keyword
MENU ▼
Read by QxMD icon Read
search

Complex Network

keyword
https://www.readbyqxmd.com/read/27923202/structure-based-optimization-of-salt-bridge-network-across-the-complex-interface-of-ptpn4-pdz-domain-with-its-peptide-ligands-in-neuroglioma
#1
Xian Xiao, Qiang-Hua He, Li-Yan Yu, Song-Qing Wang, Yang Li, Hua Yang, Ai-Hua Zhang, Xiao-Hong Ma, Yu-Jie Peng, Bing Chen
The PTP non-receptor type 4 (PTPN4) is an important regulator protein in learning, spatial memory and cerebellar synaptic plasticity; targeting the PDZ domain of PTPN4 has become as attractive therapeutic strategy for human neuroglioma. Here, we systematically examined the complex crystal structures of PTPN4 PDZ domain with its known peptide ligands; a number of charged amino acid residues were identified in these ligands and in the peptide-binding pocket of PDZ domain, which can constitute a complicated salt-bridge network across the complex interface...
November 30, 2016: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/27922834/complexity-of-generic-biochemical-circuits-topology-versus-strength-of-interactions
#2
Mikhail Tikhonov, William Bialek
The historical focus on network topology as a determinant of biological function is still largely maintained today, illustrated by the rise of structure-only approaches to network analysis. However, biochemical circuits and genetic regulatory networks are defined both by their topology and by a multitude of continuously adjustable parameters, such as the strength of interactions between nodes, also recognized as important. Here we present a class of simple perceptron-based Boolean models within which comparing the relative importance of topology versus interaction strengths becomes a quantitatively well-posed problem...
December 6, 2016: Physical Biology
https://www.readbyqxmd.com/read/27922825/model-of-turnover-kinetics-in-the-lamellipodium-implications-of-slow-and-fast-diffusing-capping-protein-and-arp2-3-complex
#3
Laura M McMillen, Dimitrios Vavylonis
Cell protrusion through polymerization of actin filaments at the leading edge of motile cells may be influenced by spatial gradients of diffuse actin and regulators. Here we study the distribution of two of the most important regulators, capping protein and Arp2/3 complex, which regulate actin polymerization in the lamellipodium through capping and nucleation of free barbed ends. We modeled their kinetics using data from prior single molecule microscopy experiments on XTC cells. These experiments have provided evidence for a broad distribution of diffusion coefficients of both capping protein and Arp2/3 complex...
December 6, 2016: Physical Biology
https://www.readbyqxmd.com/read/27922611/genetic-and-epigenomic-mechanisms-of-mammalian-circadian-transcription
#4
REVIEW
Romeo Papazyan, Yuxiang Zhang, Mitchell A Lazar
The mammalian molecular clock comprises a complex network of transcriptional programs that integrates environmental signals with physiological pathways in a tissue-specific manner. Emerging technologies are extending knowledge of basic clock features by uncovering their underlying molecular mechanisms, thus setting the stage for a 'systems' view of the molecular clock. Here we discuss how recent data from genome-wide genetic and epigenetic studies have informed the understanding of clock function. In addition to its importance in human physiology and disease, the clock mechanism provides an ideal model to assess general principles of dynamic transcription regulation in vivo...
December 6, 2016: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/27922280/ganetespib-for-small-cell-lung-cancer
#5
Deepa S Subramaniam, Eiran A Warner, Giuseppe Giaccone
Heat shock proteins (Hsps) are part of a complex network of chaperone proteins that are critically involved in the conformational maturation of intracellular proteins and regulate their degradation via the proteasome system Hsps (especially Hsp70 and Hsp90) are upregulated in many cancers and are potentially attractive therapeutic targets. Ganetespib is a potent non-geldanamycin analogue, and avoids the toxicities associated with older analogues due to its small molecular weight, lipophilicity and the absence of the benzoquinone moiety; strong pre-clinical data support its evaluation in lung cancer, especially small cell lung cancer (SCLC)...
December 6, 2016: Expert Opinion on Investigational Drugs
https://www.readbyqxmd.com/read/27922118/mining-visualizing-and-comparing-multidimensional-biomolecular-data-using-the-genomics-data-miner-gmine-web-server
#6
Carla Proietti, Martha Zakrzewski, Thomas S Watkins, Bernard Berger, Shihab Hasan, Champa N Ratnatunga, Marie-Jo Brion, Peter D Crompton, John J Miles, Denise L Doolan, Lutz Krause
Genomics Data Miner (GMine) is a user-friendly online software that allows non-experts to mine, cluster and compare multidimensional biomolecular datasets. Various powerful visualization techniques are provided, generating high quality figures that can be directly incorporated into scientific publications. Robust and comprehensive analyses are provided via a broad range of data-mining techniques, including univariate and multivariate statistical analysis, supervised learning, correlation networks, clustering and multivariable regression...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27922078/malat1-and-hotair-long-non-coding-rnas-play-opposite-role-in-estrogen-mediated-transcriptional-regulation-in-prostate-cancer-cells
#7
Aurora Aiello, Lorenza Bacci, Agnese Re, Cristian Ripoli, Francesco Pierconti, Francesco Pinto, Riccardo Masetti, Claudio Grassi, Carlo Gaetano, Pier Francesco Bassi, Alfredo Pontecorvi, Simona Nanni, Antonella Farsetti
In the complex network of nuclear hormone receptors, the long non-coding RNAs (lncRNAs) are emerging as critical determinants of hormone action. Here we investigated the involvement of selected cancer-associated lncRNAs in Estrogen Receptor (ER) signaling. Prior studies by Chromatin Immunoprecipitation (ChIP) Sequencing showed that in prostate cancer cells ERs form a complex with the endothelial nitric oxide synthase (eNOS) and that in turn these complexes associate with chromatin in an estrogen-dependent fashion...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27922073/a-single-step-method-for-rna-isolation-from-tropical-crops-in-the-field
#8
J-C Breitler, C Campa, F Georget, B Bertrand, H Etienne
The RNAzol RT reagent was used to provide pure RNA from human cells. We develop a protocol using RNAzol RT reagent to extract pure RNA from plants tissues and demonstrate that this RNA extraction method works not only at room temperature but also at elevated temperatures and provides the simplest and most effective single-step method to extract pure and undegraded RNA directly from tropical plants in the field. RNA extraction directly in a complex field environment opens up the way for studying gene-environment interactions at transcriptome level to decipher the complex regulatory network involved in multiple-stress responses...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27921393/the-role-of-the-microvascular-network-structure-on-diffusion-and-consumption-of-anti-cancer-drugs
#9
P Mascheroni, R Penta
We investigate the impact of microvascular geometry on the transport of drugs in solid tumors, focusing on the diffusion and consumption phenomena. We embrace recent advances in the asymptotic homogenization literature starting from a double Darcy, double advection-diffusion-reaction system of partial differential equations that is obtained exploiting the sharp length separation between the intercapillary distance and the average tumor size. The geometric information on the microvascular network is encoded into effective hydraulic conductivities and diffusivities, which are numerically computed by solving periodic cell problems on appropriate microscale representative cells...
December 6, 2016: International Journal for Numerical Methods in Biomedical Engineering
https://www.readbyqxmd.com/read/27921189/homogenized-constrained-mixture-models-for-anisotropic-volumetric-growth-and-remodeling
#10
F A Braeu, A Seitz, R C Aydin, C J Cyron
Constrained mixture models for soft tissue growth and remodeling have attracted increasing attention over the last decade. They can capture the effects of the simultaneous presence of multiple constituents that are continuously deposited and degraded at in general different rates, which is important to understand essential features of living soft tissues that cannot be captured by simple kinematic growth models. Recently the novel concept of homogenized constrained mixture models was introduced. It was shown that these models produce results which are very similar (and in certain limit cases even identical) to the ones of constrained mixture models based on multi-network theory...
December 5, 2016: Biomechanics and Modeling in Mechanobiology
https://www.readbyqxmd.com/read/27921134/mental-disorders-as-networks-of-problems-a-review-of-recent-insights
#11
REVIEW
Eiko I Fried, Claudia D van Borkulo, Angélique O J Cramer, Lynn Boschloo, Robert A Schoevers, Denny Borsboom
PURPOSE: The network perspective on psychopathology understands mental disorders as complex networks of interacting symptoms. Despite its recent debut, with conceptual foundations in 2008 and empirical foundations in 2010, the framework has received considerable attention and recognition in the last years. METHODS: This paper provides a review of all empirical network studies published between 2010 and 2016 and discusses them according to three main themes: comorbidity, prediction, and clinical intervention...
December 5, 2016: Social Psychiatry and Psychiatric Epidemiology
https://www.readbyqxmd.com/read/27920913/crystal-structure-of-aqua-tris-isonicotinamide-%C3%AE%C2%BAn-bis-thio-cyanato-%C3%AE%C2%BAn-cobalt-ii-2-5-hydrate
#12
Tristan Neumann, Inke Jess, Christian Näther
The asymmetric unit of the title compound, [Co(NCS)2(C6H6N2O)3(H2O)]·2.5H2O, comprises one Co(II) cation, three isonicotinamide ligands, two thio-cyanate anions, one aqua ligand and two water solvent mol-ecules in general positions, as well as one water solvent mol-ecule that is located on a twofold rotation axis. The Co(II) cations are octa-hedrally coordinated by two terminally N-bonded thio-cyanate anions, one water mol-ecule and three isonicotinamide ligands, each coordinating via the pyridine N atom. The discrete complexes are linked by inter-molecular O-H⋯O, N-H⋯O and N-H⋯S hydrogen bonding into a three-dimensional network that contains cavities in which the solvent water mol-ecules are located...
September 1, 2016: Acta Crystallographica. Section E, Crystallographic Communications
https://www.readbyqxmd.com/read/27920762/artificial-intelligence-vs-statistical-modeling-and-optimization-of-continuous-bead-milling-process-for-bacterial-cell-lysis
#13
Shafiul Haque, Saif Khan, Mohd Wahid, Sajad A Dar, Nipunjot Soni, Raju K Mandal, Vineeta Singh, Dileep Tiwari, Mohtashim Lohani, Mohammed Y Areeshi, Thavendran Govender, Hendrik G Kruger, Arshad Jawed
For a commercially viable recombinant intracellular protein production process, efficient cell lysis and protein release is a major bottleneck. The recovery of recombinant protein, cholesterol oxidase (COD) was studied in a continuous bead milling process. A full factorial response surface methodology (RSM) design was employed and compared to artificial neural networks coupled with genetic algorithm (ANN-GA). Significant process variables, cell slurry feed rate (A), bead load (B), cell load (C), and run time (D), were investigated and optimized for maximizing COD recovery...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27920733/chinese-writing-of-deaf-or-hard-of-hearing-students-and-normal-hearing-peers-from-complex-network-approach
#14
Huiyuan Jin, Haitao Liu
Deaf or hard-of-hearing individuals usually face a greater challenge to learn to write than their normal-hearing counterparts. Due to the limitations of traditional research methods focusing on microscopic linguistic features, a holistic characterization of the writing linguistic features of these language users is lacking. This study attempts to fill this gap by adopting the methodology of linguistic complex networks. Two syntactic dependency networks are built in order to compare the macroscopic linguistic features of deaf or hard-of-hearing students and those of their normal-hearing peers...
2016: Frontiers in Psychology
https://www.readbyqxmd.com/read/27920428/mitigating-herding-in-hierarchical-crowdsourcing-networks
#15
Han Yu, Chunyan Miao, Cyril Leung, Yiqiang Chen, Simon Fauvel, Victor R Lesser, Qiang Yang
Hierarchical crowdsourcing networks (HCNs) provide a useful mechanism for social mobilization. However, spontaneous evolution of the complex resource allocation dynamics can lead to undesirable herding behaviours in which a small group of reputable workers are overloaded while leaving other workers idle. Existing herding control mechanisms designed for typical crowdsourcing systems are not effective in HCNs. In order to bridge this gap, we investigate the herding dynamics in HCNs and propose a Lyapunov optimization based decision support approach - the Reputation-aware Task Sub-delegation approach with dynamic worker effort Pricing (RTS-P) - with objective functions aiming to achieve superlinear time-averaged collective productivity in an HCN...
December 2016: Scientific Reports
https://www.readbyqxmd.com/read/27919898/a-prolonged-outbreak-of-kpc-3-producing-enterobacter-cloacae-and-klebsiella-pneumoniae-driven-by-multiple-mechanisms-of-resistance-transmission-at-a-large-academic-burn-center
#16
Hajime Kanamori, Christian M Parobek, Jonathan J Juliano, David van Duin, Bruce A Cairns, David J Weber, William A Rutala
Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacter cloacae have been recently recognized in the United States. Whole-genome sequencing (WGS) has become a useful tool for analysis of outbreaks and for determining transmission networks of multidrug-resistant organisms in healthcare settings, including carbapenem-resistant Enterobacteriaceae (CRE). We experienced a prolonged outbreak of CRE of E. cloacae and K. pneumoniae over a three-year period at a large academic burn center despite rigorous infection control measures...
December 5, 2016: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/27919796/the-bad-seed-gardener-deubiquitinases-in-the-cancer-stem-cell-signaling-network-and-therapeutic-resistance
#17
REVIEW
Guan-Zhong Qiu, Wei Sun, Ming-Zhu Jin, Jing Lin, Pei-Gang Lu, Wei-Lin Jin
Tumors are comprised of highly heterogeneous populations of cells, of which only a small subset of stem-like cells possess the ability to regenerate tumors in vivo. These rare cancer stem cells (CSCs) have been regarded as the "bad seeds" accounted for tumor initiation, progression, metastasis, relapse and therapeutic resistance. CSC-targeted therapy seems to be a better avenue for radical cure of cancer. Deubiquitinases (DUBs), specifically disassembling ubiquitin chains, have been demonstrated to play an important role in rigidly maintaining the balance between ubiquitination and deubiquitination for protein quality control and homeostasis in normal circumstances...
December 2, 2016: Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/27919795/current-and-novel-insights-into-the-neurophysiology-of-migraine-and-its-implications-for-therapeutics
#18
REVIEW
Simon Akerman, Marcela Romero-Reyes, Philip R Holland
Migraine headache and its associated symptoms have plagued humans for two millennia. It is manifest throughout the world, and affects more than 1/6 of the global population. It is the most common brain disorder, and is characterized by moderate to severe unilateral headache that is accompanied by vomiting, nausea, photophobia, phonophobia, and other hypersensitive symptoms of the senses. While there is still a clear lack of understanding of its neurophysiology, it is beginning to be understood, and it seems to suggest migraine is a disorder of brain sensory processing, characterized by a generalized neuronal hyperexcitability...
December 2, 2016: Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/27919554/quantitative-structure-property-relationships-for-predicting-sorption-of-pharmaceuticals-to-sewage-sludge-during-waste-water-treatment-processes
#19
L Berthod, D C Whitley, G Roberts, A Sharpe, R Greenwood, G A Mills
Understanding the sorption of pharmaceuticals to sewage sludge during waste water treatment processes is important for understanding their environmental fate and in risk assessments. The degree of sorption is defined by the sludge/water partition coefficient (Kd). Experimental Kd values (n=297) for active pharmaceutical ingredients (n=148) in primary and activated sludge were collected from literature. The compounds were classified by their charge at pH7.4 (44 uncharged, 60 positively and 28 negatively charged, and 16 zwitterions)...
December 2, 2016: Science of the Total Environment
https://www.readbyqxmd.com/read/27919546/brain-morphometry-predicts-individual-creative-potential-and-the-ability-to-combine-remote-ideas
#20
David Bendetowicz, Marika Urbanski, Clarisse Aichelburg, Richard Levy, Emmanuelle Volle
For complex mental functions such as creative thinking, inter-individual variability is useful to better understand the underlying cognitive components and brain anatomy. Associative theories propose that creative individuals have flexible semantic associations, which allows remote elements to be formed into new combinations. However, the structural brain variability associated with the ability to combine remote associates has not been explored. To address this question, we performed a voxel-based morphometry (VBM) study and explored the anatomical connectivity of significant regions...
November 15, 2016: Cortex; a Journal Devoted to the Study of the Nervous System and Behavior
keyword
keyword
15505
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"