36 research outputs found

    Additional file 1: of Gene content dissimilarity for subclassification of highly similar microbial strains

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    This file contains the supplementary table and figures for this paper, including Table S1, Figure S1, and Figure S2. (DOCX 262 kb

    Nonequilibrium Adsorption and Reorientation Dynamics of Molecules at Electrode/Electrolyte Interfaces Probed via Real-Time Second Harmonic Generation

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    Nonequilibrium adsorption and subsequent reorientation of organic molecules at electrode/electrolyte interfaces are important steps in electrochemical reactions and other interfacial processes, yet real-time quantitative characterization and monitoring of these processes, particularly for the reorientation step, are still challenging experimentally. Herein, we investigated the nonequilibrium adsorption process of 4-(4-(diethylamino)­styryl)-<i>N</i>-methyl-pyridinium iodide (D289) molecules from acetonitrile solution onto a polycrystalline platinum electrode surface using real-time second harmonic generation (SHG) in combination with the potential step method. The time-dependent SHG curves exhibit two distinct regimes, which were interpreted with a two-step adsorption model consisting of a fast adsorption and a slow reorientation step for D289 on the surface. D289 was assumed to initially adsorb in an orientation perpendicular to the surface and then reorient to a parallel orientation. We derived a quantitative mathematical expression containing a biexponential function to fit the temporal SHG curves and obtain the rate constants for the two steps. The rate constants for fast adsorption and the slower reorientation processes show similar potential-dependent behavior: the rate decreases with an increase in the negative potential. We further proposed a molecular mechanism involving the displacement of D289 and CH<sub>3</sub>CN molecules adsorbed on the electrode interface to explain this potential-dependent behavior. On the basis of such analysis, we obtained a detailed picture of the adsorption of D289 molecules on the Pt electrode/CH<sub>3</sub>CN electrolyte, which consists of three consecutive steps: diffusion, adsorption, and reorientation. The results of this study may shed light on adsorption mechanisms at the electrode/electrolyte interface as well as at biological and other functional material interfaces

    Insight into the role of mitochondrion-related gene anchor signature in mitochondrial dysfunction of neutrophilic asthma

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    At present, targeting molecular-pharmacological therapy is still difficult in neutrophilic asthma. The investigation aims to identify and validate mitochondrion-related gene signatures for diagnosis and specific targeting therapeutics in neutrophilic asthma. Bronchial biopsy samples of neutrophilic asthma and healthy people were identified from the GSE143303 dataset and then matched with human mitochondrial gene data to obtain mitochondria-related differential genes (MitoDEGs). Signature mitochondria-related diagnostic markers were jointly screened by support vector machine (SVM) analysis, least absolute shrinkage, and selection operator (LASSO) regression. The expression of marker MitoDEGs was evaluated by validation datasets GSE147878 and GSE43696. The diagnostic value was evaluated by receiver operating characteristic (ROC) curve analysis. Meanwhile, the infiltrating immune cells were analyzed by the CIBERSORT. Finally, oxidative stress level and mitochondrial functional morphology for asthmatic mice and BEAS-2B cells were evaluated. The expression of signature MitoDEGs was verified by qPCR. 67 MitoDEGs were identified. Five signature MitoDEGs (SOD2, MTHFD2, PPTC7, NME6, and SLC25A18) were further screened out. The area under the curve (AUC) of signature MitoDEGs presented a good diagnostic performance (more than 0.9). There were significant differences in the expression of signature MitoDEGs between neutrophilic asthma and non-neutrophilic asthma. In addition, the basic features of mitochondrial dysfunction were demonstrated by in vitro and in vivo experiments. The expression of signature MitoDEGs in the neutrophilic asthma mice presented a significant difference from the control group. These MitoDEGs signatures in neutrophilic asthma may hold potential as anchor diagnostic and therapeutic targets in neutrophilic asthma.</p

    Powers for the CTP model and the MTP model.

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    <p>The powers in the upper panels correspond to the setting <i>α</i><sub>1</sub> = 0, <i>γ</i><sub>1</sub> = 1 and the lower panels correspond to setting <i>α</i><sub>1</sub> = 1, <i>γ</i><sub>1</sub> = 1. In each setting, the left panel shows the results for significance level 0.01 and the right panel shows the results for level 0.05.</p

    Density curves for two OTUs.

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    <p>The blue curve shows the density of the observed data. The green curve shows the density of predictions from the MTP model while the red curve represents the density of predictions from the CTP model.</p

    Venn diagram for the OTUs.

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    <p>Among all the 131 OTUs, 60 OTUs are not identified by any methods and the other 71 OTUs are identified by at least one method. For example, “31” in the intersection of all sets indicates that 31 OTUs are identified by all methods; while “4” located in the intersection of three sets, indicates that 4 OTUs are identified by three methods, namely, the T test, the CTP model, and the Wilcoxon test.</p

    Type I errors for the CTP model and the MTP model.

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    <p>The results in the upper panels correspond to the setting <i>α</i><sub>1</sub> = 0, <i>γ</i><sub>1</sub> = 0 and the lower panels correspond to the setting <i>α</i><sub>1</sub> = 1, <i>γ</i><sub>1</sub> = 0. In each setting, the left panel shows the results for significance level 0.01 and the right panel shows the results for level 0.05. The dashed horizontal line in each panel represents the correct <i>α</i>-level.</p

    Two-Photon-Induced Isomerization of Spiropyran/Merocyanine at the Air/Water Interface Probed by Second Harmonic Generation

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    Photochromic molecules often exhibit switchable hyperpolarizabilities upon photoisomerization between two molecular states and can be widely applied in nonlinear optical materials. Photoisomerization can occur through either one-photon or two-photon processes. Two-photon-induced isomerization has several advantages over one-photon process but has not been fully explored. In the present study, we have used second harmonic generation to investigate the two-photon-induced isomerization between spiropyran and merocyanine at the air/water interface. We show that spiropyran and merocyanine can be converted into each other reversibly with 780-nm laser-beam irradiation through two-photon processes. We also investigated the isomerization rates under various incident laser powers. Quantitative analysis revealed that the isomerization rates of spiropyran and merocyanine depend differently on the laser power. We attribute the difference to the distinct molecular structures of spiropyran and merocyanine. At the interface, nonplanar spiropyran molecules exist mainly as monomers, whereas planar merocyanine molecules form aggregates. Upon aggregation, steric hindrance effects and excitonic coupling efficiently arrest the photoisomerization of merocyanine. This work provides an in-depth understanding of two-photon-induced isomerization at the interface, which is beneficial for designing and controlling optical thin-film materials

    Type I errors of the four methods.

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    <p>The results in the upper panels correspond to the setting <i>α</i><sub>1</sub> = 0, <i>γ</i><sub>1</sub> = 0 and the lower panels correspond to setting <i>α</i><sub>1</sub> = 1, <i>γ</i><sub>1</sub> = 0. In each setting, the left panel shows the results for significance level 0.01 and the right panel shows the results for level 0.05. The dashed horizontal line in each panel represents the correct level. The results for sample size 400 can be found in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1006329#pcbi.1006329.s003" target="_blank">S1 Fig</a> in Supporting information.</p

    Fabrication of Supramolecular Chirality from Achiral Molecules at the Liquid/Liquid Interface Studied by Second Harmonic Generation

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    We present the investigation into the supramolecular chirality of 5-octadecyloxy-2-(2-pyridylazo)­phenol (PARC18) at water/1,2-dichloroethane interface by second harmonic generation (SHG). We observe that PARC18 molecules form supramolecular chirality through self-assembly at the liquid/liquid interface although they are achiral molecules. The bulk concentration of PARC18 in the organic phase has profound effects on the supramolecular chirality. By increasing bulk concentration, the enantiomeric excess at the interface first grows and then decreases until it eventually vanishes. Further analysis reveals that the enantiomeric excess is determined by the twist angle of PARC18 molecules at the interface rather than their orientational angle. At lower and higher bulk concentrations, the average twist angle of PARC18 molecules approaches zero, and the assemblies are achiral; whereas at medium bulk concentrations, the average twist angle is nonzero, so that the assemblies show supramolecular chirality. We also estimate the coverage of PARC18 molecules at the interface versus the bulk concentration and fit it to Langmuir adsorption model. The result indicates that PARC18 assemblies show strongest supramolecular chirality in a half-full monolayer. These findings highlight the opportunities for precise control of supramolecular chirality at liquid/liquid interfaces by manipulating the bulk concentration
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