Dwelling Quietly in the Rich Club: Brain Network Determinants of Slow Cortical Fluctuations

For more than a century, cerebral cartography has been driven by investigations of structural and morphological properties of the brain across spatial scales and the temporal/functional phenomena that emerge from these underlying features. The next era of brain mapping will be driven by studies that consider both of these components of brain organization simultaneously -- elucidating their interactions and dependencies. Using this guiding principle, we explored the origin of slowly fluctuating patterns of synchronization within the topological core of brain regions known as the rich club, implicated in the regulation of mood and introspection. We find that a constellation of densely interconnected regions that constitute the rich club (including the anterior insula, amygdala, and precuneus) play a central role in promoting a stable, dynamical core of spontaneous activity in the primate cortex. The slow time scales are well matched to the regulation of internal visceral states, corresponding to the somatic correlates of mood and anxiety. In contrast, the topology of the surrounding "feeder" cortical regions show unstable, rapidly fluctuating dynamics likely crucial for fast perceptual processes. We discuss these findings in relation to psychiatric disorders and the future of connectomics.Comment: 35 pages, 6 figure

Applications

Volume 3 describes how resource-aware machine learning methods and techniques are used to successfully solve real-world problems. The book provides numerous specific application examples: in health and medicine for risk modelling, diagnosis, and treatment selection for diseases in electronics, steel production and milling for quality control during manufacturing processes in traffic, logistics for smart cities and for mobile communications

Real-time decoding of question-and-answer speech dialogue using human cortical activity.

Natural communication often occurs in dialogue, differentially engaging auditory and sensorimotor brain regions during listening and speaking. However, previous attempts to decode speech directly from the human brain typically consider listening or speaking tasks in isolation. Here, human participants listened to questions and responded aloud with answers while we used high-density electrocorticography (ECoG) recordings to detect when they heard or said an utterance and to then decode the utterance's identity. Because certain answers were only plausible responses to certain questions, we could dynamically update the prior probabilities of each answer using the decoded question likelihoods as context. We decode produced and perceived utterances with accuracy rates as high as 61% and 76%, respectively (chance is 7% and 20%). Contextual integration of decoded question likelihoods significantly improves answer decoding. These results demonstrate real-time decoding of speech in an interactive, conversational setting, which has important implications for patients who are unable to communicate

Applications

Volume 3 describes how resource-aware machine learning methods and techniques are used to successfully solve real-world problems. The book provides numerous specific application examples: in health and medicine for risk modelling, diagnosis, and treatment selection for diseases in electronics, steel production and milling for quality control during manufacturing processes in traffic, logistics for smart cities and for mobile communications

Forecasting User Interests Through Topic Tag Predictions in Online Health Communities

The increasing reliance on online communities for healthcare information by patients and caregivers has led to the increase in the spread of misinformation, or subjective, anecdotal and inaccurate or non-specific recommendations, which, if acted on, could cause serious harm to the patients. Hence, there is an urgent need to connect users with accurate and tailored health information in a timely manner to prevent such harm. This paper proposes an innovative approach to suggesting reliable information to participants in online communities as they move through different stages in their disease or treatment. We hypothesize that patients with similar histories of disease progression or course of treatment would have similar information needs at comparable stages. Specifically, we pose the problem of predicting topic tags or keywords that describe the future information needs of users based on their profiles, traces of their online interactions within the community (past posts, replies) and the profiles and traces of online interactions of other users with similar profiles and similar traces of past interaction with the target users. The result is a variant of the collaborative information filtering or recommendation system tailored to the needs of users of online health communities. We report results of our experiments on an expert curated data set which demonstrate the superiority of the proposed approach over the state of the art baselines with respect to accurate and timely prediction of topic tags (and hence information sources of interest).Comment: Healthcare Informatics and NL

Modeling And Identification Of Differentially Regulated Genes Using Transcriptomics And Proteomics Data

Photosynthetic organisms are complex dynamical systems, showing a remarkable ability to adapt to different environmental conditions for their survival. Mechanisms underlying the coordination between different cellular processes in these organisms are still poorly understood. In this dissertation we utilize various computational and modeling techniques to analyze transcriptomics and proteomics data sets from several photosynthetic organisms. We try to use changes in expression levels of genes to study responses of these organisms to various environmental conditions such as availability of nutrients, concentrations of chemicals in growth media, and temperature. Three specific problems studied here are transcriptomics modifications in photosynthetic organisms under reduction-oxidation: redox) stress conditions, circadian and diurnal rhythms of cyanobacteria and the effect of incident light patterns on these rhythms, and the coordination between biological processes in cyanobacteria under various growth conditions. Under redox stresses caused by high light treatments, a strong transcriptomic level response, spread across many biological processes, is discovered in the cyanobacterium Synechocystis sp. PCC 6803. Based on statistical tests, expression levels of about 20% of genes in Synechocystis 6803 are identified as significantly affected due to influence of high light. Gene clustering methods reveal that these responses can mainly be classified as transient and consistent responses, depending on the duration of modified behaviors. Many genes related to energy production as well as energy utilization are shown to be strongly affected. Analysis of microarray data under two stress conditions, high light and DCMU treatment, combined with data mining and motif finding algorithms led to a discovery of novel transcription factor, RRTF1 that responds to redox stresses in Arabidopsis thaliana. Time course transcriptomics data from Cyanothece sp. ATCC 51142 have shown strong diurnal rhythms. By combining multiple experimental conditions and using gene classification algorithms based on Fourier scores and angular distances, it is shown that majority of the diurnal genes are in fact light responding. Only about 10% of genes in the genome are categorized as being circadian controlled. A transcription control model based on dynamical systems is employed to identify the interactions between diurnal genes. A phase oscillator network is proposed to model the behavior of different biological processes. Both these models are shown to carry biologically meaningful features. To study the coordination between different biological processes to various environment and genetic modifications, an interaction model is derived using Bayesian network approach, combining all publicly available microarray data sets for Synechocystis sp. PCC 6803. Several novel relationships between biological processes are discovered from the model. Model is used to simulate several experimental conditions, and the response of the model is shown to agree with the experimentally observed behaviors

Machine Learning Methods with Noisy, Incomplete or Small Datasets

In many machine learning applications, available datasets are sometimes incomplete, noisy or affected by artifacts. In supervised scenarios, it could happen that label information has low quality, which might include unbalanced training sets, noisy labels and other problems. Moreover, in practice, it is very common that available data samples are not enough to derive useful supervised or unsupervised classifiers. All these issues are commonly referred to as the low-quality data problem. This book collects novel contributions on machine learning methods for low-quality datasets, to contribute to the dissemination of new ideas to solve this challenging problem, and to provide clear examples of application in real scenarios

Cortical patterns and gamma genesis are modulated by reversal potentials and gap-junction diffusion

In this chapter we describe a continuum model for the cortex that includes both axon-to-dendrite chemical synapses and direct neuron-to-neuron gap-junction diffusive synapses. The effectiveness of chemical synapses is determined by the voltage of the receiving dendrite V relative to its Nernst reversal potential Vrev. Here we explore two alternative strategies for incorporating dendritic reversal potentials, and uncover surprising differences in their stability properties and model dynamics. In the “slow-soma” variant, the (Vrev - V) weighting is applied after the input flux has been integrated at the dendrite, while for “fast-soma”, the weighting is applied directly to the input flux, prior to dendritic integration. For the slow-soma case, we find that–-provided the inhibitory diffusion (via gap-junctions) is sufficiently strong–-the cortex generates stationary Turing patterns of cortical activity. In contrast, the fast-soma destabilizes in favor of standing-wave spatial structures that oscillate at low-gamma frequency ( 30-Hz); these spatial patterns broaden and weaken as diffusive coupling increases, and disappear altogether at moderate levels of diffusion. We speculate that the slow- and fast-soma models might correspond respectively to the idling and active modes of the cortex, with slow-soma patterns providing the default background state, and emergence of gamma oscillations in the fast-soma case signaling the transition into the cognitive state

Maturation trajectories of cortical resting-state networks depend on the mediating frequency band

The functional significance of resting state networks and their abnormal manifestations in psychiatric disorders are firmly established, as is the importance of the cortical rhythms in mediating these networks. Resting state networks are known to undergo substantial reorganization from childhood to adulthood, but whether distinct cortical rhythms, which are generated by separable neural mechanisms and are often manifested abnormally in psychiatric conditions, mediate maturation differentially, remains unknown. Using magnetoencephalography (MEG) to map frequency band specific maturation of resting state networks from age 7 to 29 in 162 participants (31 independent), we found significant changes with age in networks mediated by the beta (13–30 Hz) and gamma (31–80 Hz) bands. More specifically, gamma band mediated networks followed an expected asymptotic trajectory, but beta band mediated networks followed a linear trajectory. Network integration increased with age in gamma band mediated networks, while local segregation increased with age in beta band mediated networks. Spatially, the hubs that changed in importance with age in the beta band mediated networks had relatively little overlap with those that showed the greatest changes in the gamma band mediated networks. These findings are relevant for our understanding of the neural mechanisms of cortical maturation, in both typical and atypical development.This work was supported by grants from the Nancy Lurie Marks Family Foundation (TK, SK, MGK), Autism Speaks (TK), The Simons Foundation (SFARI 239395, TK), The National Institute of Child Health and Development (R01HD073254, TK), National Institute for Biomedical Imaging and Bioengineering (P41EB015896, 5R01EB009048, MSH), and the Cognitive Rhythms Collaborative: A Discovery Network (NFS 1042134, MSH). (Nancy Lurie Marks Family Foundation; Autism Speaks; SFARI 239395 - Simons Foundation; R01HD073254 - National Institute of Child Health and Development; P41EB015896 - National Institute for Biomedical Imaging and Bioengineering; 5R01EB009048 - National Institute for Biomedical Imaging and Bioengineering; NFS 1042134 - Cognitive Rhythms Collaborative: A Discovery Network