A Contact Energy Function Considering Residue Hydrophobic Environment and Its Application in Protein Fold Recognition

The three-dimensional (3D) structure prediction of proteins is an important task in bioinformatics. Finding energy functions that can better represent residue-residue and residue-solvent interactions is a crucial way to improve the prediction accuracy. The widely used contact energy functions mostly only consider the contact frequency between different types of residues; however, we find that the contact frequency also relates to the residue hydrophobic environment. Accordingly, we present an improved contact energy function to integrate the two factors, which can reflect the influence of hydrophobic interaction on the stabilization of protein 3D structure more effectively. Furthermore, a fold recognition (threading) approach based on this energy function is developed. The testing results obtained with 20 randomly selected proteins demonstrate that, compared with common contact energy functions, the proposed energy function can improve the accuracy of the fold template prediction from 20% to 50%, and can also improve the accuracy of the sequence-template alignment from 35% to 65%

ControlCom: Controllable Image Composition using Diffusion Model

Image composition targets at synthesizing a realistic composite image from a pair of foreground and background images. Recently, generative composition methods are built on large pretrained diffusion models to generate composite images, considering their great potential in image generation. However, they suffer from lack of controllability on foreground attributes and poor preservation of foreground identity. To address these challenges, we propose a controllable image composition method that unifies four tasks in one diffusion model: image blending, image harmonization, view synthesis, and generative composition. Meanwhile, we design a self-supervised training framework coupled with a tailored pipeline of training data preparation. Moreover, we propose a local enhancement module to enhance the foreground details in the diffusion model, improving the foreground fidelity of composite images. The proposed method is evaluated on both public benchmark and real-world data, which demonstrates that our method can generate more faithful and controllable composite images than existing approaches. The code and model will be available at https://github.com/bcmi/ControlCom-Image-Composition

Association between vitamin D status and cardiometabolic risk factors in adults with type 2 diabetes in Shenzhen, China

BackgroundEvidence of vitamin D status and cardiometabolic health in adults with type 2 diabetes mellitus (T2DM) is still limited. This study aimed to investigate the association between vitamin D status and cardiometabolic risk factors among adults with T2DM in Shenzhen, China.MethodsThis cross-sectional study included 164 adults (aged ≥18 years) with T2DM who were hospitalized at Peking University Shenzhen Hospital from March 1, 2023, to May 31, 2023. Serum 25-hydroxyvitamin D [25(OH)D] concentration, the active marker of vitamin D, and three major cardiometabolic risk factors including blood pressure (BP), glucose metabolism-related indicators, and blood lipid profiles were collected. Vitamin D deficiency (VDD) was defined as 25(OH)D < 20 ng/mL. Correlation, Regression, and Logistic analysis were applied to verify the association among serum 25(OH)D concentration, VDD, and 11 cardiometabolic risk factors.ResultsMedian 25(OH)D concentration was 21.78 [interquartile range (IQR)=17.51-28.05] ng/mL. The prevalence of VDD was 40.24%. Serum 25(OH)D concentration was significantly negatively correlated with diastolic BP (DBP) and glycated hemoglobin A1c (HbA1c) rather than systolic BP, plasma glucose, plasma C-peptide, and blood lipid profiles among adults with T2DM in both correlation and linear regression analysis. Furthermore, the adjusted odd ratio for poor DBP control (≥90 mmHg) of T2DM patients with VDD was 3.164 (95% confidence interval=1.303, 7.683; P=0.011) compared to those without VDD.ConclusionIn China, VDD was highly prevalent among adults with T2DM and associated with greater cardiovascular risk factors, especially with increased chances of uncontrolled DBP. These findings suggest that vitamin D levels should be monitored in T2DM patients, especially those with high DBP

Using Rhodamine 123 Accumulation in CD8+ Cells as a Surrogate Indicator to Study the P-Glycoprotein Modulating Effect of Cepharanthine Hydrochloride In Vivo

The purpose of this study was the use of rhodamine 123 (Rho123) accumulation in peripheral blood CD8+cells as a surrogate indicator to evaluate the modulating effect of P-glycoprotein (P-gp) inhibitors in the multidrug resistance (MDR) tumor-bearing mouse model. Rho123 was administered to mice, and the fluorescence level in CD8+ cells was measured. Cepharanthine hydrochloride (CH) and verapamil (VER), two P-gp inhibitors, were administered to mice 1 hour prior to Rho123 administration in vivo or added to peripheral blood 1 hour prior to Rho123 addition ex vivo. The tumor inhibition effect of 5-fluorouracil/adriamycin/cisplatin (FAP) protocol plus CH was also investigated. A concentration- or dose-response relationship was shown between the concentration and dose of CH and Rho123 accumulation or the antitumor activity. In conclusion, the measurement of Rho123 accumulation in CD8+ cells provides a surrogate assay for the screening of candidate P-gp inhibitors in preclinical trials, and CH is effective in modulating P-gp-mediated MDR in vivo

Electrochemical activity and stability of core–shell Fe2O3/Pt nanoparticles for methanol oxidation

AbstractCore–shell Fe2O3/Pt nanoparticles with amorphous iron oxide cores are successfully synthesized by a two-step chemical reduction strategy. The Pt loading can be adjusted using this preparation technique to obtain a series of chemical compositions with varying amounts of Pt precursors. The morphology, structure, and composition of the as-prepared nanoparticles are characterized by transmission electron microscopy, X-ray diffraction, energy dispersive spectroscopy, and X-ray photoelectron spectroscopy. Electrocatalytic characteristics are systematically investigated by electrochemical techniques, such as cyclic voltammetry, chronoamperometry, and in situ Fourier transform infrared spectroscopy. Compared with the E-TEK 40 wt% Pt/C catalyst, the as-made Fe2O3/Pt nanoparticles exhibit superior catalytic activity with lower peak potential and enhanced CO2 selectivity toward methanol electrooxidation in acidic medium. The highest activity is achieved by core–shell Fe2O3/Pt nanoparticles with a Fe/Pt atomic ratio of 2:1 (A g−1 of Pt) or 3:1 (mA cm−2). These nanomaterials also show much higher structural stability and tolerance to the intermediates of methanol oxidation. Methanol electrooxidation reactions with higher performance can be achieved using core–shell nanoparticles with an amorphous iron oxide core and minimum Pt loading

Tunnel splitting and quantum phase interference in biaxial ferrimagnetic particles at excited states

The tunneling splitting in biaxial ferrimagnetic particles at excited states with an explicit calculation of the prefactor of exponent is obtained in terms of periodic instantons which are responsible for tunneling at excited states and is shown as a function of magnetic field applied along an arbitrary direction in the plane of hard and medium axes. Using complex time path-integral we demonstrate the oscillation of tunnel splitting with respect to the magnitude and the direction of the magnetic field due to the quantum phase interference of two tunneling paths of opposite windings . The oscillation is gradually smeared and in the end the tunnel splitting monotonously increases with the magnitude of the magnetic field when the direction of the magnetic field tends to the medium axis. The oscillation behavior is similar to the recent experimental observation with Fe$_8$ molecular clusters. A candidate of possible experiments to observe the effect of quantum phase interference in the ferrimagnetic particles is proposed.Comment: 15 pages, 5 figures, acceptted to be pubblished in Physical Review

Regeneration of Spent Lubricant Refining Clays by Solvent Extraction

Step-by-step solvent extraction was used to regenerate spent clay by recovering the adsorbed oil in lubricating oil refining clay. Several polar and nonpolar solvents were tested, and petroleum ether (90–120°C) and ethanol (95 v%) were selected as the nonpolar and polar solvents, respectively. The spent clay was first extracted using petroleum ether (90–120°C) to obtain ideal oil and then extracted with a mixed solvent of petroleum ether (90–120°C) and ethanol (95 v%) two or three times to obtain nonideal oil before being extracted with ethanol and water. Finally, the clay was dried at 130°C to obtain regenerated clay. The total oil recovery can be more than 99 wt% of the adsorbed oil. The recovered ideal oil can be used as lubricating base oil. Shorter storage times for spent clay produce better regeneration results. The regenerated clay can be reused to refine the lubricating base oils

Coherent Dynamics of Charge Carriers in {\gamma}-InSe Revealed by Ultrafast Spectroscopy

For highly efficient ultrathin solar cells, layered indium selenide (InSe), a van der Waals solid, has shown a great promise. In this paper, we study the coherent dynamics of charge carriers generation in {\gamma}-InSe single crystals. We employ ultrafast transient absorption spectroscopy to examine the dynamics of hot electrons after resonant photoexcitation. To study the effect of excess kinetic energy of electrons after creating A exciton (VB1 to CB transition), we excite the sample with broadband pulses centered at 600, 650, 700 and 750 nm, respectively. We analyze the relaxation and recombination dynamics in {\gamma}-InSe by global fitting approach. Five decay associated spectra with their associated lifetimes are obtained, which have been assigned to intraband vibrational relaxation and interband recombination processes. We extract characteristic carrier thermalization times from 1 to 10 ps. To examine the coherent vibrations accompanying intraband relaxation dynamics, we analyze the kinetics by fitting to exponential functions and the obtained residuals are further processed for vibrational analysis. A few key phonon coherences are resolved and ab-initio quantum calculations reveal the nature of the associated phonons. The wavelet analysis is employed to study the time evolution of the observed coherences, which show that the low-frequency coherences last for more than 5 ps. Associated calculations reveal that the contribution of the intralayer phonon modes is the key determining factor for the scattering between free electrons and lattice. Our results provide fundamental insights into the photophysics in InSe and help to unravel their potential for high-performance optoelectronic devices