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Objectives Biomedical Knowledge Graphs play a pivotal role in various biomedical research domains. Concurrently, term clustering emerges as a crucial step in constructing these knowledge graphs, aiming to identify synonymous terms. Due to a lack of knowledge, previous contrastive learning models trained with Unified Medical Language System (UMLS) synonyms struggle at clustering difficult terms and do not generalize well beyond UMLS terms. In this work, we leverage the world knowledge from large language models (LLMs) and propose Contrastive Learning for Representing Terms via Explanations (CoRTEx) to enhance term representation and significantly improves term clustering. Materials and Methods The model training involves generating explanations for a cleaned subset of UMLS terms using ChatGPT. We employ contrastive learning, considering term and explanation embeddings simultaneously, and progressively introduce hard negative samples. Additionally, a ChatGPT-assisted BIRCH algorithm is designed for efficient clustering of a new ontology. Results We established a clustering test set and a hard negative test set, where our model consistently achieves the highest F1 score. With CoRTEx embeddings and the modified BIRCH algorithm, we grouped 35 580 932 terms from the Biomedical Informatics Ontology System (BIOS) into 22 104 559 clusters with O(N) queries to ChatGPT. Case studies highlight the model's efficacy in handling challenging samples, aided by information from explanations. Conclusion By aligning terms to their explanations, CoRTEx demonstrates superior accuracy over benchmark models and robustness beyond its training set, and it is suitable for clustering terms for large-scale biomedical ontologies. [ABSTRACT FROM AUTHOR]

g-C3N4/BiOI composites with different ratios were prepared by in-situ generation route at room temperature and applied in antibacterial investigation. Detailed information of the composites was characterized by XRD, TEM, HRTEM, SEM, EDS, BET, XPS, FT-IR, UV-Vis, photocurrent and EIS. The obtained g-C3N4/BiOI composites presented excellent antibacterial performance toward Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) under LED track light, with the complete inactivation of bacterial within 30 min. The decomposition of bacterial cells was observed by SEM. The bacterial mechanism was investigated by trapping experiments: holes (h+), superoxide anion free radical (O2−) and hydrogen peroxide (H2O2) were identified as active species for bacterial inactivation, and h+ had a main effect in the antibacterial process. The enhanced photocatalytic activities were assigned to an efficient separation and transition of electrons (e−) and h+ in photocatalytic antibacterial process. This work indicated the g-C3N4/BiOI composites are promising photocatalytic antibacterial materials for water disinfection. [ABSTRACT FROM AUTHOR]

The synthesis of two anthraquinone phosphoramidites is described. In both cases the anthraquinone moiety is attached via a linker to the 5-position of a uracil base, allowing incorporation at any thymidine position in an oligonucleotide sequence. Anthraquinone-modified oligonucleotides have potential applications as triplex stabilizers and fluorescence quenchers. [ABSTRACT FROM AUTHOR]

Protein-RNA interactions are central to numerous cellular processes. In this work, we present an easy and straightforward NMR-based approach to determine the RNA binding site of RNA binding proteins and to evaluate the binding of pairs of proteins to a single-stranded RNA (ssRNA) under physiological conditions, in this case in nuclear extracts. By incorporation of a 19 F atom on the ribose of different nucleotides along the ssRNA sequence, we show that, upon addition of an RNA binding protein, the intensity of the 19 F NMR signal changes when the 19 F atom is located near the protein binding site. Furthermore, we show that the addition of pairs of proteins to a ssRNA containing two 19 F atoms at two different locations informs on their concurrent binding or competition. We demonstrate that such studies can be done in a nuclear extract that mimics the physiological environment in which these protein-ssRNA interactions occur. Finally, we demonstrate that a trifluoromethoxy group (-OCF 3 ) incorporated in the 2'ribose position of ssRNA sequences increases the sensitivity of the NMR signal, leading to decreased measurement times, and reduces the issue of RNA degradation in cellular extracts., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Kara, Axer, Muskett, Bueno-Alejo, Paschalis, Taladriz-Sender, Tubasum, Vega, Zhao, Clark, Hudson, Eperon, Burley and Dominguez.)

Cysteine-rich poly comb-like protein ( CPP ) is a member of cysteine-rich transcription factors that regulates plant growth and development. In the present work, we characterized twelve CPP transcription factors encoding genes in soybean ( Glycine max ). Phylogenetic analyses classified CPP genes into six clades. Sequence logos analyses between G. max and G. soja amino acid residues exhibited high conservation. The presence of growth and stress-related cis -acting elements in the upstream regions of GmCPPs highlight their role in plant development and tolerance against abiotic stress. Ka/Ks levels showed that GmCPPs experienced limited selection pressure with limited functional divergence arising from segmental or whole genome duplication events. By using the PAN-genome of soybean, a single nucleotide polymorphism was identified in GmCPP-6 . To perform high throughput genotyping, a kompetitive allele-specific PCR (KASP) marker was developed. Association analyses indicated that GmCPP-6-T allele of GmCPP-6 (in exon region) was associated with higher thousand seed weight under both water regimes (well-water and water-limited). Taken together, these results provide vital information to further decipher the biological functions of CPP genes in soybean molecular breeding., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Nisar, Tahir, Iqbal, Sajjad, Nadeem, Qanmber, Baig, Khan, Zhao, Geng and Ur Rehman.)

HyBeacon probes have been used to characterise SNPs in the CYP2C9 and VKORC1 genes associated with variations in the efficiency of warfarin metabolism. PCR amplification of genomic DNA and probe target melting analysis provided a robust and reliable method to differentiate polymorphic sequences at these loci. Probes capped with 5'-trimethoxystilbene were found to exhibit larger fluorescence differences between hybridised and dissociated states than uncapped probes, generating melting peaks of considerably improved height. 3'-Pyrene modifications enhanced probe signal-to-noise and melting peak heights with the additional benefit of acting as PCR stoppers, and 5',3'-doubly capped probes gave the best analytical results.