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

Endovascular treatment for acute basilar artery occlusion: Descriptive analysis of the experience in a comprehensive stroke centre

Objectives: To describe the clinical and epidemiological characteristics of patients with basilar artery occlusion (BAO) treated with mechanical thrombectomy (MT) in Aragón, and to compare its anaesthetic management, technical effectivity, security, and prognosis with those of anterior circulation. Methods: 322 patients from the prospective registry of mechanical thrombectomies from Aragon were assessed: 29 with BAO and 293 with an anterior circulation large vessel occlusion. Baseline characteristics, procedural, clinical and safety outcomes variables were compared. Results: Out of 29 patients with BAO that underwent endovascular therapy (62.1% men; average age 69.8 ± 14.05 years) 18 (62.1%) received endovascular therapy (EVT) alone and 11 (37.9%) EVT plus intravenous thrombolysis. Atherothrombotic stroke was the most common etiology (41%). The BAO group had longer Door-to-groin (160 vs 141 min; P = 0.043) and Onset-to-reperfusion times (340 vs 297 min; P = 0.005), and higher use of general anaesthesia (60.7% vs 14.7%; P < 0.01). No statistically significant difference was found for Procedure time (60 vs 50 min; P = 0.231) nor the rate of successful recanalization (72.4% vs 82.7%; P = 0.171). Functional independence at 90 days was significantly worse in the BAO group (17.9% vs 38.2%; P < 0.01). Conclusions: Patients with basilar artery occlusion had higher morbimortality despite similar angiographic results. Mechanical thrombectomy for BAOs is a safe and effective procedure in selected patients. A consensus about the effect of anaesthesia has yet to be reached, for BAO general anaesthesia remains the most frequently used technique

Autonomy and forage grasses in goat farming of western France First results of a sociological survey

International audienceOur communication is based on the results of a multidisciplinary research (PSDR FLECHE-Fromages et Laits issus d'Élevages de Chèvres conduites avec de l'Herbe-2016-2020) which aims to study the potential of grass valorization in goat systems, with the dual objective of strengthening the economic resilience of farms and the social image of the dairy goat sector of Western France. The latter currently represent almost half of the national goat population and 58% of the milk supplied in France. The sociological aspect of the research concerns the representations, value systems, interests and constraint systems (technical, economic, etc.) that guide the practices of all the actors in the sector: farmers, upstream and downstream actors. The objective of this approach is to analyse, at all levels of the value chain, the incentives and obstacles to a possible transition to more grassy feeding systems. Based on 76 semi-directive interviews, this paper presents the first results of this survey by showing how contextual elements (socio-economic, professional, etc.) impact farmers' choices of practices. While, in principle, the whole goat sector seems to be converging towards an agro-ecological transition that ensures its sustainability, in practice, each of its actors is confronted with a system of constraints that limit actual developments. The articulation of these obstacles seems to lead to a kind of inertia, which prevents the adoption of practices that are nevertheless perceived as recommendable by most actors. Autonomie et fourrages herbagers dans les élevages caprins de l'Ouest de la France. Premiers résultats d'une enquête sociologique. Résumé. Notre communication s'inscrit dans le cadre d'une recherche pluridisciplinaire (Programme PSDR-FLECHE-Fromages et Laits issus d'Élevages de Chèvres conduites avec de l'Herbe-2016-2020) qui vise à étudier le potentiel de valorisation de l'herbe dans les systèmes caprins, dans le double objectif de renforcer la résilience économique des exploitations et l'image sociale des filières caprines laitières de l'Ouest de la France. Ces dernières représentent actuellement près de la moitié de l'effectif national de chèvres et 58% du lait livré en France. Le volet sociologique de la recherche porte sur les représentations, les systèmes de valeurs, les intérêts et les systèmes de contraintes (techniques, économiques, etc.) qui orientent les pratiques de l'ensemble des acteurs de la filière : éleveurs, acteurs de l'amont et de l'aval. L'objectif de cette démarche est d'analyser, à tous les niveaux de la filière, les incitations et les freins à une éventuelle transition vers des systèmes alimentaires plus herbagers. A partir de 76 entretiens semi-directifs, ce papier présente les premiers résultats de cette enquête en montrant, notamment, comment les éléments contextuels (socio-économiques, professionnels, etc.) impactent les choix des pratiques des exploitants agricoles. Si, en principe, l'ensemble de la filière caprine semble converger vers une transition agroécologique qui en assure la durabilité, dans la pratique, chacun de ses acteurs est confronté à un univers de contraintes qui limitent les évolutions effectives. L'articulation des freins relevant des différents maillons de la filière, semble ainsi déboucher sur une sorte d'inertie, qui empêche l'adoption de pratiques pourtant perçues comme souhaitables par la plupart des acteurs. Mots-clés. Autonomie-fourrages herbagers-caprins-sociologie

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