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Granger causality

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https://www.readbyqxmd.com/read/28222234/transcriptome-analysis-of-the-brassica-napus-leptosphaeria-maculans-pathosystem-identifies-receptor-signalling-and-structural-genes-underlying-plant-resistance
#1
Michael G Becker, Xuehua Zhang, Philip L Walker, Joey C Wan, Jenna L Millar, Deirdre Khan, Matthew J Granger, Jacob D Cavers, Ainsley C Chan, Dilantha W G Fernando, Mark F Belmonte
The hemibiotrophic fungal pathogen Leptosphaeria maculans is the causal agent of blackleg disease in Brassica napus (canola, oilseed rape) and causes significant yield loss worldwide. While genetic resistance has been used to mitigate the disease using traditional breeding strategies, there is little knowledge about the genes contributing to blackleg resistance. RNA sequencing and a streamlined bioinformatics pipeline identified unique genes and plant defense pathways specific to plant resistance in the B. napus-L...
February 21, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28215697/directed-network-discovery-with-dynamic-network-modeling
#2
Stefano Anzellotti, Dorit Kliemann, Nir Jacoby, Rebecca Saxe
Cognitive tasks recruit multiple brain regions. Understanding how these regions influence each other (the network structure) is an important step to characterize the neural basis of cognitive processes. Often, limited evidence is available to restrict the range of hypotheses a priori, and techniques that sift efficiently through a large number of possible network structures are needed (network discovery). This article introduces a novel modeling technique for network discovery (Dynamic Network Modeling or DNM) that builds on ideas from Granger Causality and Dynamic Causal Modeling introducing three key changes: (1) efficient network discovery is implemented with statistical tests on the consistency of model parameters across participants, (2) the tests take into account the magnitude and sign of each influence, and (3) variance explained in independent data is used as an absolute (rather than relative) measure of the quality of the network model...
February 16, 2017: Neuropsychologia
https://www.readbyqxmd.com/read/28212570/altered-amygdala-and-hippocampus-effective-connectivity-in-mild-cognitive-impairment-patients-with-depression-a-resting-state-functional-mr-imaging-study-with-granger-causality-analysis
#3
Li Juan Zheng, Gui Fen Yang, Xin Yuan Zhang, Yun Fei Wang, Ya Liu, Gang Zheng, Guang Ming Lu, Long Jiang Zhang, Ying Han
Neuroimaging studies have demonstrated that the major depression disorder would increase the risk of dementia in the older with amnestic cognitive impairment. We used granger causality analysis algorithm to explore the amygdala- and hippocampus-based directional connectivity patterns in 12 patients with major depression disorder and amnestic cognitive impairment (mean age: 69.5 ± 10.3 years), 13 amnestic cognitive impairment patients (mean age: 72.7 ± 8.5 years) and 14 healthy controls (mean age: 64.7 ± 7...
February 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28207288/equivalent-dynamic-models
#4
Peter C M Molenaar
Equivalences of two classes of dynamic models for weakly stationary multivariate time series are discussed: dynamic factor models and autoregressive models. It is shown that exploratory dynamic factor models can be rotated, yielding an infinite set of equivalent solutions for any observed series. It also is shown that dynamic factor models with lagged factor loadings are not equivalent to the currently popular state-space models, and that restriction of attention to the latter type of models may yield invalid results...
February 16, 2017: Multivariate Behavioral Research
https://www.readbyqxmd.com/read/28194095/altered-hippocampo-cerebello-cortical-circuit-in-schizophrenia-by-a-spatiotemporal-consistency-and-causal-connectivity-analysis
#5
Xi Chen, Yuchao Jiang, Lin Chen, Hui He, Li Dong, Changyue Hou, Mingjun Duan, Mi Yang, Dezhong Yao, Cheng Luo
In the current study, FOur-dimensional Consistency of local neural Activities (FOCA) analysis was used to investigate the local consistency by integrating the temporal and spatial information of the local region. In the current study, resting-state fMRI data of 69 schizophrenia patients and 70 healthy controls were collected. FOCA was utilized to investigate the local consistency. Moreover, Granger causal analysis was used to investigate causal functional connectivity among these areas, which exhibited significantly different local consistency between groups...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28169987/theta-and-beta-synchrony-coordinate-frontal-eye-fields-and-anterior-cingulate-cortex-during-sensorimotor-mapping
#6
Sahand Babapoor-Farrokhran, Martin Vinck, Thilo Womelsdorf, Stefan Everling
The frontal eye fields (FEFs) and the anterior cingulate cortex (ACC) are commonly coactivated for cognitive saccade tasks, but whether this joined activation indexes coordinated activity underlying successful guidance of sensorimotor mapping is unknown. Here we test whether ACC and FEF circuits coordinate through phase synchronization of local field potential and neural spiking activity in macaque monkeys performing memory-guided and pro- and anti-saccades. We find that FEF and ACC showed prominent synchronization at a 3-9 Hz theta and a 12-30 Hz beta frequency band during the delay and preparation periods with a strong Granger-causal influence from ACC to FEF...
February 7, 2017: Nature Communications
https://www.readbyqxmd.com/read/28167926/disrupted-causal-connectivity-anchored-in-the-posterior-cingulate-cortex-in-amnestic-mild-cognitive-impairment
#7
Hong Yang, Chengwei Wang, Yumei Zhang, Liming Xia, Zhan Feng, Deqiang Li, Shunliang Xu, Haiyan Xie, Feng Chen, Yushu Shi, Jue Wang
Amnestic mild cognitive impairment (aMCI) is a transitional stage between normal cognitive aging and Alzheimer's disease. Previous studies have found that neuronal activity and functional connectivity impaired in many functional networks, especially in the default mode network (DMN), which is related to significantly impaired cognitive and memory functions in aMCI patients. However, few studies have focused on the effective connectivity of the DMN and its subsystems in aMCI patients. The posterior cingulate cortex (PCC) is considered a crucial region in connectivity of the DMN and its key subsystem...
2017: Frontiers in Neurology
https://www.readbyqxmd.com/read/28138530/feedforward-and-feedback-frequency-dependent-interactions-in-a-large-scale-laminar-network-of-the-primate-cortex
#8
Jorge F Mejias, John D Murray, Henry Kennedy, Xiao-Jing Wang
Interactions between top-down and bottom-up processes in the cerebral cortex hold the key to understanding attentional processes, predictive coding, executive control, and a gamut of other brain functions. However, the underlying circuit mechanism remains poorly understood and represents a major challenge in neuroscience. We approached this problem using a large-scale computational model of the primate cortex constrained by new directed and weighted connectivity data. In our model, the interplay between feedforward and feedback signaling depends on the cortical laminar structure and involves complex dynamics across multiple (intralaminar, interlaminar, interareal, and whole cortex) scales...
November 2016: Science Advances
https://www.readbyqxmd.com/read/28125912/olfactory-network-differences-in-master-sommeliers-connectivity-analysis-using-granger-causality-and-graph-theoretical-approach
#9
Karthik R Sreenivasan, Xiaowei Zhuang, Sarah Banks, Virendra Mishra, Zhengshi Yang, Gopikrishna Deshpande, Dietmar Cordes
Previous studies investigating the differences in olfactory processing and judgments between trained sommeliers and controls have shown increased activations in brain regions involving higher-level cognitive processes in sommeliers. However, there is little information about the influence of expertise on causal connectivity and topological properties of the connectivity networks between these regions. Therefore, the current study focuses on addressing these questions in a functional magnetic resonance imaging (fMRI) study of olfactory perception in Master Sommeliers...
January 26, 2017: Brain Connectivity
https://www.readbyqxmd.com/read/28113234/synergetic-and-redundant-information-flow-detected-by-unnormalized-granger-causality-application-to-resting-state-fmri
#10
Sebastiano Stramaglia, Leonardo Angelini, Guorong Wu, Jesus M Cortes, Luca Faes, Daniele Marinazzo
OBJECTIVES: We develop a framework for the analysis of synergy and redundancy in the pattern of information flow between subsystems of a complex network. METHODS: The presence of redundancy and/or synergy in multivariate time series data renders difficult to estimate the neat flow of information from each driver variable to a given target. We show that adopting an unnormalized definition of Granger causality one may put in evidence redundant multiplets of variables influencing the target by maximizing the total Granger causality to a given target, over all the possible partitions of the set of driving variables...
April 28, 2016: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28113204/noninvasive-electromagnetic-source-imaging-and-granger-causality-analysis-an-electrophysiological-connectome-econnectome-approach
#11
Abbas Sohrabpour, Shuai Ye, Gregory A Worrell, Wenbo Zhang, Bin He
: Combined source imaging techniques and directional connectivity analysis can provide useful information about the underlying brain networks in a noninvasive fashion. Source imaging techniques have been used successfully to either determine the source of activity or to extract source time-courses for Granger causality analysis, previously. In this work, we utilize source imaging algorithms to both find the network nodes (regions of interest) and then extract the activation time series for further Granger causality analysis...
October 11, 2016: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28112466/tinnitus-distress-is-linked-to-enhanced-resting-state-functional-connectivity-from-the-limbic-system-to-the-auditory-cortex
#12
Yu-Chen Chen, Wenqing Xia, Huiyou Chen, Yuan Feng, Jin-Jing Xu, Jian-Ping Gu, Richard Salvi, Xindao Yin
The phantom sound of tinnitus is believed to be triggered by aberrant neural activity in the central auditory pathway, but since this debilitating condition is often associated with emotional distress and anxiety, these comorbidities likely arise from maladaptive functional connections to limbic structures such as the amygdala and hippocampus. To test this hypothesis, resting-state functional magnetic resonance imaging (fMRI) was used to identify aberrant effective connectivity of the amygdala and hippocampus in tinnitus patients and to determine the relationship with tinnitus characteristics...
January 23, 2017: Human Brain Mapping
https://www.readbyqxmd.com/read/28108924/the-nexus-of-oil-consumption-co2-emissions-and-economic-growth-in-china-japan-and-south-korea
#13
Behnaz Saboori, Ehsan Rasoulinezhad, Jinsok Sung
This article attempts to explore the nexus between oil consumption, economic growth and carbon dioxide (CO2) emissions in three East Asian oil importing countries (i.e. China, South Korea and Japan) over the period 1980-2013, by using the Granger causality, Johansen cointegration test, Generalised Impulse Response functions (GIRF) and variance decompositions. The empirical findings provide evidence for the existence of a long-run relationship between oil consumption and economic growth in China and Japan. The results also point to a uni-directional causality from running from oil consumption to economic growth in China and Japan, and from oil consumption to CO2 emissions in South Korea...
January 20, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28097334/the-role-of-cardiovascular-implantable-electronic-devices-in-the-detection-and-treatment-of-subclinical-atrial-fibrillation-a-review
#14
Paul L Hess, Jeff S Healey, Christopher B Granger, Stuart J Connolly, Paul D Ziegler, John H Alexander, Peter R Kowey, Christian T Ruff, Greg Flaker, Jonathan L Halperin, Robert G Hart, Renato D Lopes
Importance: Subclinical atrial fibrillation (AF) is associated with an increased risk for stroke. Observations: Subclinical AF is asymptomatic, short in duration, and usually detected with long-term, continuous monitoring. Most prior studies have explored its consequences using cardiovascular implantable electronic devices (CIEDs). Although current prevalence estimates are derived from study populations with prior CIEDs, 3 trials will assess the time to a first AF diagnosis among patients receiving a CIED for purposes of AF detection...
January 11, 2017: JAMA Cardiology
https://www.readbyqxmd.com/read/28090665/can-patel-s-%C3%AF-accurately-estimate-directionality-of-connections-in-brain-networks-from-fmri
#15
Yunzhi Wang, Olivier David, Xiaoping Hu, Gopikrishna Deshpande
PURPOSE: Investigating directional interactions between brain regions plays a critical role in fully understanding brain function. Consequently, multiple methods have been developed for noninvasively inferring directional connectivity in human brain networks using functional MRI (fMRI). Recent simulations by Smith et al showed that Patel's τ, a method based on higher-order statistics, was the best approach for inferring directional interactions from fMRI. Because simulations make restrictive assumptions about reality, we set out to verify this finding using experimental fMRI data obtained from a three-region network in a rat model with electrophysiological validation...
January 16, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28079528/assessing-the-evolution-of-redundancy-synergy-of-spontaneous-variability-regulation-with-age
#16
Alberto Porta, Vlasta Bari, Beatrice De Maria, Natália Maria Perseguini, Juliana Milan, Patricia Rehder-Santos, Vinícius Minatel, Anielle Takahashi, Aparecida Catai
We exploited a model-based Wiener-Granger causality method in the information domain for the evaluation of the transfer entropy (TE) and interaction TE (ITE), the latter taken as a measure of the net balance between redundancy and synergy, to describe the interactions between the spontaneous variability of heart period (HP) and systolic arterial pressure (SAP) and the effect of respiration (R) on both variables. Cardiac control was typified via the genuine TE from SAP to HP, that from R to HP, and the ITE from SAP and R to HP, while vascular control was characterized via the genuine TE from HP to SAP, that from R to SAP, and the ITE from HP and R to SAP...
January 12, 2017: Physiological Measurement
https://www.readbyqxmd.com/read/28077184/abnormalities-in-the-effective-connectivity-of-visuothalamic-circuitry-in-schizophrenia
#17
S J Iwabuchi, L Palaniyappan
BACKGROUND: Sensory-processing deficits appear crucial to the clinical expression of symptoms of schizophrenia. The visual cortex displays both dysconnectivity and aberrant spontaneous activity in patients with persistent symptoms and cognitive deficits. In this paper, we examine visual cortex in the context of the remerging notion of thalamic dysfunction in schizophrenia. We examined specific regional and longer-range abnormalities in sensory and thalamic circuits in schizophrenia, and whether these patterns are strong enough to discriminate symptomatic patients from controls...
January 12, 2017: Psychological Medicine
https://www.readbyqxmd.com/read/28065836/learning-effective-connectivity-from-fmri-using-autoregressive-hidden-markov-model-with-missing-data
#18
Shilpa Dang, Santanu Chaudhury, Brejesh Lall, Prasun Kumar Roy
BACKGROUND: Effective connectivity (EC) analysis of neuronal groups using fMRI delivers insights about functional-integration. However, fMRI signal has low-temporal resolution due to down-sampling and indirectly measures underlying neuronal activity. NEW METHOD: The aim is to address above issues for more reliable EC estimates. This paper proposes use of autoregressive hidden Markov model with missing data (AR-HMM-md) in dynamically multi-linked (DML) framework for learning EC using multiple fMRI time series...
January 5, 2017: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/27977564/vector-autoregressive-models-and-granger-causality-in-time-series-analysis-in-nursing-research-dynamic-changes-among-vital-signs-prior-to-cardiorespiratory-instability-events-as-an-example
#19
Eliezer Bose, Marilyn Hravnak, Susan M Sereika
BACKGROUND: Patients undergoing continuous vital sign monitoring (heart rate [HR], respiratory rate [RR], pulse oximetry [SpO2]) in real time display interrelated vital sign changes during situations of physiological stress. Patterns in this physiological cross-talk could portend impending cardiorespiratory instability (CRI). Vector autoregressive (VAR) modeling with Granger causality tests is one of the most flexible ways to elucidate underlying causal mechanisms in time series data...
January 2017: Nursing Research
https://www.readbyqxmd.com/read/27967128/testing-for-causality-in-reconstructed-state-spaces-by-an-optimized-mixed-prediction-method
#20
Anna Krakovská, Filip Hanzely
In this study, a method of causality detection was designed to reveal coupling between dynamical systems represented by time series. The method is based on the predictions in reconstructed state spaces. The results of the proposed method were compared with outcomes of two other methods, the Granger VAR test of causality and the convergent cross-mapping. We used two types of test data. The first test example is a unidirectional connection of chaotic systems of Rössler and Lorenz type. The second one, the fishery model, is an example of two correlated observables without a causal relationship...
November 2016: Physical Review. E
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