Data conversion strategy:A work plan to successfully complete a data conversion project in a hospital

Conversion projects are under pressure to become more efficient while facing increasing complexity. Resource limitations may restrict the transferability of clinical data, as data from a proprietary EHR system cannot seamlessly integrate with a new EHR system and conversion is needed. Converting data to ensure full accessibility in the new system can be a time-consuming and expensive process, taking weeks or even months to complete due to its complexity.Meander Medical Center is at the dawn of such a big EHR conversion project; the hospital is moving from a ‘best of breed’ strategy to an EHR suite which means that many of the current healthcare applications will be replaced by one system. The goal of this project is to define a conversion approach and strategy for Meander Medical Center. There’s done benchmarking of conversion strategies at other hospitals. Next to that, physician end-users and key stakeholders were actively involved to develop this approach. And lastly, many analysis were performed to perceive insights about the complexity of the information landscape and to determine the right variables of the strategy.Five options for the conversion strategy were defined; 1) the data quality approach, 2) the patient-centered approach, 3) the priority of healthcare professional approach, 4) a completely filled the target-EHR by AI or 5) a clean conversion but with an integrated GPT-model in our target-EHR executed on the full EHR-archive.The conclusion of this project is that Meander Medical Center should follow the data quality approach. More investigation should be done during the preparation phase on the GPT-model integration, this will facilitate healthcare professionals in the availability of key patient information. Good data quality, data availability and data accessibility play a critical role in supporting the adaptation of a new EHR system.Lastly, the project delivered a work plan to successfully complete a data conversion project in a hospital, including an overview of conversion principles and risks, an approach to execute a conversion and a framework for measuring clinical data quality

Data conversion strategy:A work plan to successfully complete a data conversion project in a hospital

Conversion projects are under pressure to become more efficient while facing increasing complexity. Resource limitations may restrict the transferability of clinical data, as data from a proprietary EHR system cannot seamlessly integrate with a new EHR system and conversion is needed. Converting data to ensure full accessibility in the new system can be a time-consuming and expensive process, taking weeks or even months to complete due to its complexity.Meander Medical Center is at the dawn of such a big EHR conversion project; the hospital is moving from a ‘best of breed’ strategy to an EHR suite which means that many of the current healthcare applications will be replaced by one system. The goal of this project is to define a conversion approach and strategy for Meander Medical Center. There’s done benchmarking of conversion strategies at other hospitals. Next to that, physician end-users and key stakeholders were actively involved to develop this approach. And lastly, many analysis were performed to perceive insights about the complexity of the information landscape and to determine the right variables of the strategy.Five options for the conversion strategy were defined; 1) the data quality approach, 2) the patient-centered approach, 3) the priority of healthcare professional approach, 4) a completely filled the target-EHR by AI or 5) a clean conversion but with an integrated GPT-model in our target-EHR executed on the full EHR-archive.The conclusion of this project is that Meander Medical Center should follow the data quality approach. More investigation should be done during the preparation phase on the GPT-model integration, this will facilitate healthcare professionals in the availability of key patient information. Good data quality, data availability and data accessibility play a critical role in supporting the adaptation of a new EHR system.Lastly, the project delivered a work plan to successfully complete a data conversion project in a hospital, including an overview of conversion principles and risks, an approach to execute a conversion and a framework for measuring clinical data quality

Integrating transposable elements in the 3D genome

Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) however, the spatial information of how genomes are folded is still only rarely integrated in experimental studies or accounted for in modelling. Whilst polymer physics is recognised as an important tool to understand the mechanisms of genome folding, in this commentary we discuss its potential applicability to aspects of TE biology. Based on recent works on the relationship between genome organisation and TE integration, we argue that existing polymer models may be extended to create a predictive framework for the study of TE integration patterns. We suggest that these models may offer orthogonal and generic insights into the integration profiles (or "topography") of TEs across organisms. In addition, we provide simple polymer physics arguments and preliminary molecular dynamics simulations of TEs inserting into heterogeneously flexible polymers. By considering this simple model, we show how polymer folding and local flexibility may generically affect TE integration patterns. The preliminary discussion reported in this commentary is aimed to lay the foundations for a large-scale analysis of TE integration dynamics and topography as a function of the three-dimensional host genome

Pre-B Cell Receptor Signaling Induces Immunoglobulin κ Locus Accessibility by Functional Redistribution of Enhancer-Mediated Chromatin Interactions

During B cell development, the precursor B cell receptor (pre-BCR) checkpoint is thought to increase immunoglobulin κ light chain (Igκ) locus accessibility to the V(D)J recombinase. Accordingly, pre-B cells lacking the pre-BCR signaling molecules Btk or Slp65 showed reduced germline Vκ transcription. To investigate whether pre-BCR signaling modulates Vκ accessibility through enhancer-mediated Igκ locus topology, we performed chromosome conformation capture and sequencing analyses. These revealed that already in pro-B cells the κ enhancers robustly interact with the ∼3.2 Mb Vκ region and its flanking sequences. Analyses in wild-type, Btk, and Slp65 single- and double-deficient pre-B cells demonstrated that pre-BCR signaling reduces interactions of both enhancers with Igκ locus flanking sequences and increases interactions of the 3′κ enhancer with Vκ genes. Remarkably, pre-BCR signaling does not significantly affect interactions between the intronic enhancer and Vκ genes, which are already robust in pro-B cells. Both enhancers interact most frequently with highly used Vκ genes, which are often marked by transcription factor E2a. We conclude that the κ enhancers interact with the Vκ region already in pro-B cells and that pre-BCR signaling induces accessibility through a functional redistribution of long-range chromatin interactions within the Vκ region, whereby the two enhancers play distinct roles

Group 2 innate lymphoid cells exhibit a dynamic phenotype in allergic airway inflammation

Group 2 innate lymphoid cells (ILC2) are implicated in allergic asthma as an early innate source of the type 2 cytokines IL-5 and IL-13. However, their induction in house dust mite (HDM)-mediated airway inflammation additionally requires T cell activation. It is currently unknown whether phenotypic differences exist between ILC2s that are activated in a T cell-dependent or T cell-independent fashion. Here, we compared ILC2s in IL-33-and HDM-driven airway inflammation. Using flow cytometry, we found that surface expression levels of various markers frequently used to identify ILC2s were dependent on their mode of activation, highly variable over time, and differed between tissue compartments, including bronchoalveolar lavage (BAL) fluid, lung, draining lymph nodes, and spleen. Whereas in vivo IL-33-activated BAL fluid ILC2s exhibited an almost uniform CD25+CD127+T1/ST2+ICOS+KLRG1+ phenotype, at a comparable time point after HDM exposure BAL fluid ILC2s had a very heterogeneous surface marker phenotype. A major fraction of HDM-activated ILC2s were CD25lowCD127+T1/ST2low ICOSlowKLRG1low, but nevertheless had the capacity to produce large amounts of type 2 cytokines. HDM-activated CD25low ILC2s in BAL fluid and lung rapidly reverted to CD25high ILC2s upon in vivo stimulation with IL-33. Genome-wide transcriptional profiling of BAL ILC2s revealed ~1,600 differentially expressed genes: HDM-stimulated ILC2s specifically expressed genes involved in the regulation of adaptive immunity through B and T cell interactions, whereas IL-33-stimulated ILC2s expressed high levels of proliferation-related and cytokine genes. In both airway inflammation models ILC2s were present in the lung submucosa close to epithelial cells, as identified by confocal microscopy. In chronic HDM-driven airway inflammation ILC2s were also found inside organized cellular infiltrates near T cells. Collectively, our findings show that ILC2s are phenotypically more heterogeneous than previously thought, whereby their surface marker and gene expression profile are highly dynamic