Insights and Challenges in Correcting Force Field Based Solvation Free Energies Using a Neural Network Potential.

We present a comprehensive study investigating the potential gain in accuracy for calculating absolute solvation free energies (ASFE) using a neural network potential to describe the intramolecular energy of the solute. We calculated the ASFE for most compounds from the FreeSolv database using the Open Force Field (OpenFF) and compared them to earlier results obtained with the CHARMM General Force Field (CGenFF). By applying a nonequilibrium (NEQ) switching approach between the molecular mechanics (MM) description (either OpenFF or CGenFF) and the neural net potential (NNP)/MM level of theory (using ANI-2x as the NNP potential), we attempted to improve the accuracy of the calculated ASFEs. The predictive performance of the results did not change when this approach was applied to all 589 small molecules in the FreeSolv database that ANI-2x can describe. When selecting a subset of 156 molecules, focusing on compounds where the force fields performed poorly, we saw a slight improvement in the root-mean-square error (RMSE) and mean absolute error (MAE). The majority of our calculations utilized unidirectional NEQ protocols based on Jarzynski's equation. Additionally, we conducted bidirectional NEQ switching for a subset of 156 solutes. Notably, only a small fraction (10 out of 156) exhibited statistically significant discrepancies between unidirectional and bidirectional NEQ switching free energy estimates.

miR-10167-3p targets TCF7L1 to inhibit bovine adipocyte differentiation and promote bovine adipocyte proliferation.

MicroRNAs (miRNAs) are widely involved in various lipogenic processes, including adipocyte proliferation and differentiation, lipid droplet formation, and adipocyte-specific gene activation. The present study aimed to investigate the gene expression profiles of bovine preadipocytes under high miR-10167-3p expression using the RNA-seq technique and to verify the functions of its downstream target genes on the proliferation and differentiation of bovine preadipocytes. First, RNA-seq identified 573 differentially expressed genes (DEGs), of which 243 were downregulated and 330 were upregulated. Then, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that 15.19% of the DEGs were enriched in pathways related to lipid metabolism. Meanwhile, dual-luciferase reporter gene assay verified the target-binding relationship between miR-10167-3p and TCF7L1. The function of TCF7L1 was assessed using several experiments in adipocytes with high TCF7L1 expression and RNA interference. The mRNA and protein expression of proliferation, differentiation, and apoptosis marker genes were detected using qPCR and western blot, respectively; lipid droplet synthesis was detected using oil red O, Nile red, and bodipy staining; adipocyte proliferation was detected by EdU; and apoptosis was detected using flow cytometry. The results revealed that TCF7L1 overexpression inhibited bovine preadipocyte differentiation and apoptosis and promoted their proliferation, with opposite results obtained with its RNA interference. These results may provide a reference for the subsequent investigation of the molecular mechanism of bovine fat deposition.

Revolutionizing cattle breeding: Gene editing advancements for enhancing economic traits.

Beef and dairy products are rich in protein and amino acids, making them highly nutritious for human consumption. The increasing use of gene editing technology in agriculture has paved the way for genetic improvement in cattle breeding via the development of the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) system. Gene sequences are artificially altered and employed in the pursuit of improving bovine breeding research through targeted knockout, knock-in, substitution, and mutation methods. This review offers a comprehensive analysis of the advancements in gene editing technology and its diverse applications in enhancing both quantitative and qualitative traits across livestock. These applications encompass areas such as meat quality, milk quality, fertility, disease resistance, environmental adaptability, sex control, horn development, and coat colour. Furthermore, the review considers prospective ideas and insights that may be employed to refine breeding traits, enhance editing efficiency, and navigate the ethical considerations associated with these advancements. The review's focus on improving the quality of beef and milk is intended to enhance the economic viability of these products. Furthermore, it constitutes a valuable resource for scholars and researchers engaged in the fields of cattle genetic improvement and breeding.

Comparing Business, Innovation, and Platform Ecosystems: A Systematic Review of the Literature.

In recent decades, the term "ecosystem" has garnered substantial attention in scholarly and managerial discourse, featuring prominently in academic and applied contexts. While individual scholars have made significant contributions to the study of various types of ecosystem, there appears to be a research gap marked by a lack of comprehensive synthesis and refinement of findings across diverse ecosystems. This paper systematically addresses this gap through a hybrid methodology, employing bibliometric and content analyses to systematically review the literature from 1993 to 2023. The primary research aim is to critically examine theoretical studies on different ecosystem types, specifically focusing on business, innovation, and platform ecosystems. The methodology of this study involves a content review of the identified literature, combining quantitative bibliometric analyses to differentiate patterns and content analysis for in-depth exploration. The core findings center on refining and summarizing the definitions of business, innovation, and platform ecosystems, shedding light on both commonalities and distinctions. Notably, the research unveils shared characteristics such as openness and diversity across these ecosystems while highlighting significant differences in terms of participants and objectives. Furthermore, the paper delves into the interconnections within these three ecosystem types, offering insights into their dynamics and paving the way for discussions on future research directions. This comprehensive examination not only advances our understanding of business, innovation, and platform ecosystems but also lays the groundwork for future scholarly inquiries in this dynamic and evolving field.

Pharmacokinetic Study of Ultrasmall Superparamagnetic Iron Oxide Nanoparticles HY-088 in Rats.

BACKGROUND AND OBJECTIVE: HY-088 injection is an ultrasmall superparamagnetic iron oxide nanoparticle (USPIOs) composed of iron oxide crystals coated with polyacrylic acid (PAA) on the surface. The purpose of this study was to investigate the pharmacokinetics, tissue distribution, and mass balance of HY-088 injection. METHODS: The pharmacokinetics of [55Fe]-HY-088 and [14C]-HY-088 were investigated in 48 SD rats by intravenous injection of 8.5 (low-dose group), 25.5 (medium-dose group), and 85 (high-dose group) mg/100 µCi/kg. Tissue distribution was studied by intravenous injection of 35 mg/100 µCi/kg in 48 SD rats, and its tissue distribution in vivo was obtained by ex vivo tissue assay. At the same time, [14C]-HY-088 was injected intravenously at a dose of 25.5 mg/100 µCi/kg into 16 SD rats, and its tissue distribution in vivo was studied by quantitative whole-body autoradiography. [14C]-HY-088 and [55Fe]-HY-088 were injected intravenously into 24 SD rats at a dose of 35 mg/100 µCi/kg, and their metabolism was observed. RESULTS: In the pharmacokinetic study, [55Fe]-HY-088 reached the maximum observed concentration (Cmax) at 0.08 h in the low- and medium-dose groups of SD rats. [14C]-HY-088 reached Cmax at 0.08 h in the three groups of SD rats. The area under the concentration-time curve (AUC) of [55Fe]-HY-088 and [14C]-HY-088 increased with increasing dose. In the tissue distribution study, [55Fe]-HY-088 and [14C]-HY-088 were primarily distributed in the liver, spleen, and lymph nodes of both female and male rats. In the mass balance study conducted over 57 days, the radioactive content of 55Fe from [55Fe]-HY-088 was primarily found in the carcass, accounting for 86.42 ± 4.18% in females and 95.46 ± 6.42% in males. The radioactive recovery rates of [14C]-HY-088 in the urine of female and male rats were 52.99 ± 5.48% and 60.66 ± 2.23%, respectively. CONCLUSIONS: Following single intravenous administration of [55Fe]-HY-088 and [14C]-HY-088 in SD rats, rapid absorption was observed. Both [55Fe]-HY-088 and [14C]-HY-088 were primarily distributed in the liver, spleen, and lymph nodes. During metabolism, the radioactivity of [55Fe]-HY-088 is mainly present in the carcass, whereas the 14C-labeled [14C]-HY-088 shell PAA is eliminated from the body mainly through the urine.