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Granger causality

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https://www.readbyqxmd.com/read/29440433/windowed-granger-causal-inference-strategy-improves-discovery-of-gene-regulatory-networks
#1
Justin D Finkle, Jia J Wu, Neda Bagheri
Accurate inference of regulatory networks from experimental data facilitates the rapid characterization and understanding of biological systems. High-throughput technologies can provide a wealth of time-series data to better interrogate the complex regulatory dynamics inherent to organisms, but many network inference strategies do not effectively use temporal information. We address this limitation by introducing Sliding Window Inference for Network Generation (SWING), a generalized framework that incorporates multivariate Granger causality to infer network structure from time-series data...
February 12, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29434570/perspectives-on-how-human-simultaneous-multi-modal-imaging-adds-directionality-to-spread-models-of-alzheimer-s-disease
#2
Julia Neitzel, Rachel Nuttall, Christian Sorg
Previous animal research suggests that the spread of pathological agents in Alzheimer's disease (AD) follows the direction of signaling pathways. Specifically, tau pathology has been suggested to propagate in an infection-like mode along axons, from transentorhinal cortices to medial temporal lobe cortices and consequently to other cortical regions, while amyloid-beta (Aβ) pathology seems to spread in an activity-dependent manner among and from isocortical regions into limbic and then subcortical regions. These directed connectivity-based spread models, however, have not been tested directly in AD patients due to the lack of an in vivo method to identify directed connectivity in humans...
2018: Frontiers in Neurology
https://www.readbyqxmd.com/read/29416530/-time-a-web-application-for-obtaining-insights-into-microbial-ecology-using-longitudinal-microbiome-data
#3
Krishanu D Baksi, Bhusan K Kuntal, Sharmila S Mande
Realization of the importance of microbiome studies, coupled with the decreasing sequencing cost, has led to the exponential growth of microbiome data. A number of these microbiome studies have focused on understanding changes in the microbial community over time. Such longitudinal microbiome studies have the potential to offer unique insights pertaining to the microbial social networks as well as their responses to perturbations. In this communication, we introduce a web based framework called 'TIME' (Temporal Insights into Microbial Ecology'), developed specifically to obtain meaningful insights from microbiome time series data...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29398362/small-networks-encode-decision-making-in-primary-auditory-cortex
#4
Nikolas A Francis, Daniel E Winkowski, Alireza Sheikhattar, Kevin Armengol, Behtash Babadi, Patrick O Kanold
Sensory detection tasks enhance representations of behaviorally meaningful stimuli in primary auditory cortex (A1). However, it remains unclear how A1 encodes decision-making. Neurons in A1 layer 2/3 (L2/3) show heterogeneous stimulus selectivity and complex anatomical connectivity, and receive input from prefrontal cortex. Thus, task-related modulation of activity in A1 L2/3 might differ across subpopulations. To study the neural coding of decision-making, we used two-photon imaging in A1 L2/3 of mice performing a tone-detection task...
January 30, 2018: Neuron
https://www.readbyqxmd.com/read/29390625/causality-analysis-of-leading-singular-value-decomposition-modes-identifies-rotor-as-the-dominant-driving-normal-mode-in-fibrillation
#5
Yaacov Biton, Avinoam Rabinovitch, Doron Braunstein, Ira Aviram, Katherine Campbell, Sergey Mironov, Todd Herron, José Jalife, Omer Berenfeld
Cardiac fibrillation is a major clinical and societal burden. Rotors may drive fibrillation in many cases, but their role and patterns are often masked by complex propagation. We used Singular Value Decomposition (SVD), which ranks patterns of activation hierarchically, together with Wiener-Granger causality analysis (WGCA), which analyses direction of information among observations, to investigate the role of rotors in cardiac fibrillation. We hypothesized that combining SVD analysis with WGCA should reveal whether rotor activity is the dominant driving force of fibrillation even in cases of high complexity...
January 2018: Chaos
https://www.readbyqxmd.com/read/29382021/altered-effective-connectivity-of-resting-state-networks-by-acupuncture-stimulation-in-stroke-patients-with-left-hemiplegia-a-multivariate-granger-analysis
#6
Cai-Hong Fu, Kuang-Shi Li, Yan-Zhe Ning, Zhong-Jian Tan, Yong Zhang, Hong-Wei Liu, Xiao Han, Yi-Huai Zou
The aim of this study was to explore the response feature of resting-state networks (RSNs) of stroke patients with left hemiplegia by acupuncture stimulation.Nineteen stroke patients with left hemiplegia and 17 controls were recruited in this study. Resting-state functional magnetic resonance imaging data before and after acupuncture were acquired using magnetic scanning. The independent component analysis (ICA) was employed to extract RSNs related to motion, sensation, cognition, and execution, including sensorimotor network (SMN), left and right frontoparietal network (LFPN and RFPN), anterior and posterior default mode network (aDMN, pDMN), visual network (VN), and salience network (SN)...
November 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29361582/auditory-neural-networks-for-attention-prefer-biologically-significant-sounds-and-exhibit-sexual-dimorphism-in-anurans
#7
Fei Xue, Xizi Yue, Yanzhu Fan, Jianguo Cui, Steven E Brauth, Yezhong Tang, Guangzhan Fang
Allocating attention to biologically relevant stimuli in a complex environment is critically important for survival and reproductive success. In humans attention modulation is regulated by the frontal cortex, and often reflected by changes in specific components of the event-related potential (ERP). Although brain networks for attention modulation have been widely studied in primates and in avian species, little is known about attention modulation in amphibians. The present study aims to investigate the attention modulation networks in an anuran species, the Emei music frog (Babina daunchina)...
January 4, 2018: Journal of Experimental Biology
https://www.readbyqxmd.com/read/29357273/progressive-reduction-in-gray-matter-in-patients-with-schizophrenia-assessed-with-mr-imaging-by-using-causal-network-analysis
#8
Yuchao Jiang, Cheng Luo, Xin Li, Mingjun Duan, Hui He, Xi Chen, Hang Yang, Jinnan Gong, Xin Chang, Marie Woelfer, Bharat B Biswal, Dezhong Yao
Purpose To investigate the temporal and causal relationships of structural changes in the brain in patients with schizophrenia. Materials and Methods T1-weighted magnetic resonance (MR) images of 97 patients with schizophrenia (29 women; mean ± standard deviation age, 41 years ± 11.5; range, 16-66 years; illness duration, 16.3 years ± 10.9; range, 0-50 years) and 126 age- and sex-matched (38 years ± 14.9; range, 18-68 years; 42 women) healthy control subjects were evaluated. The causal network of structural covariance was used to assess the causal relationships of structural changes in patients with schizophrenia...
January 19, 2018: Radiology
https://www.readbyqxmd.com/read/29354856/is-trade-openness-good-for-environment-in-south-korea-the-role-of-non-fossil-electricity-consumption
#9
Shun Zhang
The paper investigates the linkage of carbon dioxide (CO2) emissions, per capita real output, share of non-fossil electricity consumption, and trade openness in South Korea from 1971 to 2013. The empirical results indicate that the environmental Kuznets curve (EKC) is supported by autoregressive distributed lag (ARDL) test. Both short- and long-run estimates indicate that increasing non-fossil electricity consumption can mitigate environmental degradation, and increasing trade aggravates carbon dioxide emissions...
January 21, 2018: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/29352226/spatio-temporal-characteristics-of-urban-air-pollutions-and-their-causal-relationships-evidence-from-beijing-and-its-neighboring-cities
#10
Lei Jiang, Ling Bai
China has been suffering from serious air pollution for years in response to the rapid industrialization and urbanization. Notably Beijing is one of the most polluted capitals in the world. Hence, the focus of the study area is on Beijing. In the first stage, we analyze spatial and temporal characteristics of air pollution of the 6 cities while in the second stage the Granger causality test is applied to investigate whether air pollution of a city is affected by its neighbors, and vice versa. The findings are the following...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29347576/multiscale-granger-causality
#11
Luca Faes, Giandomenico Nollo, Sebastiano Stramaglia, Daniele Marinazzo
In the study of complex physical and biological systems represented by multivariate stochastic processes, an issue of great relevance is the description of the system dynamics spanning multiple temporal scales. While methods to assess the dynamic complexity of individual processes at different time scales are well established, multiscale analysis of directed interactions has never been formalized theoretically, and empirical evaluations are complicated by practical issues such as filtering and downsampling...
October 2017: Physical Review. E
https://www.readbyqxmd.com/read/29304085/a-new-test-of-multivariate-nonlinear-causality
#12
Zhidong Bai, Yongchang Hui, Dandan Jiang, Zhihui Lv, Wing-Keung Wong, Shurong Zheng
The multivariate nonlinear Granger causality developed by Bai et al. (2010) (Mathematics and Computers in simulation. 2010; 81: 5-17) plays an important role in detecting the dynamic interrelationships between two groups of variables. Following the idea of Hiemstra-Jones (HJ) test proposed by Hiemstra and Jones (1994) (Journal of Finance. 1994; 49(5): 1639-1664), they attempt to establish a central limit theorem (CLT) of their test statistic by applying the asymptotical property of multivariate U-statistic...
2018: PloS One
https://www.readbyqxmd.com/read/29288874/modeling-spike-wave-discharges-by-a-complex-network-of-neuronal-oscillators
#13
Tatiana M Medvedeva, Marina V Sysoeva, Gilles van Luijtelaar, Ilya V Sysoev
PURPOSE: The organization of neural networks and the mechanisms, which generate the highly stereotypical for absence epilepsy spike-wave discharges (SWDs) is heavily debated. Here we describe such a model which can both reproduce the characteristics of SWDs and dynamics of coupling between brain regions, relying mainly on properties of hierarchically organized networks of a large number of neuronal oscillators. MODEL: We used a two level mesoscale model. The first level consists of three structures: the nervus trigeminus serving as an input, the thalamus and the somatosensory cortex; the second level of a group of nearby situated neurons belonging to one of three modeled structures...
December 13, 2017: Neural Networks: the Official Journal of the International Neural Network Society
https://www.readbyqxmd.com/read/29238300/supervised-estimation-of-granger-based-causality-between-time-series
#14
Danilo Benozzo, Emanuele Olivetti, Paolo Avesani
Brain effective connectivity aims to detect causal interactions between distinct brain units and it is typically studied through the analysis of direct measurements of the neural activity, e.g., magneto/electroencephalography (M/EEG) signals. The literature on methods for causal inference is vast. It includes model-based methods in which a generative model of the data is assumed and model-free methods that directly infer causality from the probability distribution of the underlying stochastic process. Here, we firstly focus on the model-based methods developed from the Granger criterion of causality, which assumes the autoregressive model of the data...
2017: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/29235027/a-study-on-the-causal-effect-of-urban-population-growth-and-international-trade-on-environmental-pollution-evidence-from-china
#15
Kofi Baah Boamah, Jianguo Du, Angela Jacinta Boamah, Kingsley Appiah
This study seeks to contribute to the recent literature by empirically investigating the causal effect of urban population growth and international trade on environmental pollution of China, for the period 1980-2014. The Johansen cointegration confirmed a long-run cointegration association among the utilised variables for the case of China. The direction of causality among the variables was, consequently, investigated using the recent bootstrapped Granger causality test. This bootstrapped Granger causality approach is preferred as it provides robust and accurate critical values for statistical inferences...
December 12, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/29226709/enhanced-brain-network-activity-in-complex-movement-rhythms-a-simultaneous-fmri-eeg-study
#16
Bhim Mani Adhikari, Charles M Epstein, Mukesh Dhamala
Generating movement rhythms is known to involve a network of distributed brain regions associated with motor planning, control, execution, and perception of timing for the repertoire of motor actions. What brain areas are bound in the network and how the network activity is modulated by rhythmic complexity have not been completely explored. To contribute to answering these questions, we designed a study in which nine healthy participants performed simple to complex rhythmic finger movement tasks while undergoing simultaneous functional magnetic resonance imaging and electroencephalography (fMRI-EEG) recordings of their brain activity during the tasks and rest...
December 10, 2017: Brain Connectivity
https://www.readbyqxmd.com/read/29224721/synergistic-processing-of-visual-contours-across-cortical-layers-in-v1-and-v2
#17
Rujia Chen, Feng Wang, Hualou Liang, Wu Li
Visual cortical areas are interconnected via layer-specific feedforward and feedback projections. Such intricate connections are thought to be essential for parsing complex visual images, but the synergy among different layers in different cortical areas remains unclear. By simultaneously mapping neuronal activities across cortical depths in V1 and V2 of behaving monkeys, we identified spatiotemporally dissociable processes for grouping contour fragments and segregating background components. These processes generated and amplified contour signals within specific layers in V1 and V2...
November 17, 2017: Neuron
https://www.readbyqxmd.com/read/29211761/prophetic-granger-causality-to-infer-gene-regulatory-networks
#18
Daniel E Carlin, Evan O Paull, Kiley Graim, Christopher K Wong, Adrian Bivol, Peter Ryabinin, Kyle Ellrott, Artem Sokolov, Joshua M Stuart
We introduce a novel method called Prophetic Granger Causality (PGC) for inferring gene regulatory networks (GRNs) from protein-level time series data. The method uses an L1-penalized regression adaptation of Granger Causality to model protein levels as a function of time, stimuli, and other perturbations. When combined with a data-independent network prior, the framework outperformed all other methods submitted to the HPN-DREAM 8 breast cancer network inference challenge. Our investigations reveal that PGC provides complementary information to other approaches, raising the performance of ensemble learners, while on its own achieves moderate performance...
2017: PloS One
https://www.readbyqxmd.com/read/29204686/weather-conditions-influence-the-number-of-psychiatric-emergency-room-patients
#19
Eva Janina Brandl, Tristram A Lett, George Bakanidze, Andreas Heinz, Felix Bermpohl, Meryam Schouler-Ocak
The specific impact of weather factors on psychiatric disorders has been investigated only in few studies with inconsistent results. We hypothesized that meteorological conditions influence the number of cases presenting in a psychiatric emergency room as a measure of mental health conditions. We analyzed the number of patients consulting the emergency room (ER) of a psychiatric hospital in Berlin, Germany, between January 1, 2008, and December 31, 2014. A total of N = 22,672 cases were treated in the ER over the study period...
December 4, 2017: International Journal of Biometeorology
https://www.readbyqxmd.com/read/29190523/electromagnetic-source-imaging-using-simultaneous-scalp-eeg-and-intracranial-eeg-an-emerging-tool-for-interacting-with-pathological-brain-networks
#20
Seyed Amir Hossein Hosseini, Abbas Sohrabpour, Bin He
OBJECTIVE: The goal of this study is to investigate the performance, merits and limitations of source imaging using intracranial EEG (iEEG) recordings and to compare its accuracy to the results of EEG source imaging. Accuracy in this study, is measured both by determining the location and inter-nodal connectivity of underlying brain networks. METHODS: Systematic computer simulation studies are conducted to evaluate iEEG-based source imaging vs. EEG-based source imaging, and source imaging using both EEG and iEEG...
November 7, 2017: Clinical Neurophysiology: Official Journal of the International Federation of Clinical Neurophysiology
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