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Maryam Songhorzadeh, Karim Ansari-Asl, Alimorad Mahmoudi
Quantifying delayed directional couplings between electroencephalographic (EEG) time series requires an efficient method of causal network inference. This is especially due to the limited knowledge about the underlying dynamics of the brain activity. Recent methods based on information theoretic measures such as Transfer Entropy (TE) made significant progress on this issue by providing a model-free framework for causality detection. However, TE estimation from observed data is not a trivial task, especially when the number of variables is large which is the case in a highly complex system like human brain...
October 14, 2016: Computers in Biology and Medicine
Doanh Nguyen-Ngoc, Thuy Nguyen-Phuong
We investigate a system of two species exploiting a common resource. We consider both abiotic (i.e. with a constant resource supply rate) and biotic (i.e. with resource reproduction and self-limitation) resources. We are interested in the asymmetric competition where a given consumer is the locally superior resource exploiter (LSE) and the other is the locally inferior resource exploiter (LIE). They also interact directly via interference competition in the sense that LIE individuals can use two opposite strategies to compete with LSE individuals: we assume, in the first case, that LIE uses an avoiding strategy, i...
October 21, 2016: Acta Biotheoretica
Lauren E Marshall, Roy Koomullil, Andra R Frost, Joel L Berry
A preclinical testing model for cancer therapeutics that replicates in vivo physiology is needed to accurately describe drug delivery and efficacy prior to clinical trials. To develop an in vitro model of breast cancer that mimics in vivo drug/nutrient delivery as well as physiological size and bio-composition, it is essential to describe the mass transport quantitatively. The objective of the present study was to develop in vitro and computational models to measure mass transport from a perfusion system into a 3D extracellular matrix (ECM)...
October 21, 2016: Annals of Biomedical Engineering
Dimosthenis A Sarigiannis, Spyros P Karakitsios, Evangelos Handakas, Konstantina Simou, Ermioni Solomou, Alberto Gotti
The current study aims at a comprehensive risk characterization of bisphenol A (BPA) supported by an integrated exposure modelling framework that comprises far field and near field exposure modelling coupled to a dynamic lifetime PBTK model. Exposure analysis was done on European data of BPA food residues and human biomonitoring (HBM). The latter were further assimilated through an advanced exposure reconstruction modelling framework to estimate the corresponding external and internal systemic dose of BPA and its metabolites...
October 18, 2016: Food and Chemical Toxicology
Ana Rita Araujo, Lendert Gelens, Rahuman S M Sheriff, Silvia D M Santos
Cell division is characterized by a sequence of events by which a cell gives rise to two daughter cells. Quantitative measurements of cell-cycle dynamics in single cells showed that despite variability in G1-, S-, and G2 phases, duration of mitosis is short and remarkably constant. Surprisingly, there is no correlation between cell-cycle length and mitotic duration, suggesting that mitosis is temporally insulated from variability in earlier cell-cycle phases. By combining live cell imaging and computational modeling, we showed that positive feedback is the molecular mechanism underlying the temporal insulation of mitosis...
October 20, 2016: Molecular Cell
Liangliang Chen, Yuancheng Peng, Juan Tian, Xiaohong Wang, Zhaosheng Kong, Tonglin Mao, Ming Yuan, Yunhai Li
How cell shape is controlled is a fundamental question in developmental biology, but the genetic and molecular mechanisms that determine cell shape are largely unknown. Arabidopsis trichomes have been used as a good model system to investigate cell shape at the single-cell level. Here we describe the trichome cell shape 1 (tcs1) mutants with the reduced trichome branch number in Arabidopsis. TCS1 encodes a coiled-coil domain-containing protein. Pharmacological analyses and observations of microtubule dynamics show that TCS1 influences the stability of microtubules...
October 2016: PLoS Genetics
R Stannarius, K Harth
Disclinations in liquid crystals bear striking analogies to defect structures in a wide variety of physical systems, and their straightforward optical observability makes them excellent models to study fundamental properties of defect interactions. We employ freely suspended smectic-C films, which behave as quasi-two-dimensional polar nematics. A procedure to capture high-strength disclinations in localized spots is introduced. These disclinations are released in a controlled way, and the motion of the mutually repelling topological charges with strength +1 is studied quantitatively...
October 7, 2016: Physical Review Letters
B L Altshuler, E Cuevas, L B Ioffe, V E Kravtsov
We combine numerical diagonalization with semianalytical calculations to prove the existence of the intermediate nonergodic but delocalized phase in the Anderson model on disordered hierarchical lattices. We suggest a new generalized population dynamics that is able to detect the violation of ergodicity of the delocalized states within the Abou-Chakra, Anderson, and Thouless recursive scheme. This result is supplemented by statistics of random wave functions extracted from exact diagonalization of the Anderson model on ensemble of disordered random regular graphs (RRG) of N sites with the connectivity K=2...
October 7, 2016: Physical Review Letters
Carolina Rodriguez-Tirado, Takanori Kitamura, Yu Kato, Jeffery W Pollard, John S Condeelis, David Entenberg
Metastasis to secondary sites such as the lung, liver and bone is a traumatic event with a mortality rate of approximately 90% (1). Of these sites, the lung is the most difficult to assess using intravital optical imaging due to its enclosed position within the body, delicate nature and vital role in sustaining proper physiology. While clinical modalities (positron emission tomography (PET), magnetic resonance imaging (MRI) and computed tomography (CT)) are capable of providing noninvasive images of this tissue, they lack the resolution necessary to visualize the earliest seeding events, with a single pixel consisting of nearly a thousand cells...
October 6, 2016: Journal of Visualized Experiments: JoVE
Mon-Shu Ho, Chih-Pong Huang, Jyun-Hwei Tsai, Che-Fu Chou, Wen-Jay Lee
This paper reports an array-designed C84-embedded Si substrate fabricated using a controlled self-assembly method in an ultra-high vacuum chamber. The characteristics of the C84-embedded Si surface, such as atomic resolution topography, local electronic density of states, band gap energy, field emission properties, nanomechanical stiffness, and surface magnetism, were examined using a variety of surface analysis techniques under ultra, high vacuum (UHV) conditions as well as in an atmospheric system. Experimental results demonstrate the high uniformity of the C84-embedded Si surface fabricated using a controlled self-assembly nanotechnology mechanism, represents an important development in the application of field emission display (FED), optoelectronic device fabrication, MEMS cutting tools, and in efforts to find a suitable replacement for carbide semiconductors...
September 28, 2016: Journal of Visualized Experiments: JoVE
E A Gopalakrishnan, Yogita Sharma, Tony John, Partha Sharathi Dutta, R I Sujith
Dynamical systems can undergo critical transitions where the system suddenly shifts from one stable state to another at a critical threshold called the tipping point. The decrease in recovery rate to equilibrium (critical slowing down) as the system approaches the tipping point can be used to identify the proximity to a critical transition. Several measures have been adopted to provide early indications of critical transitions that happen in a variety of complex systems. In this study, we use early warning indicators to predict subcritical Hopf bifurcation occurring in a thermoacoustic system by analyzing the observables from experiments and from a theoretical model...
October 21, 2016: Scientific Reports
Mikyung Lee, Zhichao Liu, Ruili Huang, Weida Tong
BACKGROUND: All biological processes are inherently dynamic. Biological systems evolve transiently or sustainably according to sequential time points after perturbation by environment insults, drugs and chemicals. Investigating the temporal behavior of molecular events has been an important subject to understand the underlying mechanisms governing the biological system in response to, such as, drug treatment. The intrinsic complexity of time series data requires appropriate computational algorithms for data interpretation...
October 6, 2016: BMC Bioinformatics
Shaher Bano Mirza, Ramin Ekhteiari Salmas, M Qaiser Fatmi, Serdar Durdagi
The Klotho is known as lifespan enhancing protein involved in antagonizing the effect of Wnt proteins. Wnt proteins are stem cell regulators, and uninterrupted exposure of Wnt proteins to the cell can cause stem and progenitor cell senescence, which may lead to aging. Keeping in mind the importance of Klotho in Wnt signaling, in silico approaches have been applied to study the important interactions between Klotho and Wnt3 and Wnt3a (wingless-type mouse mammary tumor virus (MMTV) integration site family members 3 and 3a)...
October 21, 2016: Journal of Enzyme Inhibition and Medicinal Chemistry
Erfan Dashtimoghadam, Ghasem Bahlakeh, Hamed Salimi-Kenari, Mohammad Mahdi Hasani-Sadrabadi, Hamid Mirzadeh, Bo Nyström
The temperature-induced gelation of chitosan/glycerophosphate (Chs/GP) systems through physical interactions has shown great potential for various biomedical applications. In the present work, hydroxyethyl cellulose (HEC) was added to the thermosensitive Chs/GP solution to improve the mechanical strength and gel properties of the incipient Chs/HEC/GP gel in comparison with the Chs/GP hydrogel at body temperature. The physical features of the macromolecular complexes formed by the synergistic interaction between chitosan and hydroxyethyl cellulose in the presence of β-glycerophosphate disodium salt solution have been studied essentially from a rheological point of view...
October 21, 2016: Biomacromolecules
Paul R Territo, Amanda A Riley, Brian P McCarthy, Gary D Hutchins
Recent advancements in PET instrumentation have made the non-invasive assessment of cardiovascular function in small animals a reality. The majority of small animal PET systems use stationary detector gantries, thus affording high temporal resolution imaging of cardiac function. Systems designed to maximize spatial resolution and detection sensitivity employing rotating gantry designs are suboptimal when high temporal resolution imaging is needed. To overcome this limitation, the current work developed a novel view-sharing data analysis scheme suitable for dynamic cardiac PET imaging using (18)F-NaF as the tracer and tracer kinetic model analysis...
December 2016: EJNMMI Physics
P Moisset de Espanés, A Osses, I Rapaport
Fixed points are fundamental states in any dynamical system. In the case of gene regulatory networks (GRNs) they correspond to stable genes profiles associated to the various cell types. We use Kauffman's approach to model GRNs with random Boolean networks (RBNs). In this paper we explore how the topology affects the distribution of the number of fixed points in randomly generated networks. We also study the size of the basins of attraction of these fixed points if we assume the α-asynchronous dynamics (where every node is updated independently with probability 0≤α≤1)...
October 17, 2016: Bio Systems
Roland G Huber, Jan K Marzinek, Daniel A Holdbrook, Peter J Bond
Viral pathogens are a significant source of human morbidity and mortality, and have a major impact on societies and economies around the world. One of the challenges inherent in targeting these pathogens with drugs is the tight integration of the viral life cycle with the host's cellular machinery. However, the reliance of the virus on the host cell replication machinery is also an opportunity for therapeutic targeting, as successful entry- and exit-inhibitors have demonstrated. An understanding of the extracellular and intracellular structure and dynamics of the virion - as well as of the entry and exit pathways in host and vector cells - is therefore crucial to the advancement of novel antivirals...
October 17, 2016: Progress in Biophysics and Molecular Biology
Sung-Hwan Cho, Sang-Min Park, Ho-Sung Lee, Hwang-Yeol Lee, Kwang-Hyun Cho
BACKGROUND: Colorectal cancer arises from the accumulation of genetic mutations that induce dysfunction of intracellular signaling. However, the underlying mechanism of colorectal tumorigenesis driven by genetic mutations remains yet to be elucidated. RESULTS: To investigate colorectal tumorigenesis at a system-level, we have reconstructed a large-scale Boolean network model of the human signaling network by integrating previous experimental results on canonical signaling pathways related to proliferation, metastasis, and apoptosis...
October 20, 2016: BMC Systems Biology
Shehla Akbar, Fazal Subhan, Nasiara Karim, Muhammad Shahid, Nisar Ahmad, Gowhar Ali, Wajahat Mahmood, Khwaja Fawad
BACKGROUND: Diabetic neuropathy is the most prevalent, persistent and debilitating complication of diabetes mellitus often coupled with vulvodynia that may present as an isolated symptom or as a part of constellation of other neuropathic abnormalities. OBJECTIVE: Flavonoids have selective affinity for GABA receptors and 6-methoxyflavanone (6-MeOF) is a positive allosteric modulator of GABA responses at human recombinant GABAA receptors. GABAergic and opioidergic system inhibition have been shown to facilitate neuropathic pain...
October 17, 2016: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
Bonan Li, Lixin Wang, Kudzai F Kaseke, Lin Li, Mary K Seely
Soil moisture is a key variable in dryland ecosystems since it determines the occurrence and duration of vegetation water stress and affects the development of weather patterns including rainfall. However, the lack of ground observations of soil moisture and rainfall dynamics in many drylands has long been a major obstacle in understanding ecohydrological processes in these ecosystems. It is also uncertain to what extent rainfall controls soil moisture dynamics in fog dominated dryland systems. To this end, in this study, twelve to nineteen months' continuous daily records of rainfall and soil moisture (from January 2014 to August 2015) obtained from three sites (one sand dune site and two gravel plain sites) in the Namib Desert are reported...
2016: PloS One
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