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

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

Classification with minimum ambiguity under distribution heterogeneity

The traditional classification is based on the assumption that distribution of indicator variable X in one class is homogeneous. However, when data in one class comes from heterogeneous distribution, the likelihood ratio of two classes is not unique. In this paper, we construct the classification via an ambiguity criterion for the case of distribution heterogeneity of X in a single class. The separated historical data in each situation are used to estimate the thresholds respectively. The final boundary is chosen as the maximum and minimum thresholds from all situations. Our approach obtains the minimum ambiguity with a high classification accuracy allowing for a precise decision. In addition, nonparametric estimation of the classification region and theoretical properties are derived. Simulation study and real data analysis are reported to demonstrate the effectiveness of our method.</p

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

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

Antiaromaticity-Promoted Radical Stability in α‑Methyl Heterocyclics

Aromaticity is a fundamental and important concept in chemistry, and usually, the enhancement of aromaticity brings additional thermodynamic stability to a compound. Moreover, since radicals can act as intermediates in chemical reactions, they have attracted considerable attention from both experimental and theoretical chemists for a long time. However, it remains unclear whether there is a relationship between the thermodynamic stability of cyclic planar radicals and their aromaticity. In this work, using various aromaticity indices including anisotropy of the induced current density analysis and nucleus-independent chemical shifts against the radical stabilization energy, we systematically investigated the relationship between aromaticity and the thermodynamic stability of α-methyl heterocyclics. Density functional theory calculations suggest that the stronger the antiaromaticity of the original form heterocyclics, the higher the thermodynamic stability of the corresponding radicals, which is in sharp contrast to the general knowledge that aromaticity brings compounds’ thermodynamic stabilities. The principal interacting spin orbital analysis shows that the stronger the π-bond formed between the heterocyclics and the α-methyl carbon, the more spin density the radicals tend to be distributed on the heterocyclics. Thus, the strong π-bonding is one of the factors for improving the thermodynamic stability of radicals

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

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

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

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 CH₃CN 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/CH₃CN 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

Powers for the CTP model and the MTP model.

<p>The powers in the upper panels correspond to the setting <i>α</i>₁ = 0, <i>γ</i>₁ = 1 and the lower panels correspond to setting <i>α</i>₁ = 1, <i>γ</i>₁ = 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

Top 10 OTUs identified by the MTP model.

Top 10 OTUs identified by the MTP model.</p

Dual Aromaticity in Both the T₀ and S₁ States: Osmapyridinium with Phosphonium Substituents

According to Hückel’s and Baird’s rules, cyclic conjugated species are aromatic either in the ground state or in the excited state only. Thus, species with aromaticity in both states (denoted as adaptive aromaticity) are particularly rare. Here we carry out density functional theory calculations on a series of osmapyridine and osmapyridinium complexes (96 species) and find that 2 of them display adaptive aromaticity, which was verified by various aromaticity indices including HOMA, ELFπ, MCI, ACIDπ plots, and the heat of hydrogenation. Further study reveals that two osmapyridiniums containing one or two phosphonium substituents exhibit the character of the triplet ground state, which was supported by the high-level coupled cluster calculations. Our findings highlight the importance of a transition metal and phosphoniums in achieving adaptive aromaticity and the triplet ground state and may aid the design of organometallics for photochemical and molecular magnetism applications

Venn diagram for the OTUs.

<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