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https://www.readbyqxmd.com/read/28227870/identifying-disease-network-perturbations-through-regression-on-gene-expression-and-pathway-topology-analysis
#1
Georgios N Dimitrakopoulos, Panos Balomenos, Aristidis G Vrahatis, Kyriakos Sgarbas, Anastasios Bezerianos, Georgios N Dimitrakopoulos, Panos Balomenos, Aristidis G Vrahatis, Kyriakos Sgarbas, Anastasios Bezerianos, Kyriakos Sgarbas, Panos Balomenos, Georgios N Dimitrakopoulos, Anastasios Bezerianos, Aristidis G Vrahatis
In Systems Biology, network-based approaches have been extensively used to effectively study complex diseases. An important challenge is the detection of network perturbations which disrupt regular biological functions as a result of a disease. In this regard, we introduce a network based pathway analysis method which isolates casual interactions with significant regulatory roles within diseased-perturbed pathways. Specifically, we use gene expression data with Random Forest regression models to assess the interactivity strengths of genes within disease-perturbed networks, using KEGG pathway maps as a source of prior-knowledge pertaining to pathway topology...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227768/measures-of-the-brain-functional-network-that-correlate-with-alzheimer-s-neuropsychological-test-scores-an-fmri-and-graph-analysis-study
#2
Soroosh Golbabaei, Amin Dadashi, Hamid Soltanian-Zadeh, Soroosh Golbabaei, Amin Dadashi, Hamid Soltanian-Zadeh, Soroosh Golbabaei, Amin Dadashi, Hamid Soltanian-Zadeh
Neural degeneration in Alzheimer's disease (AD) leads to structural topology deformation that in turn changes brain functionality. The main aim of the present study is to find the brain's functional connectivity network (FCN) correlates of Alzheimer's psychological test scores. To this end, the brain's FCN is extracted from the resting state functional magnetic resonance images (rs-fMRI) of healthy controls and patients with AD and represented as a graph. Then, network measures are calculated from the graphs...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227620/routing-over-multi-hop-fading-wireless-body-area-networks-with-reliability-considerations
#3
Hussein Moosavi, Francis Minhthang Bui, Hussein Moosavi, Francis Minhthang Bui, Francis Minhthang Bui, Hussein Moosavi
Optimal reliable routing is studied in the context of fading wireless body area networks (WBANs). A non-cooperative game is proposed to model and analyze the strategic interactions among body-worn health-care devices when each seeks to find the most reliable path to the hub. A distributed algorithm based on the proposed game is provided and proved to converge to a multi-hop Pareto-dominant Nash topology. The game-theoretic framework is evaluated through numerical simulations in conditions approximating actual deployment of a moving ultra wideband WBAN...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227395/impaired-episodic-memory-network-in-subjects-at-high-risk-for-alzheimer-s-disease
#4
Yafeng Zhan, Jianhua Ma, Kaibin Xu, Yanhui Ding, Yue Cui, Zhengyi Yang, Yong Liu, Yafeng Zhan, Jianhua Ma, Kaibin Xu, Yanhui Ding, Yue Cui, Zhengyi Yang, Yong Liu, Yanhui Ding, Kaibin Xu, Yue Cui, Yafeng Zhan, Jianhua Ma, Zhengyi Yang, Yong Liu
Episodic memory dysfunction is one of the hallmark symptoms of Alzheimer's disease (AD) and mild cognitive impairment (MCI). This cognitive impairment may be related to abnormal brain structure and activity. Functional connectivity mapping (FCM) analysis provides a powerful tool for exploring the topology of human brain function using magnetic resonance imaging (MRI). Thus, it would be advantageous to investigate the changes in functional connectivity within the episodic memory network in a longitudinal MCI dataset, as it may be helpful in identifying a potential marker of disease progress...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227107/a-comparison-of-the-cluster-span-threshold-and-the-union-of-shortest-paths-as-objective-thresholds-of-eeg-functional-connectivity-networks-from-beta-activity-in-alzheimer-s-disease
#5
Keith Smith, Daniel Abasolo, Javier Escudero, Keith Smith, Daniel Abasolo, Javier Escudero, Javier Escudero, Keith Smith, Daniel Abasolo
The Cluster-Span Threshold (CST) is a recently introduced unbiased threshold for functional connectivity networks. This binarisation technique offers a natural trade-off of sparsity and density of information by balancing the ratio of closed to open triples in the network topology. Here we present findings comparing it with the Union of Shortest Paths (USP), another recently proposed objective method. We analyse standard network metrics of binarised networks for sensitivity to clinical Alzheimer's disease in the Beta band of Electroencephalogram activity...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227053/the-effects-of-deep-network-topology-on-mortality-prediction
#6
Hao Du, Mohammad M Ghassemi, Mengling Feng, Hao Du, Mohammad M Ghassemi, Mengling Feng, Mengling Feng, Hao Du, Mohammad M Ghassemi
Deep learning has achieved remarkable results in the areas of computer vision, speech recognition, natural language processing and most recently, even playing Go. The application of deep-learning to problems in healthcare, however, has gained attention only in recent years, and it's ultimate place at the bedside remains a topic of skeptical discussion. While there is a growing academic interest in the application of Machine Learning (ML) techniques to clinical problems, many in the clinical community see little incentive to upgrade from simpler methods, such as logistic regression, to deep learning...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226594/novel-measure-of-the-weigh-distribution-balance-on-the-brain-network-graph-complexity-applied-to-schizophrenia
#7
J Gomez-Pilar, J Poza, A Bachiller, P Nunez, C Gomez, A Lubeiro, V Molina, R Hornero, J Gomez-Pilar, J Poza, A Bachiller, P Nunez, C Gomez, A Lubeiro, V Molina, R Hornero, J Gomez-Pilar, A Bachiller, C Gomez, J Poza, P Nunez, A Lubeiro, V Molina, R Hornero
The aim of this study was to assess brain complexity dynamics in schizophrenia (SCH) patients during an auditory oddball task. For this task, we applied a novel graph measure based on the balance of the node weights distribution. Previous studies applied complexity parameters that were strongly dependent on network topology. This could bias the results, as well as making correction techniques, such as surrogating process, necessary. In the present study, we applied a novel graph complexity measure derived from the information theory: Shannon Graph Complexity (SGC)...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28225867/investigating-ego-modules-and-pathways-in-osteosarcoma-by-integrating-the-egonet-algorithm-and-pathway-analysis
#8
X Y Chen, Y H Chen, L J Zhang, Y Wang, Z C Tong
Osteosarcoma (OS) is the most common primary bone malignancy, but current therapies are far from effective for all patients. A better understanding of the pathological mechanism of OS may help to achieve new treatments for this tumor. Hence, the objective of this study was to investigate ego modules and pathways in OS utilizing EgoNet algorithm and pathway-related analysis, and reveal pathological mechanisms underlying OS. The EgoNet algorithm comprises four steps: constructing background protein-protein interaction (PPI) network (PPIN) based on gene expression data and PPI data; extracting differential expression network (DEN) from the background PPIN; identifying ego genes according to topological features of genes in reweighted DEN; and collecting ego modules using module search by ego gene expansion...
February 16, 2017: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
https://www.readbyqxmd.com/read/28225608/time-dependent-markov-state-models-for-single-molecule-force-spectroscopy
#9
Susmita Ghosh, Abhijit Chatterjee, Swati Bhattacharya
This Letter demonstrates that using time-dependent Markov state models (TD-MSMs) one can obtain molecular-scale insights into force-extension curves for a variety of stretching experiments. A master-MSM constructed at a reference extension using a handful of molecular dynamics calculations forms the basis for generating the required TD-MSM. Changes in the network topology upon stretching is related through a thermodynamic quantity termed the mechanical disposition. Proof-of-principle is provided using a stretched alanine decapeptide under a time-varying pulling force...
February 22, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28225208/weak-supramolecular-interactions-governing-parallel-and-antiparallel-dna-quadruplexes-insights-from-large-scale-qm-analysis-of-experimentally-derived-models
#10
Yevgen P Yurenko, Jan Novotný, Radek Marek
The topology and energetics of guanine (G) quadruplexes is governed by supramolecular interactions within their strands. In this work, we performed an extensive QM study of supramolecular interactions shaping the stems of (4+0) parallel (P) and (2+2) antiparallel (AP) systems. The large-scale (~ 400 atoms) models of P and AP were constructed from high-quality experimental structures. The results evidence that each of the P and AP structures is shaped by a distinct network of supramolecular interactions. The analysis of electron topological characteristics of H-bonds in P and AP systems indicates that the P model benefits from the stronger intra-tetrad H-bonding...
February 22, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28225078/distribution-of-valence-electrons-of-the-flavin-cofactor-in-nadh-cytochrome-b5-reductase
#11
Kiyofumi Takaba, Kazuki Takeda, Masayuki Kosugi, Taro Tamada, Kunio Miki
Flavin compounds such as flavin adenine dinucleotide (FAD), flavin mononucleotide and riboflavin make up the active centers in flavoproteins that facilitate various oxidoreductive processes. The fine structural features of the hydrogens and valence electrons of the flavin molecules in the protein environment are critical to the functions of the flavoproteins. However, information on these features cannot be obtained from conventional protein X-ray analyses at ordinary resolution. Here we report the charge density analysis of a flavoenzyme, NADH-cytochrome b5 reductase (b5R), at an ultra-high resolution of 0...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28224978/methylated-antibody-affinity-purification-to-improve-proteomic-identification-of-plant-rna-polymerase-pol-v-complex-and-the-interacting-proteins
#12
Guochen Qin, Jun Ma, Xiaomei Chen, Zhaoqing Chu, Yi-Min She
Affinity purification followed by enzymatic digestion and mass spectrometry has been widely utilized for the sensitive detection of interacting proteins and protein complexes in various organisms. In plants, the method is technically challenging due to the low abundance proteins, non-specific binding and difficulties of eluting interacting proteins from antibody beads. In this report, we describe a strategy to modify antibodies by reductive methylation of lysines without affecting their binding properties, followed by on-bead digestion of bound proteins with endoproteinase Lys-C...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28224148/hypercrosslinked-porous-polymer-materials-design-synthesis-and-applications
#13
REVIEW
Liangxiao Tan, Bien Tan
Hypercrosslinked polymers (HCPs) are a series of permanent microporous polymer materials initially reported by Davankov, and have received an increasing level of research interest. In recent years, HCPs have experienced rapid growth due to their remarkable advantages such as diverse synthetic methods, easy functionalization, high surface area, low cost reagents and mild operating conditions. Judicious selection of monomers, appropriate length crosslinkers and optimized reaction conditions yielded a well-developed polymer framework with an adjusted porous topology...
February 22, 2017: Chemical Society Reviews
https://www.readbyqxmd.com/read/28224024/topological-and-functional-analysis-of-nonalcoholic-steatohepatitis-through-protein-interaction-mapping
#14
Hamid Asadzadeh-Aghdaee, Vahid Mansouri, Ali Asghar Peyvandi, Fathollah Moztarzadeh, Farshad Okhovatian, Farhad Lahmi, Reza Vafaee, Mohammad Reza Zali
AIM: The corresponding proteins are important for network mapping since the interaction analysis can provide a new interpretation about disease underlying mechanisms as the aim of this study. BACKGROUD: Nonalcoholic steatohepatitis (NASH) is one of the main causes of liver disease in the world. It has been known with many susceptible proteins that play essential role in its pathogenesis. METHODS: In this paper, protein-protein interaction (PPI) network analysis of fatty liver disease retrieved from STRING db by the application of Cytoscape Software...
December 2016: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/28222386/heterogeneous-fractionation-profiles-of-meta-analytic-coactivation-networks
#15
Angela R Laird, Michael C Riedel, Mershack Okoe, Radu Jianu, Kimberly L Ray, Simon B Eickhoff, Stephen M Smith, Peter T Fox, Matthew T Sutherland
Computational cognitive neuroimaging approaches can be leveraged to characterize the hierarchical organization of distributed, functionally specialized networks in the human brain. To this end, we performed large-scale mining across the BrainMap database of coordinate-based activation locations from over 10,000 task-based experiments. Meta-analytic coactivation networks were identified by jointly applying independent component analysis (ICA) and meta-analytic connectivity modeling (MACM) across a wide range of model orders (i...
February 18, 2017: NeuroImage
https://www.readbyqxmd.com/read/28221338/pathways-towards-instability-in-financial-networks
#16
Marco Bardoscia, Stefano Battiston, Fabio Caccioli, Guido Caldarelli
Following the financial crisis of 2007-2008, a deep analogy between the origins of instability in financial systems and complex ecosystems has been pointed out: in both cases, topological features of network structures influence how easily distress can spread within the system. However, in financial network models, the details of how financial institutions interact typically play a decisive role, and a general understanding of precisely how network topology creates instability remains lacking. Here we show how processes that are widely believed to stabilize the financial system, that is, market integration and diversification, can actually drive it towards instability, as they contribute to create cyclical structures which tend to amplify financial distress, thereby undermining systemic stability and making large crises more likely...
February 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28220840/coupling-effect-of-nodes-popularity-and-similarity-on-social-network-persistence
#17
Xiaogang Jin, Cheng Jin, Jiaxuan Huang, Yong Min
Network robustness represents the ability of networks to withstand failures and perturbations. In social networks, maintenance of individual activities, also called persistence, is significant towards understanding robustness. Previous works usually consider persistence on pre-generated network structures; while in social networks, the network structure is growing with the cascading inactivity of existed individuals. Here, we address this challenge through analysis for nodes under a coevolution model, which characterizes individual activity changes under three network growth modes: following the descending order of nodes' popularity, similarity or uniform random...
February 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28216560/from-sensor-networks-to-internet-of-things-bluetooth-low-energy-a-standard-for-this-evolution
#18
Diego Hortelano, Teresa Olivares, M Carmen Ruiz, Celia Garrido-Hidalgo, Vicente López
Current sensor networks need to be improved and updated to satisfy new essential requirements of the Internet of Things, where cutting-edge applications will appear. These requirements are: total coverage, zero fails (high performance), scalability and sustainability (hardware and software). We are going to evaluate Bluetooth Low Energy as wireless transmission technology and as the ideal candidate for these improvements, due to its low power consumption, its low cost radio chips and its ability to communicate with users directly, using their smartphones or smartbands...
February 14, 2017: Sensors
https://www.readbyqxmd.com/read/28215988/a-computational-model-of-the-respiratory-network-challenged-and-optimized-by-data-from-optogenetic-manipulation-of-glycinergic-neurons
#19
Yoshitaka Oku, Swen Hülsmann
The topology of the respiratory network in the brainstem has been addressed using different computational models, which help to understand the functional properties of the system. We tested a neural mass model by comparing the result of activation and inhibition of inhibitory neurons in silico with recently published results of optogenetic manipulation of glycinergic neurons [Sherman, et al. (2015) Nat Neurosci 18:408]. The comparison revealed that a five-cell type model consisting of three classes of inhibitory neurons [I-DEC, E-AUG, E-DEC (PI)] and two excitatory populations (pre-I/I) and (I-AUG) neurons can be applied to explain experimental observations made by stimulating or inhibiting inhibitory neurons by light sensitive ion channels...
February 13, 2017: Neuroscience
https://www.readbyqxmd.com/read/28212785/the-role-of-driver-nodes-in-managing-epileptic-seizures-application-of-kuramoto-model
#20
Ali Mohseni, Shahriar Gharibzadeh, Fatemeh Bakouie
Synchronization is an important global phenomenon which could be found in a wide range of complex systems such as brain or electronic devices. However, in some circumstances the synchronized states are not desirable for the system and should be suppressed. For example, excessively synchronized activities in the brain network could be the root of neuronal disorders like epileptic seizures. According to the controllability theory of the complex networks, a minimum set of driver nodes has the ability to control the entire system...
February 15, 2017: Journal of Theoretical Biology
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