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https://www.readbyqxmd.com/read/28549920/dissecting-intrinsic-and-ligand-induced-structural-communication-in-the-%C3%AE-3-headpiece-of-integrins
#1
Angelo Felline, Michela Ghitti, Giovanna Musco, Francesca Fanelli
BACKGROUND: Graph theory is widely used to dissect structural communication in biomolecular systems. Here, graph theory-based approaches were applied to the headpiece of integrins, adhesion cell-surface receptors that transmit signals across the plasma membranes. METHODS: Protein Structure Network (PSN) analysis incorporating dynamic information either from molecular dynamics simulations or from Elastic Network Models was applied to the β3 domains from integrins αVβ3 and αIIbβ3 in their apo and ligand-bound states...
May 23, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28549824/the-hsp90-chaperone-network-modulates-candida-virulence-traits
#2
REVIEW
Teresa R O'Meara, Nicole Robbins, Leah E Cowen
Hsp90 is a conserved molecular chaperone that facilitates the folding and function of client proteins. Hsp90 function is dynamically regulated by interactions with co-chaperones and by post-translational modifications. In the fungal pathogen Candida albicans, Hsp90 enables drug resistance and virulence by stabilizing diverse signal transducers. Here, we review studies that have unveiled regulators of Hsp90 function, as well as downstream effectors that govern the key virulence traits of morphogenesis and drug resistance...
May 23, 2017: Trends in Microbiology
https://www.readbyqxmd.com/read/28549798/whole-brain-connectivity-dynamics-reflect-both-task-specific-and-individual-specific-modulation-a-multitask-study
#3
REVIEW
Hua Xie, Vince Calhoun, Javier Gonzalez-Castillo, Eswar Damaraju, Robyn Miller, Peter Bandettini, Sunanda Mitra
Functional connectivity (FC) has been widely used to study the functional organization of temporally correlated and spatially distributed brain regions. Recent studies of FC dynamics, quantified by windowed correlations, provide new insights to analyze dynamic, context-dependent reconfiguration of brain networks. A set of reoccurring whole-brain connectivity patterns at rest, referred to as FC states, have been identified, hypothetically reflecting underlying cognitive processes or mental states. We posit that the mean FC information for a given subject represents a significant contribution to the group-level FC dynamics...
May 23, 2017: NeuroImage
https://www.readbyqxmd.com/read/28549796/development-of-the-error-monitoring-system-from-ages-9-35-unique-insight-provided-by-mri-constrained-source-localization-of-eeg
#4
George A Buzzell, John E Richards, Lauren K White, Tyson V Barker, Daniel S Pine, Nathan A Fox
The ability to self-detect errors and dynamically adapt behavior is a cornerstone of higher-level cognition, requiring coordinated activity from a network of neural regions. However, disagreement exists over how the error-monitoring system develops throughout adolescence and early adulthood. The present report leveraged MRI-constrained EEG source localization to detail typical development of the error-monitoring system in a sample of 9-35 year-olds (n=43). Participants performed a flanker task while high-density EEG was recorded; structural MRIs were also acquired for all participants...
May 23, 2017: NeuroImage
https://www.readbyqxmd.com/read/28548460/internally-generated-hippocampal-sequences-as-a-vantage-point-to-probe-future-oriented-cognition
#5
REVIEW
Giovanni Pezzulo, Caleb Kemere, Matthijs A A van der Meer
Information processing in the rodent hippocampus is fundamentally shaped by internally generated sequences (IGSs), expressed during two different network states: theta sequences, which repeat and reset at the ∼8 Hz theta rhythm associated with active behavior, and punctate sharp wave-ripple (SWR) sequences associated with wakeful rest or slow-wave sleep. A potpourri of diverse functional roles has been proposed for these IGSs, resulting in a fragmented conceptual landscape. Here, we advance a unitary view of IGSs, proposing that they reflect an inferential process that samples a policy from the animal's generative model, supported by hippocampus-specific priors...
May 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28547799/the-effects-of-intransitive-competition-on-coexistence
#6
Laure Gallien, Niklaus E Zimmermann, Jonathan M Levine, Peter B Adler
Coexistence theory has been developed with an almost exclusive focus on interactions between two species, often ignoring more complex and indirect interactions, such as intransitive loops, that can emerge in competition networks. In fact, intransitive competition has typically been studied in isolation from other pairwise stabilising processes, and thus little is known about how intransitivity interacts with more traditional drivers of species coexistence such as niche partitioning. To integrate intransitivity into traditional coexistence theory, we developed a metric of growth rate when rare, Δri¯, to identify and quantify the impact of intransitive competition against a backdrop of pairwise stabilising niche differences...
May 26, 2017: Ecology Letters
https://www.readbyqxmd.com/read/28547786/the-geography-of-spatial-synchrony
#7
Jonathan A Walter, Lawrence W Sheppard, Thomas L Anderson, Jude H Kastens, Ottar N Bjørnstad, Andrew M Liebhold, Daniel C Reuman
Spatial synchrony, defined as correlated temporal fluctuations among populations, is a fundamental feature of population dynamics, but many aspects of synchrony remain poorly understood. Few studies have examined detailed geographical patterns of synchrony; instead most focus on how synchrony declines with increasing linear distance between locations, making the simplifying assumption that distance decay is isotropic. By synthesising and extending prior work, we show how geography of synchrony, a term which we use to refer to detailed spatial variation in patterns of synchrony, can be leveraged to understand ecological processes including identification of drivers of synchrony, a long-standing challenge...
May 26, 2017: Ecology Letters
https://www.readbyqxmd.com/read/28546829/vinasse-fertirrigation-alters-soil-resistome-dynamics-an-analysis-based-on-metagenomic-profiles
#8
Lucas P P Braga, Rafael F Alves, Marina T F Dellias, Acacio A Navarrete, Thiago O Basso, Siu M Tsai
Every year around 300 Gl of vinasse, a by-product of ethanol distillation in sugarcane mills, are flushed into more than 9 Mha of sugarcane cropland in Brazil. This practice links fermentation waste management to fertilization for plant biomass production, and it is known as fertirrigation. Here we evaluate public datasets of soil metagenomes mining for changes in antibiotic resistance genes (ARGs) of soils from sugarcane mesocosms repeatedly amended with vinasse. The metagenomes were annotated using the ResFam database...
2017: BioData Mining
https://www.readbyqxmd.com/read/28546808/improving-classification-performance-through-an-advanced-ensemble-based-heterogeneous-extreme-learning-machines
#9
Adnan O M Abuassba, Dezheng Zhang, Xiong Luo, Ahmad Shaheryar, Hazrat Ali
Extreme Learning Machine (ELM) is a fast-learning algorithm for a single-hidden layer feedforward neural network (SLFN). It often has good generalization performance. However, there are chances that it might overfit the training data due to having more hidden nodes than needed. To address the generalization performance, we use a heterogeneous ensemble approach. We propose an Advanced ELM Ensemble (AELME) for classification, which includes Regularized-ELM, L2-norm-optimized ELM (ELML2), and Kernel-ELM. The ensemble is constructed by training a randomly chosen ELM classifier on a subset of training data selected through random resampling...
2017: Computational Intelligence and Neuroscience
https://www.readbyqxmd.com/read/28546537/basin-stability-for-chimera-states
#10
Sarbendu Rakshit, Bidesh K Bera, Matjaž Perc, Dibakar Ghosh
Chimera states, namely complex spatiotemporal patterns that consist of coexisting domains of spatially coherent and incoherent dynamics, are investigated in a network of coupled identical oscillators. These intriguing spatiotemporal patterns were first reported in nonlocally coupled phase oscillators, and it was shown that such mixed type behavior occurs only for specific initial conditions in nonlocally and globally coupled networks. The influence of initial conditions on chimera states has remained a fundamental problem since their discovery...
May 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28545680/a-role-for-tropomyosins-in-activity-dependent-bulk-endocytosis
#11
REVIEW
R S Gormal, N Valmas, T Fath, F A Meunier
Bulk endocytosis allows stimulated neurons to take up a large portion of the presynaptic plasma membrane in order to regenerate synaptic vesicle pools. Actin, one of the most abundant proteins in eukaryotic cells, plays an important role in this process, but a detailed mechanistic understanding of the involvement of the cortical actin network is still lacking, in part due to the relatively small size of nerve terminals and the limitation of optical microscopy. We recently discovered that neurosecretory cells display a similar, albeit much larger, form of bulk endocytosis in response to secretagogue stimulation...
May 22, 2017: Molecular and Cellular Neurosciences
https://www.readbyqxmd.com/read/28545607/dynamically-weighted-evolutionary-ordinal-neural-network-for-solving-an-imbalanced-liver-transplantation-problem
#12
Manuel Dorado-Moreno, María Pérez-Ortiz, Pedro A Gutiérrez, Rubén Ciria, Javier Briceño, César Hervás-Martínez
OBJECTIVE: Create an efficient decision-support model to assist medical experts in the process of organ allocation in liver transplantation. The mathematical model proposed here uses different sources of information to predict the probability of organ survival at different thresholds for each donor-recipient pair considered. Currently, this decision is mainly based on the Model for End-stage Liver Disease, which depends only on the severity of the recipient and obviates donor-recipient compatibility...
March 2017: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/28545403/long-lasting-effect-of-obesity-on-skeletal-muscle-transcriptome
#13
Ilhem Messaoudi, Mithila Handu, Maham Rais, Suhas Sureshchandra, Byung S Park, Suzanne S Fei, Hollis Wright, Ashley E White, Ruhee Jain, Judy L Cameron, Kerri M Winters-Stone, Oleg Varlamov
BACKGROUND: Reduced physical activity and increased intake of calorically-dense diets are the main risk factors for obesity, glucose intolerance, and type 2 diabetes. Chronic overnutrition and hyperglycemia can alter gene expression, contributing to long-term obesity complications. While caloric restriction can reduce obesity and glucose intolerance, it is currently unknown whether it can effectively reprogram transcriptome to a pre-obesity level. The present study addressed this question by the preliminary examination of the transcriptional dynamics in skeletal muscle after exposure to overnutrition and following caloric restriction...
May 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28544891/emergence-of-ultrafast-sparsely-synchronized-rhythms-and-their-responses-to-external-stimuli-in-an-inhomogeneous-small-world-complex-neuronal-network
#14
Sang-Yoon Kim, Woochang Lim
We consider an inhomogeneous small-world network (SWN) composed of inhibitory short-range (SR) and long-range (LR) interneurons, and investigate the effect of network architecture on emergence of synchronized brain rhythms by varying the fraction of LR interneurons plong. The betweenness centralities of the LR and SR interneurons (characterizing the potentiality in controlling communication between other interneurons) are distinctly different. Hence, in view of the betweenness, SWNs we consider are inhomogeneous, unlike the "canonical" Watts-Strogatz SWN with nearly the same betweenness centralities...
April 28, 2017: Neural Networks: the Official Journal of the International Neural Network Society
https://www.readbyqxmd.com/read/28544890/hybrid-neuro-heuristic-methodology-for-simulation-and-control-of-dynamic-systems-over-time-interval
#15
Marcin Woźniak, Dawid Połap
Simulation and positioning are very important aspects of computer aided engineering. To process these two, we can apply traditional methods or intelligent techniques. The difference between them is in the way they process information. In the first case, to simulate an object in a particular state of action, we need to perform an entire process to read values of parameters. It is not very convenient for objects for which simulation takes a long time, i.e. when mathematical calculations are complicated. In the second case, an intelligent solution can efficiently help on devoted way of simulation, which enables us to simulate the object only in a situation that is necessary for a development process...
May 5, 2017: Neural Networks: the Official Journal of the International Neural Network Society
https://www.readbyqxmd.com/read/28544882/inference-and-evolutionary-analysis-of-genome-scale-regulatory-networks-in-large-phylogenies
#16
Christopher Koch, Jay Konieczka, Toni Delorey, Ana Lyons, Amanda Socha, Kathleen Davis, Sara A Knaack, Dawn Thompson, Erin K O'Shea, Aviv Regev, Sushmita Roy
Changes in transcriptional regulatory networks can significantly contribute to species evolution and adaptation. However, identification of genome-scale regulatory networks is an open challenge, especially in non-model organisms. Here, we introduce multi-species regulatory network learning (MRTLE), a computational approach that uses phylogenetic structure, sequence-specific motifs, and transcriptomic data, to infer the regulatory networks in different species. Using simulated data from known networks and transcriptomic data from six divergent yeasts, we demonstrate that MRTLE predicts networks with greater accuracy than existing methods because it incorporates phylogenetic information...
May 24, 2017: Cell Systems
https://www.readbyqxmd.com/read/28544647/dual-cross-linked-biofunctional-and-self-healing-networks-to-generate-user-defined-modular-gradient-hydrogel-constructs
#17
Zhao Wei, Daniel M Lewis, Yu Xu, Sharon Gerecht
Gradient hydrogels have been developed to mimic the spatiotemporal differences of multiple gradient cues in tissues. Current approaches used to generate such hydrogels are restricted to a single gradient shape and distribution. Here, a hydrogel is designed that includes two chemical cross-linking networks, biofunctional, and self-healing networks, enabling the customizable formation of modular gradient hydrogel construct with various gradient distributions and flexible shapes. The biofunctional networks are formed via Michael addition between the acrylates of oxidized acrylated hyaluronic acid (OAHA) and the dithiol of matrix metalloproteinase (MMP)-sensitive cross-linker and RGD peptides...
May 23, 2017: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/28544275/recessive-mutations-in-msto1-cause-mitochondrial-dynamics-impairment-leading-to-myopathy-and-ataxia
#18
Alessia Nasca, Chiara Scotton, Irina Zaharieva, Marcella Neri, Rita Selvatici, Olafur Thor Magnusson, Aniko Gal, David Weaver, Rachele Rossi, Annarita Armaroli, Marika Pane, Rahul Phadke, Anna Sarkozy, Francesco Muntoni, Imelda Hughes, Antonella Cecconi, György Hajnóczky, Alice Donati, Eugenio Mercuri, Massimo Zeviani, Alessandra Ferlini, Daniele Ghezzi
We report here the first families carrying recessive variants in the MSTO1 gene: compound heterozygous mutations were identified in two sisters and in an unrelated singleton case, who presented a multisystem complex phenotype mainly characterized by myopathy and cerebellar ataxia. Human MSTO1 is a poorly studied protein, suggested to have mitochondrial localization and to regulate morphology and distribution of mitochondria. As for other mutations affecting genes involved in mitochondrial dynamics, no biochemical defects typical of mitochondrial disorders were reported...
May 23, 2017: Human Mutation
https://www.readbyqxmd.com/read/28544252/soil-organic-carbon-dynamics-jointly-controlled-by-climate-carbon-inputs-soil-properties-and-soil-carbon-fractions
#19
Zhongkui Luo, Wenting Feng, Yiqi Luo, Jeff Baldock, Enli Wang
Soil organic carbon (SOC) dynamics are regulated by the complex interplay of climatic, edaphic and biotic conditions. However, the interrelation of SOC and these drivers and their potential connection networks are rarely assessed quantitatively. Using observations of SOC dynamics with detailed soil properties from 90 field trials at 28 sites under different agroecosystems across the Australian cropping regions, we investigated the direct and indirect effects of climate, soil properties, carbon (C) inputs and soil C pools (a total of 17 variables) on SOC change rate (rC , Mg C ha(-1) yr(-1) )...
May 19, 2017: Global Change Biology
https://www.readbyqxmd.com/read/28544203/observation-of-ch%C3%A2-%C3%A2-%C3%A2-%C3%AF-interactions-between-methyl-and-carbonyl-groups-in-proteins
#20
Frédéric A Perras, Dominique Marion, Jérôme Boisbouvier, David L Bryce, Michael J Plevin
Protein structure and function is dependent on myriad noncovalent interactions. Direct detection and characterization of these weak interactions in large biomolecules, such as proteins, is experimentally challenging. Herein, we report the first observation and measurement of long-range "through-space" scalar couplings between methyl and backbone carbonyl groups in proteins. These J couplings are indicative of the presence of noncovalent C-H⋅⋅⋅π hydrogen-bond-like interactions involving the amide π network...
May 22, 2017: Angewandte Chemie
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