Aneurysm Identification in Cerebral Models with Multiview Convolutional Neural Network

Stroke is the third most common cause of death and a major contributor to long-term disability worldwide. Severe stroke is most often caused by the rupture of a cerebral aneurysm, a weakened area in a blood vessel. The detection and quantification of cerebral aneurysms are essential for the prevention and treatment of aneurysmal rupture and cerebral infarction. Here, we propose a novel aneurysm detection method in a three-dimensional (3D) cerebrovascular model based on convolutional neural networks (CNNs). The multiview method is used to obtain a sequence of 2D images on the cerebral vessel branch model. The pretrained CNN is used with transfer learning to overcome the small training sample problem. The data augmentation strategy with rotation, mirroring and flipping helps improve the performance dramatically, particularly on our small datasets. The hyperparameter of the view number is determined in the task. We have applied the labeling task on 56 3D mesh models with aneurysms (positive) and 65 models without aneurysms (negative). The average accuracy of individual projected images is 87.86%, while that of the model is 93.4% with the best view number. The framework is highly effective with quick training efficiency that can be widely extended to detect other organ anomalies

Anatomical Markers Associated With the Presence of Intracranial Aneurysms in Individuals Screened for Aneurysms

BACKGROUND Hemodynamic stress is linked to the development of intracranial aneurysms (IAs) and may be influenced by anatomic variation of intracranial arteries. We assessed diameters and bifurcation angles of intracranial arteries forming the circle of Willis in a cohort of individuals screened for the presence of IAs. METHODS Individuals with and without IAs identified at screening with magnetic resonance angiography were compared. Diameters and bifurcation angles of the following arteries were measured using semiautomatic methods: A1 and A2 segments of the anterior cerebral artery, M1 and M2 segments of the middle cerebral artery, P1 segments of the posterior cerebral artery, posterior communicating artery (Pcom), internal carotid artery, vertebral artery, and basilar artery. We employed univariate general linear models to assess group differences. This included subgroup comparisons between individuals with IAs at specific locations and matched controls, and comparisons on group level between individuals with and without IAs, corrected for age and sex. RESULTS In 94 of the 1049 individuals (9.0%) included, IAs were detected. Individuals with middle cerebral artery IAs had wider ipsilateral M2–M2 bifurcation angles compared with controls (121±25° versus 97±19°; P<0.01). Individuals with anterior communicating artery IAs showed smaller angles for the A1–A2 bifurcation (106±16° versus 120±17°; P = 0.02), while those with Pcom IAs had wider Pcom–C7 bifurcation angles (147±14° versus 127±17°; P = 0.02) and smaller diameters below the ipsilateral internal carotid artery top (2.86±0.36 mm versus 3.10±0.33 mm; P = 0.03) compared with controls. CONCLUSION We found associations between wider M2–M2 bifurcation angles or narrower A1–A2 bifurcation angles and IA presence, consistent with prior literature. Moreover, we uncovered previously unexplored associations, including wider Pcom–C7 bifurcation angles and smaller internal carotid artery diameters in individuals with Pcom IAs. Future research should explore the potential of these markers in predicting IAs in at‐risk populations during follow‐up screenings

OSIRISv1.2: A named entity recognition system for sequence variants of genes in biomedical literature

<p>Abstract</p> <p>Background</p> <p>Single Nucleotide Polymorphisms, among other type of sequence variants, constitute key elements in genetic epidemiology and pharmacogenomics. While sequence data about genetic variation is found at databases such as dbSNP, clues about the functional and phenotypic consequences of the variations are generally found in biomedical literature. The identification of the relevant documents and the extraction of the information from them are hampered by the large size of literature databases and the lack of widely accepted standard notation for biomedical entities. Thus, automatic systems for the identification of citations of allelic variants of genes in biomedical texts are required.</p> <p>Results</p> <p>Our group has previously reported the development of OSIRIS, a system aimed at the retrieval of literature about allelic variants of genes <url>http://ibi.imim.es/osirisform.html</url>. Here we describe the development of a new version of OSIRIS (OSIRISv1.2, <url>http://ibi.imim.es/OSIRISv1.2.html</url>) which incorporates a new entity recognition module and is built on top of a local mirror of the MEDLINE collection and HgenetInfoDB: a database that collects data on human gene sequence variations. The new entity recognition module is based on a pattern-based search algorithm for the identification of variation terms in the texts and their mapping to dbSNP identifiers. The performance of OSIRISv1.2 was evaluated on a manually annotated corpus, resulting in 99% precision, 82% recall, and an F-score of 0.89. As an example, the application of the system for collecting literature citations for the allelic variants of genes related to the diseases intracranial aneurysm and breast cancer is presented.</p> <p>Conclusion</p> <p>OSIRISv1.2 can be used to link literature references to dbSNP database entries with high accuracy, and therefore is suitable for collecting current knowledge on gene sequence variations and supporting the functional annotation of variation databases. The application of OSIRISv1.2 in combination with controlled vocabularies like MeSH provides a way to identify associations of biomedical interest, such as those that relate SNPs with diseases.</p

Robustness of common hemodynamic indicators with respect to numerical resolution in 38 middle cerebral artery aneurysms

Background: Using computational fluid dynamics (CFD) to compute the hemodynamics in cerebral aneurysms has received much attention in the last decade. The usability of these methods depends on the quality of the computations, highlighted in recent discussions. The purpose of this study is to investigate the convergence of common hemodynamic indicators with respect to numerical resolution. Methods: 38 middle cerebral artery bifurcation aneurysms were studied at two different resolutions (one comparable to most studies, and one finer). Relevant hemodynamic indicators were collected from two of the most cited studies, and were compared at the two refinements. In addition, correlation to rupture was investigated. Results: Most of the hemodynamic indicators were very well resolved at the coarser resolutions, correlating with the finest resolution with a correlation coefficient >0.95. The oscillatory shear index (OSI) had the lowest correlation coefficient of 0.83. A logarithmic Bland-Altman plot revealed noticeable variations in the proportion of the aneurysm under low shear, as well as in spatial and temporal gradients not captured by the correlation alone. Conclusion: Statistically, hemodynamic indicators agree well across the different resolutions studied here. However, there are clear outliers visible in several of the hemodynamic indicators, which suggests that special care should be taken when considering individual assessment

Characteristics of intracranial aneurysms and subarachnoid haemorrhage in patients with polycystic kidney disease

Background and Purpose Subarachnoid haemorrhage is a common cause of death in patients with autosomal dominant polycystic kidney disease (ADPKD), but little is known about specific characteristics of subarachnoid haemorrhage and intracranial aneurysms in this group of patients. We performed a systematic review on site, size and number of aneurysms, age at time of rupture, gender, and family history in patients with ADPKD and intracranial aneurysms. We also studied the frequency of ADPKD in patients with subarachnoid haemorrhage treated in our hospital. Methods We performed a MEDLINE search and checked the reference lists of all relevant publications to identify all articles published from 1980 to 2000 on intracranial aneurysms or subarachnoid haemorrhage in ADPKD. We studied our database of patients with subarachnoid haemorrhage treated between 1978 and 1999 for the presence of ADPKD. Results We included 53 articles on 369 ADPKD patients (139 [54%] women) with 462 intracranial aneurysms. Of the 273 aneurysms with specified locations 105 (38%) were located on the middle cerebral artery in and on the anterior communicating artery in 83 patients (30%). In 253 patients with data about relatives, the family history was positive for intracranial aneurysms or subarachnoid haemorrhage in 102 (40%). The average age at which subarachnoid haemorrhage had occurred in 258 was 41 years; of 158 in whom the gender was given; 96 (52%) were women. Of the 160 patients with data on outcome, 69 (43%) had died as the result of the subarachnoid haemorrhage. Of the 1147 patients treated for aneurysmal subarachnoid haemorrhage in our institution (mean age 53 years; 65.5% women), 5 (0.44%) had ADPKD. Conclusions Compared with data on patients without ADPKD, subarachnoid haemorrhage in patients with ADPKD occurs not only often in a familial setting of subarachnoid haemorrhage, but also at an earlier age and more often in men. In patients with ADPKD, the most frequent site of aneurysms is the middle cerebral artery. The proportion of patients with ADPKD among all patients with subarachnoid haemorrhage is very small