Integrative single-cell RNA sequencing and metabolomics decipher the imbalanced lipid-metabolism in maladaptive immune responses during sepsis

BackgroundTo identify differentially expressed lipid metabolism-related genes (DE-LMRGs) responsible for immune dysfunction in sepsis.MethodsThe lipid metabolism-related hub genes were screened using machine learning algorithms, and the immune cell infiltration of these hub genes were assessed by CIBERSORT and Single-sample GSEA. Next, the immune function of these hub genes at the single-cell level were validated by comparing multiregional immune landscapes between septic patients (SP) and healthy control (HC). Then, the support vector machine-recursive feature elimination (SVM-RFE) algorithm was conducted to compare the significantly altered metabolites critical to hub genes between SP and HC. Furthermore, the role of the key hub gene was verified in sepsis rats and LPS-induced cardiomyocytes, respectively.ResultsA total of 508 DE-LMRGs were identified between SP and HC, and 5 hub genes relevant to lipid metabolism (MAPK14, EPHX2, BMX, FCER1A, and PAFAH2) were screened. Then, we found an immunosuppressive microenvironment in sepsis. The role of hub genes in immune cells was further confirmed by the single-cell RNA landscape. Moreover, significantly altered metabolites were mainly enriched in lipid metabolism-related signaling pathways and were associated with MAPK14. Finally, inhibiting MAPK14 decreased the levels of inflammatory cytokines and improved the survival and myocardial injury of sepsis.ConclusionThe lipid metabolism-related hub genes may have great potential in prognosis prediction and precise treatment for sepsis patients

Three low-mass companions around aged stars discovered by TESS

We report the discovery of three transiting low-mass companions to aged stars: a brown dwarf (TOI-2336b) and two objects near the hydrogen burning mass limit (TOI-1608b and TOI-2521b). These three systems were first identified using data from the Transiting Exoplanet Survey Satellite (TESS). TOI-2336b has a radius of $1.05\pm 0.04\ R_J$, a mass of $69.9\pm 2.3\ M_J$ and an orbital period of 7.71 days. TOI-1608b has a radius of $1.21\pm 0.06\ R_J$, a mass of $90.7\pm 3.7\ M_J$ and an orbital period of 2.47 days. TOI-2521b has a radius of $1.01\pm 0.04\ R_J$, a mass of $77.5\pm 3.3\ M_J$ and an orbital period of 5.56 days. We found all these low-mass companions are inflated. We fitted a relation between radius, mass and incident flux using the sample of known transiting brown dwarfs and low-mass M dwarfs. We found a positive correlation between the flux and the radius for brown dwarfs and for low-mass stars that is weaker than the correlation observed for giant planets.Comment: 20 pages, 13 figures; submitted to MNRA

Software for the frontiers of quantum chemistry:An overview of developments in the Q-Chem 5 package

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange–correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear–electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an “open teamware” model and an increasingly modular design

Energy decomposition analysis for exciplexes using absolutely localized molecular orbitals.

An energy decomposition analysis (EDA) scheme is developed for understanding the intermolecular interaction involving molecules in their excited states. The EDA utilizes absolutely localized molecular orbitals to define intermediate states and is compatible with excited state methods based on linear response theory such as configuration interaction singles and time-dependent density functional theory. The shift in excitation energy when an excited molecule interacts with the environment is decomposed into frozen, polarization, and charge transfer contributions, and the frozen term can be further separated into Pauli repulsion and electrostatics. These terms can be added to their counterparts obtained from the ground state EDA to form a decomposition of the total interaction energy. The EDA scheme is applied to study a variety of systems, including some model systems to demonstrate the correct behavior of all the proposed energy components as well as more realistic systems such as hydrogen-bonding complexes (e.g., formamide-water, pyridine/pyrimidine-water) and halide (F-, Cl-)-water clusters that involve charge-transfer-to-solvent excitations

High-performance oxygen barrier inorganic-organic coating for polymeric substrates

Aqueous-based inorganic–organic hybrid coating materials comprising self-assembled silica nanophase (SNAP) particles and the sodium salt of 9,10-anthraquinone-2,6-disulfonate (AQDS), an oxygen-scavenging precursor molecule, were coated onto PET films under ambient laboratory conditions using a spiral-bar coating technique. Active SNAP-based coatings containing 0.08% w/w AQDS displayed an oxygen transmission rate of 0.04 ± 0.01 cm³ mil m⁻² day⁻¹ atm⁻¹; an improvement in oxygen barrier by an order of magnitude compared with comparable coatings produced using dip-coating. The spiral-bar coating technique also provided other important technical advantages over the previously used dip-coating method, including a reduction in the AQDS concentration required in the coating solution by almost an order of magnitude. The oxygen barrier performance provided by these single-layer active SNAP-based coatings approaches that provided by other far more sophisticated multi-layer plastic barrier materials produced using vacuum-deposition methods

Elastic Reverse-Time Migration with Complex Topography

Migration is an important step in seismic data processing for oil and gas exploration. The accuracy of migration directly affects the accuracy of subsequent oil and gas reservoir characterization. Reverse-time migration is one of the most accurate migration methods at present. Multi-wave and multicomponent seismic data contain more P- and S-wave information. Making full use of multi-wave and multicomponent seismic data can offer more information about underground structure and lithology, as well as improve the accuracy of seismic exploration. Elastic reverse-time migration (ERTM) has no dip restriction and can be applied to image multi-wave and multicomponent seismic data in complex structural areas and some special lithology structures. However, the surface topography of complex regions has an influence on wavefield and seriously degrades the quality of ERTM’s migration results. We developed a new ERTM method to migrate multi-wave and multicomponent seismic data in the region with complex surface topography. We first fill the layers between the highest and lowest undulating surface with near-surface elastic parameters in a complex topography model to obtain a new model with a horizontal surface. This allows the finite difference (FD) method based on the regular rectangular grid to be used to numerically solve elastic wave equations in the model with complex topography. The decoupled wave equations are used to generate source P- and S-waves and receiver P- and S-waves to reduce crosstalk artefacts in ERTM. A topography-related filter is further used to remove the influence of surface topography on migration results. The scalar imaging condition is also applied to generate PP and PS migration images. Some numerical examples with different complex topographies demonstrate that our proposed ERTM method can remove the influence of complex topography on ERTM’s images and effectively generate high-quality ERTM images

Three-Component Microseismic Data Denoising Based on Re-Constrain Variational Mode Decomposition

Microseismic monitoring is an important technology used to evaluate hydraulic fracturing, and denoising is a crucial processing step. Analyses of the characteristics of acquired three-component microseismic data have indicated that the vertical component has a higher signal-to-noise ratio (SNR) than the two horizontal components. Therefore, we propose a new denoising method for three-component microseismic data using re-constrain variational mode decomposition (VMD). In this method, it is assumed that there is a linear relationship between the modes with the same center frequency among the VMD results of the three-component data. Then, the decomposition result of the vertical component is used as a constraint to the whole denoising effect of the three-component data. On the basis of VMD, we add a constraint condition to form the re-constrain VMD, and deduce the corresponding solution process. According to the synthesis data analysis, the proposed method can not only improve the SNR level of three-component records, it also improves the accuracy of polarization analysis. The proposed method also achieved a satisfactory effect for field data

A Novel Polarity Correction Method Developed on Cross Correlation Analysis for Downhole Migration-Based Location of Microseismic Events

Migration-based approaches depending on waveform stacking are generally used to locate the microseismic events in hydro-fracturing monitoring. A simple waveform stacking with polarity correction normally provides better results than any of the absolute value-based methods. However, the existing polarity estimation method based on cross correlation analysis selects only individual waveform as a reference waveform, which may affect the precision of migration-based methods. Therefore, a novel polarity correction method based on cross correlation analysis is introduced for a migration-based location in order to accurately locate the microseismic events in a borehole system. The proposed method selects all waveforms from one event having high signal-to-noise ratio (SNR) as corresponding reference waveforms, instead of only selecting a single high SNR waveform from one target event as the corresponding reference waveform. Compared with the above-mentioned conventional method, this proposed method provides a more accurate migration-based location of microseismic events with minimum error. The presented method was successfully tested on synthetic and field data acquired from a single monitoring well during a hydraulic fracturing process. Our study distinctly demonstrates that the proposed method provides more robust and reliable results, even in low SNR circumstances

A Novel Polarity Correction Method Developed on Cross Correlation Analysis for Downhole Migration-Based Location of Microseismic Events

Migration-based approaches depending on waveform stacking are generally used to locate the microseismic events in hydro-fracturing monitoring. A simple waveform stacking with polarity correction normally provides better results than any of the absolute value-based methods. However, the existing polarity estimation method based on cross correlation analysis selects only individual waveform as a reference waveform, which may affect the precision of migration-based methods. Therefore, a novel polarity correction method based on cross correlation analysis is introduced for a migration-based location in order to accurately locate the microseismic events in a borehole system. The proposed method selects all waveforms from one event having high signal-to-noise ratio (SNR) as corresponding reference waveforms, instead of only selecting a single high SNR waveform from one target event as the corresponding reference waveform. Compared with the above-mentioned conventional method, this proposed method provides a more accurate migration-based location of microseismic events with minimum error. The presented method was successfully tested on synthetic and field data acquired from a single monitoring well during a hydraulic fracturing process. Our study distinctly demonstrates that the proposed method provides more robust and reliable results, even in low SNR circumstances

On the Computational Characterization of Charge-Transfer Effects in Noncovalently Bound Molecular Complexes.

Charge-transfer (CT) is an important binding force in the formation of intermolecular complexes, and there have been a variety of theoretical models proposed to quantify this effect. These approaches, which typically rely on a definition of a "CT-free" state based on a partition of the system, sometimes yield significantly different results for a given intermolecular complex. Two widely used definitions of the "CT-free" state, the absolutely localized molecular orbitals (ALMO) method (where only on-fragment orbital mixings are permitted) and the constrained density functional theory (CDFT) approach (where fragment electron populations are fixed), are carefully examined in this work. Natural bond orbital (NBO) and the regularized symmetry-adapted perturbation theory (SAPT) are also briefly considered. Results for the ALMO and CDFT definitions of CT are compared on a broad range of model systems, including hydrogen-bonding systems, borane complexes, metal-carbonyl complexes, and complexes formed by water and metal cations. For most of these systems, CDFT yields a much smaller equilibrium CT energy compared to that given by the ALMO-based definition. This is mainly because the CDFT population constraint does not fully inhibit CT, which means that the CDFT "CT-free" state is in fact CT-contaminated. Examples of this contamination include (i) matching forward and backward donation (e.g., formic acid dimer) and (ii) unidirectional CT without changing fragment populations. The magnitude of the latter effect is quantified in systems such as the water dimer by employing a 3-space density constraint in addition to the orbital constraint. Furthermore, by means of the adiabatic EDA, it is shown that several observable effects of CT, such as the "pyramidalization" of the planar BH3 molecule upon the complexation with Lewis bases, already appear on the "CT-free" CDFT surface. These results reveal the essential distinctions between the ALMO and CDFT definitions of CT and suggest that the former is more consistent with accepted understanding of the role of CT in intermolecular binding