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https://www.readbyqxmd.com/read/28449397/differential-proteome-profiling-in-the-hippocampus-of-amnesic-mice
#1
Meghraj Singh Baghel, Mahendra Kumar Thakur
Amnesia or memory loss is associated with brain aging and several neurodegenerative pathologies including Alzheimer's disease (AD). This can be induced by a cholinergic antagonist scopolamine, but the underlying molecular mechanism is poorly understood. The present study of proteome profiling in the hippocampus could provide conceptual insights into the molecular mechanisms involved in amnesia. To reveal this, mice were administered scopolamine to induce amnesia and memory impairment was validated by novel object recognition test...
April 27, 2017: Hippocampus
https://www.readbyqxmd.com/read/28449392/osmotic-stress-decreases-complexity-underlying-the-electrophysiological-dynamic-in-soybean
#2
G F R Saraiva, A S Ferreira, G M Souza
Research rationale: Studies on plant electrophysiology are mostly focused on specific traits of single cells. Inspired by the complexity of the signaling network in plants and by analogies with neurons in human brains, we have sought for evidences of high complexity in the electrical dynamics of plant signaling and a likely relation with environmental cues. Central methods: An EEG-like standard protocol was adopted for high-resolution measurements of the electrical signal in Glycine max seedlings. The signals were continuously recorded in the same plants before and after the osmotic stimuli with a -2 MPa mannitol solution...
April 27, 2017: Plant Biology
https://www.readbyqxmd.com/read/28448599/simulation-of-the-dynamics-of-primary-immunodeficiencies-in-cd4-t-cells
#3
Gabriel N Teku, Mauno Vihinen
Primary immunodeficiencies (PIDs) form a large and heterogeneous group of mainly rare disorders that affect the immune system. T-cell deficiencies account for about one-tenth of PIDs, most of them being monogenic. Apart from genetic and clinical information, lots of other data are available for PID proteins and genes, including functions and interactions. Thus, it is possible to perform systems biology studies on the effects of PIDs on T-cell physiology and response. To achieve this, we reconstructed a T-cell network model based on literature mining and TPPIN, a previously published core T-cell network, and performed semi-quantitative dynamic network simulations on both normal and T-cell PID failure modes...
2017: PloS One
https://www.readbyqxmd.com/read/28448048/time-resolved-electrospray-ionization-hydrogen-deuterium-exchange-mass-spectrometry-for-studying-protein-structure-and-dynamics
#4
Cristina Lento, Shaolong Zhu, Kerene A Brown, Ruth Knox, Peter Liuni, Derek J Wilson
Intrinsically disordered proteins (IDPs) have long been a challenge to structural biologists due to their lack of stable secondary structure elements. Hydrogen-Deuterium Exchange (HDX) measured at rapid time scales is uniquely suited to detect structures and hydrogen bonding networks that are briefly populated, allowing for the characterization of transient conformers in native ensembles. Coupling of HDX to mass spectrometry offers several key advantages, including high sensitivity, low sample consumption and no restriction on protein size...
April 17, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28447851/-understanding-the-role-of-speech-production-in-reading-evidence-for-a-print-to-speech-neural-network-using-graphical-analysis-correction-to-cummine-et-al-2016
#5
(no author information available yet)
Reports an error in "Understanding the role of speech production in reading: Evidence for a print-to-speech neural network using graphical analysis" by Jacqueline Cummine, Ivor Cribben, Connie Luu, Esther Kim, Reyhaneh Bahktiari, George Georgiou and Carol A. Boliek (Neuropsychology, 2016[May], Vol 30[4], 385-397). In the article, the fifth author's name [Bakhtiari] was misspelled. The online version of this article has been corrected. (The following abstract of the original article appeared in record 2015-49069-001...
May 2017: Neuropsychology
https://www.readbyqxmd.com/read/28447220/track-weighted-dynamic-functional-connectivity-tw-dfc-a-new-method-to-study-time-resolved-functional-connectivity
#6
Fernando Calamante, Robert E Smith, Xiaoyun Liang, Andrew Zalesky, Alan Connelly
Interest in the study of brain connectivity is growing, particularly in understanding the dynamics of the structural/functional connectivity relation. Structural and functional connectivity are most often analysed independently of each other. Track-weighted functional connectivity (TW-FC) was recently proposed as a means to combine structural/functional connectivity information into a single image. We extend here TW-FC in two important ways: first, all the functional data are used without having to define a prior functional network (cf...
April 26, 2017: Brain Structure & Function
https://www.readbyqxmd.com/read/28446174/a-scalable-metabolite-supplementation-strategy-against-antibiotic-resistant-pathogen-chromobacterium-violaceum-induced-by-nad-nadh-imbalance
#7
Deepanwita Banerjee, Dharmeshkumar Parmar, Nivedita Bhattacharya, Avinash D Ghanate, Venkateswarlu Panchagnula, Anu Raghunathan
BACKGROUND: The leading edge of the global problem of antibiotic resistance necessitates novel therapeutic strategies. This study develops a novel systems biology driven approach for killing antibiotic resistant pathogens using benign metabolites. RESULTS: Controlled laboratory evolutions established chloramphenicol and streptomycin resistant pathogens of Chromobacterium. These resistant pathogens showed higher growth rates and required higher lethal doses of antibiotic...
April 26, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28446033/controls-over-spatial-and-seasonal-variations-on-isotopic-composition-of-the-precipitation-along-the-central-and-eastern-portion-of-brazil
#8
Didier Gastmans, Vinícius Santos, Juliana Aparecida Galhardi, João Felipe Gromboni, Ludmila Vianna Batista, Konrad Miotlinski, Hung Kiang Chang, José Silvio Govone
Based on Global Network Isotopes in Precipitation (GNIP) isotopic data set, a review of the spatial and temporal variability of δ(18)O and δ(2)H in precipitation was conducted throughout central and eastern Brazil, indicating that dynamic interactions between Intertropical and South Atlantic Convergence Zones, Amazon rainforest, and Atlantic Ocean determine the variations on the isotopic composition of precipitation over this area. Despite the seasonality and latitude effects observed, a fair correlation with precipitation amount was found...
April 26, 2017: Isotopes in Environmental and Health Studies
https://www.readbyqxmd.com/read/28445999/crystal-orientation-effect-on-the-subsurface-deformation-of-monocrystalline-germanium-in-nanometric-cutting
#9
Min Lai, Xiaodong Zhang, Fengzhou Fang
Molecular dynamics simulations of nanometric cutting on monocrystalline germanium are conducted to investigate the subsurface deformation during and after nanometric cutting. The continuous random network model of amorphous germanium is established by molecular dynamics simulation, and its characteristic parameters are extracted to compare with those of the machined deformed layer. The coordination number distribution and radial distribution function (RDF) show that the machined surface presents the similar amorphous state...
December 2017: Nanoscale Research Letters
https://www.readbyqxmd.com/read/28445746/crosstalk-and-the-dynamical-modularity-of%C3%A2-feed-forward-loops-in-transcriptional-regulatory-networks
#10
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/28445537/predicting-epidemic-evolution-on-contact-networks-from-partial-observations
#11
Jacopo Bindi, Alfredo Braunstein, Luca Dall'Asta
The massive employment of computational models in network epidemiology calls for the development of improved inference methods for epidemic forecast. For simple compartment models, such as the Susceptible-Infected-Recovered model, Belief Propagation was proved to be a reliable and efficient method to identify the origin of an observed epidemics. Here we show that the same method can be applied to predict the future evolution of an epidemic outbreak from partial observations at the early stage of the dynamics...
2017: PloS One
https://www.readbyqxmd.com/read/28445462/cell-diversity-and-network-dynamics-in-photosensitive-human-brain-organoids
#12
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/28445249/study-on-the-mechanisms-of-seizure-like-events-suppression-effect-by-electrical-stimulation-using-a-microelectrode-array
#13
Sora Ahn, Sumin Jo, Sang Beom Jun, Hyang Woon Lee, Seungjun Lee
In this paper, we studied the mechanisms underlying the suppression of seizure-like events (SLEs) by electrical stimulation. We conducted an in-vitro experiment using entorhinal cortex combined hippocampal slices and two convulsant drugs, bicuculline and 4-aminopyridine, to induce spontaneous SLEs. We used a microelectrode array to observe network dynamics over the entire hippocampal area simultaneously, including regions far from the stimulation site. We stimulated the entorhinal cortex region, which has been determined to be a focus of SLEs by Granger causality analysis of multichannel time series data, by an external electrode...
April 25, 2017: Neuroreport
https://www.readbyqxmd.com/read/28444934/dynamic-iminoboronate-based-boroxine-chemistry-for-the-design-of-ambient-humidity-sensitive-self-healing-polymers
#14
Sébastien Delpierre, Bertrand Willocq, Julien De Winter, Philippe Dubois, Pascal Gerbaux, Jean-Marie Raquez
Developing intrinsic self-healing polymeric materials is of great interest nowadays to extend material lifetime and/or prevent the replacement of damaged pieces. Spontaneously humidity-sensitive healable polymer network built around dynamic covalent B-O bonds was templated by using iminoboronate-based boroxine derivatives. Taking advantage of the dynamic boroxine/boronic acid equilibrium and iminoboronate chemistry, it is possible to construct polymeric materials able to self-heal without requiring any energy-demanding external activation...
April 26, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28444399/development-of-a-multipurpose-scaffold-for-the-display-of-peptide-loops
#15
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/28442760/localization-of-laplacian-eigenvectors-on-random-networks
#16
Shigefumi Hata, Hiroya Nakao
In large random networks, each eigenvector of the Laplacian matrix tends to localize on a subset of network nodes having similar numbers of edges, namely, the components of each Laplacian eigenvector take relatively large values only on a particular subset of nodes whose degrees are close. Although this localization property has significant consequences for dynamical processes on random networks, a clear theoretical explanation has not yet been established. Here we analyze the origin of localization of Laplacian eigenvectors on random networks by using a perturbation theory...
April 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28442714/mitigating-herding-in-hierarchical-crowdsourcing-networks
#17
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/28442296/an-information-theory-framework-for-dynamic-functional-domain-connectivity
#18
Victor M Vergara, Robyn Miller, Vince Calhoun
BACKGROUND: Dynamic functional network connectivity (dFNC) analyzes time evolution of coherent activity in the brain. In this technique dynamic changes are considered for the whole brain. This paper proposes an information theory framework to measure information flowing among subsets of functional networks call functional domains. NEW METHOD: Our method aims at estimating bits of information contained and shared among domains. The succession of dynamic functional states is estimated at the domain level...
April 22, 2017: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/28441880/a-three-dimensional-collagen-fiber-network-model-of-the-extracellular-matrix-for-the-simulation-of-the-mechanical-behaviors-and-micro-structures
#19
Shoubin Dong, Zetao Huang, Liqun Tang, Xiaoyang Zhang, Yongrou Zhang, Yi Jiang
The extracellular matrix (ECM) provides structural and biochemical support to cells and tissues, which is a critical factor for modulating cell dynamic behavior and intercellular communication. In order to further understand the mechanisms of the interactive relationship between cell and the ECM, we developed a three-dimensional (3D) collagen-fiber network model to simulate the micro structure and mechanical behaviors of the ECM and studied the stress-strain relationship as well as the deformation of the ECM under tension...
April 26, 2017: Computer Methods in Biomechanics and Biomedical Engineering
https://www.readbyqxmd.com/read/28441867/accurate-neural-network-description-of-surface-phonons-in-reactive-gas-surface-dynamics-n2-ru-0001
#20
Khosrow Shakouri, Jörg Behler, Joerg Meyer, Geert-Jan Kroes
Ab initio molecular dynamics (AIMD) simulations enable the accurate description of reactive molecule-surface scattering especially if energy transfer involving surface phonons is important. However, presently the computational expense of AIMD rules out its application to systems where reaction probabilities are smaller than about 1 percent. Here we show that this problem can be overcome by a high-dimensional neural network fit of the molecule-surface interaction potential, which also incorporates the dependence on phonons by taking into account all degrees of freedom of the surface explicitly...
April 25, 2017: Journal of Physical Chemistry Letters
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