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Divergent topological networks in Alzheimer's disease: a diffusion kurtosis imaging analysis

Jia-Xing Cheng, Hong-Ying Zhang, Zheng-Kun Peng, Yao Xu, Hui Tang, Jing-Tao Wu, Jun Xu
2018 Translational Neurodegeneration  
Results: We found small world characteristics of DKI networks not only in the normal subjects but also in the AD patients; Grey matter networks of AD patients tended to be a less optimized network.  ...  Brain networks were constructed by the correlation matrices of 90 regions and analyzed through graph theoretical approaches.  ...  Funding This work was supported by the National Natural Science Foundation of China (Grants NO. 81471642, 81571652, 81271211, 81471215), Natural Science Foundation of Jiangsu Province (Grants NO.BK20151592  ... 
doi:10.1186/s40035-018-0115-y pmid:29719719 pmcid:PMC5921324 fatcat:ydnifdbqmjc5bj6fhy5gdinwjm

Communication and wiring in the cortical connectome

Julian M. L. Budd, Zoltán F. Kisvárday
2012 Frontiers in Neuroanatomy  
In contrast, we have hypothesized the existence of a multi-scale principle of cortical wiring where to optimize communication there is a trade-off between spatial (construction) and temporal (routing)  ...  A popular explanation has been that axonal length is strictly minimized both within and between cortical regions.  ...  Axon arbors To analyze the wiring characteristics of single intracortical axon arbors, Budd et al. (2010) applied a range of graph theory optimization techniques to 19 in vivo reconstructions of excitatory  ... 
doi:10.3389/fnana.2012.00042 pmid:23087619 pmcid:PMC3472565 fatcat:qfykiduscvcwlpfryydpdepf6e

Artificial Neural Networks for Modelling of the Impact Toughness of Steel

D. Dunne, H. Tsuei, Z. Sterjovski
2004 ISIJ International  
The number of hidden layers and the number of processing elements in each layer determine the "topology" of the neural network and affect the accuracy of the trained network.  ...  The changes in weights are made "backwards", from the output layer through each hidden layer.  ... 
doi:10.2355/isijinternational.44.1599 fatcat:26d6imsi65dqjhxw2cdcrh3jxm

Disordered systems on various time scales: a-Si3B3N7 and homogeneous sintering [article]

J. C. Schon, A. Hannemann, G. Sethi, M. Jansen, P. Salamon, R. Frost, L. Kjeldgaard
2002 arXiv   pre-print
Modeling of materials systems for long times commonly requires the use of separation of time scale methods.  ...  We discuss this general approach and present two example systems, a-Si3B3N7 and the generation of homogeneous sinters.  ...  in the topology of the network.  ... 
arXiv:cond-mat/0212279v1 fatcat:uxphxqpwgncypkthwtr2wosb3q

Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)

Benedict Borer, Meriç Ataman, Vassily Hatzimanikatis, Dani Or, Jennifer L. Reed
2019 PLoS Computational Biology  
carbon gradients, and provides insights into dynamic community responses as a consequence of environmental changes.  ...  The model uses angular pore networks and a physically based description of the aqueous phase as a backbone for nutrient diffusion and bacterial dispersal combined with dynamic flux balance analysis to  ...  Through the integration of metabolic networks and additional intermediate metabolites in the form of acetate (to ensure mass balance of carbon within the simulation), the cooperation between the species  ... 
doi:10.1371/journal.pcbi.1007127 pmid:31216273 pmcid:PMC6583959 fatcat:h5yv22esjvhbrpacilxexpjoti

Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis

Gustavo Caetano-Anollés, M Fayez Aziz, Fizza Mughal, Frauke Gräter, Ibrahim Koç, Kelsey Caetano-Anollés, Derek Caetano-Anollés
2019 Evolutionary Bioinformatics  
Remarkably, phylogenomic analyses uncover this emergence in the rewiring of metabolomic and transcriptome-informed metabolic networks, the nanosecond dynamics of proteins, and evolving networks of metabolism  ...  The paradigm predicts the rise of hierarchical modularity in evolving networks at different timescales and complexity levels.  ...  In turn, diversification can be defined as the gradual accumulation of change and the diffusional spread of variation through time.  ... 
doi:10.1177/1176934319872980 pmid:31523127 pmcid:PMC6728656 fatcat:pundw72czjfwhc6gv2wnxktdvq

Inference of neuronal network spike dynamics and topology from calcium imaging data

Henry Lütcke, Felipe Gerhard, Friedemann Zenke, Wulfram Gerstner, Fritjof Helmchen
2013 Frontiers in Neural Circuits  
We then applied statistical neuronal network models to explore how remaining uncertainties in spike inference affect estimates of network connectivity and topological features of network organization.  ...  We define the experimental conditions suitable for inferring whether the network has a scale-free structure and determine how well hub neurons can be identified.  ...  IDENTIFICATION OF GRAPH TOPOLOGY Scale-free networks We generated scale-free networks of size 1000 neurons by constructing unweighted, undirected graphs whose degree distributions follow a power law  ... 
doi:10.3389/fncir.2013.00201 pmid:24399936 pmcid:PMC3871709 fatcat:jxxzhgrasvderm3y6fq54inoqu

Emergent Synchronous Bursting of Oxytocin Neuronal Network

Enrico Rossoni, Jianfeng Feng, Brunello Tirozzi, David Brown, Gareth Leng, Françoise Moos, Karl J. Friston
2008 PLoS Computational Biology  
Network Topology A key element of our model is the topology of network connections, which differs from all other topologies of biological networks in the literature.  ...  The topology of the networks is very different -the present network is very sparsely connected compared to others (e.g.  ... 
doi:10.1371/journal.pcbi.1000123 pmid:18636098 pmcid:PMC2440533 fatcat:syyfai3epfhpvgpctheo6nj75i

Simulation of Biochemical Reactions with ANN-Dependent Kinetic Parameter Extraction Method

Fei Tan, Jin Xu
2022 Electronics  
Swarm Optimization (PSO) algorithm to obtain the globally optimum parameters in both the simulation and data fitting.  ...  To reach our goal, we simulated the chemical or biological reactions as system of differential equations, employed artificial neural networks (ANN) to model experimentally measured data, and utilized Particle  ...  The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results'.  ... 
doi:10.3390/electronics11020216 fatcat:55qzi6mf7jewdcpwuq4t7lopnu

A Critical Evaluation of Clinical Trials in Cancer and Pharmacogenomics

I. Baianu
2012 Nature Precedings  
A Human Cancer Genomes and Epigenetics Project is proposed that can provide the essential data required for the optimal design of clinical trials with the goal of achieving significant improvements of  ...  Potentially important applications of such results are individualized human cancer therapies or, in general, 'personalized medicine' that will have to be validated through optimally designed clinical trials  ...  Mark Band, Director of the Genotyping/Transcriptomics Unit at the Keck Center, Dr.  ... 
doi:10.1038/npre.2012.7052.1 fatcat:2i2iaewtzjbizmlxbbg5zpporq

Understanding cytoskeletal avalanches using mechanical stability analysis [article]

Carlos Floyd, Herbert Levine, Christopher Jarzynski, Garegin A. Papoian
2021 arXiv   pre-print
We also find that the changes in the localization of tension and the projections of the network motion onto the vibrational normal modes are asymmetrically distributed for energy release and accumulation  ...  These cytoskeletal avalanches might indicate that the cytoskeleton's structural response to a changing cellular environment is highly sensitive, and they are therefore of significant biological interest  ...  Representing network topology as a graph We construct a graph to represent the cross-linker binding topology of cytoskeletal networks.  ... 
arXiv:2006.01884v4 fatcat:a34aajzvjjc4ji3xbo2hmq7a6a

Recruitment of 53BP1 Proteins for DNA Repair and Persistence of Repair Clusters Differ for Cell Types as Detected by Single Molecule Localization Microscopy

Elizaveta Bobkova, Daniel Depes, Jin-Ho Lee, Lucie Jezkova, Iva Falkova, Eva Pagacova, Olga Kopecna, Mariia Zadneprianetc, Alena Bacikova, Elena Kulikova, Elena Smirnova, Tatiana Bulanova (+7 others)
2018 International Journal of Molecular Sciences  
Clusters of these tags were determined as sub-units of repair foci according to SMLM parameters. The formation and relaxation of such clusters was studied.  ...  the important players participating in repair pathway decision of the cell.  ...  Since the formation of sub-units (represented by clusters of labeling points defined by SMLM parameters) within the foci has been described as a topological finding of central importance, the evolution  ... 
doi:10.3390/ijms19123713 pmid:30469529 fatcat:kbvggonkinbdpcyce36e6qtgbm

Genome-wide identification and characterisation of Aquaporins in Nicotiana tabacum and their relationships with other Solanaceae species

Annamaria De Rosa, Alexander Watson-Lazowski, John R. Evans, Michael Groszmann
2020 BMC Plant Biology  
post-translational regulatory mechanisms; collectively providing a dynamic transportation network spanning the entire plant.  ...  This study provides a comprehensive characterisation of the tobacco AQP family, and strengthens the current knowledge of AQP biology.  ...  of the Australian Plant Phenomics Facility.  ... 
doi:10.1186/s12870-020-02412-5 pmid:32517797 fatcat:g7umrpaj2zd5hbzlkz5diomwgq

Revealing sol–gel type main effects by exploring a molecular cluster behavior in model in-plane amphiphilic aggregations

N. Kruszewska, A. Gadomski
2010 Physica A: Statistical Mechanics and its Applications  
The distribution of ordered fringed micelles, and the overall crystalline inclusions of the gel phase, suggested a first-order phase change, reasonably conceivable in terms of Avrami-Kolmogorov formalism  ...  Then, the conformational behavior is distributed over the aggregations obtained, with the aim of revealing their main sol-gel type (viscoelastic) effects.  ...  enough, over them by mentioning the relevance of certain topological and geometrical sub-effects involved in any gel creation, such as the ones referring to the close-packing conditions, and those where  ... 
doi:10.1016/j.physa.2010.04.012 fatcat:t7h24ldvxfbzllesextoischci

Translational Oncogenomics and Human Cancer Interactomics: Advanced Techniques and Complex System Dynamic Approaches [chapter]

I. C.
2011 Bioinformatics - Trends and Methodologies  
Several cancer detection techniques are currently under development both in the direction of improved detection sensitivity and increased time resolution of cellular events, with the limits of single molecule  ...  Novel translational oncogenomics research is rapidly expanding through the application of advanced technology, research findings and computational tools/models to both pharmaceutical and clinical problems  ...  The characteristic diffusion time through the laserilluminated focal spot of the 0.5 µm-diameter objective increased from 0.13 to 0.20 ms for the free probe, and from 0.37 to 0.50 ms for the bound probe  ... 
doi:10.5772/18781 fatcat:op7ul67t6fak5hu5afvjknbijq
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