Mind over chatter: plastic up-regulation of the fMRI alertness network by EEG neurofeedback

EEG neurofeedback (NFB) is a brain-computer interface (BCI) approach used to shape brain oscillations by means of real-time feedback from the electroencephalogram (EEG), which is known to reflect neural activity across cortical networks. Although NFB is being evaluated as a novel tool for treating brain disorders, evidence is scarce on the mechanism of its impact on brain function. In this study with 34 healthy participants, we examined whether, during the performance of an attentional auditory oddball task, the functional connectivity strength of distinct fMRI networks would be plastically altered after a 30-min NFB session of alpha-band reduction (n=17) versus a sham-feedback condition (n=17). Our results reveal that compared to sham, NFB induced a specific increase of functional connectivity within the alertness/salience network (dorsal anterior and mid cingulate), which was detectable 30 minutes after termination of training. Crucially, these effects were significantly correlated with reduced mind-wandering 'on-task' and were coupled to NFB-mediated resting state reductions in the alpha-band (8-12 Hz). No such relationships were evident for the sham condition. Although group default-mode network (DMN) connectivity was not significantly altered following NFB, we observed a positive association between modulations of resting alpha amplitude and precuneal connectivity, both correlating positively with frequency of mind-wandering. Our findings demonstrate a temporally direct, plastic impact of NFB on large-scale brain functional networks, and provide promising neurobehavioral evidence supporting its use as a noninvasive tool to modulate brain function in health and disease

Deep Chronnectome Learning via Full Bidirectional Long Short-Term Memory Networks for MCI Diagnosis

Brain functional connectivity (FC) extracted from resting-state fMRI (RS-fMRI) has become a popular approach for disease diagnosis, where discriminating subjects with mild cognitive impairment (MCI) from normal controls (NC) is still one of the most challenging problems. Dynamic functional connectivity (dFC), consisting of time-varying spatiotemporal dynamics, may characterize "chronnectome" diagnostic information for improving MCI classification. However, most of the current dFC studies are based on detecting discrete major brain status via spatial clustering, which ignores rich spatiotemporal dynamics contained in such chronnectome. We propose Deep Chronnectome Learning for exhaustively mining the comprehensive information, especially the hidden higher-level features, i.e., the dFC time series that may add critical diagnostic power for MCI classification. To this end, we devise a new Fully-connected Bidirectional Long Short-Term Memory Network (Full-BiLSTM) to effectively learn the periodic brain status changes using both past and future information for each brief time segment and then fuse them to form the final output. We have applied our method to a rigorously built large-scale multi-site database (i.e., with 164 data from NCs and 330 from MCIs, which can be further augmented by 25 folds). Our method outperforms other state-of-the-art approaches with an accuracy of 73.6% under solid cross-validations. We also made extensive comparisons among multiple variants of LSTM models. The results suggest high feasibility of our method with promising value also for other brain disorder diagnoses.Comment: The paper has been accepted by MICCAI201

Disambiguating the role of blood flow and global signal with partial information decomposition

Global signal (GS) is an ubiquitous construct in resting state functional magnetic resonance imaging (rs-fMRI), associated to nuisance, but containing by definition most of the neuronal signal. Global signal regression (GSR) effectively removes the impact of physiological noise and other artifacts, but at the same time it alters correlational patterns in unpredicted ways. Performing GSR taking into account the underlying physiology (mainly the blood arrival time) has been proven to be beneficial. From these observations we aimed to: 1) characterize the effect of GSR on network-level functional connectivity in a large dataset; 2) assess the complementary role of global signal and vessels; and 3) use the framework of partial information decomposition to further look into the joint dynamics of the global signal and vessels, and their respective influence on the dynamics of cortical areas. We observe that GSR affects intrinsic connectivity networks in the connectome in a non-uniform way. Furthermore, by estimating the predictive information of blood flow and the global signal using partial information decomposition, we observe that both signals are present in different amounts across intrinsic connectivity networks. Simulations showed that differences in blood arrival time can largely explain this phenomenon, while using hemodynamic and calcium mouse recordings we were able to confirm the presence of vascular effects, as calcium recordings lack hemodynamic information. With these results we confirm network-specific effects of GSR and the importance of taking blood flow into account for improving de-noising methods. Additionally, and beyond the mere issue of data denoising, we quantify the diverse and complementary effect of global and vessel BOLD signals on the dynamics of cortical areas

Block Coordinate Descent for Sparse NMF

Nonnegative matrix factorization (NMF) has become a ubiquitous tool for data analysis. An important variant is the sparse NMF problem which arises when we explicitly require the learnt features to be sparse. A natural measure of sparsity is the L$_0$ norm, however its optimization is NP-hard. Mixed norms, such as L$_1$/L$_2$ measure, have been shown to model sparsity robustly, based on intuitive attributes that such measures need to satisfy. This is in contrast to computationally cheaper alternatives such as the plain L$_1$ norm. However, present algorithms designed for optimizing the mixed norm L$_1$/L$_2$ are slow and other formulations for sparse NMF have been proposed such as those based on L$_1$ and L$_0$ norms. Our proposed algorithm allows us to solve the mixed norm sparsity constraints while not sacrificing computation time. We present experimental evidence on real-world datasets that shows our new algorithm performs an order of magnitude faster compared to the current state-of-the-art solvers optimizing the mixed norm and is suitable for large-scale datasets

Joint and individual analysis of breast cancer histologic images and genomic covariates

A key challenge in modern data analysis is understanding connections between complex and differing modalities of data. For example, two of the main approaches to the study of breast cancer are histopathology (analyzing visual characteristics of tumors) and genetics. While histopathology is the gold standard for diagnostics and there have been many recent breakthroughs in genetics, there is little overlap between these two fields. We aim to bridge this gap by developing methods based on Angle-based Joint and Individual Variation Explained (AJIVE) to directly explore similarities and differences between these two modalities. Our approach exploits Convolutional Neural Networks (CNNs) as a powerful, automatic method for image feature extraction to address some of the challenges presented by statistical analysis of histopathology image data. CNNs raise issues of interpretability that we address by developing novel methods to explore visual modes of variation captured by statistical algorithms (e.g. PCA or AJIVE) applied to CNN features. Our results provide many interpretable connections and contrasts between histopathology and genetics

Open borders, closed minds: the discursive construction of national identity in North Cyprus

The article investigates the discursive construction of a Turkish Cypriot national identity by the newspapers in North Cyprus. It questions the representation and reconstruction processes of national identity within the press and examines the various practices employed to mobilize readers around certain national imaginings. Using Critical Discourse Analysis, the article analyses news reports of the opening of border crossings in Cyprus in 2003, based on their content, the strategies used in the production of national identity and the linguistic means employed in the process. In this way, the nationalist tendencies embedded in news discourses, as well as discriminatory and exclusive practices, are sought out

COINSTAC: A Privacy Enabled Model and Prototype for Leveraging and Processing Decentralized Brain Imaging Data

The field of neuroimaging has embraced the need for sharing and collaboration. Data sharing mandates from public funding agencies and major journal publishers have spurred the development of data repositories and neuroinformatics consortia. However, efficient and effective data sharing still faces several hurdles. For example, open data sharing is on the rise but is not suitable for sensitive data that are not easily shared, such as genetics. Current approaches can be cumbersome (such as negotiating multiple data sharing agreements). There are also significant data transfer, organization and computational challenges. Centralized repositories only partially address the issues. We propose a dynamic, decentralized platform for large scale analyses called the Collaborative Informatics and Neuroimaging Suite Toolkit for Anonymous Computation (COINSTAC). The COINSTAC solution can include data missing from central repositories, allows pooling of both open and ``closed'' repositories by developing privacy-preserving versions of widely-used algorithms, and incorporates the tools within an easy-to-use platform enabling distributed computation. We present an initial prototype system which we demonstrate on two multi-site data sets, without aggregating the data. In addition, by iterating across sites, the COINSTAC model enables meta-analytic solutions to converge to ``pooled-data'' solutions (i.e. as if the entire data were in hand). More advanced approaches such as feature generation, matrix factorization models, and preprocessing can be incorporated into such a model. In sum, COINSTAC enables access to the many currently unavailable data sets, a user friendly privacy enabled interface for decentralized analysis, and a powerful solution that complements existing data sharing solutions

Correction Technique for Raman Water Vapor Lidar Signal-Dependent Bias and Suitability for Water Wapor Trend Monitoring in the Upper Troposphere

The MOHAVE-2009 campaign brought together diverse instrumentation for measuring atmospheric water vapor. We report on the participation of the ALVICE (Atmospheric Laboratory for Validation, Interagency Collaboration and Education) mobile laboratory in the MOHAVE-2009 campaign. In appendices we also report on the performance of the corrected Vaisala RS92 radiosonde measurements during the campaign, on a new radiosonde based calibration algorithm that reduces the influence of atmospheric variability on the derived calibration constant, and on other results of the ALVICE deployment. The MOHAVE-2009 campaign permitted the Raman lidar systems participating to discover and address measurement biases in the upper troposphere and lower stratosphere. The ALVICE lidar system was found to possess a wet bias which was attributed to fluorescence of insect material that was deposited on the telescope early in the mission. Other sources of wet biases are discussed and data from other Raman lidar systems are investigated, revealing that wet biases in upper tropospheric (UT) and lower stratospheric (LS) water vapor measurements appear to be quite common in Raman lidar systems. Lower stratospheric climatology of water vapor is investigated both as a means to check for the existence of these wet biases in Raman lidar data and as a source of correction for the bias. A correction technique is derived and applied to the ALVICE lidar water vapor profiles. Good agreement is found between corrected ALVICE lidar measurments and those of RS92, frost point hygrometer and total column water. The correction is offered as a general method to both quality control Raman water vapor lidar data and to correct those data that have signal-dependent bias. The influence of the correction is shown to be small at regions in the upper troposphere where recent work indicates detection of trends in atmospheric water vapor may be most robust. The correction shown here holds promise for permitting useful upper tropospheric water vapor profiles to be consistently measured by Raman lidar within NDACC (Network for the Detection of Atmospheric Composition Change) and elsewhere, despite the prevalence of instrumental and atmospheric effects that can contaminate the very low signal to noise measurements in the UT

Advancing functional connectivity research from association to causation

Cognition and behavior emerge from brain network interactions, such that investigating causal interactions should be central to the study of brain function. Approaches that characterize statistical associations among neural time series-functional connectivity (FC) methods-are likely a good starting point for estimating brain network interactions. Yet only a subset of FC methods ('effective connectivity') is explicitly designed to infer causal interactions from statistical associations. Here we incorporate best practices from diverse areas of FC research to illustrate how FC methods can be refined to improve inferences about neural mechanisms, with properties of causal neural interactions as a common ontology to facilitate cumulative progress across FC approaches. We further demonstrate how the most common FC measures (correlation and coherence) reduce the set of likely causal models, facilitating causal inferences despite major limitations. Alternative FC measures are suggested to immediately start improving causal inferences beyond these common FC measures