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At least 757 records · Page 42

Development and Validation of a Non-Invasive, Chairside Oral Cavity Cancer Risk Assessment Prototype Using Machine Learning Approach

Oral cavity cancer (OCC) is associated with high morbidity and mortality rates when diagnosed at late stages. Early detection of increased risk provides an opportunity for implementing prevention strategies surrounding modifiable risk factors and screening to promote early detection and intervention. Historical evidence identified a gap in the training of primary care providers (PCPs) surrounding the examination of the oral cavity. The absence of clinically applicable analytical tools to identify patients with high-risk OCC phenotypes at point-of-care (POC) causes missed opportunities for implementing patient-specific interventional strategies. This study developed an OCC risk assessment tool prototype by applying machine learning (ML) approaches to a rich retrospectively collected data set abstracted from a clinical enterprise data warehouse. We compared the performance of six ML classifiers by applying the 10-fold cross-validation approach. Accuracy, recall, precision, specificity, area under the receiver operating characteristic curve, and recall–precision curves for the derived voting algorithm were: 78%, 64%, 88%, 92%, 0.83, and 0.81, respectively. The performance of two classifiers, multilayer perceptron and AdaBoost, closely mirrored the voting algorithm. Integration of the OCC risk assessment tool developed by clinical informatics application into an electronic health record as a clinical decision support tool can assist PCPs in targeting at-risk patients for personalized interventional care.

60 APPLIED LIFE SCIENCES↗

The Pine Ridge-Mayo National Aeronautics and Space Administration Telemedicine Project: Program Activities and Participant Reactions

OBJECTIVE: To determine the response of participants to the Pine Ridge-Mayo National Aeronautics and Space Administration telemedicine project. DESIGN: We describe a 3-month demonstration project of medical education and clinical consultations conducted by means of satellite transmission. Postparticipation questionnaires and a postproject survey were used to assess the success of the activity. MATERIAL AND METHODS: Patients and employees at the Pine Ridge Indian Health Service Hospital in southwestern South Dakota and employees at Mayo Clinic Rochester participated in a telemedicine project, after which they completed exit surveys and a postproject questionnaire to ascertain the acceptability of this mode of health care. RESULTS: Almost all Pine Ridge and Mayo Clinic participants viewed the project as beneficial. The educational sessions received favorable evaluations, and almost two-thirds of the patients who completed evaluations thought the consultation had contributed to their medical care. More than 90% of the respondents from Pine Ridge and more than 85% of the respondents from Mayo Clinic Rochester said that they would recommend participation in this project to others. More than 90% of respondents from Pine Ridge and 80% of Mayo respondents agreed with the statement that the project should continue. CONCLUSION: These data suggest that a program of clinical consultation services, professional education, and patient education available by telemedicine might be viewed as beneficial.

United States Indian Health Service↗

Goal-directed ultrasound in the detection of long-bone fractures

BACKGROUND: New portable ultrasound (US) systems are capable of detecting fractures in the remote setting. However, the accuracy of ultrasound by physicians with minimal ultrasound training is unknown. METHODS: After one hour of standardized training, physicians with minimal US experience clinically evaluated patients presenting with pain and trauma to the upper arm or leg. The investigators then performed a long-bone US evaluation, recording their impression of fracture presence or absence. Results of the examination were compared with routine plain or computer aided radiography (CT). RESULTS: 58 patients were examined. The sensitivity and specificity of US were 92.9% and 83.3%, and of the physical examination were 78.6% and 90.0%, respectively. US provided improved sensitivity with less specificity compared with physical examination in the detection of fractures in long bones. CONCLUSION: Ultrasound scans by minimally trained clinicians may be used to rule out a long-bone fracture in patients with a medium to low probability of fracture.

Validation Studies↗

Iron Heterogeneity in Early Active Multiple Sclerosis Lesions

Objective: Multiple sclerosis (MS) is a heterogeneous inflammatory demyelinating disease. Iron distribution is altered in MS patients' brains, suggesting iron liberation within active lesions amplifies demyelination and neurodegeneration. Whether the amount and distribution of iron are similar or different among different MS immunopatterns is currently unknown. Methods: We used synchrotron X-ray fluorescence imaging, histology, and immunohistochemistry to compare the iron quantity and distribution between immunopattern II and III early active MS lesions. We analyzed archival autopsy and biopsy tissue from 21 MS patients. Results: Immunopattern II early active lesions contain 64% more iron (95% confidence interval [CI] = 17-127, p = 0.004) than immunopattern III lesions, and 30% more iron than the surrounding periplaque white matter (95% CI = 3–64%, p = 0.03). Iron in immunopattern III lesions is 28% lower than in the periplaque white matter (95% CI = -40 to -14%, p < 0.001). When normalizing the iron content of early active lesions to that of surrounding periplaque white matter, the ratio is significantly higher in immunopattern II (p < 0.001). Microfocused X-ray fluorescence imaging shows that iron in immunopattern II lesions localizes to macrophages, whereas macrophages in immunopattern III lesions contain little iron. Interpretation: Iron distribution and content are heterogeneous in early active MS lesions. Iron accumulates in macrophages in immunopattern II, but not immunopattern III lesions. This heterogeneity in the two most common MS immunopatterns may be explained by different macrophage polarization, origin, or different demyelination mechanisms, and paves the way for developing new or using existing iron-sensitive magnetic resonance imaging techniques to differentiate among immunopatterns in the general nonbiopsied MS patient population.

60 APPLIED LIFE SCIENCES↗

A 1D–0D–3D coupled model for simulating blood flow and transport processes in breast tissue

In this work, we present mixed dimensional models for simulating blood flow and transport processes in breast tissue and the vascular tree supplying it. These processes are considered, to start from the aortic inlet to the capillaries and tissue of the breast. Large variations in biophysical properties and flow conditions exist in this system necessitating the use of different flow models for different geometries and flow regimes. In total, we consider four different model types. First, a system of 1D nonlinear hyperbolic partial differential equations (PDEs) is considered to simulate blood flow in larger arteries with highly elastic vessel walls. Second, we assign 1D linearized hyperbolic PDEs to model the smaller arteries with stiffer vessel walls. The third model type consists of ODE systems (0D models). It is used to model the arterioles and peripheral circulation. Finally, homogenized 3D porous media models are considered to simulate flow and transport in capillaries and tissue within the breast volume. Sink terms are used to account for the influence of the venous and lymphatic systems. Combining the four model types, we obtain two different 1D–0D–3D coupled models for simulating blood flow and transport processes: The first model results in a fully coupled 1D–0D–3D model covering the complete path from the aorta to the breast combining a generic arterial network with a patient specific breast network and geometry. The second model is a reduced one based on the separation of the generic and patient specific parts. The information from a calibrated fully coupled model is used as inflow condition for the patient specific sub-model allowing a significant computational cost reduction. Several numerical experiments are conducted to calibrate the generic model parameters and to demonstrate realistic flow simulations compared to existing data on blood flow in the human breast and vascular system. Moreover, we use two different breast vasculature and tissue data sets to illustrate the robustness of our reduced sub-model approach.

multiscale blood flow models↗

NCAPH drives breast cancer progression and identifies a gene signature that predicts luminal a tumour recurrence

Luminal A tumours generally have a favourable prognosis but possess the highest 10-year recurrence risk among breast cancers. Additionally, a quarter of the recurrence cases occur within 5 years post-diagnosis. Identifying such patients is crucial as long-term relapsers could benefit from extended hormone therapy, while early relapsers might require more aggressive treatment. We conducted a study to explore non-structural chromosome maintenance condensin I complex subunit H’s (NCAPH) role in luminal A breast cancer pathogenesis, both in vitro and in vivo, aiming to identify an intratumoural gene expression signature, with a focus on elevated NCAPH levels, as a potential marker for unfavourable progression. Our analysis included transgenic mouse models overexpressing NCAPH and a genetically diverse mouse cohort generated by backcrossing. A least absolute shrinkage and selection operator (LASSO) multivariate regression analysis was performed on transcripts associated with elevated intratumoural NCAPH levels. We found that NCAPH contributes to adverse luminal A breast cancer progression. The intratumoural gene expression signature associated with elevated NCAPH levels emerged as a potential risk identifier. Transgenic mice overexpressing NCAPH developed breast tumours with extended latency, and in Mouse Mammary Tumor Virus (MMTV)-NCAPH ErbB2 double-transgenic mice, luminal tumours showed increased aggressiveness. High intratumoural Ncaph levels correlated with worse breast cancer outcome and subpar chemotherapy response. A 10-gene risk score, termed Gene Signature for Luminal A 10 (GSLA10), was derived from the LASSO analysis, correlating with adverse luminal A breast cancer progression. The GSLA10 signature outperformed the Oncotype DX signature in discerning tumours with unfavourable outcomes, previously categorised as luminal A by Prediction Analysis of Microarray 50 (PAM50) across three independent human cohorts. This new signature holds promise for identifying luminal A tumour patients with adverse prognosis, aiding in the development of personalised treatment strategies to significantly improve patient outcomes.

60 APPLIED LIFE SCIENCES↗

Modeling inter‐reader variability in clinical target volume delineation for soft tissue sarcomas using diffusion model

Abstract Background Accurate delineation of the clinical target volume (CTV) is essential in the radiotherapy treatment of soft tissue sarcomas. However, this process is subject to inter‐reader variability due to the need for clinical assessment of risk and extent of potential microscopic spread. This can lead to inconsistencies in treatment planning, potentially impacting treatment outcomes. Most existing automatic CTV delineation methods do not account for this variability and can only generate a single CTV for each case. Purpose This study aims to develop a deep learning‐based technique to generate multiple CTV contours for each case, simulating the inter‐reader variability in the clinical practice. Methods We employed a publicly available dataset consisting of fluorodeoxyglucose positron emission tomography (FDG‐PET), x‐ray computed tomography (CT), and pre‐contrast T1‐weighted magnetic resonance imaging (MRI) scans from 51 patients with soft tissue sarcoma, along with an independent validation set containing five additional patients. An experienced reader drew a contour of the gross tumor volume (GTV) for each patient based on multi‐modality images. Subsequently, two additional readers, together with the first one, were responsible for contouring three CTVs in total based on the GTV. We developed a diffusion model‐based deep learning method that is capable of generating arbitrary number of different and plausible CTVs to mimic the inter‐reader variability in CTV delineation. The proposed model incorporates a separate encoder to extract features from the GTV masks, leveraging the critical role of GTV information in accurate CTV delineation. Results The proposed diffusion model demonstrated superior performance with the highest Dice Index (0.902 compared to values below 0.881 for state‐of‐the‐art models) and the best generalized energy distance (GED) (0.209 compared to values exceeding 0.221 for state‐of‐the‐art models). It also achieved the second‐highest recall and precision metrics among the compared ambiguous image segmentation models. Results from both datasets exhibited consistent trends, reinforcing the reliability of our findings. Additionally, ablation studies exploring different model structures and input configurations highlighted the significance of incorporating prior GTV information for accurate CTV delineation. Conclusions The proposed diffusion model successfully generates multiple plausible CTV contours for soft tissue sarcomas, effectively capturing inter‐reader variability in CTV delineation.

Dong, Yafei [Yale Biomedical Imaging Institute Yal↗

False positive PSMA PET for tumor remnants in the irradiated prostate and other interpretation pitfalls in a prospective multi-center trial

Readers need to be informed about potential pitfalls of [ 68 Ga]Ga-PSMA-11 PET interpretation. Here we report [ 68 Ga]Ga-PSMA-11 PET findings discordant with the histopathology/composite reference standard in a recently published prospective trial on 635 patients with biochemically recurrent prostate cancer. Consensus reads were false positive in 20 regions of 17/217 (8%) patients with lesion validation. Majority of the false positive interpretations (13 of 20, 65%) occurred in the context of suspected prostate (bed) relapse (T) after radiotherapy ( n = 11); other false positive findings were noted for prostate bed post prostatectomy (T, n = 2), pelvic nodes (N, n = 2), or extra pelvic lesions (M, n = 5). Major sources of false positive findings were PSMA-expressing residual adenocarcinoma with marked post-radiotherapy treatment effect. False negative interpretation occurred in 8 regions of 6/79 (8%) patients with histopathology validation, including prostate (bed) ( n = 5), pelvic nodes ( n = 1), and extra pelvic lesions ( n = 2). Lesions were missed mostly due to small metastases or adjacent bladder/urine uptake.[ 68 Ga]Ga-PSMA-11 PET at biochemical recurrence resulted in less than 10% false positive interpretations. Post-radiotherapy prostate uptake was a major source of [ 68 Ga]Ga-PSMA-11 PET false positivity. In few cases, PET correctly detects residual PSMA expression post-radiotherapy, originating however from treated, benign tissue or potentially indolent tumor remnants.

Radiology, Nuclear Medicine & Medical Imaging↗

Mass Spectrometry-Based Approaches for Clinical Biomarker Discovery in Traumatic Brain Injury

Purpose of Review: Precision treatments to address the multifaceted pathophysiology of traumatic brain injury (TBI) are desperately needed, which has led to the intense study of fluid-based protein biomarkers in TBI. Mass Spectrometry (MS) is increasingly being applied to biomarker discovery and quantification in neurological disease to explore the proteome, allowing for more flexibility in biomarker discovery than commonly encountered antibody-based assays. In this narrative review, we will provide specific examples of how MS technology has advanced translational research in traumatic brain injury (TBI) focusing on clinical studies, and looking ahead to promising emerging applications of MS to the field of Neurocritical Care. Recent Findings: Proteomic biomarker discovery using MS technology in human subjects has included the full range of injury severity in TBI, though critically ill patients can offer more options to biofluids given the need for invasive monitoring. Blood, urine, cerebrospinal fluid, brain specimens, and cerebral extracellular fluid have all been sources for analysis. Emerging evidence suggests there are distinct proteomic profiles in radiographic TBI subtypes, and that biomarkers may be used to distinguish patients sustaining TBI from healthy controls. Metabolomics may offer a window into the perturbations of ongoing cerebral insults in critically ill patients after severe TBI. Summary: Emerging MS technologies may offer biomarker discovery and validation opportunities not afforded by conventional means due to its ability to handle the complexities associated with the proteome. In conclusion, while MS techniques are relatively early in development in the neurosciences space, the potential applications to TBI and neurocritical care are likely to accelerate in the coming decade.

59 BASIC BIOLOGICAL SCIENCES↗

Hypothesis-Agnostic Network-Based Analysis of Real-World Data Suggests Ondansetron is Associated with Lower COVID-19 Any Cause Mortality

Background: The COVID-19 pandemic generated a massive amount of clinical data, which potentially hold yet undiscovered answers related to COVID-19 morbidity, mortality, long-term effects, and therapeutic solutions.Objectives: The objectives of this study were (1) to identify novel predictors of COVID-19 any cause mortality by employing artificial intelligence analytics on real-world data through a hypothesis-agnostic approach and (2) to determine if these effects are maintained after adjusting for potential confounders and to what degree they are moderated by other variables.Methods: A Bayesian statistics-based artificial intelligence data analytics tool (bAIcis®) within the Interrogative Biology® platform was used for Bayesian network learning and hypothesis generation to analyze 16,277 PCR+ patients from a database of 279,281 inpatients and outpatients tested for SARS-CoV-2 infection by antigen, antibody, or PCR methods during the first pandemic year in Central Florida. This approach generated Bayesian networks that enabled unbiased identification of significant predictors of any cause mortality for specific COVID-19 patient populations. These findings were further analyzed by logistic regression, regression by least absolute shrinkage and selection operator, and bootstrapping.Results: We found that in the COVID-19 PCR+ patient cohort, early use of the antiemetic agent ondansetron was associated with decreased any cause mortality 30 days post-PCR+ testing in mechanically ventilated patients.Conclusions: The results demonstrate how a real-world COVID-19-focused data analysis using artificial intelligence can generate unexpected yet valid insights that could possibly support clinical decision making and minimize the future loss of lives and resources.

60 APPLIED LIFE SCIENCES↗

A machine learning approach for identifying variables associated with risk of developing neutralizing antidrug antibodies to factor VIII

A key unmet need in the management of hemophilia A (HA) is the lack of clinically validated markers that are associated with the development of neutralizing antibodies to Factor VIII (FVIII) (commonly referred to as inhibitors). This study aimed to identify relevant biomarkers for FVIII inhibition using Machine Learning (ML) and Explainable AI (XAI) using the My Life Our Future (MLOF) research repository. The dataset includes biologically relevant variables such as age, race, sex, ethnicity, and the variants in the F8 gene. In addition, we previously carried out Human Leukocyte Antigen Class II (HLA-II) typing on samples obtained from the MLOF repository. Using this information, we derived other patient-specific biologically and genetically important variables. These included identifying the number of foreign FVIII derived peptides, based on the alignment of the endogenous FVIII and infused drug sequences, and the foreign-peptide HLA-II molecule binding affinity calculated using NetMHCIIpan. The data were processed and trained with multiple ML classification models to identify the top performing models. The top performing model was then chosen to apply XAI via SHAP, (SHapley Additive exPlanations) to identify the variables critical for the prediction of FVIII inhibitor development in a hemophilia A patient. Using XAI we provide a robust and ranked identification of variables that could be predictive for developing inhibitors to FVIII drugs in hemophilia A patients. These variables could be validated as biomarkers and used in making clinical decisions and during drug development. The top five variables for predicting inhibitor development based on SHAP values are: (i) the baseline activity of the FVIII protein, (ii) mean affinity of all foreign peptides for HLA DRB 3, 4, & 5 alleles, (iii) mean affinity of all foreign peptides for HLA DRB1 alleles), (iv) the minimum affinity among all foreign peptides for HLA DRB1 alleles, and (v) F8 mutation type.

60 APPLIED LIFE SCIENCES↗

Profiling B cell immunodominance after SARS-CoV-2infection reveals antibody evolution to non-neutralizing viral targets

Dissecting the evolution of memory B cells (MBCs) against SARS-CoV-2 is critical for understanding antibody recall upon secondary exposure. Here, we used single-cell sequencing to profile SARS-CoV-2-reactive B cells in 38 COVID-19 patients. Using oligo-tagged antigen baits, we isolated B cells specific to the SARS-CoV-2 spike, nucleoprotein (NP), open reading frame 8 (ORF8), and endemic human coronavirus (HCoV) spike proteins. SARS-CoV-2 spike-specific cells were enriched in the memory compartment of acutely infected and convalescent patients several months post symptom onset. With severe acute infection, substantial populations of endemic HCoV-reactive antibody-secreting cells were identified and possessed highly mutated variable genes, signifying preexisting immunity. Finally, MBCs exhibited pronounced maturation to NP and ORF8 over time, especially in older patients. Monoclonal antibodies against these targets were non-neutralizing and non-protective in vivo. These findings reveal antibody adaptation to non-neutralizing intracellular antigens during infection, emphasizing the importance of vaccination for inducing neutralizing spike-specific MBCs.

antibody↗

Functional analysis of a conserved site mutation in the DNA end processing enzyme PNKP leading to ataxia with oculomotor apraxia type 4 in humans

Polynucleotide kinase 3'-phosphatase (PNKP), an essential DNA end-processing enzyme in mammals with 3'-phosphatase and 5'-kinase activities, plays a pivotal role in multiple DNA repair pathways. Its functional deficiency has been etiologically linked to various neurological disorders. Recent reports have shown that mutation at a conserved glutamine (Gln) in PNKP leads to late-onset ataxia with oculomotor apraxia type 4 (AOA4) in humans and embryonic lethality in pigs. However, the molecular mechanism underlying such phenotypes remains elusive. Here, we report that the enzymatic activities of the mutant versus WT PNKP are comparable; however, cells expressing mutant PNKP and peripheral blood mononuclear cells (PBMCs) of AOA4 patients showed a significant amount of DNA double-strand break accumulation and consequent activation of the DNA damage response. Further investigation revealed that the nuclear localization of mutant PNKP is severely abrogated, and the mutant proteins remain primarily in the cytoplasm. Western blot analysis of AOA4 patient-derived PBMCs also revealed the presence of mutated PNKP predominantly in the cytoplasm. To understand the molecular determinants, we identified that mutation at a conserved Gln residue impedes the interaction of PNKP with importin alpha but not with importin beta, two highly conserved proteins that mediate the import of proteins from the cytoplasm into the nucleus. Collectively, our data suggest that the absence of PNKP in the nucleus leads to constant activation of the DNA damage response due to persistent accumulation of double-strand breaks in the mutant cells, triggering death of vulnerable brain cells—a potential cause of neurodegeneration in AOA4 patients.

59 BASIC BIOLOGICAL SCIENCES↗

ARCH: Large-scale knowledge graph via aggregated narrative codified health records analysis

Objective: Electronic health record (EHR) systems contain a wealth of clinical data stored as both codified data and free-text narrative notes (NLP). The complexity of EHR presents challenges in feature representation, information extraction, and uncertainty quantification. Here, to address these challenges, we proposed an efficient Aggregated naRrative Codified Health (ARCH) records analysis to generate a large-scale knowledge graph (KG) for a comprehensive set of EHR codified and narrative features. Methods: Using data from 12.5 million Veterans Affairs patients, ARCH first derives embedding vectors and generates similarities along with associated p-values to measure the strength of relatedness between clinical features with statistical certainty quantification. Next, ARCH performs a sparse embedding regression to remove indirect linkage between features to build a sparse KG. Finally, ARCH was validated on various clinical tasks, including detecting known relationships between entity pairs, predicting drug side effects, disease phenotyping, as well as sub-typing Alzheimer’s disease patients. Results: ARCH produces high-quality clinical embeddings and KG for over 60,000 codified and narrative EHR concepts. The KG and embeddings are visualized in the R-shiny powered web-API.3 ARCH achieved high accuracy in detecting EHR concept relationships, with AUCs of 0.926 (codified) and 0.861 (NLP) for similar EHR concepts, and 0.810 (codified) and 0.843 (NLP) for related pairs. It detected drug side effects with a 0.723 AUC, which improved to 0.826 after fine-tuning. Using both codified and NLP features, the detection power increased significantly. Compared to other methods, ARCH has superior accuracy and enhances weakly supervised phenotyping algorithms’ performance. Notably, it successfully categorized Alzheimer’s patients into two subgroups with varying mortality rates. Conclusion: The proposed ARCH algorithm generates large-scale high-quality semantic representations and knowledge graph for both codified and NLP EHR features, useful for a wide range of predictive modeling tasks.

Electronic health records↗

Structural basis for inhibition of coagulation factor VIII reveals a shared antigenic hotspot on the C1 domain

Hemophilia A arises from dysfunctional or deficient coagulation factor (F)VIII and leads to inefficient fibrin clot formation and uncontrolled bleeding events. The development of antibody inhibitors is a clinical complication in hemophilia A patients receiving FVIII replacement therapy. LE2E9 is an anti-C1 domain inhibitor previously isolated from a mild/moderate hemophilia A patient and disrupts FVIII interactions with von Willebrand factor and FIXa, though the intermolecular contacts that underpin LE2E9-mediated FVIII neutralization are undefined. To determine the structure of the complex between FVIII and LE2E9 and characterize its mechanism of inhibition. FVIII was bound to the antigen binding fragment (Fab) of NB2E9, a recombinant construct of LE2E9, and its structure was determined by cryogenic electron microscopy. Here, this report communicates the 3.46 Å structure of FVIII bound to NB2E9, with its epitope comprising FVIII residues S2040 to Y2043, K2065 to W2070, and R2150 to H2155. Structural analysis reveals that the LE2E9 epitope overlaps with portions of the epitope for 2A9, a murine-derived inhibitor, suggesting that these residues represent a shared antigenic region on the C1 domain between FVIII –/– mice and hemophilia A patients. Furthermore, the FVIII:NB2E9 structure elucidates the orientation of the LE2E9 glycan, illustrating how the glycan sterically blocks interactions between the FVIII C1 domain and the von Willebrand factor D' domain. A putative model of the FVIIIa:FIXa complex suggests potential clashing between the NB2E9 glycan and FIXa light chain. These results describe an antigenic “hotspot” on the FVIII C1 domain and provide a structural basis for engineering FVIII replacement therapeutics with reduced antigenicity.

60 APPLIED LIFE SCIENCES↗

A Poisson equation method for prescribing fully developed non-Newtonian inlet conditions for computational fluid dynamics simulations in models of arbitrary cross-section

Prescribing inlet boundary conditions for computational fluid dynamics (CFD) simulations of internal flow in complex geometries such as anatomical vascular models is challenging. In the absence of patient-specific inlet velocity data, a common approach for long blood vessels is to assume that the inlet flow is fully developed. In vessels of irregular cross section, however, prescribing fully developed conditions is complicated due to the lack of a general closed-form analytical solution. In this study, we develop a simple Poisson equation method for prescribing fully developed inlet conditions for the flow of either Newtonian or non-Newtonian fluids in CFD models of arbitrary cross-section. We first derive the generalized Poisson equation for fully developed flow of a non-Newtonian fluid and we then develop and verify a methodology for numerically computing the solution on any planar boundary domain. In addition, we develop a simple extension of the method for prescribing a non-orthogonal inlet velocity that represents fully developed flow from an upstream tube that is connected to the CFD inlet at a non-orthogonal angle. This may be used to investigate a common source of uncertainty in CFD simulations of internal flow that is due to a lack of information concerning the exact streamwise flow direction at the inlets. Comparison to several Newtonian and non-Newtonian benchmark verification solutions shows the method to be extremely accurate. As a practical demonstration case, we use the method to prescribe fully developed conditions on multiple non-circular inlets for the non-Newtonian flow of blood in a patient-specific model of the inferior vena cava (IVC). Finally, we further demonstrate the utility of the method by performing a sensitivity study using the patient-specific IVC model, wherein we investigate the influence of inlet velocity flow direction on the non-Newtonian IVC hemodynamics. Given its simplicity and computational efficiency, the method is shown to be far superior to alternative approaches for prescribing fully developed inlet conditions in such complicated geometries. In conclusion, to facilitate the adoption of our Poisson equation method, we have distributed our OpenFOAM source code and the associated test cases from this study as open-source software.

97 MATHEMATICS AND COMPUTING↗

PHASE: Personalized Head-based Automatic Simulation for Electromagnetic properties in 7T MRI

Accurate and individualized human head models are becoming increasingly important for electromagnetic (EM) simulations. These simulations depend on precise anatomical representations to realistically model electric and magnetic field distributions, particularly when evaluating Specific Absorption Rate (SAR) within safety guidelines. State of the art simulations use the Virtual Population due to limited public resources and the impracticality of manually annotating patient data at scale. Here, this paper introduces Personalized Head-based Automatic Simulation for EM properties (PHASE), an automated open-source toolbox that generates high-resolution, patient-specific head models for EM simulations using paired T1-weighted (T1w) magnetic resonance imaging (MRI) and computed tomography (CT) scans with 14 tissue labels. To evaluate the performance of PHASE models, we conduct semi-automated segmentation and EM simulations on 15 real human patients, serving as the gold standard reference. The PHASE model achieved comparable global SAR and localized SAR averaged over 10 grams of tissue (SAR-10g), demonstrating its potential as a promising tool for generating large-scale human model datasets in the future. The code and models of PHASE toolbox have been made publicly available: https://github.com/hrlblab/PHASE.

Deep learning↗

Structural polymorphism of amyloid fibrils in ATTR amyloidosis revealed by cryo-electron microscopy

ATTR amyloidosis is caused by the deposition of transthyretin in the form of amyloid fibrils in virtually every organ of the body, including the heart. This systemic deposition leads to a phenotypic variability that has not been molecularly explained yet. In brain amyloid conditions, previous studies suggest an association between clinical phenotype and the molecular structures of their amyloid fibrils. Here we investigate whether there is such an association in ATTRv amyloidosis patients carrying the mutation I84S. Using cryo-electron microscopy, we determined the structures of cardiac fibrils extracted from three ATTR amyloidosis patients carrying the ATTRv-I84S mutation, associated with a consistent clinical phenotype. We found that in each ATTRv-I84S patient, the cardiac fibrils exhibited different local conformations, and these variations can co-exist within the same fibril. Our finding suggests that one amyloid disease may associate with multiple fibril structures in systemic amyloidoses, calling for further studies.

59 BASIC BIOLOGICAL SCIENCES↗