Rigorous optimisation of multilinear discriminant analysis with Tucker and PARAFAC structures

Abstract Background We propose rigorously optimised supervised feature extraction methods for multilinear data based on Multilinear Discriminant Analysis (MDA) and demonstrate their usage on Electroencephalography (EEG) and simulated data. While existing MDA methods use heuristic optimisation procedures based on an ambiguous Tucker structure, we propose a rigorous approach via optimisation on the cross-product of Stiefel manifolds. We also introduce MDA methods with the PARAFAC structure. We compare the proposed approaches to existing MDA methods and unsupervised multilinear decompositions. Results We find that manifold optimisation substantially improves MDA objective functions relative to existing methods and on simulated data in general improve classification performance. However, we find similar classification performance when applied to the electroencephalography data. Furthermore, supervised approaches substantially outperform unsupervised mulitilinear methods whereas methods with the PARAFAC structure perform similarly to those with Tucker structures. Notably, despite applying the MDA procedures to raw Brain-Computer Interface data, their performances are on par with results employing ample pre-processing and they extract discriminatory patterns similar to the brain activity known to be elicited in the investigated EEG paradigms. Conclusion The proposed usage of manifold optimisation constitutes the first rigorous and monotonous optimisation approach for MDA methods and allows for MDA with the PARAFAC structure. Our results show that MDA methods applied to raw EEG data can extract discriminatory patterns when compared to traditional unsupervised multilinear feature extraction approaches, whereas the proposed PARAFAC structured MDA models provide meaningful patterns of activity

Migraine polygenic risk score associates with efficacy of migraine-specific drugs

Objective To assess whether the polygenic risk score (PRS) for migraine is associated with acute and/or prophylactic migraine treatment response. Methods We interviewed 2,219 unrelated patients at the Danish Headache Center using a semistructured interview to diagnose migraine and assess acute and prophylactic drug response. All patients were genotyped. A PRS was calculated with the linkage disequilibrium pred algorithm using summary statistics from the most recent migraine genome-wide association study comprising ∼375,000 cases and controls. The PRS was scaled to a unit corresponding to a twofold increase in migraine risk, using 929 unrelated Danish controls as reference. The association of the PRS with treatment response was assessed by logistic regression, and the predictive power of the model by area under the curve using a case-control design with treatment response as outcome. Results A twofold increase in migraine risk associates with positive response to migraine-specific acute treatment (odds ratio [OR] = 1.25 [95% confidence interval (CI) = 1.05–1.49]). The association between migraine risk and migraine-specific acute treatment was replicated in an independent cohort consisting of 5,616 triptan users with prescription history (OR = 3.20 [95% CI = 1.26–8.14]). No association was found for acute treatment with non–migraine-specific weak analgesics and prophylactic treatment response. Conclusions The migraine PRS can significantly identify subgroups of patients with a higher-than-average likelihood of a positive response to triptans, which provides a first step toward genetics-based precision medicine in migraine

Effectiveness of surgery for sciatica with disc herniation is not substantially affected by differences in surgical incidences among three countries : results from the Danish, Swedish and Norwegian spine registries

Purpose Yearly incidence of surgery for symptomatic lumbar disc herniation varies and is 29/100,000 in Sweden, 46/100,000 in Denmark and 58/100,000 in Norway. This variation was used to study whether differences in surgical incidence were associated with differences in preoperative patient characteristics as well as patient-reported outcomes. Methods Data from the national spine registers in Sweden, Denmark and Norway during 2011-2013 were pooled, and 9965 individuals, aged 18-65 years, of which 6468 had one-year follow-up data, were included in the study. Both absolute and case-mix-adjusted comparisons of the primary outcome Oswestry Disability Index (ODI) and the secondary outcomes EQ-5D-3L, and Numerical Rating Scale (NRS) for leg and back pain were performed. Case-mix adjustment was done for baseline age, sex, BMI, smoking, co-morbidity, duration of leg pain and preoperative value of the dependent variable. Results Mean improvement in the outcome variables exceeded previously described minimal clinical important change in all countries. Mean (95% CI) final scores of ODI were 18 (17-18), 19 (18-20) and 15 (15-16) in Sweden, Denmark and Norway, respectively. Corresponding results of EQ-5D-3L were 0.74 (0.73-0.75), 0.73 (0.72-0.75) and 0.75 (0.74-0.76). Results of NRS leg and back pain behaved similarly. Case-mix adjustment did not alter the findings substantially. Conclusion We found no clear association between incidence of surgery for lumbar disc herniation and preoperative patient characteristics as well as outcome, and the differences between the countries were lower than the minimal clinical important difference in all outcomes. [GRAPHICS]

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field