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https://www.readbyqxmd.com/read/28636461/genice-a-novel-framework-for-gene-network-inference-by-clustering-exhaustive-search-and-multivariate-analysis
#1
Ricardo de Souza Jacomini, David Correa Martins-Jr, Felipe Leno da Silva, Anna Helena Reali Costa
Gene network (GN) inference from temporal gene expression data is a crucial and challenging problem in systems biology. Expression data sets usually consist of dozens of temporal samples, while networks consist of thousands of genes, thus rendering many inference methods unfeasible in practice. To improve the scalability of GN inference methods, we propose a novel framework called GeNICE, based on probabilistic GNs; the main novelty is the introduction of a clustering procedure to group genes with related expression profiles and to provide an approximate solution with reduced computational complexity...
June 21, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28631354/cross-population-myelination-covariance-of-human-cerebral-cortex
#2
Zhiwei Ma, Nanyin Zhang
Cross-population covariance of brain morphometric quantities provides a measure of interareal connectivity, as it is believed to be determined by the coordinated neurodevelopment of connected brain regions. Although useful, structural covariance analysis predominantly employed bulky morphological measures with mixed compartments, whereas studies of the structural covariance of any specific subdivisions such as myelin are rare. Characterizing myelination covariance is of interest, as it will reveal connectivity patterns determined by coordinated development of myeloarchitecture between brain regions...
June 20, 2017: Human Brain Mapping
https://www.readbyqxmd.com/read/28622528/band-specific-atypical-functional-connectivity-pattern-in-childhood-autism-spectrum-disorder
#3
Tetsuya Takahashi, Teruya Yamanishi, Sou Nobukawa, Shinya Kasakawa, Yuko Yoshimura, Hirotoshi Hiraishi, Chiaki Hasegawa, Takashi Ikeda, Tetsu Hirosawa, Toshio Munesue, Haruhiro Higashida, Yoshio Minabe, Mitsuru Kikuchi
OBJECTIVE: Altered brain connectivity has been theorized as a key neural underpinning of autism spectrum disorder (ASD), but recent investigations have revealed conflicting patterns of connectivity, particularly hyper-connectivity and hypo-connectivity across age groups. The application of graph theory to neuroimaging data has become an effective approach for characterizing topographical patterns of large-scale functional networks. We used a graph approach to investigate alteration of functional networks in childhood ASD...
May 23, 2017: Clinical Neurophysiology: Official Journal of the International Federation of Clinical Neurophysiology
https://www.readbyqxmd.com/read/28618497/synchronization-of-fluctuating-delay-coupled-chaotic-networks
#4
Manuel Jiménez-Martín, Javier Rodríguez-Laguna, Otti D'Huys, Javier de la Rubia, Elka Korutcheva
We study the synchronization of chaotic units connected through time-delayed fluctuating interactions. Focusing on small-world networks of Bernoulli and Logistic units with a fixed chiral backbone, we compare the synchronization properties of static and fluctuating networks in the regime of large delays. We find that random network switching may enhance the stability of synchronized states. Synchronization appears to be maximally stable when fluctuations are much faster than the time-delay, whereas it disappears for very slow fluctuations...
May 2017: Physical Review. E
https://www.readbyqxmd.com/read/28604809/constructing-a-watts-strogatz-network-from-a-small-world-network-with-symmetric-degree-distribution
#5
Mozart B C Menezes, Seokjin Kim, Rongbing Huang
Though the small-world phenomenon is widespread in many real networks, it is still challenging to replicate a large network at the full scale for further study on its structure and dynamics when sufficient data are not readily available. We propose a method to construct a Watts-Strogatz network using a sample from a small-world network with symmetric degree distribution. Our method yields an estimated degree distribution which fits closely with that of a Watts-Strogatz network and leads into accurate estimates of network metrics such as clustering coefficient and degree of separation...
2017: PloS One
https://www.readbyqxmd.com/read/28602630/correlation-between-standardized-assessment-of-concussion-scores-and-small-world-brain-network-in-mild-traumatic-brain-injury
#6
Yan Yan, Jian Song, Guozheng Xu, Shun Yao, Chenglong Cao, Chang Li, Guibao Peng, Hao Du
This study investigated the characteristics of the small-world brain network architecture of patients with mild traumatic brain injury (MTBI), and a correlation between brain functional connectivity network properties in the resting-state fMRI and Standardized Assessment of Concussion (SAC) parameters. The neurological conditions of 22 MTBI patients and 17 normal control individuals were evaluated according to the SAC. Resting-state fMRI was performed in all subjects 3 and 7days after injury respectively. After preprocessing the fMRI data, cortex functional regions were marked using AAL90 and Dosenbach160 templates...
June 8, 2017: Journal of Clinical Neuroscience: Official Journal of the Neurosurgical Society of Australasia
https://www.readbyqxmd.com/read/28581480/rich-cell-type-specific-network-topology-in-neocortical-microcircuitry
#7
Eyal Gal, Michael London, Amir Globerson, Srikanth Ramaswamy, Michael W Reimann, Eilif Muller, Henry Markram, Idan Segev
Uncovering structural regularities and architectural topologies of cortical circuitry is vital for understanding neural computations. Recently, an experimentally constrained algorithm generated a dense network reconstruction of a ∼0.3-mm(3) volume from juvenile rat somatosensory neocortex, comprising ∼31,000 cells and ∼36 million synapses. Using this reconstruction, we found a small-world topology with an average of 2.5 synapses separating any two cells and multiple cell-type-specific wiring features...
June 5, 2017: Nature Neuroscience
https://www.readbyqxmd.com/read/28580294/gender-differences-in-the-structural-connectome-of-the-teenage-brain-revealed-by-generalized-q-sampling-mri
#8
Yeu-Sheng Tyan, Jan-Ray Liao, Chao-Yu Shen, Yu-Chieh Lin, Jun-Cheng Weng
The question of whether there are biological differences between male and female brains is a fraught one, and political positions and prior expectations seem to have a strong influence on the interpretation of scientific data in this field. This question is relevant to issues of gender differences in the prevalence of psychiatric conditions, including autism, attention deficit hyperactivity disorder (ADHD), Tourette's syndrome, schizophrenia, dyslexia, depression, and eating disorders. Understanding how gender influences vulnerability to these conditions is significant...
2017: NeuroImage: Clinical
https://www.readbyqxmd.com/read/28576097/effects-of-partial-time-delays-on-phase-synchronization-in-watts-strogatz-small-world-neuronal-networks
#9
Xiaojuan Sun, Matjaž Perc, Jürgen Kurths
In this paper, we study effects of partial time delays on phase synchronization in Watts-Strogatz small-world neuronal networks. Our focus is on the impact of two parameters, namely the time delay τ and the probability of partial time delay pdelay, whereby the latter determines the probability with which a connection between two neurons is delayed. Our research reveals that partial time delays significantly affect phase synchronization in this system. In particular, partial time delays can either enhance or decrease phase synchronization and induce synchronization transitions with changes in the mean firing rate of neurons, as well as induce switching between synchronized neurons with period-1 firing to synchronized neurons with period-2 firing...
May 2017: Chaos
https://www.readbyqxmd.com/read/28570586/inferring-and-analysis-of-social-networks-using-rfid-check-in-data-in-china
#10
Tao Liu, Lintao Yang, Shouyin Liu, Shuangkui Ge
Social networks play an important role in our daily lives. However, social ties are rather elusive to quantify, especially for large groups of subjects over prolonged periods of time. In this work, we first propose a methodology for extracting social ties from long spatio-temporal data streams, where the subjects are 17,795 undergraduates from a university of China and the data streams are the 9,147,106 time-stamped RFID check-in records left behind by them during one academic year. By several metrics mentioned below, we then analyze the structure of the social network...
2017: PloS One
https://www.readbyqxmd.com/read/28570577/partial-coupling-delay-induced-multiple-spatiotemporal-orders-in-a-modular-neuronal-network
#11
XiaoLi Yang, HuiDan Li, ZhongKui Sun
The influence of partial coupling delay on the spatiotemporal spiking dynamics is explored in a modular neuronal network. The modular neuronal network is composed of two subnetworks which present the small-world property and scale-free property, respectively. Numerical results show that spatiotemporal order that the modular network is most coherent in time and nearly synchronized in space can emerge intermittently when the coupling delays among neurons are appropriately tuned. The appropriately tuned delays are further detected to be integer multiples of the intrinsic spiking period of the modular neuronal network, which implies that the phenomenon of multiple spatiotemporal orders could be the result of a locking between the length of coupling delay and the intrinsic spiking period of the modular neuronal network...
2017: PloS One
https://www.readbyqxmd.com/read/28569517/quantifying-the-structure-of-free-association-networks-across-the-life-span
#12
Haim Dubossarsky, Simon De Deyne, Thomas T Hills
We investigate how the mental lexicon changes over the life span using free association data from over 8,000 individuals, ranging from 10 to 84 years of age, with more than 400 cue words per age group. Using network analysis, with words as nodes and edges defined by the strength of shared associations, we find that associative networks evolve in a nonlinear (U-shaped) fashion over the life span. During early life, the network converges and becomes increasingly structured, with reductions in average path length, entropy, clustering coefficient, and small world index...
June 1, 2017: Developmental Psychology
https://www.readbyqxmd.com/read/28558655/the-common-transcriptional-subnetworks-of-the-grape-berry-skin-in-the-late-stages-of-ripening
#13
Ryan Ghan, Juli Petereit, Richard L Tillett, Karen A Schlauch, David Toubiana, Aaron Fait, Grant R Cramer
BACKGROUND: Wine grapes are important economically in many countries around the world. Defining the optimum time for grape harvest is a major challenge to the grower and winemaker. Berry skins are an important source of flavor, color and other quality traits in the ripening stage. Senescent-like processes such as chloroplast disorganization and cell death characterize the late ripening stage. RESULTS: To better understand the molecular and physiological processes involved in the late stages of berry ripening, RNA-seq analysis of the skins of seven wine grape cultivars (Cabernet Franc, Cabernet Sauvignon, Merlot, Pinot Noir, Chardonnay, Sauvignon Blanc and Semillon) was performed...
May 30, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28549329/abnormal-small-world-brain-functional-networks-in-obsessive-compulsive-disorder-patients-with-poor-insight
#14
Hui Lei, Yan Cui, Jie Fan, Xiaocui Zhang, Mingtian Zhong, Jinyao Yi, Lin Cai, Dezhong Yao, Xiongzhao Zhu
BACKGROUND: There are limited data on neurobiological correlates of poor insight in obsessive-compulsive disorder (OCD). This study explored whether specific changes occur in small-world network (SWN) properties in the brain functional network of OCD patients with poor insight. METHOD: Resting-state electroencephalograms (EEGs) were recorded for 12 medication-free OCD patients with poor insight, 50 medication-free OCD patients with good insight, and 36 healthy controls...
May 20, 2017: Journal of Affective Disorders
https://www.readbyqxmd.com/read/28544891/emergence-of-ultrafast-sparsely-synchronized-rhythms-and-their-responses-to-external-stimuli-in-an-inhomogeneous-small-world-complex-neuronal-network
#15
Sang-Yoon Kim, Woochang Lim
We consider an inhomogeneous small-world network (SWN) composed of inhibitory short-range (SR) and long-range (LR) interneurons, and investigate the effect of network architecture on emergence of synchronized brain rhythms by varying the fraction of LR interneurons plong. The betweenness centralities of the LR and SR interneurons (characterizing the potentiality in controlling communication between other interneurons) are distinctly different. Hence, in view of the betweenness, SWNs we consider are inhomogeneous, unlike the "canonical" Watts-Strogatz SWN with nearly the same betweenness centralities...
April 28, 2017: Neural Networks: the Official Journal of the International Neural Network Society
https://www.readbyqxmd.com/read/28531764/disrupted-resting-brain-graph-measures-in-individuals-at-high-risk-for-alcoholism
#16
Bharath Holla, Rajanikant Panda, Ganesan Venkatasubramanian, Bharat Biswal, Rose Dawn Bharath, Vivek Benegal
Familial susceptibility to alcoholism is likely to be linked to the externalizing diathesis seen in high-risk offspring from high-density alcohol use disorder (AUD) families. The present study aimed at comparing resting brain functional connectivity and their association with externalizing symptoms and alcoholism familial density in 40 substance-naive high-risk (HR) male offspring from high-density AUD families and 30 matched healthy low-risk (LR) males without a family history of substance dependence using graph theory-based network analysis...
May 14, 2017: Psychiatry Research
https://www.readbyqxmd.com/read/28520668/structural-connectivity-related-to-persistent-symptoms-after-mild-tbi-in-adolescents-and-response-to-aerobic-training-preliminary-investigation
#17
Weihong Yuan, Shari L Wade, Catherine Quatman-Yates, Jason A Hugentobler, Paul J Gubanich, Brad G Kurowski
OBJECTIVE: To quantify structural connectivity abnormalities in adolescents with mild traumatic brain injury (mTBI) and to investigate connectivity changes following aerobic training using graph theory and diffusion tensor imaging tractography. SETTING: Outpatient research setting. PARTICIPANTS: Twenty-two children (age: 15.83 ± 1.77 years, 10 females) with 4 to 16 weeks of persistent symptoms after mTBI and a matched healthy comparison group...
May 17, 2017: Journal of Head Trauma Rehabilitation
https://www.readbyqxmd.com/read/28515708/disrupted-structural-and-functional-networks-and-their-correlation-with-alertness-in-right-temporal-lobe-epilepsy-a-graph-theory-study
#18
Wenyu Jiang, Jianping Li, Xuemei Chen, Wei Ye, Jinou Zheng
Previous studies have shown that temporal lobe epilepsy (TLE) involves abnormal structural or functional connectivity in specific brain areas. However, limited comprehensive studies have been conducted on TLE associated changes in the topological organization of structural and functional networks. Additionally, epilepsy is associated with impairment in alertness, a fundamental component of attention. In this study, structural networks were constructed using diffusion tensor imaging tractography, and functional networks were obtained from resting-state functional MRI temporal series correlations in 20 right temporal lobe epilepsy (rTLE) patients and 19 healthy controls...
2017: Frontiers in Neurology
https://www.readbyqxmd.com/read/28510210/brain-connectivity-during-encoding-and-retrieval-of-spatial-information-individual-differences-in-navigation-skills
#19
Greeshma Sharma, Klaus Gramann, Sushil Chandra, Vijander Singh, Alok Prakash Mittal
Emerging evidence suggests that the variations in the ability to navigate through any real or virtual environment are accompanied by distinct underlying cortical activations in multiple regions of the brain. These activations may appear due to the use of different frame of reference (FOR) for representing an environment. The present study investigated the brain dynamics in the good and bad navigators using Graph Theoretical analysis applied to low-density electroencephalography (EEG) data. Individual navigation skills were rated according to the performance in a virtual reality (VR)-based navigation task and the effect of navigator's proclivity towards a particular FOR on the navigation performance was explored...
May 16, 2017: Brain Informatics
https://www.readbyqxmd.com/read/28505729/optimization-of-synchronizability-in-multiplex-networks-by-rewiring-one-layer
#20
Sanjiv K Dwivedi, Murilo S Baptista, Sarika Jalan
The mathematical framework of multiplex networks has been increasingly realized as a more suitable framework for modeling real-world complex systems. In this work, we investigate the optimization of synchronizability in multiplex networks by evolving only one layer while keeping other layers fixed. Our main finding is to show the conditions under which the efficiency of convergence to the most optimal structure is almost as good as the case where both layers are rewired during an optimization process. In particular, interlayer coupling strength responsible for the integration between the layers turns out to be a crucial factor governing the efficiency of optimization even for the cases when the layer going through the evolution has nodes interacting much more weakly than those in the fixed layer...
April 2017: Physical Review. E
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