搜索结果：Cerebrovascular diseases extra

We present CaravelMetrics, a computational framework for automated cerebrovascular analysis that models vessel morphology through skeletonization-derived graph representations. The framework integrates atlas-based regional parcellation, centerline extraction, and graph construction to compute fifteen morphometric, topological, fractal, and geometric features. The features can be estimated globally from the complete vascular network or regionally within arterial territories, enabling multiscale characterization of cerebrovascular organization. Applied to 570 3D TOF-MRA scans from the IXI dataset (ages 20-86), CaravelMetrics yields reproducible vessel graphs capturing age- and sex-related variations and education-associated increases in vascular complexity, consistent with findings reported in the literature. The framework provides a scalable and fully automated approach for quantitative cerebrovascular feature extraction, supporting normative modeling and population-level studies of vascular health and aging.

We investigate model order reduction (MOR) strategies for simulating unsteady hemodynamics within cerebrovascular systems, contrasting a physics-based intrusive approach with a data-driven non-intrusive framework. High-fidelity 3D Computational Fluid Dynamics (CFD) snapshots of an idealised basilar artery bifurcation are first compressed into a low-dimensional latent space using Proper Orthogonal Decomposition (POD). We evaluate the performance of a POD-Galerkin (POD-G) model, which projects the Navier-Stokes equations onto the reduced basis, against a POD-Reservoir Computing (POD-RC) model that learns the temporal evolution of coefficients through a recurrent architecture. A multi-harmonic and multi-amplitude training signal is introduced to improve training efficiency. Both methodologies achieve computational speed-ups on the order of 10^2 to 10^3 compared to full-order simulations, demonstrating their potential as efficient and accurate surrogates for predicting flow quantities such as wall shear stress.

Univariate zero-inflated models are increasingly being used to account for excess zeros in spatio-temporal infectious disease counts. However, the multivariate case is challenging due to the need to account for correlations across space, time and disease in both the count and zero-inflated components of the model. We are interested in comparing the transmission dynamics of several co-circulating infectious diseases across space and time, where some of the diseases can be absent for long periods. We first assume there is a baseline disease that is well-established and always present in the region. The other diseases switch between periods of presence and absence in each area through a series of coupled Markov chains, which account for long periods of disease absence, disease interactions and disease spread from neighboring areas. Since we are mainly interested in comparing the diseases, we assume the cases of the present diseases in an area jointly follow an autoregressive multinomial model. We use the multinomial model to investigate whether there are associations between certain factors, such as temperature, and differences in the transmission intensity of the diseases. Inference

Brain vessel segmentation of MR scans is a critical step in the diagnosis of cerebrovascular diseases. Due to the fine vessel structure, manual vessel segmentation is time consuming. Therefore, automatic deep learning (DL) based segmentation techniques are intensively investigated. As conventional DL models yield a high complexity and lack an indication of decision reliability, they are often considered as not trustworthy. This work aims to increase trust in DL based models by incorporating epistemic uncertainty quantification into cerebrovascular segmentation models for the first time. By implementing an efficient ensemble model combining the advantages of Bayesian Approximation and Deep Ensembles, we aim to overcome the high computational costs of conventional probabilistic networks. Areas of high model uncertainty and erroneous predictions are aligned which demonstrates the effectiveness and reliability of the approach. We perform extensive experiments applying the ensemble model on out-of-distribution (OOD) data. We demonstrate that for OOD-images, the estimated uncertainty increases. Additionally, omitting highly uncertain areas improves the segmentation quality, both for in-

The rapidly increasing volume of electronic health record (EHR) data underscores a pressing need to unlock biomedical knowledge from unstructured clinical texts to support advancements in data-driven clinical systems, including patient diagnosis, disease progression monitoring, treatment effects assessment, prediction of future clinical events, etc. While contextualized language models have demonstrated impressive performance improvements for named entity recognition (NER) systems in English corpora, there remains a scarcity of research focused on clinical texts in low-resource languages. To bridge this gap, our study aims to develop multiple deep contextual embedding models to enhance clinical NER in the cardiology domain, as part of the BioASQ MultiCardioNER shared task. We explore the effectiveness of different monolingual and multilingual BERT-based models, trained on general domain text, for extracting disease and medication mentions from clinical case reports written in English, Spanish, and Italian. We achieved an F1-score of 77.88% on Spanish Diseases Recognition (SDR), 92.09% on Spanish Medications Recognition (SMR), 91.74% on English Medications Recognition (EMR), and 88.

Rare diseases are collectively common, affecting approximately one in twenty individuals worldwide. In recent years, rapid progress has been made in rare disease diagnostics due to advances in DNA sequencing, development of new computational and experimental approaches to prioritize genes and genetic variants, and increased global exchange of clinical and genetic data. However, more than half of individuals suspected to have a rare disease lack a genetic diagnosis. The Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium was initiated to study thousands of challenging rare disease cases and families and apply, standardize, and evaluate emerging genomics technologies and analytics to accelerate their adoption in clinical practice. Further, all data generated, currently representing ~7500 individuals from ~3000 families, is rapidly made available to researchers worldwide via the Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) to catalyze global efforts to develop approaches for genetic diagnoses in rare diseases (https://gregorconsortium.org/data). The majority of these families have undergone prior clinical genetic testing

3D microscopic cerebrovascular images are characterized by their high resolution, presenting significant annotation challenges, large data volumes, and intricate variations in detail. Together, these factors make achieving high-quality, efficient whole-brain segmentation particularly demanding. In this paper, we propose a novel Vessel-Pattern-Based Semi-Supervised Distillation pipeline (VpbSD) to address the challenges of 3D microscopic cerebrovascular segmentation. This pipeline initially constructs a vessel-pattern codebook that captures diverse vascular structures from unlabeled data during the teacher model's pretraining phase. In the knowledge distillation stage, the codebook facilitates the transfer of rich knowledge from a heterogeneous teacher model to a student model, while the semi-supervised approach further enhances the student model's exposure to diverse learning samples. Experimental results on real-world data, including comparisons with state-of-the-art methods and ablation studies, demonstrate that our pipeline and its individual components effectively address the challenges inherent in microscopic cerebrovascular segmentation.

The increasing size and complexity of medical imaging datasets, particularly in 3D formats, present significant barriers to collaborative research and transferability. This study investigates whether the ZFP compression technique can mitigate these challenges without compromising the performance of automated cerebrovascular segmentation, a critical first step in intracranial aneurysm detection. We apply ZFP in both its error tolerance and fixed-rate modes to a large scale, and one of the most recent, datasets in the literature, 3D medical dataset containing ground-truth vascular segmentations. The segmentation quality on the compressed volumes is rigorously compared to the uncompressed baseline (Dice approximately equals 0.8774). Our findings reveal that ZFP can achieve substantial data reduction--up to a 22.89:1 ratio in error tolerance mode--while maintaining a high degree of fidelity, with the mean Dice coefficient remaining high at 0.87656. These results demonstrate that ZFP is a viable and powerful tool for enabling more efficient and accessible research on large-scale medical datasets, fostering broader collaboration across the community.

Due to the lack of automated methods, to diagnose cerebrovascular disease, time-of-flight magnetic resonance angiography (TOF-MRA) is assessed visually, making it time-consuming. The commonly used encoder-decoder architectures for cerebrovascular segmentation utilize redundant features, eventually leading to the extraction of low-level features multiple times. Additionally, convolutional neural networks (CNNs) suffer from performance degradation when the batch size is small, and deeper networks experience the vanishing gradient problem. Methods: In this paper, we attempt to solve these limitations and propose the 3D cerebrovascular attention UNet method, named CV-AttentionUNet, for precise extraction of brain vessel images. We proposed a sequence of preprocessing techniques followed by deeply supervised UNet to improve the accuracy of segmentation of the brain vessels leading to a stroke. To combine the low and high semantics, we applied the attention mechanism. This mechanism focuses on relevant associations and neglects irrelevant anatomical information. Furthermore, the inclusion of deep supervision incorporates different levels of features that prove to be beneficial for networ

Cerebrovascular diseases (CVD) can lead to stroke and dementia. Stroke is the second leading cause of death world wide and dementia incidence is increasing by the year. There are several markers of CVD that are visible on brain imaging, including: white matter hyperintensities (WMH), acute and chronic ischaemic stroke lesions (ISL), lacunes, enlarged perivascular spaces (PVS), acute and chronic haemorrhagic lesions, and cerebral microbleeds (CMB). Brain atrophy also occurs in CVD. These markers are important for patient management and intervention, since they indicate elevated risk of future stroke and dementia. We systematically reviewed automated systems designed to support radiologists reporting on these CVD imaging findings. We considered commercially available software and research publications which identify at least two CVD markers. In total, we included 29 commercial products and 13 research publications. Two distinct types of commercial support system were available: those which identify acute stroke lesions (haemorrhagic and ischaemic) from computed tomography (CT) scans, mainly for the purpose of patient triage; and those which measure WMH and atrophy regionally and long

Segmentation in medical imaging is an essential and often preliminary task in the image processing chain, driving numerous efforts towards the design of robust segmentation algorithms. Supervised learning methods achieve excellent performances when fed with a sufficient amount of labeled data. However, such labels are typically highly time-consuming, error-prone and expensive to produce. Alternatively, semi-supervised learning approaches leverage both labeled and unlabeled data, and are very useful when only a small fraction of the dataset is labeled. They are particularly useful for cerebrovascular segmentation, given that labeling a single volume requires several hours for an expert. In addition to the challenge posed by insufficient annotations, there are concerns regarding annotation consistency. The task of annotating the cerebrovascular tree is inherently ambiguous. Due to the discrete nature of images, the borders and extremities of vessels are often unclear. Consequently, annotations heavily rely on the expert subjectivity and on the underlying clinical objective. These discrepancies significantly increase the complexity of the segmentation task for the model and consequent

Prion diseases are invariably fatal and highly infectious neurodegenerative diseases affecting humans and animals. By now there have not been some effective therapeutic approaches to treat all these prion diseases. In 2008, canine mammals including dogs (canis familials) were the first time academically reported to be resistant to prion diseases (Vaccine 26: 2601--2614 (2008)). Rabbits are the mammalian species known to be resistant to infection from prion diseases from other species (Journal of Virology 77: 2003--2009 (2003)). Horses were reported to be resistant to prion diseases too (Proceedings of the National Academy of Sciences USA 107: 19808--19813 (2010)). By now all the NMR structures of dog, rabbit and horse prion proteins had been released into protein data bank respectively in 2005, 2007 and 2010 (Proceedings of the National Academy of Sciences USA 102: 640--645 (2005), Journal of Biomolecular NMR 38:181 (2007), Journal of Molecular Biology 400: 121--128 (2010)). Thus, at this moment it is very worth studying the NMR molecular structures of horse, dog and rabbit prion proteins to obtain insights into their immunity prion diseases. This article reports the findings of th

The precise cerebrovascular segmentation in time-of-flight magnetic resonance angiography (TOF-MRA) data is crucial for clinically computer-aided diagnosis. However, the sparse distribution of cerebrovascular structures in TOF-MRA results in an exceedingly high cost for manual data labeling. The use of unlabeled TOF-MRA data holds the potential to enhance model performance significantly. In this study, we construct the largest preprocessed unlabeled TOF-MRA datasets (1510 subjects) to date. We also provide three additional labeled datasets totaling 113 subjects. Furthermore, we propose a simple yet effective pertraining strategy based on Frangi filtering, known for enhancing vessel-like structures, to fully leverage the unlabeled data for 3D cerebrovascular segmentation. Specifically, we develop a Frangi filtering-based preprocessing workflow to handle the large-scale unlabeled dataset, and a multi-task pretraining strategy is proposed to effectively utilize the preprocessed data. By employing this approach, we maximize the knowledge gained from the unlabeled data. The pretrained model is evaluated on four cerebrovascular segmentation datasets. The results have demonstrated the sup

Of the 2652 articles considered, 106 met the inclusion criteria. Review of the included papers resulted in identification of 43 chronic diseases, which were then further classified into 10 disease categories using ICD-10. The majority of studies focused on diseases of the circulatory system (n=38) while endocrine and metabolic diseases were fewest (n=14). This was due to the structure of clinical records related to metabolic diseases, which typically contain much more structured data, compared with medical records for diseases of the circulatory system, which focus more on unstructured data and consequently have seen a stronger focus of NLP. The review has shown that there is a significant increase in the use of machine learning methods compared to rule-based approaches; however, deep learning methods remain emergent (n=3). Consequently, the majority of works focus on classification of disease phenotype with only a handful of papers addressing extraction of comorbidities from the free text or integration of clinical notes with structured data. There is a notable use of relatively simple methods, such as shallow classifiers (or combination with rule-based methods), due to the interp

Livestock mobility, particularly that of small and large ruminants, is one of the main pillars of production and trade in West Africa: livestock is moved around in search of better grazing or sold in markets for domestic consumption and for festival-related activities. These movements cover several thousand kilometers and have the capability of connecting the whole West African region thus facilitating the diffusion of many animal and zoonotic diseases. Several factors shape mobility patterns even in normal years and surveillance systems need to account for such changes. In this paper, we present a procedure based on temporal network theory to identify possible sentinel locations using two indicators: vulnerability (i.e. the probability of being reached by the disease) and time of infection (i.e. the time of first arrival of the disease). Using these indicators in our structural analysis of the changing network enabled us to identify a set of nodes that could be used in an early warning system. As a case study we simulated the introduction of F.A.S.T. (Foot and Mouth Similar Transboundary) diseases in Senegal and used data taken from 2020 Sanitary certificates (LPS, laissez-passer

Is cancer a disease that can be cured or a degenerative disease which comes predominantly with old age? We give an answer based on a two-dimensional representation of diseases. These two dimensions are defined as follows. In mortality curves there is an age, namely a_c = 10 years, which plays a crucial role in the sense that the mortality rate decreases in the interval I1=(a<a_c) and increases in the interval I2=(a>a_c). The respective trends in I1 and I2 are the two parameters used in our classification of diseases. Within the framework of reliability analysis, I1 and I2 would be referred to as the "burn-in" and "wear-out" phases. This leads to define three broad groups of diseases. (AS1) Asymmetry with prevalence of I1. (AS2) Asymmetry with prevalence of I2. (S) Symmetry, with I1 and I2 both playing roles of comparable importance. Not surprisingly, among AS1-cases one finds all diseases due to congenital malformations. In the AS2-class one finds degenerative diseases, e.g. Alzheimer's disease. Among S-cases one finds most diseases due to external pathogens or to wear-out processes. Cancer is one of those mixed cases and it is closer to (AS2) than to (AS1). This representati

We introduce Disease Knowledge Transfer (DKT), a novel technique for transferring biomarker information between related neurodegenerative diseases. DKT infers robust multimodal biomarker trajectories in rare neurodegenerative diseases even when only limited, unimodal data is available, by transferring information from larger multimodal datasets from common neurodegenerative diseases. DKT is a joint-disease generative model of biomarker progressions, which exploits biomarker relationships that are shared across diseases. Our proposed method allows, for the first time, the estimation of plausible, multimodal biomarker trajectories in Posterior Cortical Atrophy (PCA), a rare neurodegenerative disease where only unimodal MRI data is available. For this we train DKT on a combined dataset containing subjects with two distinct diseases and sizes of data available: 1) a larger, multimodal typical AD (tAD) dataset from the TADPOLE Challenge, and 2) a smaller unimodal Posterior Cortical Atrophy (PCA) dataset from the Dementia Research Centre (DRC), for which only a limited number of Magnetic Resonance Imaging (MRI) scans are available. Although validation is challenging due to lack of data i

In this talk, we summarize the collider phenomenology and recent experimental results for various models of extra dimensions, including the large extra dimensions (ADD model), warped extra dimensions (Randall-Sundrum model), TeV$^{-1}$-sized extra dimensions with gauge bosons in the bulk, universal extra dimensions, and an 5D SU(5) SUSY GUT model in AdS space.

Rare disease diagnosis increasingly relies on integrating genomic, phenotypic and transcriptomic evidence, yet these signals remain difficult to reconcile within a common interpretive framework. Here we present RareCollab, an LLM-powered framework for multimodal reasoning in Mendelian disease diagnosis that integrates more than 100 diagnostic evidence signals across DNA, RNA, phenotype, curated variant-level knowledge, and in-silico pathogenicity evidence. This design enables large language models to operate as calibrated, interpretable reasoning modules rather than as a single end-to-end ranker. We applied RareCollab to 890 patients from three cohorts, including 119 Undiagnosed Diseases Network probands with paired DNA and RNA data, constituting a large systematic benchmark for multimodal rare disease diagnosis under paired genomic and transcriptomic evaluation. In this real-world multimodal benchmark, RareCollab prioritized 94% of diagnostic genes within the top 10. Across recall thresholds from top 1 to top 10, it consistently outperformed proprietary phenotype-driven LLM baselines including Claude Sonnet 4.6 and GPT-5-mini by more than 25% on average and surpassed established s