Genome-wide transcriptomic profiling of human biliary organoids infected with rotavirus

Three batches of rotavirus infected vs. uninfected: genome-wide gene expression was profiled by RNA-seq. Data shown comparison for the relative expression of all the genes

Computer use 2002-2008

During a longitudinal study at the Erasmus MC - University Medical Center, more than 1000 employees were followed using registration software on their computers. The computer users performed a variety of jobs (secretaries, researchers, managers, medical personnel, professors, etc), using a variety of software. Participants performed their daily work while the software logged mouse cursor changes (10 Hz), keystrokes, mouse clicks and mouse scroll events, whenever these events occurred. The database consists of 1296 folders (95919 files) containing data from individual computer users. The dataset can be used to perfom your own analysis or you can collaborate with the Erasmus MC Kineos Research Group to perform certain types of analysis. Possible analyses are detailed risk assessment regarding computer use and health complaints or analysis of pause, mouse and keyboard use in subgroups of computer users with specific characteristcs (such as job function, age, gender etc, etc). Due to the size of this main dataset (almost 100.000 files), the files cannot be accessed online but will be made available in another way after additional contact with DANS and/or the depositor of the data. In a separate additional database data are available on the characteristics of the computer users (such as job type, occurrence of RSI complaints, handedness, software usage). These data were collected using questionnaires sent to the participants of the study. This database will contain the same personal ID so both databases can be linked. This file can be accessed online

Supplementary Material for: Development of Best Evidence Dosing Recommendations for Term and Preterm Neonates (NeoDose Project)

Abstract: Many drugs are used off-label in neonates which leads to large variation in prescribed drugs and dosages in neonatal intensive care units (NICUs). The NeoDose project aimed to develop best evidence dosing recommendations (DRs) for term and preterm neonates using a three-step approach: 1) drug selection, 2) establishing consensus-based DRs, and 3) establishing best evidence DRs. Methods: The selection of drugs was based on frequency of prescribing, availability of a neonatal DR in the Dutch Pediatric Formulary, and the labeling status. Clinical need, pharmacological diversity, and Working Group Neonatal Pharmacology (WGNP) preferences were also taken into account, using a consensus-based approach. For the second step, we requested local dosing protocols from all ten Dutch NICUs and established consensus-based DRs within the WGNP, consisting of neonatologists, clinical pharmacologists, hospital pharmacists, and researchers. In the third step, the consensus-based DRs were compared with the available literature, using standardized PubMed searches. Results: Fourteen drugs were selected for which the local dosing protocols were collected. These protocols differed mostly in total daily dose, dosing frequency, and/or route of administration. Strikingly, almost none of the dosing protocols of these 14 drugs distinguished between preterm and term neonates. The working group established consensus-based DRs, which after literature review needed modification in 56%, mainly in terms of a dose increase. Finally, we established 37 best evidence DRs, 22 for preterm and 15 for term neonates, representing 19 indications. Conclusion: This project showed the successful three-step approach for the development of DRs for term and preterm neonates

Risk of adverse pregnancy outcomes in women with periodontal disease and the effectiveness of interventions in decreasing this risk: protocol for systematic overview of systematic reviews

Abstract Background Periodontal disease is an inflammatory disease of the tissues supporting the teeth. Women who have periodontal disease while pregnant may be at risk of adverse pregnancy outcomes. Although the association between periodontal disease and adverse pregnancy outcomes has been addressed in a considerable number of systematic reviews and meta-analyses, there are important differences in the conclusions of these reviews. Systematic reviews assessing the effectivity of various therapeutic interventions to treat periodontal disease during pregnancy to try and reduce adverse pregnancy outcomes have also arrived at different conclusions. We aim to provide a systematic overview of systematic reviews comparing the frequency of adverse pregnancy outcomes between women with and without periodontal disease and/or evaluating the effect of preventive and therapeutic interventions for periodontal disease before or during pregnancy on adverse pregnancy outcomes. Methods We will include systematic reviews reporting on studies comparing adverse pregnancy outcomes: (i) between women with or without periodontal disease before

Successful implementation of a clinical transition pathway for adolescents with juvenile-onset rheumatic and musculoskeletal diseases

Abstract Background In 2008 a clinical transition pathway for young people with juvenile-onset rheumatic and musculoskeletal diseases (jRMD) aiming at improving transitional care was instituted. Historical data on drop-out rate in our clinic was 35%, one year before the implementation of the transition pathway. This study aims to I) evaluate the effectiveness of the clinical transition pathway, II) evaluate the experiences and satisfaction of YP with the transitional process and evaluate their perceived self-management skills. Methods Young people with any jRMD transferred from the pediatric to the adult rheumatology department in our academic center were eligible to enroll in this quantitative cross-sectional observational study between 2009 and 2015. Notably in 2012, we created a dedicated adolescent JIA-clinic, located at the adult rheumatology department. Electronic patient records from all young people that were transferred between 2009 and 2015 were reviewed for drop-out of care. Young people were asked to rate a VAS for ‘satisfaction with transition’ and to complete the “on your own feet transfer experience scale” (OYOF-TES)-questionnaire regarding their experiences and satisfaction with transition. Self-management skills were measured with the “on your own feet self-efficacy scale” (OYOF-SES)-questionnaire. Results One hundred fifty-four young people were transferred to the adult department, of which 76 were transferred to the dedicated adolescent JIA-clinic. The mean age at transfer was 17.8 years for YP transferred to the adult clinic and 15.2 years for transfer to the adolescent clinic. Drop-out of care rate one year after transfer was 5.1% in the adult clinic and 1.3% in the adolescent JIA-clinic. Response rate of the returned questionnaires was 61% for the adolescent JIA clinic and 36% for the adult clinic. There was no difference between responders and non-responders in demographics and disease type besides age (non-responders were significantly younger). Young people transferred to the adult and adolescent JIA-clinic both had high scores on the satisfaction scale (7.7 and 7.5 on the VAS-scale and 72.0 and 74.5 on the OYOF-TES). Self-efficacy scores were high for both groups, with OYOF-SES 59.7 for those transferred to the adult clinic and 58.2 for those transferred to the adolescent JIA-clinic. Conclusion The implementation of the clinical transition pathway has led to a substantial improvement of patient care during the transitional process leading to low drop-out of care rate and high scores on satisfaction with transition. High scores on the self-reported self-efficacy scale suggests confidence of young people to have achieved sufficient skills to successfully manage their disease

Retrospective cohort study on factors associated with mortality in high-risk pediatric critical care patients in the Netherlands

Abstract Background High-risk patients in the pediatric intensive care unit (PICU) contribute substantially to PICU-mortality. Complex chronic conditions (CCCs) are associated with death. However, it is unknown whether CCCs also increase mortality in the high-risk PICU-patient. The objective of this study is to determine if CCCs or other factors are associated with mortality in this group. Methods Retrospective cohort study from a national PICU-database (2006–2012, n = 30,778). High-risk PICU-patients, defined as patients 30% according to either the recalibrated Pediatric Risk of Mortality-II (PRISM) or the Paediatric Index of Mortality 2 (PIM2), were included. Patients with a cardiac arrest before PICU-admission were excluded. Results In total, 492 high-risk PICU patients with mean predicted risk of 24.8% (SD 22.8%) according to recalibrated PIM2 and 40.0% (SD 23.8%) according to recalibrated PRISM were included of which 39.6% died. No association was found between CCCs and non-survival (odds ratio 0.99; 95% CI 0.62–1.59). Higher Glasgow coma scale at PICU admission was associated with lower mortality (odds ratio 0.91; 95% CI 0.87–0.96). Conclusions Complex chronic conditions are not associated with mortality in high-risk PICU patients

Using predicate and provenance information from a knowledge graph for drug efficacy screening

Abstract Background Biomedical knowledge graphs have become important tools to computationally analyse the comprehensive body of biomedical knowledge. They represent knowledge as subject-predicate-object triples, in which the predicate indicates the relationship between subject and object. A triple can also contain provenance information, which consists of references to the sources of the triple (e.g. scientific publications or database entries). Knowledge graphs have been used to classify drug-disease pairs for drug efficacy screening, but existing computational methods have often ignored predicate and provenance information. Using this information, we aimed to develop a supervised machine learning classifier and determine the added value of predicate and provenance information for drug efficacy screening. To ensure the biological plausibility of our method we performed our research on the protein level, where drugs are represented by their drug target proteins, and diseases by their disease proteins. Results Using random forests with repeated 10-fold cross-validation, our method achieved an area under the ROC curve (AUC) of 78.1% and 74.3% for two reference sets. We benchmarked against a state-of-the-art knowledge-graph technique that does not use predicate and provenance information, obtaining AUCs of 65.6% and 64.6%, respectively. Classifiers that only used predicate information performed superior to classifiers that only used provenance information, but using both performed best. Conclusion We conclude that both predicate and provenance information provide added value for drug efficacy screening

Additional file 2: of Using predicate and provenance information from a knowledge graph for drug efficacy screening

Performance for different ratios between the positive and the negative cases in the training set. This file shows the performance on a balanced test set as a function of the ratio of positive and negative cases in the training set. (XLSX 14 kb

Supplementary Material for: Determinants of Advanced Bone Age in Childhood Obesity

Background: Childhood obesity is associated with advanced bone age (BA). Previous studies suggest that androgens, oestrogens, sex hormone-binding globulin, and insulin are responsible for this phenomenon, but results are contradictory and might be biased by confounders. We aim to elucidate this matter by applying a multivariate approach. Method: We performed a correlation analysis of BA standard deviation score (SDS) with age- and sex-specific SDS for androgens, oestrogens, and with indicators of insulin secretion derived from oral glucose tolerance testing, in a group of obese children. A multivariate analysis was performed to investigate which parameters were independently predictive of BA SDS. Results: In this cohort (n = 101; mean age 10.9 years; mean BA 11.8 years; mean BMI SDS 3.3), BMI SDS was significantly correlated to BA SDS (r = 0.55, p < 0.001). In a regression analysis in the total cohort (B = 0.27, p < 0.001) as well as in females (B = 0.34, p = 0.042), males (B = 0.31, p = 0.006), and pubertal children (B = 0.32, p = 0.046), dehydroepiandrosterone sulphate (DHEAS) showed a positive, independent association with BA SDS. No association with indicators of insulin secretion was found. Conclusion: BMI SDS is highly correlated to BA SDS in obese children. Increased DHEAS has a central role in advanced BA in obese children