Sparse classification with MRI based markers for neuromuscular disease categorization

International audienceIn this paper, we present a novel method for disease classification between two patient populations based on features extracted from Magnetic Resonance Imaging (MRI) data. Anatomically meaningful features are extracted from structural data (T1- and T2-weighted MR images) and Diffusion Tensor Imaging (DTI) data, and used to train a new machine learning algorithm, the k-support SVM (ksup-SVM). The k-support regularized SVM has an inherent feature selection property, and thus it eliminates the requirement for a separate feature selection step. Our dataset consists of patients that suffer from facioscapulohumeral muscular dystrophy (FSH) and Myotonic muscular dystrophy type 1 (DM1) and our proposed method achieves a high performance. More specifically, it achieves a mean Area Under the Curve (AUC) of 0.7141 and mean accuracy 77% ± 0.013. Moreover, we provide a sparsity visualization of the features in order to indentify their discriminative value. The results suggest the potential of the combined use of MR markers to diagnose myopathies, and the general utility of the ksup-SVM. Source code is also available at https://gitorious.org/ksup-svm

Structural subnetwork evolution across the life-span: rich-club, feeder, seeder

The impact of developmental and aging processes on brain connectivity and the connectome has been widely studied. Network theoretical measures and certain topological principles are computed from the entire brain, however there is a need to separate and understand the underlying subnetworks which contribute towards these observed holistic connectomic alterations. One organizational principle is the rich-club - a core subnetwork of brain regions that are strongly connected, forming a high-cost, high-capacity backbone that is critical for effective communication in the network. Investigations primarily focus on its alterations with disease and age. Here, we present a systematic analysis of not only the rich-club, but also other subnetworks derived from this backbone - namely feeder and seeder subnetworks. Our analysis is applied to structural connectomes in a normal cohort from a large, publicly available lifespan study. We demonstrate changes in rich-club membership with age alongside a shift in importance from 'peripheral' seeder to feeder subnetworks. Our results show a refinement within the rich-club structure (increase in transitivity and betweenness centrality), as well as increased efficiency in the feeder subnetwork and decreased measures of network integration and segregation in the seeder subnetwork. These results demonstrate the different developmental patterns when analyzing the connectome stratified according to its rich-club and the potential of utilizing this subnetwork analysis to reveal the evolution of brain architectural alterations across the life-span

Improving transparency and scientific rigor in academic publishing.

Progress in basic and clinical research is slowed when researchers fail to provide a complete and accurate report of how a study was designed, executed, and the results analyzed. Publishing rigorous scientific research involves a full description of the methods, materials, procedures, and outcomes. Investigators may fail to provide a complete description of how their study was designed and executed because they may not know how to accurately report the information or the mechanisms are not in place to facilitate transparent reporting. Here, we provide an overview of how authors can write manuscripts in a transparent and thorough manner. We introduce a set of reporting criteria that can be used for publishing, including recommendations on reporting the experimental design and statistical approaches. We also discuss how to accurately visualize the results and provide recommendations for peer reviewers to enhance rigor and transparency. Incorporating transparency practices into research manuscripts will significantly improve the reproducibility of the results by independent laboratories

Psychometric evaluation of Persian nomophobia questionnaire: differential item functioning and measurement invariance across gender

Background and aims: Research examining problematic mobile phone use has increased markedly over the past 5 years and has been related to “no mobile phone phobia” (so-called nomophobia). The 20-item Nomophobia Questionnaire (NMP-Q) is the only instrument that assesses nomophobia with an underlying theoretical structure and robust psychometric testing. This study aimed to confirm the construct validity of the Persian NMP-Q using Rasch and confirmatory factor analysis (CFA) models. Methods: After ensuring the linguistic validity, Rasch models were used to examine the unidimensionality of each Persian NMP-Q factor among 3,216 Iranian adolescents and CFAs were used to confirm its four-factor structure. Differential item functioning (DIF) and multigroup CFA were used to examine whether males and females interpreted the NMP-Q similarly, including item content and NMP-Q structure. Results: Each factor was unidimensional according to the Rach findings, and the four-factor structure was supported by CFA. Two items did not quite fit the Rasch models (Item 14: “I would be nervous because I could not know if someone had tried to get a hold of me;” Item 9: “If I could not check my smartphone for a while, I would feel a desire to check it”). No DIF items were found across gender and measurement invariance was supported in multigroup CFA across gender. Conclusions: Due to the satisfactory psychometric properties, it is concluded that the Persian NMP-Q can be used to assess nomophobia among adolescents. Moreover, NMP-Q users may compare its scores between genders in the knowledge that there are no score differences contributed by different understandings of NMP-Q items

Diagnosis of Autism Spectrum Disorders Using Multi-level High-order Functional Networks Derived from Resting-State Functional MRI

Functional brain networks derived from resting-state functional magnetic resonance imaging (rs-fMRI) have been widely used for Autism Spectrum Disorder (ASD) diagnosis. Typically, these networks are constructed by calculating functional connectivity (FC) between any pair of brain regions of interest (ROIs), i.e., using Pearson's correlation between rs-fMRI time series. However, this can only be called as a low-order representation of the functional interaction, because the relationship is investigated just between two ROIs. Brain disorders might not only affect low-order FC, but also high-order FC, i.e., the higher-level relationship among multiple brain regions, which might be more crucial for diagnosis. To comprehensively characterize such relationship for better diagnosis of ASD, we propose a multi-level, high-order FC network representation that can nicely capture complex interactions among brain regions. Then, we design a feature selection method to identify those discriminative multi-level, high-order FC features for ASD diagnosis. Finally, we design an ensemble classifier with multiple linear SVMs, each trained on a specific level of FC networks, for boosting the final classification accuracy. Experimental results show that the integration of both low-order and first-level high-order FC networks achieves the best ASD diagnostic accuracy (81%). We further investigated those selected discriminative low-order and high-order FC features and found that the high-order FC features can provide complementary information to the low-order FC features in the ASD diagnosis

Sleep spindling and fluid intelligence across adolescent development: sex matters.

Evidence supports the intricate relationship between sleep electroencephalogram (EEG) spindling and cognitive abilities in children and adults. Although sleep EEG changes during adolescence index fundamental brain reorganization, a detailed analysis of sleep spindling and the spindle-intelligence relationship was not yet provided for adolescents. Therefore, adolescent development of sleep spindle oscillations were studied in a home polysomnographic study focusing on the effects of chronological age and developmentally acquired overall mental efficiency (fluid IQ) with sex as a potential modulating factor. Subjects were 24 healthy adolescents (12 males) with an age range of 15–22 years (mean: 18 years) and fluid IQ of 91–126 (mean: 104.12, Raven Progressive Matrices Test). Slow spindles (SSs) and fast spindles (FSs) were analyzed in 21 EEG derivations by using the individual adjustment method (IAM). A significant age-dependent increase in average FS density (r = 0.57; p = 0.005) was found. Moreover, fluid IQ correlated with FS density (r = 0.43; p = 0.04) and amplitude (r = 0.41; p = 0.049). The latter effects were entirely driven by particularly reliable FS-IQ correlations in females [r = 0.80 (p = 0.002) and r = 0.67 (p = 0.012), for density and amplitude, respectively]. Region-specific analyses revealed that these correlations peak in the fronto-central regions. The control of the age-dependence of FS measures and IQ scores did not considerably reduce the spindle-IQ correlations with respect to FS density. The only positive spindle-index of fluid IQ in males turned out to be the frequency of FSs (r = 0.60, p = 0.04). Increases in FS density during adolescence may index reshaped structural connectivity related to white matter maturation in the late developing human brain. The continued development over this age range of cognitive functions is indexed by specific measures of sleep spindling unraveling gender differences in adolescent brain maturation and perhaps cognitive strategy

Neural systems for speech and song in autism

Despite language disabilities in autism, music abilities are frequently preserved. Paradoxically, brain regions associated with these functions typically overlap, enabling investigation of neural organization supporting speech and song in autism. Neural systems sensitive to speech and song were compared in low-functioning autistic and age-matched control children using passive auditory stimulation during functional magnetic resonance and diffusion tensor imaging. Activation in left inferior frontal gyrus was reduced in autistic children relative to controls during speech stimulation, but was greater than controls during song stimulation. Functional connectivity for song relative to speech was also increased between left inferior frontal gyrus and superior temporal gyrus in autism, and large-scale connectivity showed increased frontal–posterior connections. Although fractional anisotropy of the left arcuate fasciculus was decreased in autistic children relative to controls, structural terminations of the arcuate fasciculus in inferior frontal gyrus were indistinguishable between autistic and control groups. Fractional anisotropy correlated with activity in left inferior frontal gyrus for both speech and song conditions. Together, these findings indicate that in autism, functional systems that process speech and song were more effectively engaged for song than for speech and projections of structural pathways associated with these functions were not distinguishable from controls