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https://www.readbyqxmd.com/read/29786557/the-gene-regulatory-network-of-mesc-differentiation-a-benchmark-for-reverse-engineering-methods
#1
Johannes Meisig, Nils Blüthgen
A large body of data have accumulated that characterize the gene regulatory network of stem cells. Yet, a comprehensive and integrative understanding of this complex network is lacking. Network reverse engineering methods that use transcriptome data to derive these networks may help to uncover the topology in an unbiased way. Many methods exist that use co-expression to reconstruct networks. However, it remains unclear how these methods perform in the context of stem cell differentiation, as most systematic assessments have been made for regulatory networks of unicellular organisms...
July 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29785073/scale-free-networks-in-metabolomics
#2
Hema Sekhar Reddy Rajula, Matteo Mauri, Vassilios Fanos
Metabolomics is an expanding discipline in biology. It is the process of portraying the phenotype of a cell, tissue or species organism using a comprehensive set of metabolites. Therefore, it is of interest to understand complex systems such as metabolomics using a scale-free topology. Genetic networks and the World Wide Web (WWW) are described as networks with complex topology. Several large networks have vertex connectivity that goes beyond a scale-free power-law distribution. It is observed that (a) networks expand constantly by the addition of recent vertices, and (b) recent vertices attach preferentially to sites that are already well connected...
2018: Bioinformation
https://www.readbyqxmd.com/read/29785055/mindfulness-training-induces-structural-connectome-changes-in-insula-networks
#3
Paul B Sharp, Bradley P Sutton, Erick J Paul, Nikolai Sherepa, Charles H Hillman, Neal J Cohen, Arthur F Kramer, Ruchika Shaurya Prakash, Wendy Heller, Eva H Telzer, Aron K Barbey
Although mindfulness meditation is known to provide a wealth of psychological benefits, the neural mechanisms involved in these effects remain to be well characterized. A central question is whether the observed benefits of mindfulness training derive from specific changes in the structural brain connectome that do not result from alternative forms of experimental intervention. Measures of whole-brain and node-level structural connectome changes induced by mindfulness training were compared with those induced by cognitive and physical fitness training within a large, multi-group intervention protocol (n = 86)...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784945/author-correction-enabling-controlling-complex-networks-with-local-topological-information
#4
Guoqi Li, Lei Deng, Gaoxi Xiao, Pei Tang, Changyun Wen, Wuhua Hu, Jing Pei, Luping Shi, H Eugene Stanley
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
May 22, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29783701/nonnative-energetic-frustrations-in-protein-folding-at-residual-level-a-simulation-study-of-homologous-immunoglobulin-like-%C3%AE-sandwich-proteins
#5
Yunxiang Sun, Feng Ding, Dengming Ming
Nonnative interactions cause energetic frustrations in protein folding and were found to dominate key events in folding intermediates. However, systematically characterizing energetic frustrations that are caused by nonnative intra-residue interactions at residual resolution is still lacking. Recently, we studied the folding of a set of homologous all- α proteins and found that nonnative-contact-based energetic frustrations are highly correlated to topology of the protein native-contact network. Here, we studied the folding of nine homologous immunoglobulin-like (Ig-like) β -sandwich proteins, and examined nonnative-contact-based energetic frustrations Gō-like model...
May 18, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29781597/single-crystalline-uio-67-type-porous-network-stable-to-boiling-water-solvent-loss-and-oxidation
#6
Yan-Lung Wong, Ka-Kit Yee, Yun-Long Hou, Jiaqian Li, Zuankai Wang, Matthias Zeller, Allen D Hunter, Zhengtao Xu
With methylthio groups flanking the carboxyl groups, the 3,3',5,5'-tetrakis(methylthio)biphenyl dicarboxylate (TMBPD) linker forms a zirconium(IV) carboxylate porous framework featuring the topology of the UiO-67 prototype, i.e., with a face-centered-cubic array of the Zr6 O4 (OH)4 clusters. Thioether functionalization proves valuable because the ZrTMBPD crystal is found to be exceptionally stable not only upon long-term exposure to air but also in boiling water and a broad range of pH conditions. The hydrophobicity of the metal-organic framework can also be tuned by simple H2 O2 oxidation, as illustrated in the water contact-angle measurement of the pristine and H2 O2 -treated ZrTMBPD solid...
May 21, 2018: Inorganic Chemistry
https://www.readbyqxmd.com/read/29778791/evolutionary-transitions-in-controls-reconcile-adaptation-with-continuity-of-evolution
#7
REVIEW
Alexander V Badyaev
Evolution proceeds by accumulating functional solutions, necessarily forming an uninterrupted lineage from past solutions of ancestors to the current design of extant forms. At the population level, this process requires an organismal architecture in which the maintenance of local adaptation does not preclude the ability to innovate in the same traits and their continuous evolution. Representing complex traits as networks enables us to visualize a fundamental principle that resolves tension between adaptation and continuous evolution: phenotypic states encompassing adaptations traverse the continuous multi-layered landscape of past physical, developmental and functional associations among traits...
May 17, 2018: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/29778329/the-kinetoplast-dna-of-the-australian-trypanosome-trypanosoma-copemani-shares-features-with-trypanosoma-cruzi-and-trypanosoma-lewisi
#8
Adriana Botero, Irit Kapeller, Crystal Cooper, Peta L Clode, Joseph Shlomai, R C Andrew Thompson
Kinetoplast DNA (kDNA) is the mitochondrial genome of trypanosomatids. It consists of a few dozen maxicircles and several thousand minicircles, all catenated topologically to form a two-dimensional DNA network. Minicircles are heterogeneous in size and sequence among species. They present one or several conserved regions that contain three highly conserved sequence blocks (CSBs). CSB-1 (10 bp sequence) and CSB-2 (8 bp sequence) present lower interspecies homology, while CSB-3 (12 bp sequence) or the Universal Minicircle Sequence (UMS) is conserved within most trypanosomatids...
May 17, 2018: International Journal for Parasitology
https://www.readbyqxmd.com/read/29776185/master-stability-functions-reveal-diffusion-driven-pattern-formation-in-networks
#9
Andreas Brechtel, Philipp Gramlich, Daniel Ritterskamp, Barbara Drossel, Thilo Gross
We study diffusion-driven pattern formation in networks of networks, a class of multilayer systems, where different layers have the same topology, but different internal dynamics. Agents are assumed to disperse within a layer by undergoing random walks, while they can be created or destroyed by reactions between or within a layer. We show that the stability of homogeneous steady states can be analyzed with a master stability function approach that reveals a deep analogy between pattern formation in networks and pattern formation in continuous space...
March 2018: Physical Review. E
https://www.readbyqxmd.com/read/29776147/sparse-dynamical-boltzmann-machine-for-reconstructing-complex-networks-with-binary-dynamics
#10
Yu-Zhong Chen, Ying-Cheng Lai
Revealing the structure and dynamics of complex networked systems from observed data is a problem of current interest. Is it possible to develop a completely data-driven framework to decipher the network structure and different types of dynamical processes on complex networks? We develop a model named sparse dynamical Boltzmann machine (SDBM) as a structural estimator for complex networks that host binary dynamical processes. The SDBM attains its topology according to that of the original system and is capable of simulating the original binary dynamical process...
March 2018: Physical Review. E
https://www.readbyqxmd.com/read/29776076/complex-network-view-of-evolving-manifolds
#11
Diamantino C da Silva, Ginestra Bianconi, Rui A da Costa, Sergey N Dorogovtsev, José F F Mendes
We study complex networks formed by triangulations and higher-dimensional simplicial complexes representing closed evolving manifolds. In particular, for triangulations, the set of possible transformations of these networks is restricted by the condition that at each step, all the faces must be triangles. Stochastic application of these operations leads to random networks with different architectures. We perform extensive numerical simulations and explore the geometries of growing and equilibrium complex networks generated by these transformations and their local structural properties...
March 2018: Physical Review. E
https://www.readbyqxmd.com/read/29774244/classification-and-characterisation-of-brain-network-changes-in-chronic-back-pain-a-multicenter-study
#12
Hiroaki Mano, Gopal Kotecha, Kenji Leibnitz, Takashi Matsubara, Aya Nakae, Nicholas Shenker, Masahiko Shibata, Valerie Voon, Wako Yoshida, Michael Lee, Toshio Yanagida, Mitsuo Kawato, Maria Joao Rosa, Ben Seymour
Background. Chronic pain is a common, often disabling condition thought to involve a combination of peripheral and central neurobiological factors. However, the extent and nature of changes in the brain is poorly understood. Methods. We investigated brain network architecture using resting-state fMRI data in chronic back pain patients in the UK and Japan (41 patients, 56 controls), as well as open data from USA. We applied machine learning and deep learning (conditional variational autoencoder architecture) methods to explore classification of patients/controls based on network connectivity...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29770832/high-strain-slide-ring-shape-memory-polycaprolactone-based-polyurethane
#13
Ruiqing Wu, Jingjuan Lai, Yi Pan, Zhaohui Zheng, Xiaobin Ding
To enable shape-memory polymer networks to achieve recoverable high deformability with a simultaneous high shape-fixity ratio and shape-recovery ratio, novel semi-crystalline slide-ring shape-memory polycaprolactone-based polyurethane (SR-SMPCLU) with movable net-points constructed by a topologically interlocked slide-ring structure was designed and fabricated. The SR-SMPCLU not only exhibited good shape fixity, almost complete shape recovery, and a fast shape-recovery speed, it also showed an outstanding recoverable high-strain capacity with 95...
May 17, 2018: Soft Matter
https://www.readbyqxmd.com/read/29767230/competing-endogenous-rna-regulatory-network-in-papillary-thyroid-carcinoma
#14
Shouhua Chen, Xiaobin Fan, He Gu, Lili Zhang, Wenhua Zhao
The present study aimed to screen all types of RNAs involved in the development of papillary thyroid carcinoma (PTC). RNA‑sequencing data of PTC and normal samples were used for screening differentially expressed (DE) microRNAs (DE‑miRNAs), long non‑coding RNAs (DE‑lncRNAs) and genes (DEGs). Subsequently, lncRNA‑miRNA, miRNA‑gene (that is, miRNA‑mRNA) and gene‑gene interaction pairs were extracted and used to construct regulatory networks. Feature genes in the miRNA‑mRNA network were identified by topological analysis and recursive feature elimination analysis...
May 11, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29764727/the-spring-of-systems-biology-driven-breeding
#15
REVIEW
Jérémy Lavarenne, Soazig Guyomarc'h, Christophe Sallaud, Pascal Gantet, Mikaël Lucas
Genetics and molecular biology have contributed to the development of rationalized plant breeding programs. Recent developments in both high-throughput experimental analyses of biological systems and in silico data processing offer the possibility to address the whole gene regulatory network (GRN) controlling a given trait. GRN models can be applied to identify topological features helping to shortlist potential candidate genes for breeding purposes. Time-series data sets can be used to support dynamic modelling of the network...
May 12, 2018: Trends in Plant Science
https://www.readbyqxmd.com/read/29764688/bridgehead-effects-and-role-of-adaptive-evolution-in-invasive-populations
#16
REVIEW
Cleo Bertelsmeier, Laurent Keller
Biological invasions are a major threat to biodiversity, agriculture, and human health. Invasive populations can be the source of additional new introductions, leading to a self-accelerating process whereby invasion begets invasion. This phenomenon, coined bridgehead effect, has been proposed to stem from the evolution of higher invasiveness in a primary introduced population. There is, however, no conclusive evidence that the success of bridgehead populations stems from the evolution of increased invasiveness...
May 12, 2018: Trends in Ecology & Evolution
https://www.readbyqxmd.com/read/29761954/-research-on-brain-white-matter-network-in-cerebral-palsy-infant
#17
Jun Li, Cheng Yang, Yuanjun Wang, Shengdong Nie
Present study used diffusion tensor image and tractography to construct brain white matter networks of 15 cerebral palsy infants and 30 healthy infants that matched for age and gender. After white matter network analysis, we found that both cerebral palsy and healthy infants had a small-world topology in white matter network, but cerebral palsy infants exhibited abnormal topological organization: increased shortest path length but decreased normalize clustering coefficient, global efficiency and local efficiency...
October 1, 2017: Sheng Wu Yi Xue Gong Cheng Xue za Zhi, Journal of Biomedical Engineering, Shengwu Yixue Gongchengxue Zazhi
https://www.readbyqxmd.com/read/29759817/enhancer-logic-and-mechanics-in-development-and-disease
#18
REVIEW
Ryan Rickels, Ali Shilatifard
Enhancers are distally located genomic cis-regulatory elements that integrate spatiotemporal cues to coordinate gene expression in a tissue-specific manner during metazoan development. Enhancer function depends on a combination of bound transcription factors and cofactors that regulate local chromatin structure, as well as on the topological interactions that are necessary for their activity. Numerous genome-wide studies concur that the vast majority of disease-associated variations occur within non-coding genomic sequences, in other words the 'cis-regulome', and this underscores their relevance for human health...
May 11, 2018: Trends in Cell Biology
https://www.readbyqxmd.com/read/29758756/resilience-of-networks-to-environmental-stress-from-regular-to-random-networks
#19
Young-Ho Eom
Despite the huge interest in network resilience to stress, most of the studies have concentrated on internal stress damaging network structure (e.g., node removals). Here we study how networks respond to environmental stress deteriorating their external conditions. We show that, when regular networks gradually disintegrate as environmental stress increases, disordered networks can suddenly collapse at critical stress with hysteresis and vulnerability to perturbations. We demonstrate that this difference results from a trade-off between node resilience and network resilience to environmental stress...
April 2018: Physical Review. E
https://www.readbyqxmd.com/read/29758747/spontaneous-repulsion-in-the-a-b%C3%A2-0-reaction-on-coupled-networks
#20
Filippos Lazaridis, Bnaya Gross, Michael Maragakis, Panos Argyrakis, Ivan Bonamassa, Shlomo Havlin, Reuven Cohen
We study the transient dynamics of an A+B→0 process on a pair of randomly coupled networks, where reactants are initially separated. We find that, for sufficiently small fractions q of cross couplings, the concentration of A (or B) particles decays linearly in a first stage and crosses over to a second linear decrease at a mixing time t_{x}. By numerical and analytical arguments, we show that for symmetric and homogeneous structures t_{x}∝(〈k〉/q)log(〈k〉/q) where 〈k〉 is the mean degree of both networks...
April 2018: Physical Review. E
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