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https://www.readbyqxmd.com/read/28637243/nanopore-sequencing-data-analysis-state-of-the-art-applications-and-challenges
#1
Alberto Magi, Roberto Semeraro, Alessandra Mingrino, Betti Giusti, Romina D'Aurizio
The nanopore sequencing process is based on the transit of a DNA molecule through a nanoscopic pore, and since the 90s is considered as one of the most promising approaches to detect polymeric molecules. In 2014, Oxford Nanopore Technologies (ONT) launched a beta-testing program that supplied the scientific community with the first prototype of a nanopore sequencer: the MinION. Thanks to this program, several research groups had the opportunity to evaluate the performance of this novel instrument and develop novel computational approaches for analyzing this new generation of data...
June 16, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28636926/enhanced-human-bone-marrow-mesenchymal-stromal-cell-adhesion-on-scaffolds-promotes-cell-survival-and-bone-formation
#2
Miryam Mebarki, Laura Coquelin, Pierre Layrolle, Séverine Battaglia, Marine Tossou, Philippe Hernigou, Hélène Rouard, Nathalie Chevallier
In order to induce an efficient bone formation with human bone marrow mesenchymal stromal cells (hBMSC) associated to a scaffold, it is crucial to determine the key points of the hBMSC action after in vivo transplantation as well as the appropriate features of a scaffold. To this aim we compared the hBMSC behavior when grafted onto two biomaterials allowing different bone potential in vivo. The cancellous devitalized Tutoplast®-processed bone (TPB) and the synthetic hydroxyapatite/β-tricalcium-phosphate (HA/βTCP) which give at 6 weeks 100% and 50% of bone formation respectively...
June 18, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28636915/probing-the-structural-dynamics-of-the-nmda-receptor-activation-by-coarse-grained-modeling
#3
Wenjun Zheng, Han Wen, Gary J Iacobucci, Gabriela K Popescu
N-Methyl-D-aspartate (NMDA) receptors are glutamate-gated excitatory channels that play essential roles in brain functions. High-resolution structures have been solved for an allosterically inhibited and agonist-bound form of a functional NMDA receptor; however, other key functional states (particularly the active open-channel state) were only resolved at moderate resolutions by cryo-electron microscopy (cryo-EM). To decrypt the mechanism of the NMDA receptor activation, structural modeling is essential to provide presently missing information about structural dynamics...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636815/accurate-characterization-of-the-pore-volume-in-microporous-crystalline-materials
#4
Daniele Ongari, Peter G Boyd, Senja Barthel, Matthew Witman, Maciej Haranczyk, Berend Smit
Pore volume is one of the main properties for the characterization of microporous crystals. It is experimentally measurable and it can also be obtained from the refined unit cell by a number of computational techniques. In this work we assess the accuracy and the discrepancies between the different computational methods which are commonly used for this purpose, i.e, geometric, helium and probe center pore volume, by studying a database of more than 5000 frameworks. We developed a new technique to fully characterize the internal void of a microporous material and to compute the probe accessible and occupiable pore volume...
June 21, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28636801/water-channels-and-barriers-formed-by-claudins
#5
REVIEW
Rita Rosenthal, Dorothee Günzel, Dian Theune, Carolina Czichos, Jörg-Dieter Schulzke, Michael Fromm
Physiological studies in leaky epithelia, like kidney proximal tubules and the small intestine, have documented water transport via both transcellular and paracellular pathways. The discovery of aquaporin water channels provided a molecular basis for transcellular water movement. In contrast, the contribution, or even existence, of a specific paracellular water pathway has been disputed for a long time, until the cation channel-forming tight junction protein claudin-2 was shown to also permit the paracellular passage of water through its pore...
June 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28636640/targeted-nanodiamonds-for-identification-of-subcellular-protein-assemblies-in-mammalian-cells
#6
Michael P Lake, Louis-S Bouchard
Transmission electron microscopy (TEM) can be used to successfully determine the structures of proteins. However, such studies are typically done ex situ after extraction of the protein from the cellular environment. Here we describe an application for nanodiamonds as targeted intensity contrast labels in biological TEM, using the nuclear pore complex (NPC) as a model macroassembly. We demonstrate that delivery of antibody-conjugated nanodiamonds to live mammalian cells using maltotriose-conjugated polypropylenimine dendrimers results in efficient localization of nanodiamonds to the intended cellular target...
2017: PloS One
https://www.readbyqxmd.com/read/28636354/rational-design-of-lithium-sulfur-battery-cathodes-based-on-experimentally-determined-maximum-active-material-thickness
#7
Michael J Klein, Gabriel M Veith, Arumugam Manthiram
Rational design of conductive carbon hosts for high energy density lithium-sulfur batteries requires an understanding of the fundamental limitations to insulating active material loading. In this work, we investigate the electrochemistry of lithium sulfide films ranging in thickness from 30 to 3500 nm. We show that films thicker than approximately 40 nm cannot be charged at local charge densities above 1 μA cm-2, and by implication, the maximum useful pore diameter is near 60 nm in a practical cathode. 'Activation' overpotentials for Li2S are identified in thicker films, resulting from polysulfide generation, but are shown not to improve the fundamental areal charge limitations...
June 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28636318/inverse-photonic-glasses-by-packing-bi-disperse-hollow-microspheres-with-uniform-cores
#8
Seung-Hyun Kim, Sofia Magkiriadou, Do Kyung Rhee, Doo Sung Lee, Pil J Yoo, Vinothan N Manoharan, Gi-Ra Yi
A major fabrication challenge is producing disordered photonic materials with angle-independent structural red color. Theoretical work has shown that such color can be produced by fabricating inverse photonic glasses with monodisperse, non-touching voids in a silica matrix. Here we demonstrate a route toward such materials and show that they have angle-independent red color. We first synthesize monodisperse hollow silica particles with precisely controlled shell thickness, then make glassy colloidal structures by mixing two types of hollow particles with the same core size and different shell thicknesses...
June 21, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28636315/fabrication-of-hierarchical-macroporous-biocompatible-scaffolds-by-combining-pickering-high-internal-phase-emulsion-templates-with-three-dimensional-printing
#9
Ting Yang, Yang Hu, Chaoyang Wang, Bernard P Binks
Biocompatible and biodegradable porous scaffolds with adjustable pore structure have aroused increasing interest in bone tissue engineering. Here, we report a facile method to fabricate hierarchical macroporous biocompatible (HmPB) scaffolds by combining Pickering high internal phase emulsion (HIPE) templates with three-dimensional (3D) printing. HmPB scaffolds composed of a polymer matrix of poly(L-lactic acid), PLLA, and poly(ε-caprolactone), PCL, are readily fabricated by solvent evaporation of 3D printed Pickering HIPEs which are stabilized by hydrophobically modified silica nanoparticles (h-SiO2)...
June 21, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28635185/antipulverization-electrode-based-on-low-carbon-triple-shelled-superstructures-for-lithium-ion-batteries
#10
Lianhai Zu, Qingmei Su, Feng Zhu, Bingjie Chen, Huanhuan Lu, Chengxin Peng, Ting He, Gaohui Du, Pengfei He, Kai Chen, Shihe Yang, Jinhu Yang, Huisheng Peng
The realization of antipulverization electrode structures, especially using low-carbon-content anode materials, is crucial for developing high-energy and long-life lithium-ion batteries (LIBs); however, this technology remains challenging. This study shows that SnO2 triple-shelled hollow superstructures (TSHSs) with a low carbon content (4.83%) constructed by layer-by-layer assembly of various nanostructure units can withstand a huge volume expansion of ≈231.8% and deliver a high reversible capacity of 1099 mAh g(-1) even after 1450 cycles...
June 21, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28634690/long-term-retromuscular-and-intraperitoneal-mesh-size-changes-within-a-randomized-controlled-trial-on-incisional-hernia-repair-including-a-review-of-the-literature
#11
P Rogmark, O Ekberg, A Montgomery
Purpose Ingrowth of fibroblasts in a polypropylene mesh may cause contraction and a later recurrence. We assessed mesh contraction in intraabdominal and retromuscular implantation after incisional hernia repair. METHODS: A cohort of patients within an RCT on laparoscopic (LHR) versus open hernia repair (OHR) had their mesh borders marked with metal clips. X-ray was performed on postoperative day 1 and after 1 year. Total length, width, and dislocation were measured. A tacker fixated large-pore polypropylene mesh was used in LHR, and a retromuscular small-pore heavy-weight mesh was sutured to the midline in OHR...
June 20, 2017: Hernia: the Journal of Hernias and Abdominal Wall Surgery
https://www.readbyqxmd.com/read/28634613/breathing-induced-new-phase-transition-in-an-mil-53-al-nh2-metal-organic-framework-under-high-methane-pressures
#12
Linius Bolinois, Tanay Kundu, Xuerui Wang, Yuxiang Wang, Zhigang Hu, Kenny Koh, Dan Zhao
The high pressure methane sorption tests on a flexible metal-organic framework [MIL-53(Al)-NH2] reveal a new phase transition to a large pore (lp) phase above 45 bar. The mixed-ligand strategy and pressure cycling tests are suggested to reduce the pressure requirement of such a phase transition for applications in natural gas storage.
June 21, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28634610/efficiently-mapping-structure-property-relationships-of-gas-adsorption-in-porous-materials-application-to-xe-adsorption
#13
A R Kaija, C E Wilmer
Designing better porous materials for gas storage or separations applications frequently leverages known structure-property relationships. Reliable structure-property relationships, however, only reveal themselves when adsorption data on many porous materials are aggregated and compared. Gathering enough data experimentally is prohibitively time consuming, and even approaches based on large-scale computer simulations face challenges. Brute force computational screening approaches that do not efficiently sample the space of porous materials may be ineffective when the number of possible materials is too large...
June 21, 2017: Faraday Discussions
https://www.readbyqxmd.com/read/28634368/preparation-and-properties-of-a-hyperbranch-structured-polyamine-adsorbent-for-carbon-dioxide-capture
#14
Hui He, Yajie Hu, Shuixia Chen, Linzhou Zhuang, Beibei Ma, Qinghua Wu
A fibrous adsorbent with amino-terminated hyperbranch structure (PP-AM-HBP-NH2) was prepared by grafting hyperbranched polyamine (HBP-NH2) onto the acrylamide-modified polypropylene (PP) fibers. The grafting of AM on PP fibers provided the active sites for introducing HBP-NH2 onto the PP fibers. This kind of "grafting to" procedure to synthesize hyperbranch-structured fiber could overcome the disadvantages of stepwise growth procedure, avoiding the complicated synthesis process and the requirement of strict experimental conditions...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28634208/ligand-and-voltage-gated-ca-2-channels-differentially-regulate-the-mode-of-vesicular-neuropeptide-release-in-mammalian-sensory-neurons
#15
Yeshi Wang, Qihui Wu, Meiqin Hu, Bin Liu, Zuying Chai, Rong Huang, Yuan Wang, Huadong Xu, Li Zhou, Lianghong Zheng, Changhe Wang, Zhuan Zhou
Neuropeptides released from dorsal root ganglion (DRG) neurons play essential roles in the neurotransmission of sensory inputs, including those underlying nociception and pathological pain. Neuropeptides are released from intracellular vesicles through two modes: a partial release mode called "kiss-and-run" (KAR) and a full release mode called "full fusion-like" (FFL). Using total internal reflection fluorescence (TIRF) microscopy, we traced the release of pH-sensitive green fluorescent protein-tagged neuropeptide Y (pHluorin-NPY) from individual dense-core vesicles in the soma and axon of single DRG neurons after Ca(2+) influx through either voltage-gated Ca(2+) channels (VGCCs) or ligand-gated transient receptor potential vanilloid 1 (TRPV1) channels...
June 20, 2017: Science Signaling
https://www.readbyqxmd.com/read/28633846/aqueous-norfloxacin-sonocatalytic-degradation-with-multilayer-flower-like-zno-in-the-presence-of-peroxydisulfate
#16
Shou-Bo Hu, Liang Li, Meng-Yu Luo, Ya-Feng Yun, Chang-Tang Chang
Multilayer ZnO nanoflowers were synthesized through a simple precipitation method and characterized by field-emission scanning electron microscopy (FE-SEM), X-ray diffraction (XRD), X-ray photoelectron spectra (XPS) and nitrogen absorption-desorption techniques. The FE-SEM images show the integrated morphology of an individual flower-like ZnO nanostructure, which is made of nano-platelets with uniform thickness (20-30nm). The average pore size and Brunauer-Emmet-Teller (BET) surface area of the as-synthesized ZnO were 27...
September 2017: Ultrasonics Sonochemistry
https://www.readbyqxmd.com/read/28633840/changes-in-pore-size-distribution-inside-sludge-under-various-ultrasonic-conditions
#17
Fang Zhao, Daolai Cheng
The pore size distribution is quite significant for determining the transport capacity of heat and moisture in sludge during the drying process. It is crucial to investigate the transformation of the pore size in sludge under sonication. In this paper, the microstructures of pores inside sludge before and after ultrasonic treatment with various ultrasonic conditions were observed using a microscope. Fractal geometry and image analysis were combined to quantitatively identify the evolution of pore size in sludge undergoing various acoustic energy densities and treatment times...
September 2017: Ultrasonics Sonochemistry
https://www.readbyqxmd.com/read/28633132/radon-emanation-from-fresh-altered-and-disturbed-granitic-rock-characterized-by-14-c-pmma-impregnation-and-autoradiography
#18
Karl-Heinz Hellmuth, Marja Siitari-Kauppi, Hannu Arvela, Antero Lindberg, Lionel Fonteneau, Paul Sardini
Radon emanation from intact samples of fresh ("BG"), altered ("Fract") and disturbed ("EDZ") Finnish granitic rock from Kuru (Finland) and its dependence on humidity and rock structural factors was studied. The pore network of the rock was characterized by microscopy and impregnation with (14)C-PMMA (polymethylmethacrylate) resin and autoradiography. The radon emanation factor was increasing linearly with the relative humidity. (14)C-PMMA autoradiography of the altered zones and the EDZ indicated significant, mineral-specific increase of porosity and porosity gradients towards the fracture surfaces (Fract) and microcracks within the EDZ...
June 13, 2017: Applied Radiation and Isotopes
https://www.readbyqxmd.com/read/28632390/atomistic-simulation-derived-insight-on-the-irreversible-structural-changes-of-si-electrode-during-fast-and-slow-delithiation
#19
Kwang Jin Kim, James Wortman, Sung-Yup Kim, Yue Qi
Quantifying the irreversible chemical and structural changes of Si during cycling remains challenging. In this study, a continuous reactive molecular dynamics delithiation algorithm, with well-controlled potential gradient and delithiation rate, was developed and used to investigate the "natural" delithiation responses of an aluminum-oxide coated silicon thin-film. Fast delithiation led to the formation of dense Si network near the surface and nanoporosity inside the a-LixSi, resulting in 141 % volume dilation and significant amount of Li trapped inside (a-Li1...
June 20, 2017: Nano Letters
https://www.readbyqxmd.com/read/28632386/synthesis-of-hierarchically-structured-hybrid-materials-by-controlled-self-assembly-of-metal-organic-framework-with-mesoporous-silica-for-co2-adsorption
#20
Chong Chen, Bingxue Li, Lijin Zhou, Zefeng Xia, Nengjie Feng, Jing Ding, Lei Wang, Hui Wan, Guofeng Guan
The HKUST-1@SBA-15 composites with hierarchical pore structure were constructed by in situ self-assembly of metal-organic framework (MOF) with mesoporous silica. The structure directing role of SBA-15 had an obvious impact on the growth of MOF crystals, which in turn affected the morphologies and structural properties of the composites. The pristine HKUST-1 and the composites with different contents of SBA-15 were characterized by XRD, N2 adsorption-desorption, SEM, TEM, FT-IR, TG, XPS, and CO2-TPD techniques...
June 20, 2017: ACS Applied Materials & Interfaces
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