| 1. |
- Ariens, Robert, et al.
(author)
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Illustrated State-of-the-Art Capsules of the ISTH 2020 Congress
- 2020
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In: RESEARCH AND PRACTICE IN THROMBOSIS AND HAEMOSTASIS. - : Wiley. - 2475-0379. ; 4:5, s. 680-713
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Research review (peer-reviewed)abstract
- The 2020 Congress of the International Society of Thrombosis and Haemostasis (ISTH) was held virtually July 12-15, 2019, due to the coronavirus disease 2019 pandemic. The congress convenes annually to discuss clinical and basic topics in hemostasis and thrombosis. Each year, the program includes State of Art (SOA) lectures given by prominent scientists. Presenters are asked to create Illustrated Capsules of their talks, which are concise illustrations with minimal explanatory text. Capsules cover major themes of the presentation, and these undergo formal peer review for inclusion in this article. Owing to the shift to a virtual congress this year, organizers reduced the program size. There were 39 SOA lectures virtually presented, and 29 capsules (9 from talks omitted from the virtual congress) were both submitted and successful in peer review, and are included in this article. Topics include the roles of the hemostatic system in inflammation, infection, immunity, and cancer, platelet function and signaling, platelet function disorders, megakaryocyte biology, hemophilia including gene therapy, phenotype tests in hemostasis, von Willebrand factor, anticoagulant factor V, computational driven discovery, endothelium, clinical and basic aspects of thrombotic microangiopathies, fibrinolysis and thrombolysis, antithrombotics in pediatrics, direct oral anticoagulant management, and thrombosis and hemostasis in pregnancy. Capsule authors invite virtual congress attendees to refer to these capsules during the live presentations and participate on Twitter in discussion. Research and Practice in Haemostasis and Thrombosis will release 2 tweets from @RPTHJournal during each presentation, using #IllustratedReview, #CoagCapsule and #ISTH2020. Readers are also welcome to utilize capsules for teaching and ongoing education.
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| 2. |
- Fang, Li Tai, et al.
(author)
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Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing
- 2021
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In: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 39:9, s. 1151-1160
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Journal article (peer-reviewed)abstract
- Tumor-normal paired DNA samples from a breast cancer cell line and a matched lymphoblastoid cell line enable calibration of clinical sequencing pipelines and benchmarking 'tumor-only' or 'matched tumor-normal' analyses. The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.
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| 3. |
- Gangannagaripalli, J., et al.
(author)
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A Standard Set of Value-Based Patient-Centered Outcomes and Measures of Overall Health in Adults
- 2022
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In: Patient-Patient Centered Outcomes Research. - : Springer Science and Business Media LLC. - 1178-1653 .- 1178-1661. ; 15:3, s. 341-351
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Journal article (peer-reviewed)abstract
- Background The definition of population-specific outcomes is an essential precondition for the implementation of value-based health care. We developed a minimum standard outcome set for overall adult health (OAH) to facilitate the implementation of value-based health care in tracking, comparing, and improving overall health care outcomes of adults across multiple conditions, which would be of particular relevance for primary care and public health populations. Methods The International Consortium for Health Outcomes Measurement (ICHOM) convened an international panel (patients, clinicians, and topic experts). Following the development of a conceptual framework, a modified Delphi method (supported by public consultations) was implemented to identify, in sequence, the relevant domains, the best instruments for measuring them, the timing of measurement, and the relevant adjustment variables. Findings Outcomes were identified in relation to overall health status and the domains of physical, mental, and social health. Three instruments covering these domains were identified: PROMIS Scale v1.2-Global Health (10 items), WHO Wellbeing Index (5 items), and the WHO Disability Assessment Schedule 2.0 (12 items). Case-mix variables included a range of sociodemographic and biometric measures. Yearly measurement was proposed for all outcomes and most case-mix variables. Interpretation The ICHOM OAH Standard Set has been developed through consensus-based methods based on predefined criteria following high standards for the identification and selection of high-quality measures The involvements of a wide range of stakeholders supports the acceptability of the set, which is readily available for use and feasibility testing in clinical settings.
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| 4. |
- Gepner, B. D., et al.
(author)
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Evaluation of GHBMC, THUMS and SAFER Human Body Models in Frontal Impacts in Reclined Postures
- 2022
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In: Conference proceedings International Research Council on the Biomechanics of Injury, IRCOBI. - 2235-3151. ; 2022-September, s. 116-143
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Conference paper (peer-reviewed)abstract
- Virtual tools, such as human body models (HBMs), can support advances in vehicle development and restraint system design. The goal of this study is to evaluate selected HBMs against data from recent reclined post-mortem human subject (PMHS) tests. Three HBMs - the Global Human Body Modelling Consortium detailed model v.6.0, Total Human Model for Safety v.6.0, and SAFER HBM v.10 - were used in this study. The models were positioned with respect to the average PMHS position and utlised a previously developed environment model. The HBMs were evaluated comparing belt engagement, boundary forces and displacements (in the seat and belt), and the trajectories of the head, T1, T8, T11, L1, L3, and pelvis. The HBMs' belt engagement, boundary forces and displacements, and X-direction (fore-aft) trajectories were all generally consistent with the PMHS. All HBMs predicted more downward motion of the head and T1 compared to the PMHS. The HBMs also showed rearward pelvis pitch at peak lap belt force, opposite to the PMHS. Some of these differences were associated with differences in flexion of the lumbar spine. This is the first study to provide an in-depth evaluation of multiple reclined HBMs in frontal crashes compared to reclined PMHS.
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| 5. |
- Tushak, Sophia K., et al.
(author)
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Evaluation of the GHBMC Lumbar Spine in Sub-injurious and Injurious Loading
- 2022
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In: Conference proceedings International Research Council on the Biomechanics of Injury, IRCOBI. - 2235-3151. ; 2022-September, s. 866-883
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Conference paper (peer-reviewed)abstract
- Accurate prediction of lumbar spine response and how it relates to kinematics, kinetics, and injury is critical since lumbar spine loading is predicted to be amplified in reclined postures. The objective was to evaluate the Global Human Body Models Consortium (GHBMC) lumbar spine (v5.1.1) model relative to postmortem human subjects (PMHS) in two different loading modes using data from recent experiments. The model's whole ligamentous lumbar spine was first evaluated in sub-injurious quasi-static loading in multiple directions with three different levels of axial compression. Compared to PMHS, the GHBMC responses varied widely across loading direction and axial compression level, exhibiting higher stiffness in some conditions and lower stiffness in other conditions. Then, three-vertebra sections of the model's ligamentous lumbar spine were subjected to high-rate compression-flexion loading to failure. Compared to PMHS, GHBMC responses and stiffness coefficients did not display the same bilinear response behavior, but instead displayed linear behavior. Additionally, the GHBMC and PMHS did not respond similarly when increased levels of axial compression were applied. The outcomes from this study shed light on the usefulness of the model.
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| 6. |
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| 7. |
- Xiao, Wenming, et al.
(author)
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Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing
- 2021
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In: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 39:9, s. 1141-1150
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Journal article (peer-reviewed)abstract
- Recommendations are given on optimal read coverage and selection of calling algorithm to maximize the reproducibility of cancer mutation detection in whole-genome or whole-exome sequencing. Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study has addressed the effects of cross-site reproducibility, nor the biological, technical and computational factors that influence variant identification. Here we report a systematic interrogation of somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy at six different centers. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), we evaluated the reproducibility of different sample types with varying input amount and tumor purity, and multiple library construction protocols, followed by processing with nine bioinformatics pipelines. We found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, genomic copy content and the global imbalance score (GIV; G > T/C > A). Finally, taking into account library preparation protocol, tumor content, read coverage and bioinformatics processes concomitantly, we recommend actionable practices to improve the reproducibility and accuracy of NGS experiments for cancer mutation detection.
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