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https://www.readbyqxmd.com/read/28231448/finding-the-optimal-tradeoffs
#1
Shibin Mathew, Amy E Thurber, Suzanne Gaudet
Computational analyses of a half-million circuit topologies provide a rationale for why certain fold-change detection topologies are more prevalent in nature.
February 22, 2017: Cell Systems
https://www.readbyqxmd.com/read/28231324/a-framework-for-analyzing-contagion-in-assortative-banking-networks
#2
Thomas R Hurd, James P Gleeson, Sergey Melnik
We introduce a probabilistic framework that represents stylized banking networks with the aim of predicting the size of contagion events. Most previous work on random financial networks assumes independent connections between banks, whereas our framework explicitly allows for (dis)assortative edge probabilities (i.e., a tendency for small banks to link to large banks). We analyze default cascades triggered by shocking the network and find that the cascade can be understood as an explicit iterated mapping on a set of edge probabilities that converges to a fixed point...
2017: PloS One
https://www.readbyqxmd.com/read/28230817/common%C3%A2-chemical%C3%A2-inductors%C3%A2-of%C3%A2-replication%C3%A2-stress-%C3%A2-focus%C3%A2-on%C3%A2-cell-based%C3%A2-studies
#3
REVIEW
Eva Vesela, Katarina Chroma, Zsofia Turi, Martin Mistrik
DNA replication is a highly demanding process regarding the energy and material supply and must be precisely regulated, involving multiple cellular feedbacks. The slowing down or stalling of DNA synthesis and/or replication forks is referred to as replication stress (RS). Owing to the complexity and requirements of replication, a plethora of factors may interfere and challenge the genome stability, cell survival or affect the whole organism. This review outlines chemical compounds that are known inducers of RS and commonly used in laboratory research...
February 21, 2017: Biomolecules
https://www.readbyqxmd.com/read/28230364/modeling-protein-conformational-transition-pathways-using-collective-motions-and-the-lasso-method
#4
Thomas W Hayes, Iain H Moal
Many proteins can adopt multiple distinct conformational states which often play different functional roles. Previous studies have shown that the underlying global dynamics through which these states are accessed are, at least in part, encoded by the protein's topology. In this work we present a method for generating transition pathways between states by perturbing the protein towards a target conformational state along thermally accessible collective motions calculated from the starting conformation. Specifically, the least absolute shrinkage and selection operator (LASSO) is used to identify the most parsimonious route along soft modes calculated using the anisotropic network model...
February 23, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28230166/a-universal-indicator-of-critical-state-transitions-in-noisy-complex-networked-systems
#5
Junhao Liang, Yanqing Hu, Guanrong Chen, Tianshou Zhou
Critical transition, a phenomenon that a system shifts suddenly from one state to another, occurs in many real-world complex networks. We propose an analytical framework for exactly predicting the critical transition in a complex networked system subjected to noise effects. Our prediction is based on the characteristic return time of a simple one-dimensional system derived from the original higher-dimensional system. This characteristic time, which can be easily calculated using network data, allows us to systematically separate the respective roles of dynamics, noise and topology of the underlying networked system...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28230164/dynamical-majorana-edge-modes-in-a-broad-class-of-topological-mechanical-systems
#6
Emil Prodan, Kyle Dobiszewski, Alokik Kanwal, John Palmieri, Camelia Prodan
Mechanical systems can display topological characteristics similar to that of topological insulators. Here we report a large class of topological mechanical systems related to the BDI symmetry class. These are self-assembled chains of rigid bodies with an inversion centre and no reflection planes. The particle-hole symmetry characteristic to the BDI symmetry class stems from the distinct behaviour of the translational and rotational degrees of freedom under inversion. This and other generic properties led us to the remarkable conclusion that, by adjusting the gyration radius of the bodies, one can always simultaneously open a gap in the phonon spectrum, lock-in all the characteristic symmetries and generate a non-trivial topological invariant...
February 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28230047/electrically-tunable-artificial-gauge-potential-for-polaritons
#7
Hyang-Tag Lim, Emre Togan, Martin Kroner, Javier Miguel-Sanchez, Atac Imamoğlu
Neutral particles subject to artificial gauge potentials can behave as charged particles in magnetic fields. This fascinating premise has led to demonstrations of one-way waveguides, topologically protected edge states and Landau levels for photons. In ultracold neutral atoms, effective gauge fields have allowed the emulation of matter under strong magnetic fields leading to realization of Harper-Hofstadter and Haldane models. Here we show that application of perpendicular electric and magnetic fields effects a tunable artificial gauge potential for two-dimensional microcavity exciton polaritons...
February 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28229152/an-anionic-metal-organic-framework-with-ternary-building-units-for-rapid-and-selective-adsorption-of-dyes
#8
Shuo Yao, Tong Xu, Nian Zhao, Lirong Zhang, Qisheng Huo, Yunling Liu
A novel metal-organic framework, [(CH3)2NH2]2[Cu3O(SO4)3Cu2L2(DMF)(H2O)]·9DMF (JLU-Liu39) H2L = pyridine-3,5-bis(phenyl-4-carboxylic acid), has been successfully synthesized under solvothermal conditions. Structure analysis indicates that the framework of JLU-Liu39 is constructed by ternary building units which include a rare hexa-nuclear [Cu6O2(SO4)6] cluster, a classical [Cu2(CO2)4] paddlewheel, and a 3-connected hetero-N, O donor ligand. The whole 3D framework possesses a (3,4,4)-connected fjh topology and a large window size of 25...
February 23, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28229131/discovering-cortical-folding-patterns-in-neonatal-cortical-surfaces-using-large-scale-dataset
#9
Yu Meng, Gang Li, Li Wang, Weili Lin, John H Gilmore, Dinggang Shen
The cortical folding of the human brain is highly complex and variable across individuals. Mining the major patterns of cortical folding from modern large-scale neuroimaging datasets is of great importance in advancing techniques for neuroimaging analysis and understanding the inter-individual variations of cortical folding and its relationship with cognitive function and disorders. As the primary cortical folding is genetically influenced and has been established at term birth, neonates with the minimal exposure to the complicated postnatal environmental influence are the ideal candidates for understanding the major patterns of cortical folding...
October 2016: Medical Image Computing and Computer-assisted Intervention: MICCAI ..
https://www.readbyqxmd.com/read/28228094/sfreemap-a-simulation-free-tool-for-stochastic-mapping
#10
Diego Pasqualin, Marcos Barbeitos, Fabiano Silva
BACKGROUND: Stochastic mapping is frequently used in comparative biology to simulate character evolution, enabling the probabilistic computation of statistics such as number of state transitions along a tree and distribution of states in its internal nodes. Common implementations rely on Continuous-time Markov Chain simulations whose parameters are difficult to adjust and subjected to inherent inaccuracy. Thus, researchers must run a large number of simulations in order to obtain adequate estimates...
February 22, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28228022/electron-nuclear-wave-packet-dynamics-through-a-conical-intersection
#11
Kilian Hader, Julian Albert, E K U Gross, Volker Engel
We investigate the coupled electron-nuclear dynamics in a model system showing a conical intersection (CoIn) between two excited state potential energy surfaces. Within the model, a single electron and nucleus move in two dimensions in an external static field. It is demonstrated that the nuclear density conserves its initial Gaussian shape when directly passing the CoIn, whereas the electronic density remains approximately constant. This is in sharp contrast to the picture which evolves from an analysis within the basis of adiabatic electronic states...
February 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28227912/a-hybrid-discrete-continuous-model-of-in-vitro-spheroid-tumor-growth-and-drug-response
#12
Giorgos Tzedakis, Evangelos Liapis, Eleftheria Tzamali, Giannis Zacharakis, Vangelis Sakkalis, Giorgos Tzedakis, Evangelos Liapis, Eleftheria Tzamali, Giannis Zacharakis, Vangelis Sakkalis, Giannis Zacharakis, Vangelis Sakkalis, Evangelos Liapis, Giorgos Tzedakis, Eleftheria Tzamali
Anti-cancer therapy efficacy in solid tumors mainly depends on drug transportation through the vasculature system and the extracellular matrix, on diffusion gradients and clonal heterogeneity within the tumor mass, as well as on the responses of the individual tumor cells to drugs and their interactions with each other and their local microenvironment. In this work, we develop a mathematical predictive model for tumor growth and drug response based on 3D spheroids experiments that possess several in vivo features of tumors and are considered better for drug screening...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227870/identifying-disease-network-perturbations-through-regression-on-gene-expression-and-pathway-topology-analysis
#13
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/28227813/a-110-nw-in-channel-sigma-delta-converter-for-large-scale-neural-recording-implants
#14
M Rezaei, E Maghsoudloo, M Sawan, B Gosselin, M Rezaei, E Maghsoudloo, M Sawan, B Gosselin, M Rezaei, E Maghsoudloo, M Sawan, B Gosselin
Advancement in wireless and microsystems technology have ushered in new devices that can directly interface with the central nervous system for stimulating and/or monitoring neural circuitry. In this paper, we present an ultra low-power sigma-delta analog-to-digital converter (ADC) intended for utilization into large-scale multi-channel neural recording implants. This proposed design, which provides a resolution of 9 bits using a one-bit oversampled ADC, presents several desirable features that allow for an in-channel ADC scheme, where one sigma-delta converter is provided for each channel, enabling development of scalable systems that can interface with different types of high-density neural microprobes...
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
#15
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
#16
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/28227524/a-feasibility-study-of-using-event-related-potential-as-a-biometrics
#17
Yih-Choung Yu, Sicheng Wang, Lisa A Gabel, Yih-Choung Yu, Sicheng Wang, Lisa A Gabel, Lisa A Gabel, Yih-Choung Yu, Sicheng Wang
The use of an individual's neural response to stimuli (the event-related potential or ERP) has potential as a biometric because it is highly resistant to fraud relative to other conventional authentication systems. P300 is an ERP in human electroencephalography (EEG) that occurs in response to an oddball stimulus when an individual is actively engaged in a target detection task. Because P300 is consistently detectable from almost every subject, it is considered a potential signal for biometric applications...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227427/inexact-coronary-tree-matching-algorithm-with-artificial-nodes
#18
Helene Feuillatre, Jean-Claude Nunes, Christine Toumoulin, Helene Feuillatre, Jean-Claude Nunes, Christine Toumoulin, Jean-Claude Nunes, Helene Feuillatre, Christine Toumoulin
Coronary tree matching is applied to plan percutaneous vascular procedures. This work, which allows following each segment of non-isomorphic coronary trees over time, precedes the determination of the best 2D angiography view from C-arm acquisition system for angioplasty procedure. To match two 3D coronary trees which represent two successive cardiac phases, we adapted a reference inexact tree matching algorithm based on association graph and maximum clique. To improve the pair-wise matching performance of our approach, artificial nodes are introduced to take into account the topology variation between 3D vascular trees...
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
#19
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
#20
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
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