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    A Virtual Lab Maturity Model for Guiding the Co-Development of Advanced Virtual Research Environments
    (2025-08-26) Zhao, Zhiming; Kissling, W. Daniel; Hengeveld, Geerten M; Athanasiadis, Ioannis; Soetaert, Karline; Hof, Andries
    Advanced data science and AI technologies, such as Digital Twins, offer new avenues for innovation in addressing complex scientific problems. However, developing an effective Virtual Research Environment (VRE) to realize these innovation potentials is technically challenging. Incorporating the emerging technologies into the research lifecycle as a new problem-solving paradigm requires assembling diverse software and technological components, which are often not yet fully production-ready. Additionally, successful implementations are often limited to demonstrator cases that are difficult to generalize, leading to significant development risks when creating mature services within a VRE intended for large scientific communities. While agile practices can support development by promoting close engagement with end users throughout the process, their iterative nature does not inherently guarantee the evolution of a technically sustainable solution, potentially increasing risks in project delay or even failure. This paper introduces a Virtual Lab Maturity Framework designed to facilitate the co-development process between end users and development teams, ensuring a more coordinated and sustainable approach to building effective VREs.
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    Titanium carbide MXenes - Early identification of safety, sustainability and regulatory issues
    (2025-09-17) Ouhajji, Samia; Swart, Elmer; Völker, Doris; Schwirn, Kathrin; Fadeel, Bengt; Oomen, Agnes G
    Two-dimensional (2D) carbides and nitrides, collectively known as MXenes, are advanced materials known for their unique properties, including exceptional electrical conductivity, large surface area, and tuneable surface functionalities. MXenes have gained significant attention, due to their potential in energy storage, biomedicine, and environmental remediation. However, the safe and sustainable implementation of these materials is hindered by critical gaps in safety, sustainability, and regulatory data. This study applies the OECD's Early4AdMa anticipatory risk governance tool to systematically identify potential risks and challenges associated with titanium carbide (TiC) MXenes, the most extensively studied of the MXenes. We highlight critical uncertainties around human health and environmental impacts, stemming from discrepancies in acute toxicity studies, insufficient data on pulmonary exposure, genotoxicity, and long-term effects, and limited understanding of environmental fate and ecotoxicity. These knowledge gaps are sustained by the lack of harmonised guidance on sample preparation and dosimetry tailored to the unique morphology of MXenes. Moreover, life-cycle assessments demonstrate the high environmental cost of conventional synthesis methods, underlining the need for greener, energy-efficient alternatives and sustainable innovation approaches. In addition to addressing these knowledge gaps, a key follow-up action is the evaluation of the need to update regulatory guidance documents related to material characterization relevant for such 2D materials (e.g., lateral size, layers, and terminal groups) to ensure comprehensive risk assessment. The present study not only identifies actions to improve the safety and sustainability of TiC MXenes, but also provides a basis for the evaluation of other emerging materials.
  • PublicationMetadata only
    Correction: Kuypers et al. Evaluation of Neonatal Screening Programs for Tyrosinemia Type 1 Worldwide. Int. J. Neonatal Screen. 2024, 10, 82
    (2025-09-01) Kuypers, Allysa M; Bouva, Marelle J; Loeber, J Gerard; Boelen, Anita; Dekkers, Eugenie; Petritis, Konstantinos; Pickens, C Austin; The Isns Representatives; van Spronsen, Francjan J; Heiner-Fokkema, M Rebecca
    The authors wish to make the following correction to their paper published in the [...].
  • PublicationMetadata only
    Comparing DNA Isolation and Preparation Protocols for Dried Blood Spots in the Context of Genomic Newborn Screening
    (2025-09-03) Duintjer, Annelotte J; Imholz, Sandra; Pico-Knijnenburg, Ingrid; Heuperman, Adinda; Hodemaekers, Hennie; Deutekom, Eva S; Voorhoeve, Els; Dollé, Martijn ET; van der Burg, Mirjam
    Due to rapid technical advancements and increasing cost-effectiveness, the potential application of next-generation sequencing (NGS) in newborn screening (NBS) has raised great interest worldwide. Genomic NBS offers the possibility to improve current NBS programs when applied as follow-up tier, and, as first-tier, allows for inclusion of conditions lacking a detectable biomarker for conventional NBS. Obtaining enough high-quality DNA from typically limited dried blood spot (DBS) material to meet NGS requirements can be challenging. Selecting a DNA isolation method for genomic NBS requires balancing technical performance and laboratory feasibility with optimal cost-effectiveness. Ten DNA isolation protocols, including two column-based, five lysis-based, and three semi-automated magnetic bead-based protocols, were evaluated on technical outcomes and performance in targeted amplicon sequencing. Additionally, estimated costs, hands-on time, turnaround time, scalability, and plastic footprint were assessed. Although technical outcomes, including yield, purity, and molecular weight, differed between methods, qualitative results in amplicon sequencing, as defined by read output, mapping, and coverage depth, were found sufficient and comparable for various protocols. In conclusion, both technical requirements and operational parameters are crucial when selecting a DNA isolation protocol and will depend on the NGS application as well as the NBS approach, as either first-tier or follow-up tier.
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    Design, development, and testing of a new multi-locus sequence typing scheme for the zoonotic pathogen
    (2025-08-14) Troell, Karin; Stensvold, Christen Rune; Sannella, Anna Rosa; Betson, Martha; Östlund, Emma; Chalmers, Rachel M; Chaudhry, Umer; Davidson, Rebecca; Davies, Lauren; Ignatius, Ralf; de Jong, Anton; Karadjian, Gregory; Adjou, Karim; Klotz, Christian; Ptochos, Sokratis; Robinson, Guy; Roelfsema, Jeroen; Soba, Barbara; Sroka, Jacek; Vatta, Paolo; Wensman, Jonas Johansson; Cacciò, Simone M
    The zoonotic parasite is an important global cause of diarrheal disease in humans and young ruminants. Molecular typing is essential to track transmission routes and identify clusters of cases. Here, we developed a novel multi-locus sequence typing (MLST) scheme based on single nucleotide polymorphisms (SNPs) in unlinked markers. Coding regions with high variability were identified by comparing whole genome sequences (WGS) from 43 human- and 92 ruminant-derived samples collected across Europe. We first selected 18 markers and showed that they provide high discrimination among the samples with WGS data, with 88% of the MLSTs being singletons. Next, we defined a MLST based on eight genetically unlinked markers and generated sequence data from 305  samples, collected from four different host species and 13 European countries. We consolidated a set of 365 fully genotyped samples, characterized by the presence of 154 different MLSTs, 105 of which were singletons. Network analyses showed no complete clustering of samples by host species or country of origin at the European scale. We further showed that samples with subtypes that are common in Europe are divided into many MLSTs by the new scheme, highlighting its increased discriminatory ability. However, the applicability of the scheme in public health settings is limited by its cost, turnaround time, and scalability. To achieve discrimination of samples based on SNPs, a large number of loci needs to be analysed, and this is feasible using amplicon sequencing technologies.

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