Deconvolution of bulk blood eQTL effects into immune cell subpopulations

BACKGROUND: Expression quantitative trait loci (eQTL) studies are used to interpret the function of disease-associated genetic risk factors. To date, most eQTL analyses have been conducted in bulk tissues, such as whole blood and tissue biopsies, which are likely to mask the cell type-context of the eQTL regulatory effects. Although this context can be investigated by generating transcriptional profiles from purified cell subpopulations, current methods to do this are labor-intensive and expensive. We introduce a new method, Decon2, as a framework for estimating cell proportions using expression profiles from bulk blood samples (Decon-cell) followed by deconvolution of cell type eQTLs (Decon-eQTL). RESULTS: The estimated cell proportions from Decon-cell agree with experimental measurements across cohorts (R ≥ 0.77). Using Decon-cell, we could predict the proportions of 34 circulating cell types for 3194 samples from a population-based cohort. Next, we identified 16,362 whole-blood eQTLs and deconvoluted cell type interaction (CTi) eQTLs using the predicted cell proportions from Decon-cell. CTi eQTLs show excellent allelic directional concordance with eQTL (≥ 96-100%) and chromatin mark QTL (≥87-92%) studies that used either purified cell subpopulations or single-cell RNA-seq, outperforming the conventional interaction effect. CONCLUSIONS: Decon2 provides a method to detect cell type interaction effects from bulk blood eQTLs that is useful for pinpointing the most relevant cell type for a given complex disease. Decon2 is available as an R package and Java application (https://github.com/molgenis/systemsgenetics/tree/master/Decon2) and as a web tool (www.molgenis.org/deconvolution)

Additional file 1: of Glatiramer acetate treatment persistence - but not adherence - in multiple sclerosis patients is predicted by health-related quality of life and self-efficacy: a prospective web-based patient-centred study (CAIR study)

Data on adherence, persistence, self-efficacy, HRQoL, gender and disease duration. (XLSX 25 kb

Study into the Impact of Nutrition on Children with Attention-deficit hyperactivity disorder - ADHD (INCA Study)

Dutch randomised controlled trial into the effects of food on the behaviour of a random group of school-going children meeting the DSM-IV criteria for ADHD, including immunological testing. This INCA study is registered as an International Standard Randomised Controlled Trial, number ISRCTN 76063113

TriGraphSlant - benchmark set for writer identification - writers were asked to write in unnatural slant

This is the TrigraphSlant (Img version) Distribution, release 18/3/2011 This distribution contains 188 images of scanned handwritten text, scanned at resolution 300dpi Canon LiDE 25, grey scale, by 47 Dutch writers, four pages per writer, from four writing conditions, one condition per page. The conditions are: 1. [AN] Copy text A in your natural handwriting. 2. [BN] Copy text B in your natural handwriting. 3. [BL] Copy text B and slant your handwriting to the left as much as possible. 4. [BR] Copy text B and slant your handwriting to the right as much as possible. The codes AN, BN, BL and BR refer to subsets into which the collected pages of the writers were subdivided. AN represents a collection of authentic documents; BN, BL and BR can be seen as collections of questioned documents. To avoid structural effects of fatigue, the order of item 3 and 4 was randomized at each collection: half of the subjects wrote the BR page before the BL page. The data were collected at three sites, in three cities: The Hague: NFI (N...), Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen (D...) and the Artificial Intelligence Dept. of University of Groningen (R...) Copyright The International Unipen Foundation, 2010, All rights reserve

SWAP70 is a universal GEF-like adaptor for tethering actin to phagosomes

We recently identified a key role for SWAP70 as the tethering factor stabilizing F-actin filaments on the surface of phagosomes in human dendritic cells by interacting both with Rho-family GTPases and the lipid phosphatidylinositol (3,4)-bisphosphate. In this study, we aimed to investigate whether this role of SWAP70 was general among immune phagocytes. Our data reveal that SWAP70 is recruited to early phagosomes of macrophages and dendritic cells from both human and mouse. The putative inhibitor of SWAP70 sanguinarine blocked phagocytosis and F-actin polymerization, supporting a key role for SWAP70 in phagocytosis as demonstrated previously with knock-down. Moreover, SWAP70 was recently shown to sequester the F-actin severing protein cofilin and we investigated this relationship in phagocytosis. Our data show an increased activation of cellular cofilin upon siRNA knockdown of SWAP70. Finally, we explored whether SWAP70 would be recruited to the immune synapse between dendritic cells and T cells required for antigen presentation, as the formation of such synapses depends on F-actin. However, we observed that SWAP70 was depleted at immune synapses and specifically was recruited to phagosomes. Our data support an essential and specific role for SWAP70 in tethering and stabilizing F-actin to the phagosomal surface in a wide range of phagocytes

Supplementary Material for: Cognitive Remediation Therapy Does Not Enhance Treatment Effect in Obsessive-Compulsive Disorder and Anorexia Nervosa: A Randomized Controlled Trial

Background: Guideline-recommended therapies are moderately successful in the treatment of obsessive-compulsive disorder (OCD) and anorexia nervosa (AN), leaving room for improvement. Cognitive inflexibility, a common trait in both disorders, is likely to prevent patients from engaging in treatment and from fully benefiting from existing therapies. Cognitive remediation therapy (CRT) is a practical augmentation intervention aimed at ameliorating this impairing cognitive style prior to disorder-specific therapy. Objective: To compare the effectiveness of CRT and a control treatment that was not aimed at enhancing flexibility, named specialized attention therapy (SAT), as add-ons to treatment as usual (TAU). Methods: In a randomized controlled multicenter clinical trial, 71 adult patients with OCD and 61 with AN were randomized to ten twice-weekly sessions with either CRT or SAT, followed by TAU. Patients were evaluated at baseline, post-CRT/SAT, and after 6 and 12 months, with outcomes being quantified using the Yale-Brown Obsessive Compulsive Scale for OCD and the Eating Disorder Examination Questionnaire for AN. Results: Across study groups, most importantly CRT+TAU was not superior to control treatment (SAT)+TAU in reducing OCD and AN pathology. Contrary to expectations, SAT+TAU may have been more effective than CRT+TAU in patients being treated for OCD. Conclusions: CRT did not enhance the effect of TAU for OCD and AN more than SAT. Unexpectedly, SAT, the control condition, may have had an augmentation effect on TAU in OCD patients. Although this latter finding may have been due to chance, the effect of SAT delivered as a pretreatment add-on intervention for adults with OCD and AN merits future efforts at replication

Supplementary Material for: Bronchoscopic Lung Volume Reduction Treatment Using Endobronchial Valves for Emphysema: Emerging Questions

Medicin

Translation and transcultural validation of the Dutch hospital for special surgery paediatric functional activity brief scale (HSS Pedi-FABS)

Abstract Background There is a need for a validated simple Dutch paediatric activity scale. The purpose was to translate and transculturally validate the Dutch Hospital for Special Surgery Paediatric Functional Activity Brief Scale (HSS Pedi-FABS) questionnaire in healthy children and adolescents. Methods The original HSS Pedi-FABS was translated forward and backward and was transculturally adapted after performing a pilot study among children and professionals. The final version of the Dutch HSS Pedi-FABS was validated in healthy children and adolescents aged 10 to 18 years old. Children who had any condition or injury limiting their normal physical activity were excluded. The interval between the first questionnaire T0 (HSS Pedi-FABS, Physical Activity Questionnaire for children or adolescents (PAQ-C/A) and Tegner activity scale) and the second questionnaire T1 (HSS Pedi-FABS) was 2 weeks. Construct validity, interpretability and reliability were evaluated. Content validity was evaluated through cognitive interviews among a smaller group of children and through a questionnaire among professionals. Results To evaluate content validity, 9 children and adolescents were interviewed, and 30 professionals were consulted. Content validity among professionals showed a relevance of less than 85% for most items on construct. However, content validity among children was good with a 92% score for item relevance. Readability was scored at a reading level of 11- to 12-year-olds. The validation group consisted of 110 healthy children and adolescents (mean age of 13.9 years ±2.6). Construct validity was considered good as 8 out of 10 hypotheses were confirmed. The Dutch HSS Pedi-FABS showed no floor or ceiling effect. Analysis of the internal consistency in the validation group resulted in a Cronbach’s alpha of 0.82. Test-retest reliability was evaluated among 69 children and adolescents and revealed an Intraclass Correlation Coefficient (ICC) of 0.76. Conclusion The Dutch HSS Pedi-FABS showed good psychometric properties in a healthy Dutch paediatric and adolescent population. Limitations of the current Dutch HSS Pedi-FABS are content validity on construct of items reported by professionals