Adapting the complexity level of a serious game to the proficiency of players

As games are continuously assessing the player, this assessment can be used to adapt the complexity of a game to the proficiency of the player in real time. We performed an experiment to examine the role of dynamic adaptation. In one condition, participants played a version of our serious game for triage training that automatically adapted the complexity level of the presented cases to how well the participant scored previously. Participants in the control condition played a version of the game with no adaptation. The adapted version was significantly more efficient and resulted in higher learning gains per instructional case, but did not lead to a difference in engagement. Adapting games to the proficiency of the player could make serious games more efficient learning tools

Automated Selection of Hotspots (ASH): enhanced automated segmentation and adaptive step finding for Ki67 hotspot detection in adrenal cortical cancer

BACKGROUND: In prognosis and therapeutics of adrenal cortical carcinoma (ACC), the selection of the most active areas in proliferative rate (hotspots) within a slide and objective quantification of immunohistochemical Ki67 Labelling Index (LI) are of critical importa

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

Cloning, tissue expression, and mapping of a human photolyase homolog with similarity to plant blue-light receptors

Enzymatic photoreactivation is a DNA repair mechanism that removes UV- induced pyrimidine dimer lesions by action of a single enzyme, photolyase, and visible light. Its presence has been demonstrated in a wide variety of organisms, ranging from simple prokaryotes to higher eukaryotes. We have isolated a human gene encoding a 66-kDa protein that shows clear overall homology to known bacterial photolyase genes. The human gene product is more similar to plant blue-light receptors within class I ph

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

Pollitt syndrome patients carry mutation in TTDN1

Complete human genome sequencing was used to identify the causative mutation in a family with Pollitt syndrome (MIM #. 275550), comprising two non-consanguineous parents and their two affected children. The patient's symptoms were reminiscent of the non-photosensitive form of recessively inherited trichothiodystrophy (TTD). A mutation in the TTDN1/. C7orf11 gene, a gene that is known to be involved in non-photosensitive TTD, had been excluded by others by Sanger sequencing. Unexpectedly, we did find a homozygous single-base pair deletion in the coding region of this gene, a mutation that is known to cause non-photosensitive TTD. The deleterious variant causing a frame shift at amino acid 93 (C326delA) followed the right mode of inheritance in the family and was independently validated using conventional DNA sequencing. We expect this novel DNA sequencing technology to help redefine phenotypic and genomic variation in patients with (mono) genetic disorders in an unprecedented manner

The effect of fantasy on learning and recall of declarative knowledge in AR game-based learning

With increasing research attention on the application of Augmented Reality (AR) and Game elements in education, fantasy elements as imaginary, fictional game features have been shown to improve learners’ motivation and are critical to engaging and immersive experiences in AR game-based learning. With its affordance of enriching real-life education with virtual effects, AR game-based learning has shown its potential to improve recall performance in previous research. However, educators and researchers have concerns regarding the effect of employing fantasy game elements in AR game-based learning, suggesting learning with such elements will add cognitive load for children leading to a lower recall. To explore the effect of AR and fantasy in game-based learning for recalling declarative knowledge, we conducted an experiment involving 98 children participants and 26 adult participants from the Netherlands and China, using our own designed AR game- ChemiKami AR. We used a mixed ANOVA to identify the effect of fantasy and AR on knowledge recall. This study showed that using AR fantasy in game-based learning can improve recall of declarative knowledge and increase learning effectiveness in classroom learning contexts for children. We offer insights and guidelines for designing AR and fantasy experiences that enhance declarative knowledge recall for target groups with different ages, learning capacities, and cultural backgrounds.</p