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https://www.readbyqxmd.com/read/29675146/efficient-prediction-of-reaction-paths-through-molecular-graph-and-reaction-network-analysis
#1
Yeonjoon Kim, Jin Woo Kim, Zeehyo Kim, Woo Youn Kim
Despite remarkable advances in computational chemistry, prediction of reaction mechanisms is still challenging, because investigating all possible reaction pathways is computationally prohibitive due to the high complexity of chemical space. A feasible strategy for efficient prediction is to utilize chemical heuristics. Here, we propose a novel approach to rapidly search reaction paths in a fully automated fashion by combining chemical theory and heuristics. A key idea of our method is to extract a minimal reaction network composed of only favorable reaction pathways from the complex chemical space through molecular graph and reaction network analysis...
January 28, 2018: Chemical Science
https://www.readbyqxmd.com/read/29670045/what-we-know-about-the-brain-structure-function-relationship
#2
REVIEW
Karla Batista-García-Ramó, Caridad Ivette Fernández-Verdecia
How the human brain works is still a question, as is its implication with brain architecture: the non-trivial structure–function relationship. The main hypothesis is that the anatomic architecture conditions, but does not determine, the neural network dynamic. The functional connectivity cannot be explained only considering the anatomical substrate. This involves complex and controversial aspects of the neuroscience field and that the methods and methodologies to obtain structural and functional connectivity are not always rigorously applied...
April 18, 2018: Behavioral Sciences
https://www.readbyqxmd.com/read/29668696/the-minimal-abc-trees-with-b1-branches
#3
Darko Dimitrov, Zhibin Du, Carlos M da Fonseca
The atom-bond connectivity index (or, for short, ABC index) is a molecular structure descriptor bridging chemistry to graph theory. It is probably the most studied topological index among all numerical parameters of a graph that characterize its topology. For a given graph G = (V, E), the ABC index of G is defined as [Formula: see text], where di denotes the degree of the vertex i, and ij is the edge incident to the vertices i and j. A combination of physicochemical and the ABC index properties are commonly used to foresee the bioactivity of different chemical composites...
2018: PloS One
https://www.readbyqxmd.com/read/29664012/current-phase-relation-from-graphs-and-diagrams-and-application-to-thick-ferromagnetic-josephson-junctions
#4
I Margaris, V Paltoglou, N Flytzanis
In this work we present a method of representing terms in the current-phase-relation of a ballistic Josephson junction by combinations of diagrams, used in previous work to represent an equivalent of the matching condition determinant of the junction. This is accomplished by the expansion of the logarithm of this determinant in Taylor series and keeping track of surviving terms, i.e. terms that do not annihilate each other. The types of the surviving terms are represented by connected graphs, whose points represent diagrammatic terms of the determinant expansion...
April 17, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/29662443/emotion-regulation-and-complex-brain-networks-association-between-expressive-suppression-and-efficiency-in-the-fronto-parietal-network-and-default-mode-network
#5
Junhao Pan, Liying Zhan, ChuanLin Hu, Junkai Yang, Cong Wang, Li Gu, Shengqi Zhong, Yingyu Huang, Qian Wu, Xiaolin Xie, Qijin Chen, Hui Zhou, Miner Huang, Xiang Wu
Emotion regulation (ER) refers to the "implementation of a conscious or non-conscious goal to start, stop or otherwise modulate the trajectory of an emotion" (Etkin et al., 2015). Whereas multiple brain areas have been found to be involved in ER, relatively little is known about whether and how ER is associated with the global functioning of brain networks. Recent advances in brain connectivity research using graph-theory based analysis have shown that the brain can be organized into complex networks composed of functionally or structurally connected brain areas...
2018: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/29651014/altered-connection-properties-of-important-network-hubs-may-be-neural-risk-factors-for-individuals-with-primary-insomnia
#6
Xuming Liu, Jiyong Zheng, Bi-Xia Liu, Xi-Jian Dai
Primary insomnia (PIs) is highly prevalent and can lead to adverse socioeconomic impacts, but the underlying mechanism of its complex brain network impairment remains largely unknown. Functional studies are too few and diverse in methodology, which makes it difficult to glean general conclusions. To answer this question, we first used graph theory-based network analyse, together with seed-based functional connectivity approach, to characterize the topology architecture of whole-brain functional networks associated with PIs...
April 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29624619/time-estimation-and-beta-segregation-an-eeg-study-and-graph-theoretical-approach
#7
Amir Hossein Ghaderi, Shadi Moradkhani, Arvin Haghighatfard, Fatemeh Akrami, Zahra Khayyer, Fuat Balcı
Elucidation of the neural correlates of time perception constitutes an important research topic in cognitive neuroscience. The focus to date has been on durations in the millisecond to seconds range, but here we used electroencephalography (EEG) to examine brain functional connectivity during much longer durations (i.e., 15 min). For this purpose, we conducted an initial exploratory experiment followed by a confirmatory experiment. Our results showed that those participants who overestimated time exhibited lower activity of beta (18-30 Hz) at several electrode sites...
2018: PloS One
https://www.readbyqxmd.com/read/29618992/fronto-temporal-connectivity-predicts-ect-outcome-in-major-depression
#8
Amber M Leaver, Benjamin Wade, Megha Vasavada, Gerhard Hellemann, Shantanu H Joshi, Randall Espinoza, Katherine L Narr
Background: Electroconvulsive therapy (ECT) is arguably the most effective available treatment for severe depression. Recent studies have used MRI data to predict clinical outcome to ECT and other antidepressant therapies. One challenge facing such studies is selecting from among the many available metrics, which characterize complementary and sometimes non-overlapping aspects of brain function and connectomics. Here, we assessed the ability of aggregated, functional MRI metrics of basal brain activity and connectivity to predict antidepressant response to ECT using machine learning...
2018: Frontiers in Psychiatry
https://www.readbyqxmd.com/read/29616603/snack-food-as-a-modulator-of-human-resting-state-functional-connectivity
#9
Andrea Mendez-Torrijos, Silke Kreitz, Claudiu Ivan, Laura Konerth, Julie Rösch, Monika Pischetsrieder, Gunther Moll, Oliver Kratz, Arnd Dörfler, Stefanie Horndasch, Andreas Hess
OBJECTIVE: To elucidate the mechanisms of how snack foods may induce non-homeostatic food intake, we used resting state functional magnetic resonance imaging (fMRI), as resting state networks can individually adapt to experience after short time exposures. In addition, we used graph theoretical analysis together with machine learning techniques (support vector machine) to identifying biomarkers that can categorize between high-caloric (potato chips) vs. low-caloric (zucchini) food stimulation...
April 4, 2018: CNS Spectrums
https://www.readbyqxmd.com/read/29601886/a-method-to-assess-randomness-of-functional-connectivity-matrices
#10
Victor M Vergara, Qingbao Yu, Vince D Calhoun
BACKGROUND: Functional magnetic resonance imaging (fMRI) allows for the measurement of functional connectivity of the brain. In this context, graph theory has revealed distinctive non-random connectivity patterns. However, the application of graph theory to fMRI often utilizes non-linear transformations (absolute value) to extract edge representations. NEW METHOD: In contrast, this work proposes a mathematical framework for the analysis of randomness directly from functional connectivity assessments...
March 27, 2018: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/29599714/clustering-coefficients-for-correlation-networks
#11
Naoki Masuda, Michiko Sakaki, Takahiro Ezaki, Takamitsu Watanabe
Graph theory is a useful tool for deciphering structural and functional networks of the brain on various spatial and temporal scales. The clustering coefficient quantifies the abundance of connected triangles in a network and is a major descriptive statistics of networks. For example, it finds an application in the assessment of small-worldness of brain networks, which is affected by attentional and cognitive conditions, age, psychiatric disorders and so forth. However, it remains unclear how the clustering coefficient should be measured in a correlation-based network, which is among major representations of brain networks...
2018: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/29596059/a-brain-age-model-for-preterm-infants-based-on-functional-connectivity
#12
Mario Lavanga, Ofelie De Wel, Alexander Caicedo Dorado, Katrien Jansen, Anneleen Dereymaeker, Gunnar Naulaers, Sabine Van Huffel
In this study, the development of EEG functional connectivity during early development has been investigated in order to provide a predictive age model for premature infants. The functional connectivity has been assessed via the coherency function (its imaginary part (<i>ImCoh</i>) and its mean squared magnitude (<i>MSC</i>)), the phase locking value (<i>PLV</i>) and the mutual information (<i>MI</i>) in a dataset of 30 patients, partially described and employed in previous studies...
March 29, 2018: Physiological Measurement
https://www.readbyqxmd.com/read/29564025/decoding-the-different-states-of-visual-attention-using-functional-and-effective-connectivity-features-in-fmri-data
#13
Behdad Parhizi, Mohammad Reza Daliri, Mehdi Behroozi
The present paper concentrates on the impact of visual attention task on structure of the brain functional and effective connectivity networks using coherence and Granger causality methods. Since most studies used correlation method and resting-state functional connectivity, the task-based approach was selected for this experiment to boost our knowledge of spatial and feature-based attention. In the present study, the whole brain was divided into 82 sub-regions based on Brodmann areas. The coherence and Granger causality were applied to construct functional and effective connectivity matrices...
April 2018: Cognitive Neurodynamics
https://www.readbyqxmd.com/read/29536173/task-and-domain-specific-modulation-of-functional-connectivity-in-the-ventral-and-dorsal-object-processing-pathways
#14
Frank E Garcea, Quanjing Chen, Roger Vargas, Darren A Narayan, Bradford Z Mahon
A whole-brain network of regions collectively supports the ability to recognize and use objects-the Tool Processing Network. Little is known about how functional interactions within the Tool Processing Network are modulated in a task-dependent manner. We designed an fMRI experiment in which participants were required to either generate object pantomimes or to carry out a picture matching task over the same images of tools, while holding all aspects of stimulus presentation constant across the tasks. The Tool Processing Network was defined with an independent functional localizer, and functional connectivity within the network was measured during the pantomime and picture matching tasks...
March 13, 2018: Brain Structure & Function
https://www.readbyqxmd.com/read/29535678/progressively-disrupted-brain-functional-connectivity-network-in-subcortical-ischemic-vascular-cognitive-impairment-patients
#15
Linqiong Sang, Lin Chen, Li Wang, Jingna Zhang, Ye Zhang, Pengyue Li, Chuanming Li, Mingguo Qiu
Cognitive impairment caused by subcortical ischemic vascular disease (SIVD) has been elucidated by many neuroimaging studies. However, little is known regarding the changes in brain functional connectivity networks in relation to the severity of cognitive impairment in SIVD. In the present study, 20 subcortical ischemic vascular cognitive impairment no dementia patients (SIVCIND) and 20 dementia patients (SIVaD) were enrolled; additionally, 19 normal controls were recruited. Each participant underwent a resting-state functional MRI scan...
2018: Frontiers in Neurology
https://www.readbyqxmd.com/read/29532601/alpine-glacial-relict-species-losing-out-to-climate-change-the-case-of-the-fragmented-mountain-hare-population-lepus-timidus-in-the-alps
#16
Maik Rehnus, Kurt Bollmann, Dirk R Schmatz, Klaus Hackländer, Veronika Braunisch
Alpine and Arctic species are considered to be particularly vulnerable to climate change, which is expected to cause habitat loss, fragmentation and-ultimately-extinction of cold-adapted species. However, the impact of climate change on glacial relict populations is not well understood, and specific recommendations for adaptive conservation management are lacking. We focused on the mountain hare (Lepus timidus) as a model species and modelled species distribution in combination with patch and landscape-based connectivity metrics...
March 13, 2018: Global Change Biology
https://www.readbyqxmd.com/read/29531963/modulating-the-resting-state-functional-connectivity-patterns-of-language-processing-areas-in-the-human-brain-with-anodal-transcranial-direct-current-stimulation-applied-over-the-broca-s-area
#17
Jianwei Cao, Hanli Liu, George Alexandrakis
Cortical circuit reorganization induced by anodal transcranial direct current stimulation (tDCS) over the Broca's area of the dominant language hemisphere in 13 healthy adults was quantified by functional near-infrared spectroscopy (fNIRS). Transient cortical reorganization patterns in steady-state functional connectivity (seed-based and graph theory analysis) and temporal functional connectivity (sliding window correlation analysis) were recorded before, during, and after applying high current tDCS (1 mA, 8 min)...
April 2018: Neurophotonics
https://www.readbyqxmd.com/read/29527484/alteration-of-brain-network-topology-in-hiv-associated-neurocognitive-disorder-a-novel-functional-connectivity-perspective
#18
Anas Z Abidin, Adora M DSouza, Mahesh B Nagarajan, Lu Wang, Xing Qiu, Giovanni Schifitto, Axel Wismüller
HIV is capable of invading the brain soon after seroconversion. This ultimately can lead to deficits in multiple cognitive domains commonly referred to as HIV-associated neurocognitive disorders (HAND). Clinical diagnosis of such deficits requires detailed neuropsychological assessment but clinical signs may be difficult to detect during asymptomatic injury of the central nervous system (CNS). Therefore neuroimaging biomarkers are of particular interest in HAND. In this study, we constructed brain connectivity profiles of 40 subjects (20 HIV positive subjects and 20 age-matched seronegative controls) using two different methods: a non-linear mutual connectivity analysis approach and a conventional method based on Pearson's correlation...
2018: NeuroImage: Clinical
https://www.readbyqxmd.com/read/29520363/pattern-formation-over-multigraphs
#19
Andras Gyorgy, Murat Arcak
Two of the most common pattern formation mechanisms are Turing-patterning in reaction-diffusion systems and lateral inhibition of neighboring cells. In this paper, we introduce a broad dynamical model of interconnected modules to study the emergence of patterns, with the above mentioned two mechanisms as special cases. Our results do not restrict the number of modules or their complexity, allow multiple layers of communication channels with possibly different interconnection structure, and do not assume symmetric connections between two connected modules...
January 2018: IEEE Transactions on Network Science and Engineering
https://www.readbyqxmd.com/read/29517975/temporal-transitions-of-spontaneous-brain-activity
#20
Zhiwei Ma, Nanyin Zhang
Spontaneous brain activity, typically investigated using resting-state fMRI (rsfMRI), provides a measure of inter-areal resting-state functional connectivity (RSFC). Although it has been established that RSFC is non-stationary, previous dynamic rsfMRI studies mainly focused on revealing the spatial characteristics of dynamic RSFC patterns, but the temporal relationship between these RSFC patterns remains elusive. Here we investigated the temporal organization of characteristic RSFC patterns in awake rats and humans...
March 8, 2018: ELife
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