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https://www.readbyqxmd.com/read/27923064/sparse-regression-based-structure-learning-of-stochastic-reaction-networks-from-single-cell-snapshot-time-series
#1
Anna Klimovskaia, Stefan Ganscha, Manfred Claassen
Stochastic chemical reaction networks constitute a model class to quantitatively describe dynamics and cell-to-cell variability in biological systems. The topology of these networks typically is only partially characterized due to experimental limitations. Current approaches for refining network topology are based on the explicit enumeration of alternative topologies and are therefore restricted to small problem instances with almost complete knowledge. We propose the reactionet lasso, a computational procedure that derives a stepwise sparse regression approach on the basis of the Chemical Master Equation, enabling large-scale structure learning for reaction networks by implicitly accounting for billions of topology variants...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27923046/mitochondria-and-caspases-tune-nmnat-mediated-stabilization-to-promote-axon-regeneration
#2
Li Chen, Derek M Nye, Michelle C Stone, Alexis T Weiner, Kyle W Gheres, Xin Xiong, Catherine A Collins, Melissa M Rolls
Axon injury can lead to several cell survival responses including increased stability and axon regeneration. Using an accessible Drosophila model system, we investigated the regulation of injury responses and their relationship. Axon injury stabilizes the rest of the cell, including the entire dendrite arbor. After axon injury we found mitochondrial fission in dendrites was upregulated, and that reducing fission increased stabilization or neuroprotection (NP). Thus axon injury seems to both turn on NP, but also dampen it by activating mitochondrial fission...
December 6, 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27922865/additional-value-of-early-phase-18f-fp-cit-pet-image-for-differential-diagnosis-of-atypical-parkinsonism
#3
Soyoung Jin, Minyoung Oh, Seung Jun Oh, Jungsu S Oh, Sang Ju Lee, Sun Ju Chung, Jae Seung Kim
PURPOSE: Regional cerebral perfusion is coupled to metabolism in general. Early perfusion dominant imaging using F-FP-CIT PET (pCIT) may provide complementary information to delayed dopamine transporter dominant images. We investigated the ability of pCIT to differentiate atypical Parkinson disorder from Parkinson disease (PD) compared to FDG and the image quality for optimizing the acquisition time. METHODS: Sixty-seven subjects [PD, 23 subjects; multiple system atrophy-cerebellar type (MSA-C), 27 subjects; MSA-Parkinson type (MSA-P), 12 subjects; and progressive supranuclear palsy (PSP), 5 subjects] underwent F-FP-CIT and FDG PET...
December 3, 2016: Clinical Nuclear Medicine
https://www.readbyqxmd.com/read/27922830/ligand-receptor-binding-kinetics-in-surface-plasmon-resonance-cells-a-monte-carlo-analysis
#4
Jacob Carroll, Matthew Raum, Kimberly Forsten-Williams, Uwe C Täuber
Surface plasmon resonance (SPR) chips are widely used to measure association and dissociation rates for the binding kinetics between two species of chemicals, e.g., cell receptors and ligands. It is commonly assumed that ligands are spatially well mixed in the SPR region, and hence a mean-field rate equation description is appropriate. This approximation however ignores the spatial fluctuations as well as temporal correlations induced by multiple local rebinding events, which become prominent for slow diffusion rates and high binding affinities...
December 6, 2016: Physical Biology
https://www.readbyqxmd.com/read/27922611/genetic-and-epigenomic-mechanisms-of-mammalian-circadian-transcription
#5
REVIEW
Romeo Papazyan, Yuxiang Zhang, Mitchell A Lazar
The mammalian molecular clock comprises a complex network of transcriptional programs that integrates environmental signals with physiological pathways in a tissue-specific manner. Emerging technologies are extending knowledge of basic clock features by uncovering their underlying molecular mechanisms, thus setting the stage for a 'systems' view of the molecular clock. Here we discuss how recent data from genome-wide genetic and epigenetic studies have informed the understanding of clock function. In addition to its importance in human physiology and disease, the clock mechanism provides an ideal model to assess general principles of dynamic transcription regulation in vivo...
December 6, 2016: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/27922190/clc-3-promotes-osteogenic-differentiation-in-mc3t3-e1-cell-after-dynamic-compression
#6
Dawei Wang, Hao Wang, Feng Gao, Kun Wang, Fusheng Dong
ClC-3 chloride channel has been proved to have a relationship with the expression of osteogenic markers during osteogenesis, persistent static compression can upregulate the expression of ClC-3 and regulate osteodifferentiation in osteoblasts. However, there was no study about the relationship between the expression of ClC-3 and osteodifferentiation after dynamic compression. In this study, we applied dynamic compression on MC3T3-E1 cells to detect the expression of ClC-3, runt-related transcription factor 2 (Runx2), bone morphogenic protein-2 (BMP-2), osteopontin (OPN), nuclear-associated antigen Ki67 (Ki67) and proliferating cell nuclear antigen (PCNA) in biopress system, then we investigated the expression of these genes after dynamic compression with Chlorotoxin (specific ClC-3 chloride channel inhibitor) added...
December 6, 2016: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/27921997/comparative-molecular-dynamics-study-of-dimeric-and-monomeric-forms-of-hiv-1-protease-in-ligand-bound-and-unbound-state
#7
Monikaben Padariya, Umesh Kalathiya
Human immunodeficiency virus type 1 protease is a viral-encoded enzyme and it is essential for replication and assembly of the virus. Inactivation of HIV-1 protease causes production of immature, noninfectious viral particles and thus HIV-1 protease is an attractive target in anti-AIDS drug design. In our current work, we performed molecular dynamics (MD) calculations (500 ns) for two different ligands (COM5 - designed in our previous study, and Darunavir) and made effort to understand dynamics behaviour of our designed compound COM5...
December 6, 2016: General Physiology and Biophysics
https://www.readbyqxmd.com/read/27921453/integrating-ion-mobility-spectrometry-into-mass-spectrometry-based-exposome-measurements-what-can-it-add-and-how-far-can-it-go
#8
Thomas O Metz, Erin S Baker, Emma L Schymanski, Ryan S Renslow, Dennis G Thomas, Tim J Causon, Ian K Webb, Stephan Hann, Richard D Smith, Justin G Teeguarden
Measuring the exposome remains a challenge due to the range and number of anthropogenic molecules that are encountered in our daily lives, as well as the complex systemic responses to these exposures. One option for improving the coverage, dynamic range and throughput of measurements is to incorporate ion mobility spectrometry (IMS) into current MS-based analytical methods. The implementation of IMS in exposomics studies will lead to more frequent observations of previously undetected chemicals and metabolites...
January 2017: Bioanalysis
https://www.readbyqxmd.com/read/27921393/the-role-of-the-microvascular-network-structure-on-diffusion-and-consumption-of-anti-cancer-drugs
#9
P Mascheroni, R Penta
We investigate the impact of microvascular geometry on the transport of drugs in solid tumors, focusing on the diffusion and consumption phenomena. We embrace recent advances in the asymptotic homogenization literature starting from a double Darcy, double advection-diffusion-reaction system of partial differential equations that is obtained exploiting the sharp length separation between the intercapillary distance and the average tumor size. The geometric information on the microvascular network is encoded into effective hydraulic conductivities and diffusivities, which are numerically computed by solving periodic cell problems on appropriate microscale representative cells...
December 6, 2016: International Journal for Numerical Methods in Biomedical Engineering
https://www.readbyqxmd.com/read/27921372/a-fuzzy-neural-network-sliding-mode-controller-for-vibration-suppression-in-robotically-assisted-minimally-invasive-surgery
#10
Hongqiang Sang, Chenghao Yang, Fen Liu, Jintian Yun, Guoguang Jin
BACKGROUND: It is very important for robotically assisted minimally invasive surgery to achieve a high-precision and smooth motion control. However, the surgical instrument tip will exhibit vibration caused by nonlinear friction and unmodeled dynamics, especially when the surgical robot system is attempting low-speed, fine motion. METHODS: A fuzzy neural network sliding mode controller (FNNSMC) is proposed to suppress vibration of the surgical robotic system. Nonlinear friction and modeling uncertainties are compensated by a Stribeck model, a radial basis function (RBF) neural network and a fuzzy system, respectively...
December 2016: International Journal of Medical Robotics + Computer Assisted Surgery: MRCAS
https://www.readbyqxmd.com/read/27921306/applying-a-family-resilience-framework-in-training-practice-and-research-mastering-the-art-of-the-possible
#11
Froma Walsh
With growing interest in systemic views of human resilience, this article updates and clarifies our understanding of the concept of resilience as involving multilevel dynamic processes over time. Family resilience refers to the functioning of the family system in dealing with adversity: Assessment and intervention focus on the family impact of stressful life challenges and the family processes that foster positive adaptation for the family unit and all members. The application of a family resilience framework is discussed and illustrated in clinical and community-based training and practice...
December 2016: Family Process
https://www.readbyqxmd.com/read/27921169/drying-kinetics-of-deformable-and-cracking-nano-porous-gels
#12
J Thiery, E Keita, S Rodts, D Courtier Murias, T Kodger, A Pegoraro, P Coussot
The desiccation of porous materials encompasses a wide range of technological and industrial processes and is acutely sensitive to the hierarchical structure of the porous materials resulting in complex dynamics which are challenging to unravel. Macroscopic observations of the surface and geometry of model colloidal gels during desiccation under controlled air flow highlight the role of crack formation in drying. The density of cracks and their rate of appearance depend on the initial solid fraction of the gels and their adherence to the substrate...
December 2016: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/27921099/thermoresponsive-microgels-containing-trehalose-as-soft-matrices-for-3d-cell-culture
#13
Małgorzata Burek, Sylwia Waśkiewicz, Anna Lalik, Sebastian Student, Tadeusz Bieg, Ilona Wandzik
A series of thermoresponsive glycomicrogels with trehalose in the cross-links or with trehalose in the cross-links and as pending moieties was synthesized. These materials were obtained by surfactant-free precipitation copolymerization of N-isopropylacrylamide and various amounts of trehalose monomers. The resultant particles showed a spherical shape and a submicrometer hydrodynamic size with a narrow size distribution. At 25 °C, glycomicrogels in solutions with physiological ionic strength formed stable colloids, which further gelled upon heating to physiological temperature forming a macroscopic hydrogel with an interconnected porous structure...
December 6, 2016: Biomaterials Science
https://www.readbyqxmd.com/read/27920753/neuroproteomics-and-systems-biology-approach-to-identify-temporal-biomarker-changes-post-experimental-traumatic-brain-injury-in-rats
#14
Firas H Kobeissy, Joy D Guingab-Cagmat, Zhiqun Zhang, Ahmed Moghieb, Olena Y Glushakova, Stefania Mondello, Angela M Boutté, John Anagli, Richard Rubenstein, Hisham Bahmad, Amy K Wagner, Ronald L Hayes, Kevin K W Wang
Traumatic brain injury (TBI) represents a critical health problem of which diagnosis, management, and treatment remain challenging. TBI is a contributing factor in approximately one-third of all injury-related deaths in the United States. The Centers for Disease Control and Prevention estimate that 1.7 million people suffer a TBI in the United States annually. Efforts continue to focus on elucidating the complex molecular mechanisms underlying TBI pathophysiology and defining sensitive and specific biomarkers that can aid in improving patient management and care...
2016: Frontiers in Neurology
https://www.readbyqxmd.com/read/27920428/mitigating-herding-in-hierarchical-crowdsourcing-networks
#15
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 2016: Scientific Reports
https://www.readbyqxmd.com/read/27920427/mixing-of-quantum-states-a-new-route-to-creating-optical-activity
#16
Anvar S Baimuratov, Nikita V Tepliakov, Yurii K Gun'ko, Alexander V Baranov, Anatoly V Fedorov, Ivan D Rukhlenko
The ability to induce optical activity in nanoparticles and dynamically control its strength is of great practical importance due to potential applications in various areas, including biochemistry, toxicology, and pharmaceutical science. Here we propose a new method of creating optical activity in originally achiral quantum nanostructures based on the mixing of their energy states of different parities. The mixing can be achieved by selective excitation of specific states or via perturbing all the states in a controllable fashion...
December 2016: Scientific Reports
https://www.readbyqxmd.com/read/27920388/human-drivers-of-ecological-and-evolutionary-dynamics-in-emerging-and-disappearing-infectious-disease-systems
#17
REVIEW
Mary A Rogalski, Camden D Gowler, Clara L Shaw, Ruth A Hufbauer, Meghan A Duffy
Humans have contributed to the increased frequency and severity of emerging infectious diseases, which pose a significant threat to wild and domestic species, as well as human health. This review examines major pathways by which humans influence parasitism by altering (co)evolutionary interactions between hosts and parasites on ecological timescales. There is still much to learn about these interactions, but a few well-studied cases show that humans influence disease emergence every step of the way. Human actions significantly increase dispersal of host, parasite and vector species, enabling greater frequency of infection in naive host populations and host switches...
January 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27919984/clinical-significances-of-preoperative-classification-of-intrahepatic-cholangiocarcinoma-different-characteristics-of-perihilar-vs-peripheral-icc
#18
Yo-Ichi Yamashita, Huanlin Wang, Takeshi Kurihara, Eiji Tsujita, Akihiro Nishie, Katsunori Imai, Daisuke Hashimoto, Akira Chikamoto, Shinichi Aishima, Hideo Baba
BACKGROUND: The aim of this study was to evaluate the clinical significance of preoperative classification of intrahepatic cholangiocarcinoma (ICC) into perihilar and peripheral types using dynamic computed tomography (CT). PATIENTS AND METHODS: A retrospective cohort study was performed to analyze the differences in clinical characteristics between perihilar and peripheral ICC samples from patients between 1990-2014. RESULTS: A total of 87 patients were divided into three ICC subtypes; perihilar (n=34), peripheral (n=44), and unclassifiable ICC (n=9)...
December 2016: Anticancer Research
https://www.readbyqxmd.com/read/27919816/surface-rearrangement-of-adsorbed-egcg-mucin-complexes-on-hydrophilic-surfaces
#19
J McColl, R Horvath, G E Yakubov, J J Ramsden
The kinetic adsorption-desorption behaviour of porcine gastric mucin in the presence of physiologically relevant concentrations of the polyphenol epigallocatechin gallate (EGCG) was investigated using high-resolution kinetic optical waveguide lightmode spectroscopy (OWLS) and atomic force microscopy (AFM). Comparison with dynamic light scattering results from EGCG-mucin mixtures indicates that discrete particles are formed whose size increases with increasing EGCG:mucin ratio. These particles are deduced to be the adsorbing entities, which fuse on the surface to form complex surface layers...
December 2, 2016: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/27919729/noradrenergic-modulation-of-evoked-dopamine-release-and-ph-shift-in-the-mouse-dorsal-hippocampus-and-ventral-striatum
#20
Adam Z Weitemier, Thomas J McHugh
Rapid monoamine release in the dorsal hippocampus is not well characterized, despite its postulated role in modulating fast hippocampal circuit dynamics. We measured monoamine release in the dorsal hippocampus upon stimulation of the ventral tegmental area (VTA) with fast-scan cyclic voltammetry in anesthetized norepinephrine-depleted and non-depleted mice. Within the hippocampus, norepinephrine depletion altered the ability of α2 adrenergic compounds and transporter blockers to modulate the small, evoked monoamine signal...
December 2, 2016: Brain Research
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