The eDAL Suite: Tools and Concepts for Primary Data Citation

Retrieval and citation of primary data is the important factor in the approaching age of “data science”. Digital data are easily shared, and just as easily wiped or lost. The problem of keeping on-line data accessible and
retrievable is especially difficult for SME like plant breeders plant biotech companies as well as research projects in this domain.
Intension of eDAL is the provisioning of an information retrieval and data citation infrastructure that meets the requirements of the “data science” age and implements a re-usable platform for data retrieval, data
citation, and data publication. Like a shopping cart, the idea is to combine a search engine and a data cart, which retrieves, rank and collect query relevant data from crop plant data centers

25-Hydroxyvitamin D and Peripheral Immune Mediators:Results from Two Nationwide Danish Pediatric Cohorts

(1) Background: We aimed to examine if 25-hydroxyvitamin D (25(OH)D) was related to the peripheral immunological and inflammatory signature both at birth, and in newly diagnosed patients with childhood type 1 diabetes (T1D) and their healthy controls; (2) Methods: The birth cohort consisted of 470 patients and 500 healthy controls. Dried blood samples were collected from the neonates in the period 1981–1999. The newly diagnosed cohort consisted of 460 patients and 453 siblings. Serum samples were collected in the period 1997–2005. A variety of peripheral immune mediators were measured and compared to total 25(OH)D levels (25(OH)D2 + 25(OH)D3). For each immune mediator, the relative change (RC) in the mean level was modeled by robust log-normal regression and correction for multiple testing was performed; (3) Results: Two associations were identified; there was a negative association between 25(OH)D (10 nmol/L increase) and leptin (RC (95% confidence interval (CI)), 0.98 (0.96; 1.00)), and a positive association between 25(OH)D (10 nmol/L increase) and the chemokine, chemokine (c-x-c motif) ligand (CXCL) 8 (RC (95% CI), 1.07 (1.01; 1.13)); (4) Conclusion: CXCL8 and leptin have significant associations with levels of 25(OH)D in the newly diagnosed cohort. These results do not indicate a strong influence of 25(OH)D on the peripheral immunological or inflammatory signature

Microbiological point of care testing before antibiotic prescribing in primary care:considerable variations between practices

BACKGROUND: Point-of-care testing (POCT) in primary care may improve rational antibiotic prescribing. We examined use of POCT in Denmark, including patient- and general practitioner (GP)-related predictors. METHODS: We linked nationwide health care databases to assess POCT use (C-reactive protein (CRP), group A streptococcal (GAS) antigen swabs, bacteriological cultures, and urine test strips) per 1,000 overall GP consultations, 2004–2013. We computed odds ratios (OR) of POCT in patients prescribed antibiotics according to patient and GP age and sex, GP practice type, location, and workload. RESULTS: The overall use of POCT in Denmark increased by 45.8% during 2004–2013, from 147.2 per 1,000 overall consultations to 214.8. CRP tests increased by 132%, bacteriological cultures by 101.7% while GAS swabs decreased by 8.6%. POCT preceded 28% of antibiotic prescriptions in 2004 increasing to 44% in 2013. The use of POCT varied more than 5-fold among individual practices, from 54.9 to 394.7 per 1,000 consultations in 2013. POCT use varied substantially with patient age, and males were less likely to receive POCT than females (adjusted OR = 0.75, 95% CI 0.74-0.75) driven by usage of urine test strips among females (18% vs. 7%). Odds of POCT were higher among female GPs and decreased with higher GP age, with lowest usage among male GPs >60 years. GP urban/rural location and workload had little impact. CONCLUSION: GPs use POCT increasingly with the highest use among young female GPs. In 2013, 44% of all antibiotic prescriptions were preceded by POCT but testing rates vary greatly across individual GPs

The LAILAPS Search Engine: A Feature Model for Relevance Ranking in Life Science Databases

Efficient and effective information retrieval in life sciences is one of the most pressing challenge in bioinformatics. The incredible growth of life science databases to a vast network of interconnected information systems is to the same extent a big challenge and a great chance for life science research. The knowledge found in the Web, in particular in life-science databases, are a valuable major resource. In order to bring it to the scientist desktop, it is essential to have well performing search engines. Thereby, not the response time nor the number of results is important. The most crucial factor for millions of query results is the relevance ranking. In this paper, we present a feature model for relevance ranking in life science databases and its implementation in the LAILAPS search engine. Motivated by the observation of user behavior during their inspection of search engine result, we condensed a set of 9 relevance discriminating features. These features are intuitively used by scientists, who briefly screen database entries for potential relevance. The features are both sufficient to estimate the potential relevance, and efficiently quantifiable. The derivation of a relevance prediction function that computes the relevance from this features constitutes a regression problem. To solve this problem, we used artificial neural networks that have been trained with a reference set of relevant database entries for 19 protein queries. Supporting a flexible text index and a simple data import format, this concepts are implemented in the LAILAPS search engine. It can easily be used both as search engine for comprehensive integrated life science databases and for small in-house project databases. LAILAPS is publicly available for SWISSPROT data at http://lailaps.ipk-gatersleben.d

No Contribution of GAD-65 and IA-2 Autoantibodies around Time of Diagnosis to the Increasing Incidence of Juvenile Type 1 Diabetes:A 9-Year Nationwide Danish Study

Aims. A new perspective on autoantibodies as pivotal players in the pathogenesis of type 1 diabetes (T1D) has recently emerged. Our key objective was to examine whether increased levels of autoantibodies against the β-cell autoantigens glutamic acid decarboxylase (isoform 65) (GADA) and insulinoma associated antigen-2A (IA-2A) mirrored the 3.4% annual increase in incidence of T1D. Methods. From the Danish Childhood Diabetes Register, we randomly selected 500 patients and 500 siblings for GADA and IA-2A analysis (1997 through 2005). Blood samples were taken within three months after onset. A robust log-normal regression model was used. Nine hundred children and adolescents had complete records and were included in the analysis. Cochran-Armitage test for trend was used to evaluate changes in prevalence of autoantibody positivity by period. Results. No significant changes in levels of GADA and IA-2A were found over our 9-year study period. No trends in autoantibody positivity—in either patients or siblings—were found. Levels of GADA and IA-2A were significantly associated with HLA risk groups and GADA with age. Conclusion. The prevalence of positivity and the levels of GADA and IA-2A have not changed between 1997 and 2005 in newly diagnosed patients with T1D and their siblings without T1D

Association between Neonatal Whole Blood Iron Content and Cytokines, Adipokines, and Other Immune Response Proteins

(1) Background: High iron associates with inflammation and type 1 diabetes (T1D). Iron is essential not only for neonatal development but also for infectious microorganisms. The neonatal immune system is immature, and innate immunity prevails before immunocompetence develops. (2) Methods: In 398 newborns from the Danish Newborn Screening Biobank, we examined if whole blood iron (WB-Iron) content were associated with cytokines, adipokines, C-reactive protein (CRP), and mannose-binding lectin (MBL) in non-infected healthy neonates, and if these associations differed in newborns who later developed T1D (cases) (n = 199). WB-Iron was quantified using laser ablation inductively coupled plasma mass spectrometry on the neonatal dried blood spots. For each analyte, the relative change (RC) in the mean level was modeled by robust log-normal regression. (3) Results: A one unit increase in neonatal WB-Iron was associated with a 38% decrease in mean interleukin (IL)-6 levels (0.62; 95% CI: 0.40–0.95, p = 0.03), and a 37% decrease in mean MBL levels (0.63; 95% CI: 0.41–0.95, p = 0.03), but was not statistically significant after correction for multiple testing. (4) Conclusions: In summary, we found that higher neonatal WB-iron content was inversely associated with IL-6 and MBL, which may increase susceptibility to infections

Pædagogisk selvtræning for lærere og studerende

I dette working paper præsenteres og diskuteres et e-læringskoncept: Pædagogisk Selvtræning. Først vises den medietekniske udformning. Dernæst præsenteres et læringsteoretisk grundlag for konceptet ud fra K. Illeris, 2001. Det starter ud fra de læringsprocesser (kognitive, psykodynamiske og sociale), som foregår i brugere af konceptet, lærere så vel som studerende. Ud fra denne model diskuteres, hvordan denne viden kan være vejledende for lærerens resp. den studerendes direkte aktivitet i klasselokalet. Problemet for brugeren (en lærer eller en student) er dels at diagnosticere situationen på holdet, ved eksamen e.l. og dels at finde/vælge en reaktionsmåde, der er relevant hertil. Det er disse kompetencer, Pædagogisk Selvtræning søger at udvikle. Til sidst diskuteres, hvordan Pædagogisk Selvtræning kan videreudvikles og indplaceres ift. andre, fx IT-baserede undervisningsformer

Perinatal Whole Blood Zinc Status and Cytokines, Adipokines, and Other Immune Response Proteins

(1) Background: Zinc is an essential micronutrient and zinc deficiency is associated with immune dysfunction. The neonatal immune system is immature, and therefore an optimal neonatal zinc status may be important. The aim of this study was to investigate the possible association between neonatal whole blood (WB)-Zinc content and several immune markers. (2) Methods: In total, 398 healthy newborns (199 who later developed type 1 diabetes and 199 controls) from the Danish Newborn Screening Biobank had neonatal dried blood spots (NDBS) analyzed for WB-Zinc content and (i) cytokines: Interleukin (IL)-1β, IL-4, IL-6, IL-8, IL-10, IL-12 (p70), interferon gamma, tumor necrosis factor alpha, and transforming growth factor beta; (ii) adipokines: leptin and adiponectin; (iii) other immune response proteins: C-reactive protein (CRP), and mannose-binding lectin (MBL), and soluble triggering receptors expressed on myeloid cells1 (sTREM-1). WB-Zinc content was determined using laser ablation inductively coupled plasma mass spectrometry. For each analyte, the relative change in mean level was modelled by a robust log-normal model regression. (3) Results: No association was found between WB-Zinc content and all the immune response markers in either the unadjusted or adjusted models overall or when stratifying by case status. (4) Conclusions: In healthy Danish neonates, WB-Zinc content was not associated with cytokines, adipokines, CRP, MBL or sTREM, which does not indicate a strong immunological function of neonatal zinc status

High neonatal blood iron content is associated with the risk of childhood type 1 diabetes mellitus

(1) Background: Iron requirement increases during pregnancy and iron supplementation is therefore recommended in many countries. However, excessive iron intake may lead to destruction of pancreatic β-cells. Therefore, we aim to test if higher neonatal iron content in blood is associated with the risk of developing type 1 diabetes mellitus (T1D) in childhood; (2) Methods: A case-control study was conducted, including 199 children diagnosed with T1D before the age of 16 years from 1991 to 2005 and 199 controls matched on date of birth. Information on confounders was available in 181 cases and 154 controls. Iron was measured on a neonatal single dried blood spot sample and was analyzed by laser ablation inductively coupled plasma mass spectrometry. Multivariate logistic regression was used to evaluate if iron content in whole blood was associated with the risk of T1D; (3) Results: A doubling of iron content increased the odds of developing T1D more than two-fold (odds ratio (95% CI), 2.55 (1.04; 6.24)). Iron content increased with maternal age (p = 0.04) and girls had higher content than boys (p = 0.01); (4) Conclusions: Higher neonatal iron content associates to an increased risk of developing T1D before the age of 16 years. Iron supplementation during early childhood needs further investigation, including the causes of high iron in neonates