qtl.outbred: Interfacing outbred line cross data with the R/qtl mapping software

Background qtl.outbred is an extendible interface in the statistical environment, R, for combining quantitative trait loci (QTL) mapping tools. It is built as an umbrella package that enables outbred genotype probabilities to be calculated and/or imported into the software package R/qtl. Findings Using qtl.outbred, the genotype probabilities from outbred line cross data can be calculated by interfacing with a new and efficient algorithm developed for analyzing arbitrarily large datasets (included in the package) or imported from other sources such as the web-based tool, GridQTL. Conclusion qtl.outbred will improve the speed for calculating probabilities and the ability to analyse large future datasets. This package enables the user to analyse outbred line cross data accurately, but with similar effort than inbred line cross data.

Formal caregivers' perceptions of quality of care for older people : associating factors

Background: Despite the growing number of studies concerning quality of care for older people, there is a lack of studies depicting factors associated with good quality of care from the formal caregivers' perspective. The aim was to describe formal caregivers' perceptions of quality of care for older people in the community and explore factors associated with these perceptions. In total, 70 nursing assistants, 163 enrolled nurses and 198 registered nurses from 14 communities in central Sweden participated in the study. They filled out the following questionnaires: a modified version of Quality from the Patient's Perspective, Creative Climate Questionnaire, Stress of Conscience Questionnaire, items regarding education and competence, Health Index and Sense of coherence questionnaire. The overall response rate was 57 % (n = 431). Results: In the perceived reality of quality of care respondents assessed the highest mean value in the dimension medical-technical competence and physical technical conditions and lower values in the dimensions; identity-oriented approach, socio-cultural atmosphere and in the context specific dimension. The caregivers estimated their competence and health rather high, had lower average values in sense of coherence and organizational climate and low values in stress of conscience. Conculsions: The PR of quality of care were estimated higher among NA/ENs compared to RNs. Occupation, organizational climate and stress of conscience were factors associated with quality of care that explained 42 % of the variance. Competence, general health and sense of coherence were not significantly associated to quality of care. The mentioned factors explaining quality of care might be intertwined and showed that formal caregivers' working conditions are of great importance for quality of care.

Inflammation, oxidative stress, glomerular filtration rate, and albuminuria in elderly men : a cross-sectional study

BACKGROUND: The role of inflammation and oxidative stress in mild renal impairment in the elderly is not well studied. Accordingly, we aimed at investigating the associations between estimated glomerular filtration rate (eGFR), albumin/creatinine ratio (ACR), and markers of different inflammatory pathways and oxidative stress in a community based cohort of elderly men. FINDINGS: Cystatin C-based GFR, ACR, and biomarkers of cytokine-mediated inflammation (interleukin-6, high-sensitivity C-reactive protein[CRP], serum amyloid A[SAA]), cyclooxygenase-mediated inflammation (urinary prostaglandin F2alpha [PGF2alpha]), and oxidative stress (urinary F2 isoprostanes) were assessed in the Uppsala Longitudinal Study of Adult Men(n = 647, mean age 77 years). RESULTS: In linear regression models adjusting for age, BMI, smoking, blood pressure, LDL-cholesterol, HDL-cholesterol, triglycerides, and treatment with statins, ACE-inhibitors, ASA, and anti-inflammatory agents, eGFR was inversely associated with CRP, interleukin-6, and SAA (beta-coefficient -0.13 to -0.19, p < 0.001 for all), and positively associated with urinary F2-isoprostanes (beta-coefficient 0.09, p = 0.02). In line with this, ACR was positively associated with CRP, interleukin-6, and SAA (beta- coefficient 0.09-0.12, p < 0.02 for all), and negatively associated with urinary F2-isoprostanes (beta-coefficient -0.12, p = 0.002). The associations were similar but with lower regression coefficients in a sub-sample with normal eGFR (>60 ml/min/1.73 m2, n = 514), with the exception that F2-isoprostane and SAA were no longer associated with eGFR. CONCLUSION: Our data indicate that cytokine-mediated inflammation is involved in the early stages of impaired kidney function in the elderly, but that cyclooxygenase-mediated inflammation does not play a role at this stage. The unexpected association between higher eGFR/lower albuminuria and increased F2-isoprostanes in urine merits further studies.

Exploring critical literacy in Swedish education : Introductory notes

This article is an introductory note to The thematic section in this issue of Education Inquiry has its background in the need for research interpreting literacy from a critical perspective. Teaching literacy is not solely about technical reading skills but is also about understanding and the making of meaning. From that point of view, teaching must also consider the use of language, the context within which language is used, and issues of power. The thematic section includes five articles about critical literacy in Swedish education. The contributions were developed after a workshop conducted by Professor Hilary Janks, University of the Witwatersrand, Johannesburg. She introduces the framework of a critical literacy theory in the first article of the issue. Further, the contributions of Swedish scholars are united in their interest in applying a mode of critical literacy designed by Janks to different practices, sites and speech-events, for example policy documents, home reading, teaching and learning practices. The articles offer a wide perspective of critical literacy in education and further understanding of the complex processes in teaching.