A General Tensor Prediction Framework Based on Graph Neural Networks

Graph neural networks (GNNs) have been shown to be extremely flexible and accurate in predicting the physical properties of molecules and crystals. However, traditional invariant GNNs are not compatible with directional properties, which currently limits their usage to the prediction of only invariant scalar properties. To address this issue, here we propose a general framework, i.e., an edge-based tensor prediction graph neural network, in which a tensor is expressed as the linear combination of the local spatial components projected on the edge directions of clusters with varying sizes. This tensor decomposition is rotationally equivariant and exactly satisfies the symmetry of the local structures. The accuracy and universality of our new framework are demonstrated by the successful prediction of various tensor properties from first to third order. The framework proposed in this work will enable GNNs to step into the broad field of prediction of directional properties

sj-doc-1-inq-10.1177_00469580231171820 – Supplemental material for Association Between Sleep and Cognition of Older Adults in Rural Areas: A Cross-Sectional Study

Supplemental material, sj-doc-1-inq-10.1177_00469580231171820 for Association Between Sleep and Cognition of Older Adults in Rural Areas: A Cross-Sectional Study by Wenjia Meng, Tianlin Gao, Yang Zhong and Ling Ge in INQUIRY: The Journal of Health Care Organization, Provision, and Financing</p

Number of chemosensory receptor genes in vertebrates.

<p>The numbers of each bar represent the number of functional (intact) and pseudogenes of OR, TAAR, V1R, V2R, T1R and T2R genes. The blue and orange bars represent the number of functional genes and pseudogenes, respectively.</p

The web interface of CRDB.

<p>A) Snapshot of the CRDB home page. B) Result of phylogenetic tree of primate T1R genes.</p

lncRNA MEG3 inhibits the growth of hepatocellular carcinoma cells by sponging miR-9-5p to upregulate SOX11

The long non-coding RNA (lncRNA) maternally expressed gene 3 (MEG3), a tumor suppressor, is critical for the carcinogenesis and progression of different cancers, including hepatocellular carcinoma (HCC). To date, the roles of lncRNA MEG3 in HCC are not well illustrated. Therefore, this study used western blot and qRT-PCR to evaluate the expression of MEG3, miR-9-5p, and Sex determining Region Y-related HMG-box 11 (SOX11) in HCC tissues and cell lines. RNA pull-down and luciferase reporter assay were used to evaluate these molecular interactions. 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide and flow cytometry detected the viability and apoptosis of HCC cells, respectively. The results showed that MEG3 and SOX11 were poorly expressed but miR-9-5p was highly expressed in HCC. The expression levels of these molecules suggested a negative correlation between MEG3 and miR-9-5p and a positive correlation with SOX11, confirmed by Pearson's correlation analysis and biology experiments. Furthermore, MEG3 could combine with miR-9-5p, and SOX11 was a direct target of miR-9-5p. Moreover, MEG3 over-expression promoted cell apoptosis and growth inhibition in HCC cells through sponging miR-9-5p to up-regulate SOX11. Therefore, the interactions among MEG3, miR-9-5p, and SOX11 might offer a novel insight for understanding HCC pathogeny and provide potential diagnostic markers and therapeutic targets for HCC.</div

Thermodynamics in Separation for the Ternary System 1,2-Ethanediol + 1,2-Propanediol + 2,3-Butanediol

The thermodynamic data in distillation, i.e., isobaric vapor–liquid equilibrium data, have been measured for the three binary systems of 1,2-ethanediol + 1,2-propanediol, 1,2-ethanediol + 2,3-butanediol, and 1,2-propanediol + 2,3-butanediol at 101.3 kPa. The accuracy of the experimental data was confirmed by both Herington test and Van Ness test. The thermodynamic properties of the vapor phase have been calculated with the Hayden–O’Connell equation in consideration of nonideality. The liquid activity coefficients have been satisfactorily correlated with the Wilson, NRTL, and UNIQUAC models, while the estimated results from the UNIFAC model are not satisfactory. The corresponding binary interaction parameters of the three models Wilson, NRTL, and UNIQUAC were calculated and used to obtain the residual curves of the ternary system 1,2-ethanediol + 1,2-propanediol + 2,3-butanediol. Based on all of the preceding results, a two-column distillation process has been designed to obtain the required products

Luminescent Turn-On Upconversion Nanoprobes for Monitoring NADH In Vivo

Mitochondrial damage is implicated with a variety of pathological processes and is featured by the dramatically raised NADH level. To date, the detection and in situ imaging of NADH in living animals is still a challenge. Herein, we designed an upconversion luminescent nanoprobe for the in vivo imaging of NADH. The Nile blue (NB) with a strong absorption band at 500–700 nm can quench the red luminescence of the upconversion nanoparticle at 654 nm by the fluorescence resonance energy transfer effect. Under the presence of NADH, the NB was bleached, so that the fluorescence of the probe was “turned on”. The nanoprobe achieved highly selective detection of NADH, and the in vivo monitoring of NADH was also demonstrated on living mice

Free Energetics and the Role of Water in the Permeation of Methyl Guanidinium across the Bilayer–Water Interface: Insights from Molecular Dynamics Simulations Using Charge Equilibration Potentials

Combining umbrella sampling molecular dynamics (MD) simulations, the weighted histogram analysis method (WHAM) for unbiasing probabilities, and polarizable charge equilibration force fields, we compute the potential of mean force for the reversible transfer of methyl guanidinium from bulk solution to the center of a model DPPC bilayer. A 5 kcal/mol minimum in the potential of mean force profile for membrane permeation suggests that the analogue will preferentially reside in the headgroup region of the lipid, qualitatively in agreement with previously published results. We find the potential of mean force for permeation to be approximately 28 kcal/mol (relative to the minimum in the headgroups), within the range of values reported for similar types of simulations using fixed-charge force fields. From analysis of the lipid structure, we find that the lipid deformation leads to a substantial destabilizing contribution to the free energy of the methyl guanidinium as it resides in the bilayer center, though this deformation allows more efficient stabilization by water defects and transient pores. Water in the bilayer core stabilizes the charged residue. The role of water in stabilizing or destabilizing the solute as it crosses the bilayer depends on bulk electrolyte concentration. In 1 M KCl solution, the water contribution to the potential of mean force is stabilizing over the entire range of the permeation coordinate, with the sole destabilizing force originating from the anionic species in solution. Conversely, methyl guanidinium experiences net destabilization from water in the absence of electrolyte. The difference in solvent contributions to permeation free energy is traced to a local effect arising from differences in water density in the bilayer–water solution interface, thus leading to starkly opposite net forces on the permeant. The origin of the local water density differential rests with the penetration of hydrated chloride anions into the solution–bilayer interface. Finally, water permeation into the bilayer is required for the deformation of individual lipid molecules and permeation of ions into the membrane. From simulations where water is first excluded from the bilayer center where methyl guanidinium is restrained and then, after equilibration, allowed to enter the bilayer, we find that in the absence of any water defects/permeation into the bilayer, the lipid headgroups do not follow the methyl guanidinium. Only when water enters the bilayer do we see deformation of individual lipid molecules to associate with the amino acid analogue at bilayer center

Data_Sheet_2_COVID-19 Risk Assessment for the Tokyo Olympic Games.doc

Introduction: As of June 7, 2021, the outbreak of Coronavirus Disease 2019 (COVID-19) has spread to more than 200 countries. The global number of reported cases is more than 172.9 million, with more than 3.7 million deaths, and the number of infected individuals is still growing rapidly. Consequently, events and activities around the world were canceled or postponed, and the preparation for sporting events were greatly challenged. Under such circumstances, about 11,000 athletes from ~206 countries are arriving in Tokyo for the 32nd Summer Olympic Games. Therefore, it is urgently necessary to assess the occurrence and spread risk of COVID-19 for the Games.Objectives: To explore effective prevention and control measures for COVID-19 in large international events through simulations of different interventions according to risk assessment.Methods: We used a random model to calculate the number of initial infected patients and used Poisson distribution to determine the number of initial infected patients based on the number of countries involved. Furthermore, to simulate the COVID-19 transmission, the susceptible-exposed-symptomatic-asymptomatic-recovered-hospitalized (SEIARH) model was established based on the susceptible-exposed-infectious-recovered (SEIR) mathematical model of epidemic diseases. According to risk assessment indicators produced by different scenarios of the simulated interventions, the risk of COVID-19 transmission in Tokyo Olympic Games was assessed.Results: The current COVID-19 prevention measures proposed by the Japan Olympic Committee need to be enhanced. And large-scale vaccination will effectively control the spread of COVID-19. When the protective efficacy of vaccines is 78.1% or 89.8%, and if the vaccination rate of athletes reaches 80%, an epidemic prevention barrier can be established.</p

Data_Sheet_1_COVID-19 Risk Assessment for the Tokyo Olympic Games.doc

Introduction: As of June 7, 2021, the outbreak of Coronavirus Disease 2019 (COVID-19) has spread to more than 200 countries. The global number of reported cases is more than 172.9 million, with more than 3.7 million deaths, and the number of infected individuals is still growing rapidly. Consequently, events and activities around the world were canceled or postponed, and the preparation for sporting events were greatly challenged. Under such circumstances, about 11,000 athletes from ~206 countries are arriving in Tokyo for the 32nd Summer Olympic Games. Therefore, it is urgently necessary to assess the occurrence and spread risk of COVID-19 for the Games.Objectives: To explore effective prevention and control measures for COVID-19 in large international events through simulations of different interventions according to risk assessment.Methods: We used a random model to calculate the number of initial infected patients and used Poisson distribution to determine the number of initial infected patients based on the number of countries involved. Furthermore, to simulate the COVID-19 transmission, the susceptible-exposed-symptomatic-asymptomatic-recovered-hospitalized (SEIARH) model was established based on the susceptible-exposed-infectious-recovered (SEIR) mathematical model of epidemic diseases. According to risk assessment indicators produced by different scenarios of the simulated interventions, the risk of COVID-19 transmission in Tokyo Olympic Games was assessed.Results: The current COVID-19 prevention measures proposed by the Japan Olympic Committee need to be enhanced. And large-scale vaccination will effectively control the spread of COVID-19. When the protective efficacy of vaccines is 78.1% or 89.8%, and if the vaccination rate of athletes reaches 80%, an epidemic prevention barrier can be established.</p