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Complex Network

Tomaž Šolc, Mihael Mohorčič, Carolina Fortuna
Lack of unallocated spectrum and increasing demand for bandwidth in wireless networks is forcing new devices and technologies to share frequency bands. Spectrum sensing is a key enabler for frequency sharing and there is a large body of existing work on signal detection methods. However a unified methodology that would be suitable for objective comparison of detection methods based on experimental evaluations is missing. In this paper we propose such a methodology comprised of seven steps that can be applied to evaluate methods in simulation or practical experiments...
2018: PloS One
Alex D Bird, Magnus J E Richardson
Short-term synaptic depression, caused by depletion of releasable neurotransmitter, modulates the strength of neuronal connections in a history-dependent manner. Quantifying the statistics of synaptic transmission requires stochastic models that link probabilistic neurotransmitter release with presynaptic spike-train statistics. Common approaches are to model the presynaptic spike train as either regular or a memory-less Poisson process: few analytical results are available that describe depressing synapses when the afferent spike train has more complex, temporally correlated statistics such as bursts...
June 22, 2018: PLoS Computational Biology
Isabel Forner-Piquer, Constantinos C Mylonas, Josep Calduch-Giner, Francesca Maradonna, Giorgia Gioacchini, Marco Allarà, Fabiana Piscitelli, Vincenzo Di Marzo, Jaume Pérez-Sánchez, Oliana Carnevali
The increasing manufacture of plastics and their mismanagement has turned plastic into a ubiquitous waste in the marine environment. Among all the substances conforming the plastic items, the effects of a dietary Bisphenol A (BPA) and Di-isononyl phthalate (DiNP) have been evaluated in adult male gilthead sea bream, focusing on their effects in the modulation of the Endocannabinoid System (ECS). In zebrafish, the ECS has been recently chosen as a new target for the activity of some Endocrine Disrupting Chemicals (EDC), since it represents a complex lipid signaling network essential for the well-being of the organisms...
June 19, 2018: Environment International
Annette Pisanski, Silvia Pagliardini
Breathing at rest is typically characterized by three phases: active inspiration, post-inspiration (or stage 1 expiration), and passive expiration (or stage 2 expiration). Breathing during periods of increased respiratory demand, on the other hand, engages active expiration through recruitment of abdominal muscles in order to increase ventilation. It is currently hypothesized that different phases of the respiratory rhythm are driven by three coupled oscillators: the preBötzinger Complex, driving inspiration, the parafacial respiratory group (pFRG), driving active expiration and the post-inspiratory Complex, driving post-inspiration...
June 19, 2018: Respiratory Physiology & Neurobiology
Louis Anthony Tony Cox
Sufficiently high and prolonged inhalation exposures to some respirable elongated mineral particles (REMPs), notably including amphibole asbestos fibers, can increase risk of inflammation-mediated diseases including malignant mesothelioma, pleural diseases, fibrosis, and lung cancer. Chronic inflammation involves ongoing activation of the NLRP3 inflammasome, which enables immune cells to produce potent proinflammatory cytokines IL-1β and IL-18. Reactive oxygen species (ROS) (in particular, mitochondrial ROS) contribute to NRLP3 activation via a well-elucidated mechanism involving oxidation of reduced thioredoxin and association of thioredoxin-interacting protein with NLRP3...
June 19, 2018: Toxicology and Applied Pharmacology
Michael Hendriksen
Phylogenetic networks are a generalisation of phylogenetic trees that allow for more complex evolutionary histories that include hybridisation-like processes. It is of considerable interest whether a network can be considered 'tree-like' or not, which leads to the introduction of tree-based networks in the rooted, binary context. Tree-based networks are those networks which can be constructed by adding additional edges into a phylogenetic tree, called the base tree. Previous extensions have considered extending to the binary, unrooted case and the nonbinary, rooted case...
June 19, 2018: Mathematical Biosciences
Ancor Sanz-Garcia, Thorsten Rings, Klaus Lehnertz
Objective and Approach: Investigating properties of evolving functional brain networks has become a valuable tool to characterize the complex dynamics of the epileptic brain. 
 Such networks are usually derived from electroencephalograms (EEG) recorded with sensors implanted chronically into deeper structures of the brain and/or placed onto the cortex.
 It is still unclear, however, whether the use of different sensors for an identification of network nodes affects properties
 of functional brain networks...
June 22, 2018: Physiological Measurement
Cosmika Goswami, Stephen Fox, Matthew Holden, Martin Connor, Alistair Leanord, Thomas J Evans
Bacteraemia caused by Escherichia coli is a growing problem with a significant mortality. The factors that influence the acquisition and outcome of these infections are not clear. Here, we have linked detailed genetic data from the whole-genome sequencing of 162 bacteraemic isolates collected in Scotland, UK, in 2013-2015, with clinical data in order to delineate bacterial and host factors that influence the acquisition in hospital or the community, outcome and antibiotic resistance. We identified four major sequence types (STs) in these isolates: ST131, ST69, ST73 and ST95...
June 22, 2018: Microbial Genomics
Ahmed A Moustafa, Hogyoung Kim, Rasha S Albeltagy, Ola H El-Habit, Asim B Abdel-Mageed
MicroRNAs (miRNAs) are a small functional non-coding RNAs that post-transcriptionally regulate gene expression through mRNA degradation or translational repression. miRNAs are key regulatory components of various cellular networks. Current evidence support that multiple mammalian genome-encoded miRNAs impact the cellular biology, including proliferation, apoptosis, differentiation, and tumorigenesis, by targeting specific subsets of mRNAs. This minireview is focused on the current themes underlying the interactions between miRNAs and their mRNA targets and pathways in prostate tumorigenesis and progression, and their potential clinical utility as biomarkers for prostate cancer...
June 2018: Experimental Biology and Medicine
Stephen Kelly, Malcolm I Heywood
Algorithms that learn through environmental interaction and delayed rewards, or reinforcement learning, increasingly face the challenge of scaling to dynamic, highdimensional, and partially observable environments. Significant attention is being paid to frameworks from deep learning, which scale to high-dimensional data by decomposing the task through multi-layered neural networks. While effective, the representation is complex and computationally demanding. In this work we propose a framework based on Genetic Programming which adaptively complexifies policies through interaction with the task...
June 22, 2018: Evolutionary Computation
He Huang, Dan-Li Wang, Yingming Zhao
Lysine crotonylation (Kcr) is a recently identified PTM that is regulated by an acetyltransferase, p300. The p300-catalyzed histone Kcr is able to stimulate transcription to a greater degree than the well-studied histone lysine acetylation (Kac). Despite these progresses, the global Kcr substrates regulated by p300 remain largely unknown, hindering efforts to establish mechanistic links between Kcr and p300-mediated phenotypes. Here, we used quantitative proteomics to characterize the p300-regulated lysine crotonylome in wild type (WT) and p300 knockout (KO) cells...
June 22, 2018: Proteomics
Xiao-Jun Cai, Lei Wang, Chun-Mei Hu
Minimal hepatic encephalopathy (MHE), a complex neuropsychological complication of cirrhosis, is characterized by delayed reaction time and the inhibition of abnormal response. This network meta-analysis (NMA) was adopted to compare the efficacy of five drugs including lactulose, probiotics, rifaximin, acetyl-L-carnitine (ALC), and L-Ornithine L-aspartate (LOLA) in the treatment of MHE. The Cochrane Library, PubMed, and Embase databases were searched for any existing entail on these five drugs from the inception to February 2018, including Randomized controlled trials (RCTs)...
June 22, 2018: Journal of Cellular Biochemistry
Giulia Maurizi, Lucia Babini, Lucio Della Guardia
Adipose tissue is a dynamic endocrine organ playing a pivotal role in metabolism modulation. Adipocytes differentiation requires a highly orchestrated series of changes of gene expression in precursor cells. At the same time, white mature adipocytes are plastic cells able to reversibly transdifferentiate toward fibroblast-like cells via the liposecretion process, returning back to a non-committed status of the cells. In particular, adipose tissue microenvironment along with external signaling molecules such as adipokines, cytokines and growth factors can regulate adipocytes physiology through complex molecular networks...
June 22, 2018: Journal of Cellular Physiology
Rongrong Guo, Bo Wang, Ling Lin, Guo Cheng, Sihong Zhou, Shuyu Xie, Xiaofang Shi, Muming Cao, Ying Zhang, Xianjin Bai
The fruitfulness of grapevines ( Vitis vinifera L.) is determined to a large extent by the differentiation of uncommitted meristems, especially in the second-crop production of some varieties, where the intermediate of inflorescence and tendril accounts for a significant proportion in two-crop-a-year grape culture system. The differentiation of uncommitted lateral meristem was reported to be regulated by a network, whose backbone was composed of several floral meristem identity genes. In the present study, the phylogenetics of grape floral meristem identity genes with their orthologues in other species, and their conserved domain and interaction networks were analysed...
June 2018: Journal of Genetics
Jordan K Villa, Yichi Su, Lydia M Contreras, Ming C Hammond
In bacteria and archaea, small RNAs (sRNAs) regulate complex networks through antisense interactions with target mRNAs in trans, and riboswitches regulate gene expression in cis based on the ability to bind small-molecule ligands. Although our understanding and characterization of these two important regulatory RNA classes is far from complete, these RNA-based mechanisms have proven useful for a wide variety of synthetic biology applications. Besides classic and contemporary applications in the realm of metabolic engineering and orthogonal gene control, this review also covers newer applications of regulatory RNAs as biosensors, logic gates, and tools to determine RNA-RNA interactions...
May 2018: Microbiology Spectrum
Stefan G Hofmann, Joshua Curtiss
Contemporary classification systems assume that psychiatric disorders are expressions of latent disease entities. However, some critics point to the comorbidity problem and other issues that question the validity of the latent disease model. An alternative to this traditional view is the complex network approach. This approach assumes that disorders exist as systems of inter-connected elements, without requiring that the elements are expressions of latent disease entities. Depending on the structure of the network, change can occur abruptly once the network reaches a tipping point...
June 21, 2018: European Journal of Clinical Investigation
Luca Cera, Christoph A Schalley
Self-organization in synthetic chemical systems is quickly developing into a powerful strategy for designing new functional materials. As self-organization requires the system to exist far from thermodynamic equilibrium, chemists have begun to go beyond the classical equilibrium self-assembly that is often applied in bottom-up supramolecular synthesis, and to learn about the surprising and unpredicted emergent properties of chemical systems that are characterized by a higher level of complexity and extended reactivity networks...
June 21, 2018: Advanced Materials
Adam Bertscher, Leslie London, Marsha Orgill
Alcohol is a major contributor to the Non-Communicable Disease burden in South Africa. In 2000, 7.1% of all deaths and 7% of total disability-adjusted life years were ascribed to alcohol-related harm in the country. Regulations proposed to restrict alcohol advertising in South Africa present an evidence-based upstream intervention. Research on policy formulation in low- and middle-income countries is limited. This study aims to describe and explore the policy formulation process of the 2013 draft Control of Marketing of Alcoholic Beverages Bill in South Africa between March 2011 and May 2017...
June 21, 2018: Health Policy and Planning
Masahiro Kanai, Yuichi Maeda, Yukinori Okada
Summary: Rapid advances in high-throughput sequencing technologies have enabled more efficient acquisition of massive amount of multi-omics data. However, interpretation of the underlying relationships across multi-omics networks has not been fully succeeded, partly due to the lack of effective methods in visualization. To aid interpretation of the results from such multi-omics data, we here present Grimon (Graphical interface to visualize multi-omics networks), an R package that visualizes high-dimensional multi-layered data sets in three-dimensional parallel coordinates...
June 19, 2018: Bioinformatics
Georgy Derevyanko, Sergei Grudinin, Yoshua Bengio, Guillaume Lamoureux
Motivation: The computational prediction of a protein structure from its sequence generally relies on a method to assess the quality of protein models. Most assessment methods rank candidate models using heavily engineered structural features, defined as complex functions of the atomic coordinates. However, very few methods have attempted to learn these features directly from the data. Results: We show that deep convolutional networks can be used to predict the ranking of model structures solely on the basis of their raw three-dimensional atomic densities, without any feature tuning...
June 19, 2018: Bioinformatics
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