Technical note: A knowledge graph approach to registering tumour specific data of patient-candidates for proton therapy in the Netherlands.

The registration of multi-source radiation oncology data is a time-consuming and labour-intensive procedure. The standardisation of data collection offers the possibility for the acquisition of quality data for research and clinical purposes. With this study, we present an overview of the different tumour group data lists in the Dutch national proton therapy registry. Furthermore, as a representative example of the workings of these different tumour-specific knowledge graphs, we present the FAIR (Findable, Accessible, Interoperable, Reusable) data principles-compliant knowledge graph approach describing the head and neck tumour variables using radiotherapy domain ontologies and semantic web technologies. Our goal is to provide the radiotherapy community with a flexible and interoperable data model for data exchange between centres. We highlight data variables that are needed for models used in the model-based approach (MBA), which ensures a fair selection of patients that will benefit most from proton therapy.

Breast cancer patients' most important quality of life themes for a radiotherapy decision aid.

BACKGROUND AND AIM: The BRASA patient decision aid (BRASA-PtDA) facilitates shared decision making for breast cancer patients (BCPs) facing a radiotherapy treatment decision. During evaluations, patients indicated the wish for quantitative information on side effects. Therefore, this study assessed BCPs opinion on which and how information on side effects should be incorporated in the BRASA-PtDA. METHODS: A workshop was organized with BCPs (n = 9), researchers (n = 5) and clinicians (n = 3). Subsequently, a survey was sent to BCPs (n = 744) investigating the generalisability of the workshop findings, and posing additional questions. The survey entailed multiple choice questions on quality of life themes, the use of a decision aid and risk communication. RESULTS: The workshop revealed BCPs wish for a layered, all encompassing information system. Information on the impact of side effects on daily life was preferred above the risk of these side effects. The survey revealed that important quality of life (QoL) themes were having energy (81%; n = 605), arm function (61%; n = 452), pain (55%; n = 410). Despite the focus on qualitative effects in the workshop, 89% of the survey respondents also wanted to be informed on individualized risks of side effects. 54% Of the survey respondents had never heard of a PtDA. CONCLUSIONS: BCPs preferred information on the impact of side effects, but also their individualized risks on side effects. Most important QoL themes were having enough energy, arm function and pain. Consequently, the BRASA-PtDA should be reshaped, starting with quality of life themes, rather than side effects.

Independent validation of a dysphagia dose response model for the selection of head and neck cancer patients to proton therapy.

Background and purpose: The model based approach involves the use of normal tissue complication models for selection of head and neck cancer patients to proton therapy. Our goal was to validate the clinical utility of the related dysphagia model using an independent patient cohort. Materials and Methods: A dataset of 277 head and neck cancer (pharynx and larynx) patients treated with (chemo)radiotherapy between 2019 and 2021 was acquired. For the evaluation of the model discrimination we used statistical metrics such as the sensitivity, specificity and the area under the receiver operating characteristic curve. After the validation we evaluated if the dysphagia model can be improved using the closed testing procedure, the Brier and the Hosmer-Lemeshow score. Results: The performance of the original normal tissue complication probability model for dysphagia grade II-IV at 6 months was good (AUC = 0.80). According to the graphical calibration assessment, the original model showed underestimated dysphagia risk predictions. The closed testing procedure indicated that the model had to be updated and selected a revised model with new predictor coefficients as an optimal model. The revised model had also satisfactory discrimination (AUC = 0.83) with improved calibration. Conclusion: The validation of the normal tissue complication probability model for grade II-IV dysphagia was successful in our independent validation cohort. However, the closed testing procedure indicated that the model should be updated with new coefficients.

Making radiotherapy more efficient with FAIR data.

Given the rapid growth of artificial intelligence (AI) applications in radiotherapy and the related transformations toward the data-driven healthcare domain, this article summarizes the need and usage of the FAIR (Findable, Accessible, Interoperable, Reusable) data principles in radiotherapy. This work introduces the FAIR data concept, presents practical and relevant use cases and the future role of the different parties involved. The goal of this article is to provide guidance and potential applications of FAIR to various radiotherapy stakeholders, focusing on the central role of medical physicists.

A knowledge graph representation of baseline characteristics for the Dutch proton therapy research registry.

Cancer registries collect multisource data and provide valuable information that can lead to unique research opportunities. In the Netherlands, a registry and model-based approach (MBA) are used for the selection of patients that are eligible for proton therapy. We collected baseline characteristics including demographic, clinical, tumour and treatment information. These data were transformed into a machine readable format using the FAIR (Findable, Accessible, Interoperable, Reusable) data principles and resulted in a knowledge graph with baseline characteristics of proton therapy patients. With this approach, we enable the possibility of linking external data sources and optimal flexibility to easily adapt the data structure of the existing knowledge graph to the needs of the clinic.

FAIR-compliant clinical, radiomics and DICOM metadata of RIDER, interobserver, Lung1 and head-Neck1 TCIA collections.

PURPOSE: One of the most frequently cited radiomics investigations showed that features automatically extracted from routine clinical images could be used in prognostic modeling. These images have been made publicly accessible via The Cancer Imaging Archive (TCIA). There have been numerous requests for additional explanatory metadata on the following datasets - RIDER, Interobserver, Lung1, and Head-Neck1. To support repeatability, reproducibility, generalizability, and transparency in radiomics research, we publish the subjects' clinical data, extracted radiomics features, and digital imaging and communications in medicine (DICOM) headers of these four datasets with descriptive metadata, in order to be more compliant with findable, accessible, interoperable, and reusable (FAIR) data management principles. ACQUISITION AND VALIDATION METHODS: Overall survival time intervals were updated using a national citizens registry after internal ethics board approval. Spatial offsets of the primary gross tumor volume (GTV) regions of interest (ROIs) associated with the Lung1 CT series were improved on the TCIA. GTV radiomics features were extracted using the open-source Ontology-Guided Radiomics Analysis Workflow (O-RAW). We reshaped the output of O-RAW to map features and extraction settings to the latest version of Radiomics Ontology, so as to be consistent with the Image Biomarker Standardization Initiative (IBSI). Digital imaging and communications in medicine metadata was extracted using a research version of Semantic DICOM (SOHARD, GmbH, Fuerth; Germany). Subjects' clinical data were described with metadata using the Radiation Oncology Ontology. All of the above were published in Resource Descriptor Format (RDF), that is, triples. Example SPARQL queries are shared with the reader to use on the online triples archive, which are intended to illustrate how to exploit this data submission. DATA FORMAT: The accumulated RDF data are publicly accessible through a SPARQL endpoint where the triples are archived. The endpoint is remotely queried through a graph database web application at http://sparql.cancerdata.org. SPARQL queries are intrinsically federated, such that we can efficiently cross-reference clinical, DICOM, and radiomics data within a single query, while being agnostic to the original data format and coding system. The federated queries work in the same way even if the RDF data were partitioned across multiple servers and dispersed physical locations. POTENTIAL APPLICATIONS: The public availability of these data resources is intended to support radiomics features replication, repeatability, and reproducibility studies by the academic community. The example SPARQL queries may be freely used and modified by readers depending on their research question. Data interoperability and reusability are supported by referencing existing public ontologies. The RDF data are readily findable and accessible through the aforementioned link. Scripts used to create the RDF are made available at a code repository linked to this submission: https://gitlab.com/UM-CDS/FAIR-compliant_clinical_radiomics_and_DICOM_metadata.

Mean platelet volume as a diagnostic marker for cardiovascular disease: drawbacks of preanalytical conditions and measuring techniques.

After the first description of platelets more than a century ago, the knowledge about their origin and function grew continuously. The development of the impedance method as a completely automated assay allowed integrating mean platelet volume (MPV) measurement as a routine parameter of the complete blood count. This enabled us to focus more on the association of platelet function and size. Since then, many authors described MPV as a marker of platelet reactivity and risk factor for cardiovascular diseases. Hence, the preanalytical variability of this parameter is known from its introduction as standard laboratory value. Unfortunately no preanalytical standards have been implemented. This review shows the high variability in the literature with MPV as a risk factor for cardiovascular disease. After a brief description of the biology of platelets, we provide an in-depth survey of the measurement methods and their drawbacks. Finally, we propose a possible approach to standardization.

The effects of pneumatic tube system transport on ROTEM analysis and contact activation assessed by thrombin generation test.

UNLABELLED: Thromboelastometry (ROTEM) is a popular point-of-care test. It generates results quickly and may benefit individualised guided haemostatic therapy. However, processing of specimens by non-technicians might decrease the quality and reproducibility of results. Centralised laboratory equipment receiving specimens through a pneumatic tube system (PTS) could avoid this. This study aimed to evaluate the influence of PTS transport on ROTEM results and its contribution to contact activation assessed by thrombin generation (TG). METHODS: Specimens from 44 patients were drawn immediately after arterial puncture. Two were anticoagulated by citrate and two by citrate/corn trypsin inhibitor, a Factor XIIa pathway inhibitor. Both types of samples were transported by walking and PTS. Subsequently, analysis was performed: ROTEM on citrated blood, and TG on citrated and corn trypsin inhibitor (CTI) blood using either 0 or 1 pM tissue factor (TF). RESULTS: In ROTEM analysis the NATEM assay showed significant differences. The EXTEM assay revealed small significant differences for clot formation time: 65 seconds (SD ± 20) versus 67 seconds (SD ± 17), and alpha angle 79° (SD ± 3) versus 77° (SD ± 3). The results remained within reference range. TG was not significantly affected by the type of tube transport, independent of the amount of TF. CONCLUSION: PTS for ROTEM analysis is feasible except for NATEM assays. The amount of contact activation via Factor XIIa in terms of TG is independent of transport type. However, due to the different characteristics of pneumatic systems, hospitals should check its impact on the results before introducing this route of transport.