observado a partir do horizonte B em solos do tabuleiros sertanejos, do Nordeste do Brasil