Progressive and accurate assembly of multi-domain protein structures from cryo-EM density maps

ABSTRACTProgress in cryo-electron microscopy (cryo-EM) has provided the potential for large-size protein structure determination. However, the solution rate for multi-domain proteins remains low due to the difficulty in modeling inter-domain orientations. We developed DEMO-EM, an automatic method to assemble multi-domain structures from cryo-EM maps through a progressive structural refinement procedure combining rigid-body domain fitting and flexible assembly simulations with deep neural network inter-domain distance profiles. The method was tested on a large-scale benchmark set of proteins containing up to twelve continuous and discontinuous domains with medium-to-low-resolution density maps, where DEMO-EM produced models with correct inter-domain orientations (TM-score >0.5) for 98% of cases and significantly outperformed the state-of-the-art methods. DEMO-EM was applied to SARS-Cov-2 coronavirus genome and generated models with average TM-score/RMSD of 0.97/1.4Å to the deposited structures. These results demonstrated an efficient pipeline that enables automated and reliable large-scale multi-domain protein structure modeling with atomic-level accuracy from cryo-EM maps.

A disfluent font does not help people to solve math and non-math problems regardless of their numeracy [Preprint]

Prior research has suggested that perceptual disfluency activates analytical processing and increases the solution rate of mathematical problems with appealing but incorrect answers (i.e., the Cognitive Reflection Test, hereafter CRT). However, a recent meta-analysis does not support such a conclusion. We tested here whether insufficient numerical ability can account for this discrepancy. In a 2(font: fluent vs. disfluent; between-subjects factor) × 2 (CRT: Numerical vs Verbal; within-subjects factor) design, 310 participants solved numerical and verbal CRT problems, followed by a measure of numerical ability. We found strong support against the disfluent font effect on the problem-solving rate for math as well as non-math problems regardless of participants’ numeracy. The updated meta-analysis (k = 18) yielded close-to-zero effect, Hedge’s g = -0.01, 95% CI[-0.05, 0.03] and decisive evidence against the disfluency effect on math problems, BF0+ = 151.6. Thus, perceptual disfluency does not help people solve math and non-math problems.

Competition kinetics of OH radical reactions with oxygenated organic compounds in aqueous solution: rate constants and internal optical absorption effects

Atmospheric aqueous phase rate constants are determined and the effect of optical absorbers in competition kinetics is studied.

Determination of the reactivity of CaSO4 · 2H2O

Reactivity of energy gypsum was investigated. The method is based on the conversion reaction of aqueous suspension of gypsum with ammonium carbonate solution. Rate of the conversion of all investigated samples, including gypsum originating from flue gas desulphurization (FGD), was high and 80 % conversion was achieved during one hour. It was found that there is a correlation between BET specific surface and the rate of the conversion reaction.

Effects Different Processing Techniques for Flavonoids from Buckwheat and Antioxidative

the flavonoid existing in buckwheat is one of the important physiological active substances. This paper studies the baking and cooking, high pressure treatment on the effect of flavonoids from buckwheat and buckwheat grains. Results showed that buckwheat hull has little effect on processing of total flavonoids, after baking, cooking and hyperbaric treatment, buckwheat flavonoids solution rate increased by more than 70%. Instead, made of buckwheat flour dough, is greatly influenced by processing, adding a certain concentration of salt can alleviate the degradation of rutin in buckwheat, but relief is unlikely.

Synthesis and Performance Characterization of Highly Active Samarium Doped TiO2 Nanopowder

In the experiment, the tetrabutyl titanate and samarium trinitrate were used as raw material, samarium doped TiO2 powder was prepared by sol-gel method. Main factors that affect the TiO2 nanoparticles, such as catalyst, ratio of raw materials, and calcination temperature of the preparation process were studied. TiO2 powder was characterized by using XRD, UV-vis, IR to determine the crystal structure, grain size and spectral properties. The results show that, the amount of catalyst is 50mg, the calcination temperature is 500 °C, samarium doping ratio is 0.4%, and the visible light photocatalytic degradation time at 60min, the degradation of methyl orange solution rate of 20mg/L can reach 42.8%. Samples with anatase as the main, in the catalyst preparation process, due to the synergistic effects of samarium doping, the modified TiO2 absorption band of different redshift, enhanced the catalytic activity of TiO2 visible light.

Preparation and Optical Properties of Lanthanum Doped Ultra-Fine TiO2 Photocatalyst

In the experiment, the tetrabutyl titanate and lanthanum nitrate were used as raw material, lanthanum doped TiO2 powder was prepared by sol-gel method, were characterized by using XRD, UV-vis, IR to determine the crystal structure, grain size and spectral properties. The results showed that the calcination temperature is 600 °C, lanthanum doping ratio is 0.6%, the amount of catalyst is 50mg and the visible light photocatalytic degradation time at 60min, the degradation of methyl orange solution rate of 20mg/L can reach 36%. Samples with anatase as the main, in the catalyst preparation process, due to the synergistic effects of lanthanum doping, the modified TiO2 absorption band of different redshift, enhanced the catalytic activity of TiO2 visible light.

Development of Lecithin Nanoemulsion Based Organogels for Permeation Enhancement of Metoprolol through Rat Skin

Background. Drugs with low oral bioavailability due to the first pass metabolism are good candidates for transdermal delivery.Objectives.The aim of this work was preparation of transdermal nanoemulsion of metoprolol which has high first pass metabolism.Methods. Three commercially available types of lecithin (200, 100p, and 170), three short chain alcohol (n-butanol, isopropyl alcohol, and n-propanol), and isopropyl myristate (IPM) were used as surfactant, cosurfactant, and oil phase, respectively. The aqueous phase was composed of metoprolol tartrate. Nanoemulsions with different surfactant/cosurfactant weight ratio, various amounts of drug, and different types of alcohol were prepared, and their phase diagrams were studied. Drug release, permeability, and diffusion coefficient of the drug were studied using hairless rat skin.Results. A significant increase in drug solution rate was observed with increasing the metoprolol content in the nanoemulsions, while it decreased when lecithin concentration increased from 40% to 60%. Increasing the water content resulted in a significant increase in metoprolol release. N-butanol enhanced the drug flux from nanoemulsions more than n-propanol and isopropyl alcohol. The o/w nanoemulsions of metoprolol showed high flux and permeability through the skin.Conclusion. Both w/o and o/w nanoemulsions of metoprolol could enhance permeation and diffusion of metoprolol through rat skin.