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https://www.readbyqxmd.com/read/28212305/epigenetic-landscape-during-coronavirus-infection
#1
Alexandra Schäfer, Ralph S Baric
Coronaviruses (CoV) comprise a large group of emerging human and animal pathogens, including the highly pathogenic severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) strains. The molecular mechanisms regulating emerging coronavirus pathogenesis are complex and include virus-host interactions associated with entry, replication, egress and innate immune control. Epigenetics research investigates the genetic and non-genetic factors that regulate phenotypic variation, usually caused by external and environmental factors that alter host expression patterns and performance without any change in the underlying genotype...
February 15, 2017: Pathogens
https://www.readbyqxmd.com/read/28212095/identifying-bacterial-essential-genes-based-on-a-feature-integrated-method
#2
Yan Lin, Fa-Zhan Zhang, Kai Xue, Yi-Zhou Gao, Feng-Biao Guo
Essential genes are those genes of an organism that are considered to be crucial for its survival. Identification of essential genes is therefore of great significance to advance our understanding of the principles of cellular life. We have developed a novel computational method, which can effectively predict bacterial essential genes by extracting and integrating homologous features, protein domain feature, gene intrinsic features and network topological features. By performing the principal component regression (PCR) analysis for Escherichia coli MG1655, we established a classification model with the average area under curve (AUC) value of 0...
February 15, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28212087/dual-deep-network-for-visual-tracking
#3
Zhizhen Chi, Hongyang Li, Huchuan Lu, Minghsuan Yang
Visual tracking addresses the problem of identifying and localizing an unknown target in a video given the target specified by a bounding box in the first frame. In this paper, we propose a dual network to better utilize features among layers for visual tracking. It is observed that features in higher layers encode semantic context while its counterparts in lower layers are sensitive to discriminative appearance. Thus we exploit the hierarchical features in different layers of a deep model and design a dual structure to obtain better feature representation from various streams, which is rarely investigated in previous work...
February 15, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28212072/neural-network-based-solutions-for-stochastic-optimal-control-using-path-integrals
#4
Karthikeyan Rajagopal, Sivasubramanya Nadar Balakrishnan, Jerome R Busemeyer
In this paper, an offline approximate dynamic programming approach using neural networks is proposed for solving a class of finite horizon stochastic optimal control problems. There are two approaches available in the literature, one based on stochastic maximum principle (SMP) formalism and the other based on solving the stochastic Hamilton-Jacobi-Bellman (HJB) equation. However, in the presence of noise, the SMP formalism becomes complex and results in having to solve a couple of backward stochastic differential equations...
March 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28211533/integration-of-microrna-and-mrna-expression-profiles-in-the-skin-of-systemic-sclerosis-patients
#5
Bin Zhou, Xiao Xia Zuo, Yi Sha Li, Si Ming Gao, Xiao Dan Dai, Hong Lin Zhu, Hui Luo
MicroRNAs (miRNAs) play important roles in the fibrosis of systemic sclerosis (SSc). However, the underlying miRNA-mRNA regulatory network is not fully understood. A systemic investigation of the role of miRNAs would be very valuable for increasing our knowledge of the pathogenesis of SSc. Here, we combined miRNA and mRNA expression profiles and bioinformatics analyses and then performed validation experiments. we identified 21 miRNAs and 2698 mRNAs that were differentially expressed in SSc. Among these, 17 miRNAs and their 33 target mRNAs (55 miRNA-mRNA pairs) were involved in Toll-like receptor, transforming growth factor β and Wnt signalling pathways...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28211524/epigenetic-and-genetic-dissections-of-uv-induced-global-gene-dysregulation-in-skin-cells-through-multi-omics-analyses
#6
Yao Shen, Milda Stanislauskas, Gen Li, Deyou Zheng, Liang Liu
To elucidate the complex molecular mechanisms underlying the adverse effects UV radiation (UVR) on skin homeostasis, we performed multi-omics studies to characterize UV-induced genetic and epigenetic changes. Human keratinocytes from a single donor treated with or without UVR were analyzed by RNA-seq, exome-seq, and H3K27ac ChIP-seq at 4 h and 72 h following UVR. Compared to the relatively moderate mutagenic effects of UVR, acute UV exposure induced substantial epigenomic and transcriptomic alterations, illuminating a previously underappreciated role of epigenomic and transcriptomic instability in skin pathogenesis...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28211449/translational-use-of-event-related-potentials-to-assess-circuit-integrity-in-asd
#7
REVIEW
Meera E Modi, Mustafa Sahin
Deficits in social cognition are the defining characteristic of autism spectrum disorder (ASD). Social cognition requires the integration of several neural circuits in a time-sensitive fashion, so impairments in social interactions could arise as a result of alterations in network connectivity. Electroencephalography (EEG) has revealed abnormalities in event related potentials (ERPs) evoked by auditory and visual sensory stimuli in humans with ASD, indicating disruption of neural connectivity. Similar abnormalities in sensory-evoked ERPs have been observed in animal models of ASD, suggesting that ERPs have the potential to provide a translational biomarker of the disorder...
February 17, 2017: Nature Reviews. Neurology
https://www.readbyqxmd.com/read/28211026/social-networks-and-health-status-in-the-elderly-the-anziani-in-rete-population-based-study
#8
Luca Bianchetti, Flaminio Squazzoni, Niccolò Casnici, Devis Bianchini, Emirena Garrafa, Claudia Archetti, Valentina Romano, Luca Rozzini, Michele Melchiori, Chiara Fiorentini, Daniela Uberti, Stefano Calza, Alessandra Marengoni
BACKGROUND: Certain features of the social environment could maintain and even improve not only psychological well-being, but also health and cognition of the elderly. AIMS: We tested the association between social network characteristics and the number of chronic diseases in the elderly. METHODS: A randomized sample of the elderly population of Brescia, Italy, was evaluated (N = 200, age ≥65 years). We performed a comprehensive geriatric assessment, including information on socio-demographic variables (family, friendships, and acquaintance contacts)...
February 16, 2017: Aging Clinical and Experimental Research
https://www.readbyqxmd.com/read/28210983/multi-view-ensemble-classification-of-brain-connectivity-images-for-neurodegeneration-type-discrimination
#9
Michele Fratello, Giuseppina Caiazzo, Francesca Trojsi, Antonio Russo, Gioacchino Tedeschi, Roberto Tagliaferri, Fabrizio Esposito
Brain connectivity analyses using voxels as features are not robust enough for single-patient classification because of the inter-subject anatomical and functional variability. To construct more robust features, voxels can be aggregated into clusters that are maximally coherent across subjects. Moreover, combining multi-modal neuroimaging and multi-view data integration techniques allows generating multiple independent connectivity features for the same patient. Structural and functional connectivity features were extracted from multi-modal MRI images with a clustering technique, and used for the multi-view classification of different phenotypes of neurodegeneration by an ensemble learning method (random forest)...
February 16, 2017: Neuroinformatics
https://www.readbyqxmd.com/read/28209199/making-life-difficult-for-clostridium-difficile-augmenting-the-pathogen-s-metabolic-model-with-transcriptomic-and-codon-usage-data-for-better-therapeutic-target-characterization
#10
Sara Saheb Kashaf, Claudio Angione, Pietro Lió
BACKGROUND: Clostridium difficile is a bacterium which can infect various animal species, including humans. Infection with this bacterium is a leading healthcare-associated illness. A better understanding of this organism and the relationship between its genotype and phenotype is essential to the search for an effective treatment. Genome-scale metabolic models contain all known biochemical reactions of a microorganism and can be used to investigate this relationship. RESULTS: We present icdf834, an updated metabolic network of C...
February 16, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28209158/gene-regulatory-network-underlying-the-immortalization-of-epithelial-cells
#11
Luis Fernando Méndez-López, Jose Davila-Velderrain, Elisa Domínguez-Hüttinger, Christian Enríquez-Olguín, Juan Carlos Martínez-García, Elena R Alvarez-Buylla
BACKGROUND: Tumorigenic transformation of human epithelial cells in vitro has been described experimentally as the potential result of spontaneous immortalization. This process is characterized by a series of cell-state transitions, in which normal epithelial cells acquire first a senescent state which is later surpassed to attain a mesenchymal stem-like phenotype with a potentially tumorigenic behavior. In this paper we aim to provide a system-level mechanistic explanation to the emergence of these cell types, and to the time-ordered transition patterns that are common to neoplasias of epithelial origin...
February 16, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28208787/a-web-of-things-based-emerging-sensor-network-architecture-for-smart-control-systems
#12
Murad Khan, Bhagya Nathali Silva, Kijun Han
The Web of Things (WoT) plays an important role in the representation of the objects connected to the Internet of Things in a more transparent and effective way. Thus, it enables seamless and ubiquitous web communication between users and the smart things. Considering the importance of WoT, we propose a WoT-based emerging sensor network (WoT-ESN), which collects data from sensors, routes sensor data to the web, and integrate smart things into the web employing a representational state transfer (REST) architecture...
February 9, 2017: Sensors
https://www.readbyqxmd.com/read/28208633/compact-planar-ultrawideband-antennas-with-3-5-5-2-5-8-ghz-triple-band-notched-characteristics-for-internet-of-things-applications
#13
Jian Dong, Qianqian Li, Lianwen Deng
Ultrawideband (UWB) antennas, as core devices in high-speed wireless communication, are widely applied to mobile handsets, wireless sensor networks, and Internet of Things (IoT). A compact printed monopole antenna for UWB applications with triple band-notched characteristics is proposed in this paper. The antenna has a very compact size of 10 x 16 mm2 and is composed of a square slotted radiation patch and a narrow rectangular ground plane on the back of the substrate. First, by etching a pair of inverted T-shaped slots at the bottom of the radiation patch, one notched band at 5-6 GHz for rejecting the Wireless Local Area Network (WLAN) is generated...
February 10, 2017: Sensors
https://www.readbyqxmd.com/read/28208616/immunoinformatics-features-linked-to-leishmania-vaccine-development-data-integration-of-experimental-and-in-silico-studies
#14
Rory C F Brito, Frederico G Guimarães, João P L Velloso, Rodrigo Corrêa-Oliveira, Jeronimo C Ruiz, Alexandre B Reis, Daniela M Resende
Leishmaniasis is a wide-spectrum disease caused by parasites from Leishmania genus. There is no human vaccine available and it is considered by many studies as apotential effective tool for disease control. To discover novel antigens, computational programs have been used in reverse vaccinology strategies. In this work, we developed a validation antigen approach that integrates prediction of B and T cell epitopes, analysis of Protein-Protein Interaction (PPI) networks and metabolic pathways. We selected twenty candidate proteins from Leishmania tested in murine model, with experimental outcome published in the literature...
February 10, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28208522/re-integrative-analyses-reveal-a-long-noncoding-rna-mediated-sponge-regulatory-network-in-prostate-cancer
#15
Anthony Atala
No abstract text is available yet for this article.
March 2017: Journal of Urology
https://www.readbyqxmd.com/read/28208505/solving-the-two-dimensional-fokker-planck-equation-for-strongly-correlated-neurons
#16
Taşkın Deniz, Stefan Rotter
Pairs of neurons in brain networks often share much of the input they receive from other neurons. Due to essential nonlinearities of the neuronal dynamics, the consequences for the correlation of the output spike trains are generally not well understood. Here we analyze the case of two leaky integrate-and-fire neurons using an approach which is nonperturbative with respect to the degree of input correlation. Our treatment covers both weakly and strongly correlated dynamics, generalizing previous results based on linear response theory...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28208394/optimizing-synchronization-stability-of-the-kuramoto-model-in-complex-networks-and-power-grids
#17
Bo Li, K Y Michael Wong
Maintaining the stability of synchronization state is crucial for the functioning of many natural and artificial systems. In this study, we develop methods to optimize the synchronization stability of the Kuramoto model by minimizing the dominant Lyapunov exponent. Using the recently proposed cut-set space approximation of the steady states, we greatly simplify the objective function, and further derive its gradient and Hessian with respect to natural frequencies, which leads to an efficient algorithm with the quasi-Newton's method...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28208338/synchronization-and-long-time-memory-in-neural-networks-with-inhibitory-hubs-and-synaptic-plasticity
#18
Elena Bertolotti, Raffaella Burioni, Matteo di Volo, Alessandro Vezzani
We investigate the dynamical role of inhibitory and highly connected nodes (hub) in synchronization and input processing of leaky-integrate-and-fire neural networks with short term synaptic plasticity. We take advantage of a heterogeneous mean-field approximation to encode the role of network structure and we tune the fraction of inhibitory neurons f_{I} and their connectivity level to investigate the cooperation between hub features and inhibition. We show that, depending on f_{I}, highly connected inhibitory nodes strongly drive the synchronization properties of the overall network through dynamical transitions from synchronous to asynchronous regimes...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28208023/transcriptomic-profiling-of-human-hippocampal-progenitor-cells-treated-with-antidepressants-and-its-application-in-drug-repositioning
#19
Timothy R Powell, Tytus Murphy, Sang H Lee, Jack Price, Sandrine Thuret, Gerome Breen
Current pharmacological treatments for major depressive disorder (MDD) are ineffective in a significant proportion of patients, and the identification of new antidepressant compounds has been difficult. 'Connectivity mapping' is a method that can be used to identify drugs that elicit similar downstream effects on mRNA levels when compared to current treatments, and thus may point towards possible repositioning opportunities. We investigated genome-wide transcriptomic changes to human hippocampal progenitor cells treated with therapeutically relevant concentrations of a tricyclic antidepressant (nortriptyline) and a selective serotonin reuptake inhibitor (escitalopram)...
January 1, 2017: Journal of Psychopharmacology
https://www.readbyqxmd.com/read/28207958/shared-care-requires-a-shared-vision-communities-of-clinical-practice-in-a-primary-care-setting
#20
Jessica Young, Tony Egan, Chrystal Jaye, Martyn Williamson, Anna Askerud, Peter Raude, Maree Penese
AIMS AND OBJECTIVES: To understand how a vision of care is formed and shared by patients and the primary care professionals involved in their care. BACKGROUND: To achieve the best health outcomes, it is important for patients and those who care for them to have a mutual understanding about what is important to the patient in their everyday life and why, and what care is necessary to realise this vision. Shared or team care does not necessarily translate to a consistent and integrated approach to a patient's care...
February 16, 2017: Journal of Clinical Nursing
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