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https://www.readbyqxmd.com/read/28645171/upsetr-an-r-package-for-the-visualization-of-intersecting-sets-and-their-properties
#1
Jake R Conway, Alexander Lex, Nils Gehlenborg
Motivation: Venn and Euler diagrams are a popular yet inadequate solution for quantitative visualization of set intersections. A scalable alternative to Venn and Euler diagrams for visualizing intersecting sets and their properties is needed. Results: We developed UpSetR, an open source R package that employs a scalable matrix-based visualization to show intersections of sets, their size, and other properties. Availability: UpSetR is available at https://github...
June 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28645036/influence-of-surface-states-on-blinking-characteristics-of-single-colloidal-cdse-cds-zns-core-multishell-quantum-dot
#2
Hao Xu, Hjalmar Brismar, Ying Fu
We carefully characterized the fluorescence blinking of single colloidal CdSe-CdS/ZnS core-multishell quantum dots (QDs) with different surface modifications, including octadecylamine (ODA) coated QDs dispersed in chloroform, aqueous 3-mercaptopropionic acids (3MPA) coated QDs in HEPES solution treated by Ca(2+) ions and ethylene glycol tetraacetic acid (EGTA, Ca(2+) chelator), and aqueous 3MPA-QDs treated by glycerol. It was found that the on- and off-state probability density distributions displayed different rules...
June 16, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28645029/phytoavailability-of-cr-in-silene-vulgaris-the-role-of-soil-plant-genotype-and-bacterial-rhizobiome
#3
P García-Gonzalo, A E Pradas Del Real, M Pirredda, M J Gismera, M C Lobo, A Pérez-Sanz
Understanding the metal behavior at the soil-root interface is of utmost significance for a successful implementation of phytoremediation. In this study, we investigated the differences in chromium (Cr) uptake, chemical changes in soil solution and the shifts in rhizosphere bacterial communities of two genotypes of Silene vulgaris (SV21, SV38) with different tolerance to Cr. A greenhouse experiment was performed in two soils that differed on pH and organic matter (OM) content. An industrial sludge with high content in Cr was used as pollution source...
June 20, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/28645018/take-over-performance-in-evasive-manoeuvres
#4
Riender Happee, Christian Gold, Jonas Radlmayr, Sebastian Hergeth, Klaus Bengler
We investigated after effects of automation in take-over scenarios in a high-end moving-base driving simulator. Drivers performed evasive manoeuvres encountering a blocked lane in highway driving. We compared the performance of drivers 1) during manual driving, 2) after automated driving with eyes on the road while performing the cognitively demanding n-back task, and 3) after automated driving with eyes off the road performing the visually demanding SuRT task. Both minimum time to collision (TTC) and minimum clearance towards the obstacle disclosed a substantial number of near miss events and are regarded as valuable surrogate safety metrics in evasive manoeuvres...
June 20, 2017: Accident; Analysis and Prevention
https://www.readbyqxmd.com/read/28644982/assessment-of-sublethal-endpoints-after-chronic-exposure-of-the-nematode-caenorhabditis-elegans-to-palladium-platinum-and-rhodium
#5
Gerhard Schertzinger, Sonja Zimmermann, Daniel Grabner, Bernd Sures
The aim of this study was to investigate chronic effects of the platinum-group elements (PGE) palladium (Pd), platinum (Pt) and rhodium (Rh) on the nematode Caenorhabditis elegans. Aquatic toxicity testing was carried out according to ISO 10872 by determining 96 h EC50 values for sublethal endpoints, including growth, fertility and reproduction. Single PGE standard solutions were used as metal source. Based on the EC50 values for Pt, reproduction (96 h EC50 = 497 μg/L) was the most sensitive endpoint followed by fertility (96 h EC50 = 726 μg/L) and growth (96 h EC50 = 808 μg/L)...
June 20, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28644959/generation-and-characterization-of-aptamers-targeting-factor-xia
#6
R S Woodruff, I Ivanov, I M Verhamme, M-F Sun, D Gailani, B A Sullenger
BACKGROUND: The plasma protease factor XIa (FXIa) has become a target of interest for therapeutics designed to prevent or treat thrombotic disorders. METHODS: We used a solution-based, directed evolution approach called systematic evolution of ligands by exponential enrichment (SELEX) to isolate RNA aptamers that target the FXIa catalytic domain. RESULTS: Two aptamers, designated 11.16 and 12.7, were identified that bound to previously identified anion binding and serpin bindings sites on the FXIa catalytic domain...
June 9, 2017: Thrombosis Research
https://www.readbyqxmd.com/read/28644896/how-fast-is-a-collective-bacterial-state-established
#7
Mikkel Lindstrøm Sørensen, Peter Dahl, Thomas Sams
Bacteria in a biofilm colony have the capacity to monitor the size and growth conditions for the colony and modify their phenotypical behaviour to optimise attacks, defence, migration, etc. The quorum sensing systems controlling this involve production and sensing of diffusive signal molecules. Frequently, quorum sensing systems carry a positive feedback loop which produces a switch at a threshold size of the colony. This all-or-none switch can be beneficial to create a sudden attack, leaving a host little time to establish a defence...
2017: PloS One
https://www.readbyqxmd.com/read/28644807/depth-image-inpainting-improving-low-rank-matrix-completion-with-low-gradient-regularization
#8
Hongyang Xue, Shengming Zhang, Deng Cai
We address the task of single depth image inpainting. Without the corresponding color images, previous or next frames, depth image inpainting is quite challenging. One natural solution is to regard the image as a matrix and adopt the low rank regularization just as color image inpainting. However, the low rank assumption does not make full use of the properties of depth images. A shallow observation inspires us to penalize the non-zero gradients by sparse gradient regularization. However, statistics show that though most pixels have zero gradients, there is still a non-ignorable part of pixels whose gradients are small but nonzero...
June 21, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28644798/joint-alignment-of-multiple-point-sets-with-batch-and-incremental-expectation-maximization
#9
Dimitrios Georgios Evangelidis, Radu Horaud
This paper addresses the problem of registering multiple point sets. Solutions to this problem are often approximated by repeatedly solving for pairwise registration, which results in an uneven treatment of the sets forming a pair: a model set and a data set. The main drawback of this strategy is that the model set may contain noise and outliers, which negatively affects the estimation of the registration parameters. In contrast, the proposed formulation treats all the point sets on an equal footing. Indeed, all the points are drawn from a central Gaussian mixture, hence the registration is cast into a clustering problem...
June 21, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28644758/an-independent-shopping-experience-for-wheelchair-users-through-augmented-reality-and-rfid
#10
Zulqarnain Rashid, Rafael Pous, Christopher S Norrie
People with physical and mobility impairments continue to struggle to attain independence in the performance of routine activities and tasks. For example, browsing in a store and interacting with products located beyond an arm's length may be impossible without the enabling intervention of a human assistant. This research article describes a study undertaken to design, develop, and evaluate potential interaction methods for motor-impaired individuals, specifically those who use wheelchairs. Our study includes a user-centered approach, and a categorization of wheelchair users based upon the severity of their disability and their individual needs...
June 23, 2017: Assistive Technology: the Official Journal of RESNA
https://www.readbyqxmd.com/read/28644647/quasi-low-dimensional-electron-gas-with-one-populated-band-as-a-testing-ground-for-time-dependent-density-functional-theory-of-mesoscopic-systems
#11
Vladimir U Nazarov
We find an exact analytical solution to the exchange-only time-dependent density-functional theory (TDDFT) problem for a significant class of quasi-low-dimensional (QLD) materials: QLD electron gas with only one band filled in the direction perpendicular to the layer or wire. The theory yields the TD exchange potential as an explicit nonlocal operator of the TD spin density. The dressed interband (image states) excitation spectra of quasi-two-dimensional electron gas are obtained, while the comparison with the Kohn-Sham transitions provides insights into the qualitative and quantitative role of the many-body interactions...
June 9, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28644630/expanding-the-therapeutic-potential-of-the-iron-chelator-deferasirox-in-the-development-of-aqueous-stable-ti-iv-anticancer-complexes
#12
Sergio A Loza-Rosas, Alexandra M Vázquez-Salgado, Kennett I Rivero, Lenny J Negrón, Yamixa Delgado, Josué A Benjamín-Rivera, Angel L Vázquez-Maldonado, Timothy B Parks, Charlene Munet-Colón, Arthur D Tinoco
The recent X-ray structure of titanium(IV)-bound human serum transferrin (STf) exhibiting citrate as a synergistic anion reveals a difference in Ti(IV) coordination versus iron(III), the metal endogenously delivered by the protein to cells. This finding enriches our bioinspired drug design strategy for Ti(IV)-based anticancer therapeutics, which applies a family of Fe(III) chelators termed chemical transferrin mimetic (cTfm) ligands to inhibit Fe bioavailability in cancer cells. Deferasirox, a drug used for iron overload disease, is a cTfm ligand that models STf coordination to Fe(III), favoring Fe(III) binding versus Ti(IV)...
June 23, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28644618/exploring-new-assembly-modes-of-uranyl-terephthalate-templated-syntheses-and-structural-regulation-of-a-series-of-rare-2d-%C3%A2-3d-polycatenated-frameworks
#13
Lei Mei, Cong-Zhi Wang, Liu-Zheng Zhu, Zeng-Qiang Gao, Zhi-Fang Chai, John K Gibson, Wei-Qun Shi
The reaction of uranyl nitrate with terephthalic acid (H2TP) under hydrothermal conditions in the presence of an organic base, 1,3-(4,4'-bispyridyl)propane (BPP) or 4,4'-bipyridine (BPY), provided four uranyl terephthalate compounds with different entangled structures by a pH-tuning method. [UO2(TP)1.5](H2BPP)0.5·2H2O (1) obtained in a relatively acidic solution (final aqueous pH, 4.28) crystallizes in the form of a noninterpenetrated honeycomb-like two-dimensional network structure. An elevation of the solution pH (final pH, 5...
June 23, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28644616/importance-of-a-fully-anharmonic-treatment-of-equilibrium-isotope-fractionation-properties-of-dissolved-ionic-species-as-evidenced-by-li-aq
#14
Romain Dupuis, Magali Benoit, Mark E Tuckerman, Merlin Méheut
Equilibrium fractionation of stable isotopes is critically important in fields ranging from chemistry, including medicinal chemistry, electrochemistry, geochemistry, and nuclear chemistry, to environmental science. The dearth of reliable estimates of equilibrium fractionation factors, from experiment or from natural observations, has created a need for accurate computational approaches. Because isotope fractionation is a purely quantum mechanical phenomenon, exact calculation of fractionation factors is nontrivial...
June 23, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28644553/structural-insights-into-the-inclusion-complexes-between-clomiphene-citrate-and-%C3%AE-cyclodextrin-the-mechanism-of-preferential-isomeric-selection
#15
Arti Maheshwari, Harish Saraswat, Santosh Kumar Upadhyay
A major challenge in pharmaceuticals for clinical applications is to alter the solubility, stability, and toxicity of drug molecules in living systems. Cyclodextrins (CDs) have the ability to form host-guest inclusion complexes with pharmaceuticals for further development of new drug formulations. The inclusion complex of clomiphene citrate (CL), a poorly water-soluble drug, with native β-cyclodextrin (β-CD) was characterized by a one and two-dimensional nuclear magnetic resonance (NMR) spectroscopic approach and also by molecular docking techniques...
June 23, 2017: Chirality
https://www.readbyqxmd.com/read/28644511/bacteriophage-tail-tube-assembly-studied-by-proton-detected-4d-solid-state-nmr
#16
Maximilian Zinke, Pascal Fricke, Camille Samson, Songhwan Hwang, Joseph Wall, Sascha Lange, Sophie Zinn-Justin, Adam Lange
Obtaining unambiguous resonance assignments remains a major bottleneck in solid-state NMR studies of protein structure and dynamics. Particularly for supramolecular assemblies with large subunits (>150 residues), the analysis of crowded spectral data presents a challenge, even if three-dimensional (3D) spectra are used. Here, we present a proton-detected 4D solid-state NMR assignment procedure that is tailored for large assemblies. The key to recording 4D spectra with three indirect carbon or nitrogen dimensions with their inherently large chemical shift dispersion lies in the use of sparse non-uniform sampling (as low as 2%)...
June 23, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28644482/one-thousand-fold-enhancement-of-high-field-liquid-nuclear-magnetic-resonance-signals-at-room-temperature
#17
Guoquan Liu, Marcel Levien, Niels Karschin, Giacomo Parigi, Claudio Luchinat, Marina Bennati
Nuclear magnetic resonance (NMR) is a fundamental spectroscopic technique for the study of biological systems and materials, molecular imaging and the analysis of small molecules. It detects interactions at very low energies and is thus non-invasive and applicable to a variety of targets, including animals and humans. However, one of its most severe limitations is its low sensitivity, which stems from the small interaction energies involved. Here, we report that dynamic nuclear polarization in liquid solution and at room temperature can enhance the NMR signal of (13)C nuclei by up to three orders of magnitude at magnetic fields of ∼3 T...
July 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28644468/observation-of-electron-transfer-mediated-decay-in-aqueous-solution
#18
Isaak Unger, Robert Seidel, Stephan Thürmer, Marvin N Pohl, Emad F Aziz, Lorenz S Cederbaum, Eva Muchová, Petr Slavíček, Bernd Winter, Nikolai V Kryzhevoi
Photoionization is at the heart of X-ray photoelectron spectroscopy (XPS), which gives access to important information on a sample's local chemical environment. Local and non-local electronic decay after photoionization-in which the refilling of core holes results in electron emission from either the initially ionized species or a neighbour, respectively-have been well studied. However, electron-transfer-mediated decay (ETMD), which involves the refilling of a core hole by an electron from a neighbouring species, has not yet been observed in condensed phase...
July 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28644431/an-in-vitro-study-on-the-efficacy-of-removing-calcium-hydroxide-from-curved-root-canal-systems-in-root-canal-therapy
#19
Ying Wang, Li-Yang Guo, Hong-Zhi Fang, Wen-Ling Zou, Ying-Ming Yang, Yuan Gao, Hui Yang, Tao Hu
To compare the efficacy of various irrigants (citric acid, ethylenediaminetetraacetic acid (EDTA) and NaOCl) and techniques in removing Ca(OH)2 in two types of curved root canal systems, simulated root canals with specific curvatures were used to investigate the effects of different irrigants and instruments on Ca(OH)2 removal. The optimal methods were verified on extracted human teeth. Simulated root canals were assigned to one of two groups based on the irrigation solution: 10% citric acid or 2.5% NaOCl. Each group was divided into four subgroups according to the technique used to remove Ca(OH)2...
June 23, 2017: International Journal of Oral Science
https://www.readbyqxmd.com/read/28644423/probing-the-interaction-of-dielectric-nanoparticles-with-supported-lipid-membrane-coatings-on-nanoplasmonic-arrays
#20
Abdul Rahim Ferhan, Gamaliel Junren Ma, Joshua A Jackman, Tun Naw Sut, Jae Hyeon Park, Nam-Joon Cho
The integration of supported lipid membranes with surface-based nanoplasmonic arrays provides a powerful sensing approach to investigate biointerfacial phenomena at membrane interfaces. While a growing number of lipid vesicles, protein, and nucleic acid systems have been explored with nanoplasmonic sensors, there has been only very limited investigation of the interactions between solution-phase nanomaterials and supported lipid membranes. Herein, we established a surface-based localized surface plasmon resonance (LSPR) sensing platform for probing the interaction of dielectric nanoparticles with supported lipid bilayer (SLB)-coated, plasmonic nanodisk arrays...
June 23, 2017: Sensors
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