Effectiveness and cost-effectiveness of a nurse-delivered intervention to improve adherence to treatment for HIV : a pragmatic, multicentre, open-label, randomised clinical trial

This trial was funded from public money by the Netherlands Organisation for Health Research and Development (ZonMW; grant number 171002208). Aardex provided support on the development of the study website. We thank all the HIV nurses and physicians from the seven HIV clinics involved in the AIMS study for their input and collaboration (Academic Medical Centre, Slotervaart hospital, and St. Lucas-Andreas hospital, all in Amsterdam; the Leiden University Medical Centre, Leiden; HAGA hospital, The Hague; Erasmus Medical Centre, Rotterdam; and Isala clinic, Zwolle), the study participants, and the Stichting HIV Monitoring (SHM) for their support in accessing the SHM database for identifying patient inclusion criteria and developing the Markov model. Finally, we thank and remember Herman Schaalma (deceased) for his contribution to the study design and grant application.Peer reviewedPostprin

Cost-effectiveness and Cost-utility of the Adherence Improving Self-management Strategy in Human Immunodeficiency Virus Care : A Trial-based Economic Evaluation

This study was funded by ZonMw (the Netherlands), program Doelmatigheidsonderzoek (grant number 171002208). This funding source had no role in study design, data collection, analysis, interpretation, or writing of the report. All authors declare that they have no competing interests. We thank the HIV-nurses and physicians from the seven HIV-clinics who were involved in the AIMSstudy (Academic Medical Center, Amsterdam; Slotervaart Hospital, Amsterdam; St. Lucas-Andreas Hospital, Amsterdam; the Leiden University Medical Center, Leiden; Haga Teaching Hospital, Den Haag; Erasmus Medical Center, Rotterdam; Isala Clinics, Zwolle) for their input and collaboration. We also would like to express our gratitude to the study participants. Written informed consent was obtained from each patient. The study has been approved by the ethics committee of each participating center.Peer reviewedPostprin

Analysis of >3400 worldwide eggplant accessions reveals two independent domestication events and multiple migration-diversification routes

Eggplant (Solanum melongena) is an important Solanaceous crop, widely cultivated and consumed in Asia, the Mediterranean basin, and Southeast Europe. Its domestication centers and migration and diversification routes are still a matter of debate. We report the largest georeferenced and genotyped collection to this date for eggplant and its wild relatives, consisting of 3499 accessions from seven worldwide genebanks, originating from 105 countries in five continents. The combination of genotypic and passport data points to the existence of at least two main centers of domestication, in Southeast Asia and the Indian subcontinent, with limited genetic exchange between them. The wild and weedy eggplant ancestor S. insanum shows admixture with domesticated S. melongena, similar to what was described for other fruit-bearing Solanaceous crops such as tomato and pepper and their wild ancestors. After domestication, migration and admixture of eggplant populations from different regions have been less conspicuous with respect to tomato and pepper, thus better preserving ‘local’ phenotypic characteristics. The data allowed the identification of misclassified and putatively duplicated accessions, facilitating genebank management. All the genetic, phenotypic, and passport data have been deposited in the Open Access G2P-SOL database, and constitute an invaluable resource for understanding the domestication, migration and diversification of this cosmopolitan vegetabl

Twist exome capture allows for lower average sequence coverage in clinical exome sequencing

Background Exome and genome sequencing are the predominant techniques in the diagnosis and research of genetic disorders. Sufficient, uniform and reproducible/consistent sequence coverage is a main determinant for the sensitivity to detect single-nucleotide (SNVs) and copy number variants (CNVs). Here we compared the ability to obtain comprehensive exome coverage for recent exome capture kits and genome sequencing techniques. Results We compared three different widely used enrichment kits (Agilent SureSelect Human All Exon V5, Agilent SureSelect Human All Exon V7 and Twist Bioscience) as well as short-read and long-read WGS. We show that the Twist exome capture significantly improves complete coverage and coverage uniformity across coding regions compared to other exome capture kits. Twist performance is comparable to that of both short- and long-read whole genome sequencing. Additionally, we show that even at a reduced average coverage of 70× there is only minimal loss in sensitivity for SNV and CNV detection. Conclusion We conclude that exome sequencing with Twist represents a significant improvement and could be performed at lower sequence coverage compared to other exome capture techniques

A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Purpose Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock

Analysis of >3400 worldwide eggplant accessions reveals two independent domestication events and multiple migration‐diversification routes

SUMMARY Eggplant ( Solanum melongena ) is an important Solanaceous crop, widely cultivated and consumed in Asia, the Mediterranean basin, and Southeast Europe. Its domestication centers and migration and diversification routes are still a matter of debate. We report the largest georeferenced and genotyped collection to this date for eggplant and its wild relatives, consisting of 3499 accessions from seven worldwide genebanks, originating from 105 countries in five continents. The combination of genotypic and passport data points to the existence of at least two main centers of domestication, in Southeast Asia and the Indian subcontinent, with limited genetic exchange between them. The wild and weedy eggplant ancestor S. insanum shows admixture with domesticated S. melongena , similar to what was described for other fruit‐bearing Solanaceous crops such as tomato and pepper and their wild ancestors. After domestication, migration and admixture of eggplant populations from different regions have been less conspicuous with respect to tomato and pepper, thus better preserving ‘local’ phenotypic characteristics. The data allowed the identification of misclassified and putatively duplicated accessions, facilitating genebank management. All the genetic, phenotypic, and passport data have been deposited in the Open Access G2P‐SOL database, and constitute an invaluable resource for understanding the domestication, migration and diversification of this cosmopolitan vegetable.Significance Statement Genotypic, passport and geographical origin data from 3499 worldwide accessions of eggplant and its wild relatives were collected, curated, analyzed, and deposited in a ‘one stop shop’ Open Access database. The identified polymorphisms and georeferencing data led to the identification of two main centers of domestication of eggplant – in Southeast Asia and the Indian subcontinent – and of its migration and diversification routes. Identification of putatively duplicated and misclassified accessions will facilitate genebank management

Type 2 Diabetes Monocyte MicroRNA and mRNA Expression: Dyslipidemia Associates with Increased Differentiation-Related Genes but Not Inflammatory Activation a11111

Abstract There is increasing evidence that inflammatory macrophages in adipose tissue are involved in insulin resistance of type 2 diabetes (T2D). Due to a relative paucity of data on circulating monocytes in T2D, it is unclear whether the inflammatory changes of adipose tissue macrophages are reflected in these easily accessible cells. Objective To study the expression pattern of microRNAs and mRNAs related to inflammation in T2D monocytes. Design A microRNA finding study on monocytes of T2D patients and controls using array profiling was followed by a quantitative Real Time PCR (qPCR) study on monocytes of an Ecuadorian validation cohort testing the top over/under-expressed microRNAs. In addition, monocytes of the validation cohort were tested for 24 inflammation-related mRNAs and 2 microRNAs previously found deregulated in (auto)-inflammatory monocytes. Results In the finding study, 142 significantly differentially expressed microRNAs were identified, 15 having the strongest power to discriminate T2D patients from controls (sensitivity 66%, specificity 90%). However, differences in expression of these microRNAs between patients and controls were small. On the basis of >1.4 or <0.6-fold change expression 5 microRNAs were selected for further validation. One microRNA (miR-34c-5p) was validated as significantly over-expressed in T2D monocytes. In addition, we found over expression of 3 mRNAs (CD9, DHRS3 and PTPN7) in the validation cohort. These mRNAs are important for cell morphology, adhesion, shape change, and cell differentiation. Classical inflammatory genes (e.g. TNFAIP3) were only over-expressed in monocytes of patients with normal serum lipids. Remarkably, in dyslipidemia, there was a reduction in the expression of inflammatory genes (e.g. ATF3, DUSP2 and PTGS2). Conclusions The expression profile of microRNAs/mRNAs in monocytes of T2D patients indicates an altered adhesion, differentiation, and shape change potential. Monocyte inflammatory activation was only found in patients with normal serum lipids. Abnormal lipid values coincided with a reduced monocyte inflammatory state

Effectiveness and cost-effectiveness of a nurse-delivered intervention to improve adherence to treatment for HIV: a pragmatic, multicentre, open-label, randomised clinical trial

No high-quality trials have provided evidence of effectiveness and cost-effectiveness of HIV treatment adherence intervention strategies. We therefore examined the effectiveness and cost-effectiveness of the Adherence Improving self-Management Strategy (AIMS) compared with treatment as usual.publisher: Elsevier articletitle: Effectiveness and cost-effectiveness of a nurse-delivered intervention to improve adherence to treatment for HIV: a pragmatic, multicentre, open-label, randomised clinical trial journaltitle: The Lancet Infectious Diseases articlelink: http://dx.doi.org/10.1016/S1473-3099(16)30534-5 associatedlink: http://dx.doi.org/10.1016/S1473-3099(17)30106-8 content_type: article copyright: © 2017 Elsevier Ltd. All rights reserved.status: publishe

Hierarchical cluster analysis of the tested genes and microRNAs of the monocytes of Ecuadorian type 2 diabetic patients and controls in the validation cohort.

<p>On the left, the fold change values between the T2D group and the non-diabetic controls were determined from normalized Ct values (Ct gene/Ct reference gene ABL) by the ΔΔCt method (2−ΔΔCt, User Bulletin 2; Applied Biosystems, Foster City, CA). Data were standardized to the non-diabetic control subjects. The fold change of each gene in the non-diabetic control subjects is therefore 1. Differences between groups were tested using t tests for independent samples. This table shows that 2 microRNAs (MiR-34c-5p and miR-576-3p) were significantly higher expressed in the monocytes of the T2D patients compared to non-diabetic controls. Also, 4 genes (of the 24 tested) were significantly different expressed (PTGS2 lower, and CD9, DHRS3 and PTPN7 significantly higher). The heatmap and dendrogram present the result of the hierarchical clustering of the genes. Three major clusters were found: Cluster A contains inflammatory compounds and includes miR-410 and miR-576-3p. Cluster B contains inflammatory compounds and factors involved with migration/differentiation/metabolism; Cluster C only consists of migration/metabolic factors. MiR-138, miR-574-3p, miR-146a and miR-34c-5p formed a sub-cluster within cluster C and strongly clustered together.</p