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https://www.readbyqxmd.com/read/28088672/using-discrete-multi-physics-for-detailed-exploration-of-hydrodynamics-in-an-in-vitro-colon-system
#1
A Alexiadis, K Stamatopoulos, W Wen, H K Batchelor, S Bakalis, M Barigou, M J H Simmons
We developed a mathematical model that describes the motion of viscous fluids in the partially-filled colon caused by the periodic contractions of flexible walls (peristalsis). In-vitro data are used to validate the model. The model is then used to identify two fundamental mechanisms of mass transport: the surfing mode and the pouring mode. The first mechanism is faster, but only involves the surface of the liquid. The second mechanism causes deeper mixing, and appears to be the main transport mechanism. Based on the gained understanding, we propose a series of measures that can improve the reliability of in-vitro models...
January 9, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28088643/molecular-mechanisms-of-bio-catalysis-of-heme-extraction-from-hemoglobin
#2
Serzhan Sakipov, Olga Rafikova, Maria G Kurnikova, Ruslan Rafikov
Red blood cell hemolysis in sickle cell disease (SCD) releases free hemoglobin. Extracellular hemoglobin and its degradation products, free heme and iron, are highly toxic due to oxidative stress induction and decrease in nitric oxide availability. We propose an approach that helps to eliminate extracellular hemoglobin toxicity in SCD by employing a bacterial protein system that evolved to extract heme from extracellular hemoglobin. NEAr heme Transporter (NEAT) domains from iron-regulated surface determinant proteins from Staphylococcus aureus specifically bind free heme as well as facilitate its extraction from hemoglobin...
January 7, 2017: Redox Biology
https://www.readbyqxmd.com/read/28088631/an-esipt-based-two-photon-fluorescent-probe-detection-of-hydrogen-peroxide-in-live-cells-and-tissues
#3
Liyi Zhou, Yongbo Peng, Qianqian Wang, Qinlu Lin
A variety of diseases associated with human aging, which have a strong oxidative stress, but connecting age-related diseases and oxidative stress of the basic molecular mechanisms still insufficiently understood. Oxidative stress origins from the unregulated production of reactive oxygen species (ROS), and oxidative damaging to tissues and organs from subsequent oxidation-reduction chemistry by cellular mismanagement. In particular, H2O2 is a major by-product of ROS in live organisms and a common marker for oxidative stress, and its dynamic equilibrium can have various physiological and pathological consequences...
January 9, 2017: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/28088616/patient-agency-and-contested-notions-of-disability-in-social-assistance-applications-in-south-africa
#4
Gabrielle Kelly
Problems in fairly allocating welfare and health resources are very often located in the spaces where citizens interact directly with state workers. This study draws on observations of doctor-patient encounters in disability assessments for the South African disability grant (DG) to examine how doctor-patient interactions and patient agency shape social welfare allocation in a context of high poverty and inequality. Data were gathered via interviews with healthcare workers and observations of doctor-patient interactions in twelve clinics and three hospitals in the Western Cape province between October 2013 and August 2014...
January 9, 2017: Social Science & Medicine
https://www.readbyqxmd.com/read/28088574/time-dependence-of-the-enhancement-effect-of-chemical-enhancers-molecular-mechanisms-of-enhancing-kinetics
#5
Xiaochang Liu, Peng Quan, Shanshan Li, Chao Liu, Yuan Zhao, Yongshan Zhao, Liang Fang
Chemical enhancers are widely used for facilitating drug penetration in transdermal drug delivery system (TDDS). However, there is a lack of knowledge about how the enhancement effect changes over time. In this study, on the basis of kinetic parameters of enhancement effect, molecular details of the dynamic enhancement process was described and a new hypothesis of the recovery mechanism of the skin barrier function was proposed. Using pretreated skin and flurbiprofen patch, the effects of Azone (AZ) and menthol decanoate (MT-10) were evaluated with in vitro permeation experiment and further confirmed by confocal laser scanning microscopy (CLSM) and TEWL...
January 11, 2017: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/28088484/optimal-trajectories-of-brain-state-transitions
#6
Shi Gu, Richard F Betzel, Marcelo G Mattar, Matthew Cieslak, Philip R Delio, Scott T Grafton, Fabio Pasqualetti, Danielle S Bassett
The complexity of neural dynamics stems in part from the complexity of the underlying anatomy. Yet how white matter structure constrains how the brain transitions from one cognitive state to another remains unknown. Here we address this question by drawing on recent advances in network control theory to model the underlying mechanisms of brain state transitions as elicited by the collective control of region sets. We find that previously identified attention and executive control systems are poised to affect a broad array of state transitions that cannot easily be classified by traditional engineering-based notions of control...
January 11, 2017: NeuroImage
https://www.readbyqxmd.com/read/28088482/combined-spatiotemporal-ica-stica-for-continuous-and-dynamic-lag-structure-analysis-of-mreg-data
#7
Ville Raatikainen, Niko Huotari, Vesa Korhonen, Aleksi Rasila, Janne Kananen, Lauri Raitamaa, Tuija Keinänen, Jussi Kantola, Osmo Tervonen, Vesa Kiviniemi
This study investigated lag structure in the resting-state fMRI by applying a novel independent component (ICA) method to magnetic resonance encephalography (MREG) data. Briefly, the spatial ICA (sICA) was used for defining the frontal and back nodes of the default mode network (DMN), and the temporal ICA (tICA), which is enabled by the high temporal resolution of MREG (TR=100ms), was used to separate both neuronal and physiological components of these two spatial map regions. Subsequently, lag structure was investigated between the frontal (DMNvmpf) and posterior (DMNpcc) DMN nodes using both conventional method with all-time points and a sliding-window approach...
January 11, 2017: NeuroImage
https://www.readbyqxmd.com/read/28088456/development-of-a-predictive-model-for-the-long-term-stability-assessment-of-drug-in-adhesive-transdermal-films-using-polar-pressure-sensitive-adhesives-as-carrier-matrix
#8
Clémence Chenevas-Paule, Hans-Michael Wolff, Mark Ashton, Martin Schubert, Kalliopi Dodou
Drug crystallization in transdermal drug delivery systems (TDDS) is a critical quality defect. The impact of drug load and hydration on the physical stability of polar (acrylic) drug-in-adhesive (DIA) films was investigated with the objective to identify predictive formulation parameters with respect to drug solubility and long-term stability. Medicated acrylic films were prepared over a range of drug concentrations below and above saturation solubility; and were characterized by FTIR, differential scanning calorimetry (DSC), polarized microscopy and Dynamic Vapor Sorption (DVS) analysis...
January 11, 2017: Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28088192/nucleotide-diversity-inflation-as-a-genome-wide-response-to-experimental-lifespan-extension-in-drosophila-melanogaster
#9
Pawel Michalak, Lin Kang, Pernille M Sarup, Mads F Schou, Volker Loeschcke
BACKGROUND: Evolutionary theory predicts that antagonistically selected alleles, such as those with divergent pleiotropic effects in early and late life, may often reach intermediate population frequencies due to balancing selection, an elusive process when sought out empirically. Alternatively, genetic diversity may increase as a result of positive frequency-dependent selection and genetic purging in bottlenecked populations. RESULTS: While experimental evolution systems with directional phenotypic selection typically result in at least local heterozygosity loss, we report that selection for increased lifespan in Drosophila melanogaster leads to an extensive genome-wide increase of nucleotide diversity in the selected lines compared to replicate control lines, pronounced in regions with no or low recombination, such as chromosome 4 and centromere neighborhoods...
January 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28088161/efficient-free-energy-calculations-by-combining-two-complementary-tempering-sampling-methods
#10
Liangxu Xie, Lin Shen, Zhe-Ning Chen, Mingjun Yang
Although energy barriers can be efficiently crossed in the reaction coordinate (RC) guided sampling, this type of method suffers from identification of the correct RCs or requirements of high dimensionality of the defined RCs for a given system. If only the approximate RCs with significant barriers are used in the simulations, hidden energy barriers with small to medium height would exist in other degrees of freedom (DOFs) relevant to the target process and consequently cause the problem of insufficient sampling...
January 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28088156/path-integral-approach-to-the-wigner-representation-of-canonical-density-operators-for-discrete-systems-coupled-to-harmonic-baths
#11
Andrés Montoya-Castillo, David R Reichman
We derive a semi-analytical form for the Wigner transform for the canonical density operator of a discrete system coupled to a harmonic bath based on the path integral expansion of the Boltzmann factor. The introduction of this simple and controllable approach allows for the exact rendering of the canonical distribution and permits systematic convergence of static properties with respect to the number of path integral steps. In addition, the expressions derived here provide an exact and facile interface with quasi- and semi-classical dynamical methods, which enables the direct calculation of equilibrium time correlation functions within a wide array of approaches...
January 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28088151/phase-transition-of-a-symmetric-diblock-copolymer-induced-by-nanorods-with-different-surface-chemistry
#12
Yu-Qi Guo, Jun-Xing Pan, Min-Na Sun, Jin-Jun Zhang
We investigate the phase transition of a symmetric diblock copolymer induced by nanorods with different surface chemistry. The results demonstrate that the system occurs the phase transition from a disordered structure to ordered parallel lamellae and then to the tilted layered structure as the number of rods increases. The dynamic evolution of the domain size and the order parameter of the microstructure are also examined. Furthermore, the influence of rod property, rod-phase interaction, rod-rod interaction, rod length, and polymerization degree on the behavior of the polymer system is also investigated systematically...
January 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28088143/fokker-planck-quantum-master-equation-for-mixed-quantum-semiclassical-dynamics
#13
Jin-Jin Ding, Yao Wang, Hou-Dao Zhang, Rui-Xue Xu, Xiao Zheng, YiJing Yan
We revisit Caldeira-Leggett's quantum master equation representing mixed quantum-classical theory, but with limited applications. Proposed is a Fokker-Planck quantum master equation theory, with a generic bi-exponential correlation function description on semiclassical Brownian oscillators' environments. The new theory has caustic terms that bridge between the quantum description on primary systems and the semiclassical or quasi-classical description on environments. Various parametrization schemes, both analytical and numerical, for the generic bi-exponential environment bath correlation functions are proposed and scrutinized...
January 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28088142/colloidal-transport-by-active-filaments
#14
Raj Kumar Manna, P B Sunil Kumar, R Adhikari
Enhanced colloidal transport beyond the limit imposed by diffusion is usually achieved through external fields. Here, we demonstrate the ballistic transport of a colloidal sphere using internal sources of energy provided by an attached active filament. The latter is modeled as a chain of chemo-mechanically active beads connected by potentials that enforce semi-flexibility and self-avoidance. The fluid flow produced by the active beads and the forces they mediate are explicitly taken into account in the overdamped equations of motion describing the colloid-filament assembly...
January 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28088140/ring-polymer-molecular-dynamics-studies-on-the-rate-coefficient-of-the-abstraction-channel-of-hydrogen-plus-ethane-propane-and-dimethyl-ether
#15
Qingyong Meng, Jun Chen
To accurately compute the rates of the abstraction channels of hydrogen plus ethane (Et), propane (Pr), and dimethyl ether (DME), ring-polymer molecular dynamics (RPMD) method is used in conjunction with the recently constructed local permutation invariant polynomial neural-networks potential energy surface of the parent H + CH4 system [Q. Meng et al., J. Chem. Phys. 144, 154312 (2016)]. For H + Et, one of the H atoms in CH4 of the parent system is replaced by a methyl group, while for the H + DME reaction, it is replaced by the methoxyl group...
January 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28088138/fast-simulation-of-brownian-dynamics-in-a-crowded-environment
#16
Stephen Smith, Ramon Grima
Brownian dynamics simulations are an increasingly popular tool for understanding spatially extended biochemical reaction systems. Recent improvements in our understanding of the cellular environment show that volume exclusion effects are fundamental to reaction networks inside cells. These systems are frequently studied by incorporating inert hard spheres (crowders) into three-dimensional Brownian dynamics (BD) simulations; however these methods are extremely slow owing to the sheer number of possible collisions between particles...
January 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28088137/forces-on-nuclei-moving-on-autoionizing-molecular-potential-energy-surfaces
#17
Nimrod Moiseyev
Autoionization of molecular systems occurs in diatomic molecules and in small biochemical systems. Quantum chemistry packages enable calculation of complex potential energy surfaces (CPESs). The imaginary part of the CPES is associated with the autoionization decay rate, which is a function of the molecular structure. Molecular dynamics simulations, within the framework of the Born-Oppenheimer approximation, require the definition of a force field. The ability to calculate the forces on the nuclei in bio-systems when autoionization takes place seems to rely on an understanding of radiative damages in RNA and DNA arising from the release of slow moving electrons which have long de Broglie wavelengths...
January 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28088094/organ-on-a-chip-for-assessing-environmental-toxicants
#18
REVIEW
Soohee Cho, Jeong-Yeol Yoon
Man-made xenobiotics, whose potential toxicological effects are not fully understood, are oversaturating the already-contaminated environment. Due to the rate of toxicant accumulation, unmanaged disposal, and unknown adverse effects to the environment and the human population, there is a crucial need to screen for environmental toxicants. Animal models and in vitro models are ineffective models in predicting in vivo responses due to inter-species difference and/or lack of physiologically-relevant 3D tissue environment...
January 11, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28088081/lead-pb-2-and-copper-cu-2-remediation-from-water-using-superparamagnetic-maghemite-%C3%AE-fe2o3-nanoparticles-synthesized-by-flame-spray-pyrolysis-fsp
#19
Shalini Rajput, Lok P Singh, Charles U Pittman, Dinesh Mohan
Superparamagnetic maghemite (γ-Fe2O3) nanoparticles of controllable morphology were successfully synthesized using a flame spray pyrolysis (FSP) technique. Their physico-chemical properties, size, morphology, and surface chemistries were determined using X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), transmission electron microscopy (TEM), selected area electron diffraction patterns (SAED), SEM-EDX, scanning electron microscopy (SEM), and pHZPC(6.3). Elemental contents before and after adsorption were identified using energy dispersive X-ray fluorescence (ED-XRF), energy dispersive X-ray analysis (EDX) and elemental mapping...
November 27, 2016: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28087980/the-significance-of-glypican-3-expression-profiling-in-the-tumor-cellular-origin-theoretical-system-for-hepatocellular-carcinoma-progression
#20
Ran Xue, Jiliang Feng, Qinghua Meng, Fudong Lv, Yueke Zhu, Hongwei Yu, Shijie Zhang, Chenzhao Song, Lin Sun, Zhujun Yue, Shuai Feng, Ruiwen Che, Qian Xiang, Xiaodan Jing
AIMS: Glypican-3(GPC3) expression is correlated with poor prognosis and progression in hepatocellular carcinoma (HCC). HCC progression can be associated with the differentiation status of tumor cell before malignant transformation. Our aim was to investigate the dynamic expression of GPC3 during tumor cells differentiation and to explore the role and theoretical significance of GPC3 in malignant essence of HCC. METHODS: The expressions of tissue GPC3 and alpha-fetoprotein (AFP) were detected by immunohistochemical staining...
January 14, 2017: Journal of Gastroenterology and Hepatology
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