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https://www.readbyqxmd.com/read/28239715/clustering-in-vibrated-monolayers-of-granular-rods
#1
M González-Pinto, F Borondo, Y Martínez-Ratón, E Velasco
We investigate the ordering properties of vertically-vibrated monolayers of granular cylinders in a circular container at high packing fraction. In line with previous works by other groups, we identify liquid-crystalline ordering behaviour similar to that of two-dimensional hard rectangular particles subject to thermal equilibrium fluctuations. However, due to dissipation, there is a much stronger tendency for particles to cluster into parallel arrangements in the granular system. These clusters behave as a polydisperse mixture of long life-time 'superparticles', and some aspects of the system behaviour can be understood by applying mean-field theories for equilibrium hard rectangles, based on two-body correlations, to these 'superparticles'...
February 27, 2017: Soft Matter
https://www.readbyqxmd.com/read/28239705/chemical-communication-and-dynamics-of-droplet-emulsions-in-networks-of-belousov-zhabotinsky-micro-oscillators-produced-by-microfluidics
#2
Kristian Torbensen, Federico Rossi, Sandra Ristori, Ali Abou-Hassan
Chemical communication leading to synchronization and collective behaviour of dynamic elements, such as cell colonies, is a widespread phenomenon with biological, physical and chemical importance. Such synchronization between elements proceeds via chemical communication by emmision, interdiffusion and reception of specific messenger molecules. On a lab scale, these phenomena can be modeled by encapsulating an oscillating chemical reaction, which serves as a signal (information) sender/receiver element, inside microcompartments such as droplet emulsions, liposomes and polymersomes...
February 27, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28239424/non-covalent-interactions-in-controlling-ph-responsive-behaviors-of-self-assembled-nanosystems
#3
Yang Li, Zhaohui Wang, Qi Wei, Min Luo, Gang Huang, Baran D Sumer, Jinming Gao
Self-assembly and associated dynamic and reversible non-covalent interactions are the basis of protein biochemistry (e.g., protein folding) and development of sophisticated nanomaterial systems that can respond to and amplify biological signals. In this study, we report a systematic investigation of non-covalent interactions that affect the pH responsive behaviors and resulting supramolecular self-assembly of a series of ultra-pH sensitive (UPS) block copolymers. Increase of hydrophobic and π-π stacking interactions led to the decrease of pKa values...
October 14, 2016: Polymer Chemistry
https://www.readbyqxmd.com/read/28238128/nanoparticle-tracking-analysis-for-determination-of-hydrodynamic-diameter-concentration-and-zeta-potential-of-polyplex-nanoparticles
#4
David R Wilson, Jordan J Green
Nanoparticle tracking analysis (NTA) is a recently developed nanoparticle characterization technique that offers certain advantages over dynamic light scattering for characterizing polyplex nanoparticles in particular. Dynamic light scattering results in intensity-weighted average measurements of nanoparticle characteristics. In contrast, NTA directly tracks individual particles, enabling concentration measurements as well as the direct determination of number-weighted particle size and zeta-potential. A direct number-weighted assessment of nanoparticle characteristics is particularly useful for polydisperse samples of particles, including many varieties of gene delivery particles that can be prone to aggregation...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28237086/pseudomonas-aeruginosa-produces-aspirin-insensitive-eicosanoids-and-contributes-to-the-eicosanoid-profile-of-polymicrobial-biofilms-with-candida-albicans
#5
Ruan Fourie, Ruan Ells, Gabré Kemp, Olihile M Sebolai, Jacobus Albertyn, Carolina H Pohl
The interaction of clinically relevant microorganisms is the focus of various studies, e.g. the interaction between the pathogenic yeast, Candida albicans, and the bacterium, Pseudomonas aeruginosa. During infection both release arachidonic acid, which they can transform into eicosanoids. This study evaluated the production of prostaglandin E2, prostaglandin F2α and 15-hydroxyeicosatetraenoic acid by biofilms of P. aeruginosa and C. albicans. The influence of co-incubation, acetylsalicylic acid and nordihydroguaiaretic acid on biofilm formation and eicosanoid production was evaluated...
February 2017: Prostaglandins, Leukotrienes, and Essential Fatty Acids
https://www.readbyqxmd.com/read/28236031/structural-dependence-of-meh-ppv-chromism-in-solution
#6
Carlos E T de Magalhães, Ranylson M L Savedra, Karina S Dias, Rodrigo Ramos, Melissa F Siqueira
The chromism observed in the MEH-PPV polymer in tetrahydrofuran (THF) solution is discussed as a function of the structural morphology of the backbone chains. To evaluate this phenomenon, we carried out simulations employing a hybrid methodology using molecular dynamics and quantum mechanical approaches. Our results support the hypothesis that the morphological order-disorder transition is related to the change from red to blue phase observed experimentally. The morphological disorder is associated with total or partial twisted arrangements in the polymer backbone, which induces an electronic conjugation length more confined to shorter segments...
March 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28236030/insights-from-molecular-modeling-into-the-selective-inhibition-of-cathepsin-s-by-its-inhibitor
#7
Sabahuddin Ahmad, Mohammad Imran Siddiqi
Cathepsin S has been demonstrated to play a crucial role in the remodeling of extracellular matrix proteins such as elastin and collagen, which in turn contribute to the structural integrity of the cardiovascular wall. Atherosclerotic lesions, aneurysm formation, plaque rupture, thrombosis, and calcification are some of the cardiovascular disorders related to cathepsin S. A highly selective inhibitor of human as well as animal cathepsin S, RO5444101, was recently reported to attenuate the progression of atherosclerotic lesions...
March 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28235879/experimental-manipulation-shows-a-greater-influence-of-population-than-dietary-perturbation-on-the-microbiome-of-tyrophagus-putrescentiae
#8
Tomas Erban, Ondrej Ledvinka, Marta Nesvorna, Jan Hubert
Tyrophagus putrescentiae (TP) is inhabited by bacteria that differ among mite populations (strains) and diets. Here, we investigated how the microbiome and fitness of TP are altered by dietary perturbations and mite populations. Four TP populations, referred to as Dog, Koppert, Laboratory and Phillips, underwent a perturbation, i.e., a dietary switch from a rearing diet to two experimental diets. The microbiome was investigated by sequencing the V1-V3 portion of the 16S rRNA gene, and selected bacterial taxa were quantified by qPCR using group/taxa-specific primers...
February 24, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28235785/emergence-of-communities-and-diversity-in-social-networks
#9
Xiao Han, Shinan Cao, Zhesi Shen, Boyu Zhang, Wen-Xu Wang, Ross Cressman, H Eugene Stanley
Communities are common in complex networks and play a significant role in the functioning of social, biological, economic, and technological systems. Despite widespread interest in detecting community structures in complex networks and exploring the effect of communities on collective dynamics, a deep understanding of the emergence and prevalence of communities in social networks is still lacking. Addressing this fundamental problem is of paramount importance in understanding, predicting, and controlling a variety of collective behaviors in society...
February 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28235764/cellular-and-molecular-identity-of-tumor-associated-macrophages-in-glioblastoma
#10
Zhihong Chen, Xi Feng, Cameron J Herting, Virginia Alvarez Garcia, Kai Nie, Winnie W Pong, Rikke Rasmussen, Bhakti Dwivedi, Sandra Seby, Susanne A Wolf, David H Gutmann, Dolores Hambardzumyan
In glioblastoma (GBM), tumor--associated macrophages (TAM) represent up to one half of the cells of the tumor mass, including both infiltrating macrophages and resident brain microglia. In an effort to delineate the temporal and spatial dynamics of TAM composition during gliomagenesis, we employed two genetically engineered mouse models where oncogenic drivers and fluorescent reporters were expressed coordinately under the control of the monocyte/microglia--selective Cx3cr1 or Ccr2 promoters, respectively. Using this approach, we demonstrated that CX3CR1LoCCR2Hi monocytes were recruited to the glioblastoma, where they transitioned to CX3CR1HiCCR2Lo macrophages and CX3CR1HiCCR2- microglia--like cells...
February 24, 2017: Cancer Research
https://www.readbyqxmd.com/read/28231498/bone-specific-poly-ethylene-sodium-phosphate-bearing-biodegradable-nanoparticles
#11
Yuya Hirano, Yasuhiko Iwasaki
Chemotherapy is the most reliable treatment for osteoporosis and osseous metastases. To facilitate better drug delivery for bone treatments, a novel preparation of polymeric nanoparticles with high affinity to bone has been prepared. Two-step synthesis of cholesteryl-functionalized poly(ethylene sodium phosphate) (Ch-PEPn·Na) was performed via ring-opening polymerization of cyclic phosphoesters and the demethylation. The molecular weight of Ch-PEPn·Na could be well controlled by changing the ratio of cholesterol and cyclic phosphoesters...
February 16, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28231402/ex-vivo-visualization-of-human-ciliated-epithelium-and-quantitative-analysis-of-induced-flow-dynamics-by-using-optical-coherence-tomography
#12
Yuye Ling, Xinwen Yao, Ute A Gamm, Emilio Arteaga-Solis, Charles W Emala, Michael A Choma, Christine P Hendon
BACKGROUND AND OBJECTIVE: Cilia-driven mucociliary clearance is an important self-defense mechanism of great clinical importance in pulmonary research. Conventional light microscopy possesses the capability to visualize individual cilia and its beating pattern but lacks the throughput to assess the global ciliary activities and flow dynamics. Optical coherence tomography (OCT), which provides depth-resolved cross-sectional images, was recently introduced to this area. MATERIALS AND METHODS: Fourteen de-identified human tracheobronchial tissues are directly imaged by two OCT systems: one system centered at 1,300 nm with 6...
February 23, 2017: Lasers in Surgery and Medicine
https://www.readbyqxmd.com/read/28230867/ultrafast-electron-and-hole-transfer-dynamics-of-a-solar-cell-dye-containing-hole-acceptors-on-mesoporous-tio2-and-al2o3
#13
Mirko Scholz, Oliver Flender, Gerrit Boschloo, Kawon Oum, Thomas Lenzer
The stability of dye cations against recombination with conduction band electrons in mesoporous TiO2 electrodes is a key property for improving light harvesting in dye-sensitised solar cells. Using ultrafast transient broadband absorption spectroscopy, we monitor efficient intramolecular hole transfer in the solar cell dye E6 having two peripheral triarylamine acceptors. After photoexcitation, two hole transfer mechanisms are identified: a concerted mechanism for electron injection and hole transfer (2.4 ps) and a sequential mechanism with time constants of 3...
February 23, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28230533/thermophoretic-transport-of-ionic-liquid-droplets-in-carbon-nanotubes
#14
Rakesh Rajegowda, Sridhar Kannam, Remco Hartkamp, Sarith P Sathian
Thermal-gradient induced transport of ionic liquid (IL) and water droplets through a carbon nanotube (CNT) is investigated in this study using molecular dynamics simulations. Energetic analysis indicates that IL transport through a CNT is driven primarily by the fluid-solid interaction, while fluid-fluid interactions dominate in water-CNT systems. Droplet diffusion analysis via the Moment Scaling Spectrum reveals sub-diffusive motion of the IL droplet, in contrast to the self-diffusive motion of the water droplet...
February 23, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28230348/nmr-structures-of-gcn4p-are-largely-conserved-when-ion-pairs-are-disrupted-at-acidic-ph-but-show-a-relaxation-of-the-coiled-coil-superhelix
#15
Anne R Kaplan, Megan R Brady, Mark W Maciejewski, Richard A Kammerer, Andrei T Alexandrescu
To understand the roles ion pairs play in stabilizing coiled coils we determined NMR structures of GCN4p at three pH values. At pH 6.6 all acidic residues are fully charged, at pH 4.4 they are half-charged, and at pH 1.5 they are protonated and uncharged. The α-helix monomer and coiled coil structures of GCN4p are largely conserved, except for a loosening of the coiled coil quaternary structure with decreasing pH. Differences going from neutral to acidic pH include (i) an unwinding of the coiled coil superhelix due to the loss of inter-chain ion pair contacts, (ii) a small increase in the separation of the monomers in the dimer, (iii) a loosening of knobs-into-holes packing motifs, and (iv) an increased separation between oppositely charged residues that participate in ion pairs at neutral pH...
February 23, 2017: Biochemistry
https://www.readbyqxmd.com/read/28230186/glycan-independent-binding-and-internalization-of-human-igm-to-fcmr-its-cognate-cellular-receptor
#16
Katy A Lloyd, Jiabin Wang, Britta C Urban, Daniel M Czajkowsky, Richard J Pleass
IgM is the first antibody to be produced in immune responses and plays an important role in the neutralization of bacteria and viruses. Human IgM is heavily glycosylated, featuring five N-linked glycan sites on the μ chain and one on the J-chain. Glycosylation of IgG is known to modulate the effector functions of Fcγ receptors. In contrast, little is known about the effect of glycosylation on IgM binding to the human Fcμ receptor (hFCMR). In this study, we identify the Cμ4 domain of IgM as the target of hFCMR, and show that binding and internalization of IgM by hFCMR is glycan-independent...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28230164/dynamical-majorana-edge-modes-in-a-broad-class-of-topological-mechanical-systems
#17
Emil Prodan, Kyle Dobiszewski, Alokik Kanwal, John Palmieri, Camelia Prodan
Mechanical systems can display topological characteristics similar to that of topological insulators. Here we report a large class of topological mechanical systems related to the BDI symmetry class. These are self-assembled chains of rigid bodies with an inversion centre and no reflection planes. The particle-hole symmetry characteristic to the BDI symmetry class stems from the distinct behaviour of the translational and rotational degrees of freedom under inversion. This and other generic properties led us to the remarkable conclusion that, by adjusting the gyration radius of the bodies, one can always simultaneously open a gap in the phonon spectrum, lock-in all the characteristic symmetries and generate a non-trivial topological invariant...
February 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28230046/gel-phase-formation-in-dilute-triblock-copolyelectrolyte-complexes
#18
Samanvaya Srivastava, Marat Andreev, Adam E Levi, David J Goldfeld, Jun Mao, William T Heller, Vivek M Prabhu, Juan J de Pablo, Matthew V Tirrell
Assembly of oppositely charged triblock copolyelectrolytes into phase-separated gels at low polymer concentrations (<1% by mass) has been observed in scattering experiments and molecular dynamics simulations. Here we show that in contrast to uncharged, amphiphilic block copolymers that form discrete micelles at low concentrations and enter a phase of strongly interacting micelles in a gradual manner with increasing concentration, the formation of a dilute phase of individual micelles is prevented in polyelectrolyte complexation-driven assembly of triblock copolyelectrolytes...
February 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28229437/pharmacokinetic-modeling-of-11-c-flumazenil-kinetics-in-the-rat-brain
#19
Isadora Lopes Alves, David Vállez García, Andrea Parente, Janine Doorduin, Rudi Dierckx, Ana Maria Marques da Silva, Michel Koole, Antoon Willemsen, Ronald Boellaard
BACKGROUND: Preferred models for the pharmacokinetic analysis of [(11)C]flumazenil human studies have been previously established. However, direct translation of these models and settings to animal studies might be sub-optimal. Therefore, this study evaluates pharmacokinetic models for the quantification of [(11)C]flumazenil binding in the rat brain. Dynamic (60 min) [(11)C]flumazenil brain PET scans were performed in two groups of male Wistar rats (tracer dose (TD), n = 10 and pre-saturated (PS), n = 2)...
December 2017: EJNMMI Research
https://www.readbyqxmd.com/read/28228589/capsid-phosphorylation-state-and-hepadnavirus-virion-secretion
#20
Xiaojun Ning, Suresh H Basagoudanavar, Kuancheng Liu, Laurie Luckenbaugh, Duoqian Wei, Chunyan Wang, Bo Wei, Yingren Zhao, Taotao Yan, William Delaney, Jianming Hu
The C-terminal domain (CTD) of hepadnavirus core protein is involved in multiple steps of viral replication. In particular, CTD is initially phosphorylated at multiple sites to facilitate viral RNA packaging into immature nucleocapsids (NCs) and the early stage of viral DNA synthesis. For the avian hepadnavirus, the duck hepatitis B virus (DHBV), CTD is dephosphorylated subsequently to facilitate the late stage of viral DNA synthesis and to stabilize NCs containing mature viral DNA. The role of CTD phosphorylation in virion secretion, if any, has remained unclear...
February 22, 2017: Journal of Virology
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