Constructing Priors that Penalize the Complexity of Gaussian Random Fields

Priors are important for achieving proper posteriors with physically meaningful covariance structures for Gaussian random fields (GRFs) since the likelihood typically only provides limited information about the covariance structure under in-fill asymptotics. We extend the recent Penalised Complexity prior framework and develop a principled joint prior for the range and the marginal variance of one-dimensional, two-dimensional and three-dimensional Mat\'ern GRFs with fixed smoothness. The prior is weakly informative and penalises complexity by shrinking the range towards infinity and the marginal variance towards zero. We propose guidelines for selecting the hyperparameters, and a simulation study shows that the new prior provides a principled alternative to reference priors that can leverage prior knowledge to achieve shorter credible intervals while maintaining good coverage. We extend the prior to a non-stationary GRF parametrized through local ranges and marginal standard deviations, and introduce a scheme for selecting the hyperparameters based on the coverage of the parameters when fitting simulated stationary data. The approach is applied to a dataset of annual precipitation in southern Norway and the scheme for selecting the hyperparameters leads to concervative estimates of non-stationarity and improved predictive performance over the stationary model

Marginal Folate Deficiency as a Possible Cause of Hyperhomocysteinaemia in Stroke Patients

Peer Reviewe

International Stroke Genetics Consortium recommendations for studies of genetics of stroke outcome and recovery

Numerous biological mechanisms contribute to outcome after stroke, including brain injury, inflammation, and repair mechanisms. Clinical genetic studies have the potential to discover biological mechanisms affecting stroke recovery in humans and identify intervention targets. Large sample sizes are needed to detect commonly occurring genetic variations related to stroke brain injury and recovery. However, this usually requires combining data from multiple studies where consistent terminology, methodology, and data collection timelines are essential. Our group of expert stroke and rehabilitation clinicians and researchers with knowledge in genetics of stroke recovery here present recommendations for harmonizing phenotype data with focus on measures suitable for multicenter genetic studies of ischemic stroke brain injury and recovery. Our recommendations have been endorsed by the International Stroke Genetics Consortium

Exploring a New Class of Non-stationary Spatial Gaussian Random Fields with Varying Local Anisotropy

Gaussian random fields (GRFs) constitute an important part of spatial modelling, but can be computationally infeasible for general covariance structures. An efficient approach is to specify GRFs via stochastic partial differential equations (SPDEs) and derive Gaussian Markov random field (GMRF) approximations of the solutions. We consider the construction of a class of non-stationary GRFs with varying local anisotropy, where the local anisotropy is introduced by allowing the coefficients in the SPDE to vary with position. This is done by using a form of diffusion equation driven by Gaussian white noise with a spatially varying diffusion matrix. This allows for the introduction of parameters that control the GRF by parametrizing the diffusion matrix. These parameters and the GRF may be considered to be part of a hierarchical model and the parameters estimated in a Bayesian framework. The results show that the use of an SPDE with non-constant coefficients is a promising way of creating non-stationary spatial GMRFs that allow for physical interpretability of the parameters, although there are several remaining challenges that would need to be solved before these models can be put to general practical use

Predominance of caudate nucleus lesions in acute ischemic stroke patients with impairments in language and speech

Background and purpose. Whereas traditional views of language processing in the brain have assumed that the language function is concentrated to a limited number of cortical areas (Broca’s and Wernicke’s areas), current knowledge points at a much more complex system of language and speech processing involving many brain areas, both cortical and subcortical. The purpose of the current study was to make an unbiased assessment of which cerebral areas are affected in first-ever acute ischemic stroke patients identified as having language and speech impairments according to the National Institute of Health Stroke Scale (NIHSS). Methods. Data from thirty-four patients with language and speech impairments, with a score of 1-3 on item 9 on the NIHSS, following ischemic stroke was collected from the Lund Stroke Register. MRI images acquired up to 20 days after stroke onset were used to create an overlap lesion image using MRIcron software. Results. The classical language areas, Wernicke’s and Broca’s area, were affected in less than one fourth of the patients. The most frequently affected region was a subcortical region - the left caudate nucleus and the adjacent corona radiata. Conclusions. These findings contribute to the growing body of evidence that the basal ganglia have a crucial role in the control over language and speech processing

Variations in apolipoprotein D and sigma non-opioid intracellular receptor 1 genes with relation to risk, severity and outcome of ischemic stroke

Background: In experimental studies, the apolipoprotein D (APOD) and the sigma receptor type 1 (SIGMAR1) have been related to processes of brain damage, repair and plasticity. Methods: We examined blood samples from 3081 ischemic stroke (IS) patients and 1595 control subjects regarding 10 single nucleotide polymorphisms (SNPs) in the APOD (chromosomal location 3q29) and SIGMAR1 (chromosomal location 9p13) genes to find possible associations with IS risk, IS severity (NIHSS-score) and recovery after IS (modified Rankin Scale, mRS, at 90 days). Simple/multiple logistic regression and Spearman's rho were utilized for the analyses. Results: Among the SNPs analyzed, rs7659 within the APOD gene showed a possible association with stroke risk (OR = 1.12; 95% CI: 1.01-1.25; P = 0.029) and stroke severity (NIHSS >= 16) (OR = 0.70; 95% CI: 0.54-0.92; P = 0.009) when controlling for age, sex and vascular risk factors for stroke. No SNP showed an association with stroke recovery (mRS). Conclusions: We conclude that the SNP rs7659 within the APOD gene might be related to risk and severity of ischemic stroke in patients

Does non-stationary spatial data always require non-stationary random fields?

A stationary spatial model is an idealization and we expect that the true dependence structures of physical phenomena are spatially varying, but how should we handle this non-stationarity in practice? We study the challenges involved in applying a flexible non-stationary model to a dataset of annual precipitation in the conterminous US, where exploratory data analysis shows strong evidence of a non-stationary covariance structure. The aim of this paper is to investigate the modelling pipeline once non-stationarity has been detected in spatial data. We show that there is a real danger of over-fitting the model and that careful modelling is necessary in order to properly account for varying second-order structure. In fact, the example shows that sometimes non-stationary Gaussian random fields are not necessary to model non-stationary spatial data.Comment: Minor change from previous version. arXiv admin note: text overlap with arXiv:1306.040

Updated Stroke Gene Panels : Rapid evolution of knowledge on monogenic causes of stroke

This article updates our previous Stroke Gene Panels (SGP) from 2017. Online Mendelian Inheritance in Man and PubMed were searched. We divided detected genes into two SGP groups, SGP1: genes reported in at least one person with stroke and associated with one or more clinical subgroups: large artery atherosclerotic, large artery non-atherosclerotic (tortuosity, dolichoectasia, aneurysm, non-atherosclerotic dissection or occlusion), cerebral small vessel diseases, cardio-embolic (arrhythmia, heart defect, cardiomyopathy), coagulation dysfunctions (venous thrombosis, arterial thrombosis, bleeding tendency), intracerebral hemorrhage, vascular malformations (cavernoma, arteriovenous malformations) and metabolism disorders; and SGP2: genes related to diseases that may predispose to stroke. We identified 168 SGP1 genes, 70 of these were validated for clinical practice. We also detected 72 SGP2 genes. Nine genes were removed because of conflicting evidence. The number of genes increased from 168 to 240 during 4.5-years, reflecting a dynamic evolution and the need for regular updates for research and clinical use.Peer reviewe

Three-phase traffic theory and two-phase models with a fundamental diagram in the light of empirical stylized facts

Despite the availability of large empirical data sets and the long history of traffic modeling, the theory of traffic congestion on freeways is still highly controversial. In this contribution, we compare Kerner's three-phase traffic theory with the phase diagram approach for traffic models with a fundamental diagram. We discuss the inconsistent use of the term "traffic phase" and show that patterns demanded by three-phase traffic theory can be reproduced with simple two-phase models, if the model parameters are suitably specified and factors characteristic for real traffic flows are considered, such as effects of noise or heterogeneity or the actual freeway design (e.g. combinations of off- and on-ramps). Conversely, we demonstrate that models created to reproduce three-phase traffic theory create similar spatiotemporal traffic states and associated phase diagrams, no matter whether the parameters imply a fundamental diagram in equilibrium or non-unique flow- density relationships. In conclusion, there are different ways of reproducing the empirical stylized facts of spatiotemporal congestion patterns summarized in this contribution, and it appears possible to overcome the controversy by a more precise definition of the scientific terms and a more careful comparison of models and data, considering effects of the measurement process and the right level of detail in the traffic model used.Comment: 18 pages in the published article, 13 figures, 2 table