Integrating Geodesign and game experiments for negotiating urban development

In this article we explore an expansion of geodesign to analyze processes of competition and cooperation by combining it with game-theoretical modelling and experiments. We test the applicability of facilitating these two fields in an integrated workshop by analysing the case study of oversupply of development sites in the Liemers corridor. Two workshops were held, with representatives of the six municipalities involved and with the regional and provincial authority, in which participants negotiated over the distribution of the supply of development sites. The workshops were performed around an interactive MapTable, with spatial information (from GIS) and financial information (from the game-theoretical model) being visualized in real-time. The integrated workshops were assessed to discover differences in terms of process and outcomes, and they examine whether and how learning takes place. We conclude that the combination of game theory and geodesign provides added value for planning support by facilitating a realistic discussion, and negotiation that is strongly connected to real-life locations, and by aiming at designing a common, collaborative solution. Through the integrated workshop learning about the problem of oversupply in financial and geographical terms and also about each other’s motives and behaviour is stimulated

Kwel en natuurontwikkeling in het Binnenveld tussen de Neder-Rijn en Veenedaal.

Geohydrologie onderdeel Gelderse Valle

ImmunoGlobulin galaxy (IGGalaxy) for simple determination and quantitation of immunoglobulin heavy chain rearrangements from NGS

Background: Sequence analysis of immunoglobulin heavy chain (IGH) gene rearrangements and frequency analysis is a powerful tool for studying the immune repertoire, immune responses and immune dysregulation in health and disease. The challenge is to provide user friendly, secure and reproducible analytical services that are available for both small and large laboratories which are determining VDJ repertoire using NGS technology. Results: In this study we describe ImmunoGlobulin Galaxy (IGGalaxy)- a convenient web based application for analyzing next-generation sequencing results and reporting IGH gene rearrangements for both repertoire and clonality studies. IGGalaxy has two analysis options one using the built in igBLAST algorithm and the second using output from IMGT; in either case repertoire summaries for the B-cell populations tested are available. IGGalaxy supports multi-sample and multi-replicate input analysis for both igBLAST and IMGT/HIGHV-QUEST. We demonstrate the technical validity of this platform using a standard dataset, S22, used for benchmarking the performance of antibody alignment utilities with a 99.9 % concordance with previous results. Re-analysis of NGS data from our samples of RAG-deficient patients demonstrated the validity and user friendliness of this tool. Conclusions: IGGalaxy provides clinical researchers with detailed insight into the repertoire of the B-cell population per individual sequenced and between control and pathogenic genomes. IGGalaxy was developed for 454 NGS results but is capable of analyzing alternative NGS data (e.g. Illumina, Ion Torrent). We demonstrate the use of a Galaxy virtual machine to determine the VDJ repertoire for reference data and from B-cells taken from immune deficient patients. IGGalaxy is available as a VM for download and use on a desktop PC or on a server

IReport: A generalised Galaxy solution for integrated experimental reporting

Background: Galaxy offers a number of visualisation options with components, such as Trackster, Circster and Galaxy Charts, but currently lacks the ability to easily combine outputs from different tools into a single view or report. A number of tools produce HTML reports as output in order to combine the various output files from a single tool; however, this requires programming and knowledge of HTML, and the reports must be custom-made for each new tool.Findings: We have developed a generic and flexible reporting tool for Galaxy, iReport, that allows users to create interactive HTML reports directly from the Galaxy UI, with the ability to combine an arbitrary number of outputs from any number of different tools. Content can be organised into different tabs, and interactivity can be added to components. To demonstrate the capability of iReport we provide two publically available examples, the first is an iReport explaining about iReports, created for, and using content from the recent Galaxy Community Conference 2014. The second is a genetic report based on a trio analysis to determine candidate pathogenic variants which uses our previously developed Galaxy toolset for whole-genome NGS analysis, CGtag. These reports may be adapted for outputs from any sequencing platform and any results, such as omics data, non-high throughput results and clinical variables.Conclusions: iReport provides a secure, collaborative, and flexible web-based reporting system that is compatible with Galaxy (and non-Galaxy) generated content. We demonstrate its value with a real-life example of reporting genetic trio-analysis

Time-trends in disease characteristics and comorbidities in patients with chronic hepatitis B in the period 1980–2020

Background & aims: The incidence of chronic hepatitis B (CHB) is declining due to successful implementation of vaccination programs and widespread use of antiviral therapy. We aimed to study time-trends in disease characteristics and comorbidities in newly referred CHB patients. Methods: : We collected information on hepatitis B virus (HBV) related disease characteristics (including hepatitis B e-antigen (HBeAg) status, viremia, stage of liver fibrosis and indication for treatment and/or hepatocellular carcinoma (HCC) surveillance) and presence of comorbidities in all CHB patients referred to our center from 1980 through 2020. Patient characteristics were compared according to referral date (before 2000, between 2000 and 2010 and after 2010). Results: : We identified 1515 eligible patients. Patients referred after 2010 were older (36 versus 34 years, p < 0.001), more often non-Caucasian (82.3% versus 55.0%, p < 0.001) and more frequently HBeAg negative (81.5% versus 49.8%, p < 0.001) when compared to patients referred before 2000. Adjusted for ethnicity, sex and age, patients referred after 2010 were less likely to have significant fibrosis (adjusted odds ratio [aOR]:0.178, p < 0.001) or indication for antiviral therapy (aOR:0.342, p < 0.001) but were more likely to be affected by the metabolic syndrome (aOR:1.985, p = 0.013), hepatic steatosis (aOR:1.727, p < 0.001) and metabolic dysfunction associated fatty liver disease (MAFLD) (aOR:1.438, p = 0.013). Conclusions: : The characteristics of the CHB populations are changing. Newly referred patients are older, have less active HBV related liver disease but are more likely to be co-affected by MAFLD. These findings provide guidance for adequate allocation of resources to cope with the changing characteristics of the CHB population

Exome-wide analysis of the discovehr cohort reveals novel candidate pharmacogenomic variants for clinical pharmacogenomics

Recent advances in next-generation sequencing technology have led to the production of an unprecedented volume of genomic data, thus further advancing our understanding of the role of genetic variation in clinical pharmacogenomics. In the present study, we used whole exome sequencing data from 50,726 participants, as derived from the DiscovEHR cohort, to identify pharmacogenomic variants of potential clinical relevance, according to their occurrence within the PharmGKB database. We further assessed the distribution of the identified rare and common pharmacogenomics variants amongst different GnomAD subpopulations. Overall, our findings show that the use of publicly available sequence data, such as the DiscovEHR dataset and GnomAD, provides an opportunity for a deeper understanding of genetic variation in pharmacogenes with direct implications in clinical pharmacogenomics

CGtag: Complete genomics toolkit and annotation in a cloud-based Galaxy

Background: Complete Genomics provides an open-source suite of command-line tools for the analysis of their CG-formatted mapped sequencing files. Determination of; for example, the functional impact of detected variants, requires annotation with various databases that often require command-line and/or programming experience; thus, limiting their use to the average research scientist. We have therefore implemented this CG toolkit, together with a number of annotation, visualisation and file manipulation tools in Galaxy called CGtag (Complete Genomics Toolkit and Annotation in a Cloud-based Galaxy).Findings: In order to provide research scientists with web-based, simple and accurate analytical and visualisation applications for the selection of candidate mutations from Complete Genomics data, we have implemented the open-source Complete Genomics tool set, CGATools, in Galaxy. In addition we implemented some of the most popular command-line annotation and visualisation tools to allow research scientists to select candidate pathological mutations (SNV, and indels). Furthermore, we have developed a cloud-based public Galaxy instance to host the CGtag toolkit and other associated modules.Conclusions: CGtag provides a user-friendly interface to all research scientists wishing to select candidate variants from CG or other next-generation sequencing platforms' data. By using a cloud-based infrastructure, we can also assure sufficient and on-demand computation and storage resources to handle the analysis tasks. The tools are freely available for use from an NBIC/CTMM-TraIT (The Netherlands Bioinformatics Center/Center for Translational Molecular Medicine) cloud-based Galaxy instance, or can be installed to a local (production) Galaxy via the NBIC Galaxy tool shed

Precursor lesions of vulvar squamous cell carcinoma – histology and biomarkers: A systematic review

The precursor lesion of vulvar squamous cell carcinoma (VSCC), namely vulvar intraepithelial neoplasia (VIN), is classified as: human papillomavirus (HPV)-related high grade squamous intraepithelial lesion (HSIL), and HPV-independent differentiated VIN (dVIN). Traditionally, histology and immunohistochemistry (IHC) have been the basis of diagnosis and classification of VIN. HSIL shows conspicuous histological atypia, and positivity on p16-IHC, whereas dVIN shows less obvious histological atypia, and overexpression or null-pattern on p53-IHC. For both types of VIN, other diagnostic immunohistochemical markers have also been evaluated. Molecular characterization of VIN has been attempted in few recent studies, and novel genotypic subtypes of HPV-independent VSCC and VIN have been identified. This systematic review appraises the VSCC precursors identified so far, focusing on histology and biomarkers (immunohistochemical and molecular). To gain further insights into the carcinogenesis and to identify additional potential biomarkers, gene expression omnibus (GEO) datasets on VSCC were analyzed; the results are presented