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https://www.readbyqxmd.com/read/28641269/a-model-based-tool-for-the-analysis-and-design-of-gene-regulatory-network
#1
Liliana Ironi, Ettore Lanzarone
Computational and mathematical models have significantly contributed to the rapid progress in the study of gene regulatory networks (GRN), but researchers still lack a reliable model-based framework for computer-aided analysis and design. Such tool should both reveal the relation between network structure and dynamics and find parameter values and/or constraints that enable the simulated dynamics to reproduce specific behaviors. This paper addresses these issues and proposes a computational framework that facilitates network analysis or design...
June 19, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28636629/minimal-oscillating-subnetwork-in-the-huang-ferrell-model-of-the-mapk-cascade
#2
Otto Hadač, František Muzika, Vladislav Nevoral, Michal Přibyl, Igor Schreiber
Prompted by the recent growing evidence of oscillatory behavior involving MAPK cascades we present a systematic approach of analyzing models and elucidating the nature of biochemical oscillations based on reaction network theory. In particular, we formulate a minimal biochemically consistent mass action subnetwork of the Huang-Ferrell model of the MAPK signalling that provides an oscillatory response when a parameter controlling the activation of the top-tier kinase is varied. Such dynamics are either intertwined with or separated from the earlier found bistable/hysteretic behavior in this model...
2017: PloS One
https://www.readbyqxmd.com/read/28636047/decoding-the-regulatory-mechanism-of-glucose-and-insulin-induced-phosphatidylinositol-3-4-5-trisphosphate-dynamics-in-%C3%AE-cells
#3
Tagari Samanta, Peeyush Sharma, Dwijendra Kukri, Sandip Kar
In MIN6 pancreatic β-cells, glucose and insulin act in a synergistic manner to regulate the dynamics of Phosphatidylinositol (3,4,5)-trisphosphate (PIP3). However, the precise regulatory mechanism behind such an experimentally observed synergy is poorly understood. In this article, we propose a phenomenological mathematical model for studying the glucose and insulin driven PIP3 activation dynamics under various stimulatory conditions to unfold the mechanism responsible for the observed synergy. The modeling study reveals that the experimentally observed oscillation in PIP3 dynamics with disparate time scales for different external glucose doses is mainly orchestrated by the complex dynamic regulation of cytosolic Ca(2+) in β-cells...
June 21, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28636005/mass-mobility-and-ms-n-measurements-of-single-ions-using-charge-detection-mass-spectrometry
#4
Andrew G Elliott, Conner C Harper, Haw-Wei Lin, Evan R Williams
Charge detection mass spectrometry is used to measure the mass, charge, MS(n) and mobility of an individual ion produced by electrospray ionization of a 8 MDa polyethylene glycol sample. The charge detection mass spectrometer is an electrostatic ion trap that uses cone electrodes and a single tube detector and can detect ions for up to the full trapping time of 4.0 s. The time-domain signal induced on the detector tube by a single multiply charged ion can be complex owing to sequential fragmentation of the original precursor ion as well as increasing oscillation frequencies of the single ion owing to collisions with background gas that reduce the kinetic energy of the ion inside the trap...
June 21, 2017: Analyst
https://www.readbyqxmd.com/read/28634743/comminuted-olecranon-fractures-biomechanical-testing-of-locked-versus-minifragment-non-locked-plate-fixation
#5
David S Wellman, Scott M Tucker, Josh R Baxter, Nadine C Pardee, Lionel E Lazaro, Christopher S Smith, Dean G Lorich, David L Helfet
INTRODUCTION: Open reduction and internal fixation has long been accepted as optimal treatment for displaced olecranon fractures based on poor results seen with conservative management. With the presence of comminution, tension-band wiring constructs are contraindicated due to tendency to compress through fragments, thereby shortening the articular segment. Therefore, plate fixation is typically employed. Our hypothesis was that in a comminuted fracture model, 2.7 mm reconstruction plating without locking screws will perform equally to 3...
June 20, 2017: Archives of Orthopaedic and Trauma Surgery
https://www.readbyqxmd.com/read/28634499/three-input-gate-logic-circuits-on-chemically-assembled-single-electron-transistors-with-organic-and-inorganic-hybrid-passivation-layers
#6
Yutaka Majima, Guillaume Hackenberger, Yasuo Azuma, Shinya Kano, Kosuke Matsuzaki, Tomofumi Susaki, Masanori Sakamoto, Toshiharu Teranishi
Single-electron transistors (SETs) are sub-10-nm scale electronic devices based on conductive Coulomb islands sandwiched between double-barrier tunneling barriers. Chemically assembled SETs with alkanethiol-protected Au nanoparticles show highly stable Coulomb diamonds and two-input logic operations. The combination of bottom-up and top-down processes used to form the passivation layer is vital for realizing multi-gate chemically assembled SET circuits, as this combination enables us to connect conventional complementary metal oxide semiconductor (CMOS) technologies via planar processes...
2017: Science and Technology of Advanced Materials
https://www.readbyqxmd.com/read/28634173/a-comparison-of-2-respiratory-devices-for-sputum-clearance-in-adults-with-non-cystic-fibrosis-bronchiectasis
#7
Yasmin R Silva, Tracy A Greer, Lucy C Morgan, Frank Li, Claude S Farah
BACKGROUND: Airway clearance techniques are a vital part of routine care for patients with bronchiectasis. There is no clear superior modality. The Flutter combines oscillations (6-20Hz) and positive expiratory pressure; the Lung Flute combines positive expiratory pressure and low frequency acoustic waves (18-22Hz), to augment clearance. This project aimed to compare these devices. METHODS: This was a randomized crossover study of adult subjects with stable non-cystic fibrosis bronchiectasis (expectorating >25 mL/d)...
June 20, 2017: Respiratory Care
https://www.readbyqxmd.com/read/28634086/towards-building-a-more-complex-view-of-the-lateral-geniculate-nucleus-recent-advances-in-understanding-its-role
#8
REVIEW
Masoud Ghodrati, Seyed-Mahdi Khaligh-Razavi, Sidney R Lehky
The lateral geniculate nucleus (LGN) has often been treated in the past as a linear filter that adds little to retinal processing of visual inputs. Here we review anatomical, neurophysiological, brain imaging, and modeling studies that have in recent years built up a much more complex view of LGN. These include effects related to nonlinear dendritic processing, cortical feedback, synchrony and oscillations across LGN populations, as well as involvement of LGN in higher level cognitive processing Although recent studies have provided valuable insights into early visual processing including the role of LGN, a unified model of LGN responses to real-world objects has not yet been developed...
June 17, 2017: Progress in Neurobiology
https://www.readbyqxmd.com/read/28633970/unified-neural-field-theory-of-brain-dynamics-underlying-oscillations-in-parkinson-s-disease-and-generalized-epilepsies
#9
E J Müller, S J van Albada, J W Kim, P A Robinson
The mechanisms underlying pathologically synchronized neural oscillations in Parkinson's disease (PD) and generalized epilepsies are explored in parallel via a physiologically-based neural field model of the corticothalamic-basal ganglia (CTBG) system. The basal ganglia (BG) are approximated as a single effective population and their roles in the modulation of oscillatory dynamics of the corticothalamic (CT) system and vice versa are analyzed. In addition to normal EEG rhythms, enhanced activity around 4 Hz and 20 Hz exists in the model, consistent with the characteristic frequencies observed in PD...
June 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28633830/accompanying-the-frequency-shift-of-the-nonlinear-resonance-of-a-gas-bubble-using-a-dual-frequency-excitation
#10
Matthieu Guédra, Claude Inserra, Bruno Gilles
An asymptotic method is applied to analyze the nonlinear oscillations of a gas bubble driven by a dual-frequency excitation. More specifically, the latter is considered as a combination of two neighboring, incommensurate frequencies and is treated as a nonstationary excitation. This implies that both amplitude and phase of the bubble response are slowly oscillating at the time scale of the frequency difference, thus leading to a regime of aperiodic oscillations. The approximate solution is successfully compared with numerical simulations and reveals the possibility of achieving larger bubble response amplitude compared to the monofrequency excitation for sufficiently high driving pressure and specific values of the frequency difference...
September 2017: Ultrasonics Sonochemistry
https://www.readbyqxmd.com/read/28633817/computational-study-of-state-equation-effect-on-single-acoustic-cavitation-bubble-s-phenomenon
#11
Kaouther Kerboua, Oualid Hamdaoui
Many models have been established to study the evolution of the bubble dynamics and chemical kinetics within a single acoustic cavitation bubble during its oscillation. The content of the bubble is a gas medium that generates the evolution of a chemical mechanism governed by the internal bubble conditions. These gases are described by a state equation, linking the pressure to the volume, temperature and species amounts, and influencing simultaneously the dynamical, the thermal and the mass variation in the cavitation bubble...
September 2017: Ultrasonics Sonochemistry
https://www.readbyqxmd.com/read/28633816/a-derivation-of-the-stable-cavitation-threshold-accounting-for-bubble-bubble-interactions
#12
Matthieu Guédra, Corentin Cornu, Claude Inserra
The subharmonic emission of sound coming from the nonlinear response of a bubble population is the most used indicator for stable cavitation. When driven at twice their resonance frequency, bubbles can exhibit subharmonic spherical oscillations if the acoustic pressure amplitude exceeds a threshold value. Although various theoretical derivations exist for the subharmonic emission by free or coated bubbles, they all rest on the single bubble model. In this paper, we propose an analytical expression of the subharmonic threshold for interacting bubbles in a homogeneous, monodisperse cloud...
September 2017: Ultrasonics Sonochemistry
https://www.readbyqxmd.com/read/28633524/charge-migration-in-eyring-walter-and-kimball-s-1944-model-of-the-electronically-excited-hydrogen-molecule-ion
#13
Dennis J Diestler, Gunter Hermann, Jörn Manz
In an elementary variational treatment of the electronic structure of H2+ Eyring, Walter and Kimball (EWK) serendipitously discovered charge migration (CM) in 1944. Using an analytic expression for the electronic probability density (EPD), they found that if the electron is initially localized on one of the protons (by taking the initial state to be a superposition of the ground and first-excited electronic energy eigenstates), then it oscillates adiabatically between fixed protons with a period T inversely proportional to the energy gap between the eigenstates...
June 21, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28632848/effect-of-gabapentin-memantine-on-the-infantile-nystagmus-syndrome-in-the-zebrafish-model-implications-for-the-therapy-of-ocular-motor-diseases
#14
Stefan Yu Bögli, Maresa Afthinos, Melody Ying-Yu Huang
Purpose: Infantile nystagmus syndrome (INS) is a disorder characterized by typical horizontal eye oscillations. Due to the uncertain etiology of INS, developing specific treatments remains difficult. Single reports demonstrated, on limited measures, alleviating effects of gabapentin and memantine. In the current study, we employed the zebrafish INS model belladonna (bel) to conduct an in-depth study of how gabapentin and memantine interventions alleviate INS signs, which may further restore visual conditions in affected subjects...
June 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28632774/short-term-eeg-dynamics-and-neural-generators-evoked-by-navigational-images
#15
Axelle Leroy, Carlos Cevallos, Ana-Maria Cebolla, Stéphanie Caharel, Bernard Dan, Guy Cheron
The ecological environment offered by virtual reality is primarily supported by visual information. The different image contents and their rhythmic presentation imply specific bottom-up and top-down processing. Because these processes already occur during passive observation we studied the brain responses evoked by the presentation of specific 3D virtual tunnels with respect to 2D checkerboard. For this, we characterized electroencephalograhy dynamics (EEG), the evoked potentials and related neural generators involved in various visual paradigms...
2017: PloS One
https://www.readbyqxmd.com/read/28632666/change-in-calcaneal-bone-strength-in-long-term-care-residents-treated-with-low-intensity-pulsed-ultrasound
#16
Hiroyasu Okuizumi, Kiyoshi Koyano, Kazuya Kurosawa, Naoto Kamide, Ayako Soyano
OBJECTIVE: We examined the effect of low-intensity pulsed ultrasound (LIPUS) on bone strength in osteoporotic elderly residents. MATERIALS AND METHODS: This was a randomized controlled trial. Elderly residents with osteoporosis in a long-term care facility were treated with LIPUS (oscillation frequency 100 KHz) that involved treatment of the heel bone for 2 minutes a day. The selection of the treated heel was decided randomly with a personal computer. The heel bone mineral density before and after treatment was measured by calcaneal quantitative ultrasound (GE-1000 Express)...
July 2017: Journal of Orthopaedic Trauma
https://www.readbyqxmd.com/read/28631615/phonon-drag-magnetoquantum-oscillations-in-graphene
#17
S S Kubakaddi, Tutul Biswas, Tarun Kanti Ghosh
A theory of low-temperature phonon-drag magnetothermopower [Formula: see text] is presented in graphene in a quantizing magnetic field. [Formula: see text] is found to exhibit quantum oscillations as a function of magnetic field B and electron concentration n e . The amplitude of the oscillations is found to increase (decrease) with increasing B (n e ). The behavior of [Formula: see text] is also investigated as a function of temperature. A large value of [Formula: see text] (∼few hundreds of μV K(-1)) is predicted...
June 20, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/28630968/designing-self-powered-materials-systems-that-perform-pattern-recognition
#18
Yan Fang, Victor V Yashin, Steven P Levitan, Anna C Balazs
Inspired by the advances in both materials and computer science, we describe efforts to design "materials that compute" where the material and the computer are the same entity. Using theory and simulation, we devise systems that integrate the behavior of self-oscillating gels and fundamental concepts from oscillator-based computing. We specifically focus on gels that undergo the Belousov-Zhabotinsky (BZ) reaction and thus exhibit self-sustained oscillations. In our models, we couple the BZ gel to an overlaying piezoelectric (PZ) cantilever to create a BZ-PZ unit...
June 20, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28630900/reconstructed-storm-tracks-reveal-three-centuries-of-changing-moisture-delivery-to-north-america
#19
Erika K Wise, Matthew P Dannenberg
Moisture delivery to western North America is closely linked to variability in the westerly storm tracks of midlatitude cyclones, which are, in turn, modified by larger-scale features such as the El Niño-Southern Oscillation system. Instrumental and modeling data suggest that extratropical storm tracks may be intensifying and shifting poleward due to anthropogenic climate change, but it is difficult to separate recent trends from natural variability because of the large amount of decadal and longer variation in storm tracks and their limited instrumental record...
June 2017: Science Advances
https://www.readbyqxmd.com/read/28630468/neurofeedback-learning-modifies-the-incidence-rate-of-alpha-spindles-but-not-their-duration-and-amplitude
#20
Alexei Ossadtchi, Tatiana Shamaeva, Elizaveta Okorokova, Victoria Moiseeva, Mikhail A Lebedev
Although the first experiments on alpha-neurofeedback date back nearly six decades ago, when Joseph Kamiya reported successful operant conditioning of alpha-rhythm in humans, the effectiveness of this paradigm in various experimental and clinical settings is still a matter of debate. Here, we investigated the changes in EEG patterns during a continuously administered neurofeedback of P4 alpha activity. Two days of neurofeedback training were sufficient for a significant increase in the alpha power to occur...
June 19, 2017: Scientific Reports
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