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https://www.readbyqxmd.com/read/28445746/crosstalk-and-the-dynamical-modularity-of%C3%A2-feed-forward-loops-in-transcriptional-regulatory-networks
#1
Michael A Rowland, Ahmed Abdelzaher, Preetam Ghosh, Michael L Mayo
Network motifs, such as the feed-forward loop (FFL), introduce a range of complex behaviors to transcriptional regulatory networks, yet such properties are typically determined from their isolated study. We characterize the effects of crosstalk on FFL dynamics by modeling the cross regulation between two different FFLs and evaluate the extent to which these patterns occur in vivo. Analytical modeling suggests that crosstalk should overwhelmingly affect individual protein-expression dynamics. Counter to this expectation we find that entire FFLs are more likely than expected to resist the effects of crosstalk (≈20% for one crosstalk interaction) and remain dynamically modular...
April 25, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28445735/a-design-principle-for-an-autonomous-post-translational-pattern-formation
#2
Shuhei S Sugai, Koji L Ode, Hiroki R Ueda
Previous autonomous pattern-formation models often assumed complex molecular and cellular networks. This theoretical study, however, shows that a system composed of one substrate with multisite phosphorylation and a pair of kinase and phosphatase can generate autonomous spatial information, including complex stripe patterns. All (de-)phosphorylation reactions are described with a generic Michaelis-Menten scheme, and all species freely diffuse without pre-existing gradients. Computational simulation upon >23,000,000 randomly generated parameter sets revealed the design motifs of cyclic reaction and enzyme sequestration by slow-diffusing substrates...
April 25, 2017: Cell Reports
https://www.readbyqxmd.com/read/28445589/a-network-engineering-perspective-on-probing-and-perturbing-cognition-with-neurofeedback
#3
REVIEW
Danielle S Bassett, Ankit N Khambhati
Network science and engineering provide a flexible and generalizable tool set to describe and manipulate complex systems characterized by heterogeneous interaction patterns among component parts. While classically applied to social systems, these tools have recently proven to be particularly useful in the study of the brain. In this review, we describe the nascent use of these tools to understand human cognition, and we discuss their utility in informing the meaningful and predictable perturbation of cognition in combination with the emerging capabilities of neurofeedback...
April 26, 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28445462/cell-diversity-and-network-dynamics-in-photosensitive-human-brain-organoids
#4
Giorgia Quadrato, Tuan Nguyen, Evan Z Macosko, John L Sherwood, Sung Min Yang, Daniel R Berger, Natalie Maria, Jorg Scholvin, Melissa Goldman, Justin P Kinney, Edward S Boyden, Jeff W Lichtman, Ziv M Williams, Steven A McCarroll, Paola Arlotta
In vitro models of the developing brain such as three-dimensional brain organoids offer an unprecedented opportunity to study aspects of human brain development and disease. However, the cells generated within organoids and the extent to which they recapitulate the regional complexity, cellular diversity and circuit functionality of the brain remain undefined. Here we analyse gene expression in over 80,000 individual cells isolated from 31 human brain organoids. We find that organoids can generate a broad diversity of cells, which are related to endogenous classes, including cells from the cerebral cortex and the retina...
April 26, 2017: Nature
https://www.readbyqxmd.com/read/28445397/radiation-and-thyroid-cancer
#5
REVIEW
Elisabetta Albi, Samuela Cataldi, Andrea Lazzarini, Michela Codini, Tommaso Beccari, Francesco Saverio Ambesi-Impiombato, Francesco Curcio
Radiation-induced damage is a complex network of interlinked signaling pathways, which may result in apoptosis, cell cycle arrest, DNA repair, and cancer. The development of thyroid cancer in response to radiation, from nuclear catastrophes to chemotherapy, has long been an object of study. A basic overview of the ionizing and non-ionizing radiation effects of the sensitivity of the thyroid gland on radiation and cancer development has been provided. In this review, we focus our attention on experiments in cell cultures exposed to ionizing radiation, ultraviolet light, and proton beams...
April 26, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28445220/catalyzing-interdisciplinary-research-and-training-initial-outcomes-and-evolution-of-the-affinity-research-collaboratives-model
#6
Katya Ravid, Francesca Seta, David Center, Gloria Waters, David Coleman
Team science has been recognized as critical to solving increasingly complex biomedical problems and advancing discoveries in the prevention, diagnosis, and treatment of human disease. In 2009, the Evans Center for Interdisciplinary Biomedical Research (ECIBR) was established in the Department of Medicine at Boston University School of Medicine as a new organizational paradigm to promote interdisciplinary team science. The ECIBR is made up of affinity research collaboratives (ARCs), consisting of investigators from different departments and disciplines who come together to study biomedical problems that are relevant to human disease and not under interdisciplinary investigation at the university...
April 25, 2017: Academic Medicine: Journal of the Association of American Medical Colleges
https://www.readbyqxmd.com/read/28444887/morphological-study-of-the-atrioventricular-conduction-system-and-purkinje-fibers-in-yak
#7
Deyong Duan, Sijiu Yu, Yan Cui, Chaoxu Li
We studied the morphology of the atrioventricular conduction system (AVCS) and Purkinje fibers of the yak. Light and transmission electron microscopy were used to study the histological features of AVCS. The distributional characteristics of the His-bundle, the left bundle branch (LBB), right bundle branch (RBB), and Purkinje fiber network of yak hearts were examined using gross dissection, ink injection, and ABS casting. The results showed that the atrioventricular node (AVN) of yak located in the right side of interatrial septum and had a flattened ovoid shape...
April 26, 2017: Journal of Morphology
https://www.readbyqxmd.com/read/28444516/trap-nesting-hymenoptera-and-their-network-with-parasites-in-recovered-riparian-forests-brazil
#8
G J Araujo, R Fagundes, Y Antonini
Different aspects of human activities can cause environmental change that endanger species persistence, alter species distributions, and lead to changes in antagonistic and mutualistic interactions, whereas deforestation and flooding of riparian forest results in landscapes consisting of patchily distributed riparian forest fragments in a matrix of pastures, plantations, and urban areas. Therefore, we assessed the richness, abundance, and trophic interactions of trap-nesting Hymenoptera and their parasites at four patches of restored riparian forest and at one reference natural fragment, of different sizes and ages, located at the Volta Grande Reservoir, in Minas Gerais and São Paulo states to answer the following questions: (1) Does the richness and abundance of cavity-nesting bees and wasps differ in riparian forest fragments according to the seasonal periods? (2) Does the composition of cavity-nesting bees and wasps vary among restoration and reference sites and between climate seasons (wet and dry)? (3) How do the degrees of specialization of the parasites vary among the patches of forest? We recorded 12 species of wasps, eight of bees, and nine species of parasites...
April 25, 2017: Neotropical Entomology
https://www.readbyqxmd.com/read/28444481/peer-victimization-and-suicidal-thoughts-and-behaviors-in-depressed-adolescents
#9
Jeremy G Stewart, Linda Valeri, Erika C Esposito, Randy P Auerbach
Suicide is a leading cause of death among youth worldwide, and depressed adolescents are at a significantly elevated risk to report suicidal ideation, planning, and attempts. Peer victimization is a robust predictor of adolescent suicidal thoughts and behaviors (STBs), but little research has focused on why bullying leads to suicidal thoughts and behaviors. To address this empirical gap, we recruited 340 (246 female) depressed adolescents ages 13-19 (M = 15.59, SD = 1.41) within 48 h of admission for acute psychiatric treatment...
April 25, 2017: Journal of Abnormal Child Psychology
https://www.readbyqxmd.com/read/28444399/development-of-a-multipurpose-scaffold-for-the-display-of-peptide-loops
#10
Maxim Rossmann, Sandra J Greive, Tommaso Moschetti, Michael Dinan, Marko Hyvönen
Protein-protein interactions (PPIs) determine a wide range of biological processes and analysis of these dynamic networks is increasingly becoming a mandatory tool for studying protein function. Using the globular ATPase domain of recombinase RadA as a scaffold, we have developed a peptide display system (RAD display), which allows for the presentation of target peptides, protein domains or full-length proteins and their rapid recombinant production in bacteria. The design of the RAD display system includes differently tagged versions of the scaffold, which allows for flexibility in the protein purification method, and chemical coupling for small molecule labeling or surface immobilization...
April 24, 2017: Protein Engineering, Design & Selection: PEDS
https://www.readbyqxmd.com/read/28444127/hla-class-i-binding-prediction-via-convolutional-neural-networks
#11
Yeeleng S Vang, Xiaohui Xie
Motivation: Many biological processes are governed by protein-ligand interactions. One such example is the recognition of self and nonself cells by the immune system. This immune response process is regulated by the major histocompatibility complex (MHC) protein which is encoded by the human leukocyte antigen (HLA) complex. Understanding the binding potential between MHC and peptides can lead to the design of more potent, peptide-based vaccines and immunotherapies for infectious autoimmune diseases...
April 21, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28444052/healthcare-regions-and-their-care-networks-an-organizational-systemic-model-for-sus
#12
Lenir Santos
This paper describes a comprehensive effort to develop studies regarding Brazil's Unified Healthcare System (SUS), as a result of the combination of public services in a network that follows a region-based rationale (tripartite organization). The SUS emerges from such an integration and should be organized as such. The intention is to demonstrate that this type of organization is essential, given that Brazil is organized as a Federation, and all three governmental levels are, in a broad sense, equally responsible for healthcare...
April 2017: Ciência & Saúde Coletiva
https://www.readbyqxmd.com/read/28444049/healthcare-financing-decentralization-and-regional-health-planning-federal-transfers-and-the-healthcare-networks-in-minas-gerais-brazil
#13
Laura Monteiro de Castro Moreira, Felipe Ferré, Eli Iola Gurgel Andrade
The Decrees 4279/10 and 7508/11 established norms to guide health politics, with impacts on funding of the Middle and High Complexity Hospital and Outpatient. To verify the effects on the consolidation of care networks in Minas Gerais, we performed an analytical-descriptive study of the National Health Fund from 2006 to 2014. We observed decentralization of responsibilities, accompanied of resources and innovative financing mechanisms, resulting expansion of the network care model. The federal government definitions suggest reduction of the autonomy and limitation of regional solutions...
April 2017: Ciência & Saúde Coletiva
https://www.readbyqxmd.com/read/28444032/thoughts-on-the-development-of-active-regional-public-health-systems
#14
Ademar Arthur Chioro Dos Reis, Ana Paula Menezes Sóter, Lumena Almeida Castro Furtado, Silvana Souza da Silva Pereira
Decentralization and regionalization are strategic themes for reforms in the health system. This paper analyzes the complex process of health regionalization being developed in Brazil. This paper identifies that the normative framework from the Brazilian National Health System, SUS has made advances with respect to its institutionalization and overcoming the initial centrality involved in municipalization. This has strengthened the development of regionalization and the intergovernmental agreement on health but the evidence points to the need to promote a revision...
April 2017: Ciência & Saúde Coletiva
https://www.readbyqxmd.com/read/28443326/ionic-liquid-silica-precursors-via-solvent-free-sol-gel-process-and-their-application-in-epoxy-amine-network-a-theoretical-experimental-study
#15
Magdalena Perchacz, Ricardo Keitel Donato, Leandro Seixas, Alexander Zhigunov, Rafal Konefal, Magdalena Serkis-Rodzeń, Hynek Benes
This work describes the solvent-free sol-gel synthesis of epoxy-functionalized silica-based precursors, in the presence of 1-butyl-3-methylimidazolium-based ionic liquids (ILs) containing different anions - chloride (Cl(-)) and methanesulfonate (MeSO3(-)). The IL-driven sol-gel mechanisms were investigated in details using experimental characterizations ((29)Si NMR and ATR FTIR spectroscopy) and a theoretical computational method based on density functional theory (DFT). We observed a complex IL's influence on both hydrolysis and condensation steps, involving especially H-bonding and Coulomb coupling stabilization of the process intermediates...
April 26, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28443014/the-topographical-mapping-in-drosophila-central-complex-network-and-its-signal-routing
#16
Po-Yen Chang, Ta-Shun Su, Chi-Tin Shih, Chung-Chuan Lo
Neural networks regulate brain functions by routing signals. Therefore, investigating the detailed organization of a neural circuit at the cellular levels is a crucial step toward understanding the neural mechanisms of brain functions. To study how a complicated neural circuit is organized, we analyzed recently published data on the neural circuit of the Drosophila central complex, a brain structure associated with a variety of functions including sensory integration and coordination of locomotion. We discovered that, except for a small number of "atypical" neuron types, the network structure formed by the identified 194 neuron types can be described by only a few simple mathematical rules...
2017: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/28442998/glial-cell-line-derived-neurotrophic-factor-gene-delivery-in-parkinson-s-disease-a-delicate-balance-between-neuroprotection-trophic-effects-and-unwanted-compensatory-mechanisms
#17
REVIEW
Liliane Tenenbaum, Marie Humbert-Claude
Glial cell line-derived neurotrophic factor (GDNF) and Neurturin (NRTN) bind to a receptor complex consisting of a member of the GDNF family receptor (GFR)-α and the Ret tyrosine kinase. Both factors were shown to protect nigro-striatal dopaminergic neurons and reduce motor symptoms when applied terminally in toxin-induced Parkinson's disease (PD) models. However, clinical trials based on intraputaminal GDNF protein administration or recombinant adeno-associated virus (rAAV)-mediated NRTN gene delivery have been disappointing...
2017: Frontiers in Neuroanatomy
https://www.readbyqxmd.com/read/28442785/hunter-gatherer-social-networks-and-reproductive-success
#18
Abigail E Page, Nikhil Chaudhary, Sylvain Viguier, Mark Dyble, James Thompson, Daniel Smith, Gul D Salali, Ruth Mace, Andrea Bamberg Migliano
Individuals' centrality in their social network (who they and their social ties are connected to) has been associated with fertility, longevity, disease and information transmission in a range of taxa. Here, we present the first exploration in humans of the relationship between reproductive success and different measures of network centrality of 39 Agta and 38 BaYaka mothers. We collected three-meter contact ('proximity') networks and reproductive histories to test the prediction that individual centrality is positively associated with reproductive fitness (number of living offspring)...
April 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28442714/mitigating-herding-in-hierarchical-crowdsourcing-networks
#19
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 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/28442501/chlorokb-a-web-application-for-the-integration-of-knowledge-related-to-chloroplast-metabolic-network
#20
Pauline Gloaguen, Sylvain Bournais, Claude Alban, Stephane Ravanel, Daphne Seigneurin-Berny, Michel Matringe, Marianne Tardif, Marcel Kuntz, Myriam Ferro, Christophe Bruley, Norbert Rolland, Yves Vandenbrouck, Gilles Curien
CONTEXT: Higher plants, as autotrophic organisms, are effective sources of molecules. They hold great promise for metabolic engineering, but the behavior of plant metabolism at the network level is still incompletely described. Although structural models (stoichiometry matrices) and pathway databases are extremely useful, they cannot describe the complexity of the metabolic context and new tools are required to visually represent integrated biocurated knowledge for use by both humans and computers...
April 25, 2017: Plant Physiology
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