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Directional Terms01:14

Directional Terms

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Directional terms are essential for describing the relative locations of different body structures. For instance, an anatomist might describe one band of tissue as "inferior to" another, or a physician might describe a tumor as "superficial to" a deeper body structure. These terms often use comparative terms in pairs to trace out the relative locations of one body part to another or descriptions of body tissues like the deeper ones from superficially present with reference to...
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Ras-related nuclear protein or Ran is a small G protein that cycles between its GTP and GDP bound states. Ran specific regulators, a Ran GTPase Activating Protein or RanGAP present in the cytosol and a Ran guanine nucleotide exchange factor or RanGEF present inside the nucleus regulate GTP/GDP exchange. A high concentration of GTP inside the cells, in addition to this asymmetric distribution of  Ran-specific regulators, leads to a higher RanGTP concentration inside the nucleus. This...
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Ortho–para directors are substituent groups attached to the benzene ring and direct the addition of an electrophile to the positions ortho or para to the substituent. All electron-donating groups are considered ortho–para directors. They donate electrons to the ring and make the ring more electron-rich. The ring is therefore susceptible to the addition of electrophiles. Substituents such as amino, hydroxy, or alkoxy, containing lone pairs on the atom adjacent to the ring, donate...
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Cells can detect chemical cues in their environment and reorganize the cytoskeleton to migrate toward them or away from them. This directional migration, called chemotaxis, is essential during embryogenesis and development, immune response, tissue repair and regeneration, and reproduction. These chemical cues can either attract or repel the cell's movement. For example, axon development is determined by a combination of chemoattractants and chemorepellents that direct the growing axon...
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Substituents on the benzene ring that direct an incoming electrophile to undergo substitution at the meta position are called meta directors. All meta directors either have a positive charge on the atom directly bonded to the ring or a partial positive charge. These groups function by withdrawing electrons from the ring through inductive and resonance effects. Consider the carbocation intermediates formed upon the addition of an electrophile on nitrobenzene at the...
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Acceleration occurs when velocity changes in magnitude (an increase or decrease in speed), direction, or both. Although acceleration is in the direction of the change in velocity, it is not always in the direction of motion. When an object slows down, its acceleration is opposite to the direction of its motion. This is commonly referred to as deceleration. However, the term deceleration can cause confusion in analysis because it is not a vector; it does not point to a specific direction with...
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    This study enhances the Biomedical Relation Extraction Dataset (BioRED) by adding entity role directionality, crucial for understanding biological networks. A novel multi-task language model successfully identifies relationships and entity roles, outperforming existing models.

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    Area of Science:

    • Bioinformatics
    • Computational Biology
    • Natural Language Processing

    Background:

    • Biological relation networks are vital for understanding complex biological mechanisms.
    • The rapid expansion of biomedical literature presents challenges for updating these networks.
    • Existing datasets like BioRED aid automated relation extraction but lack entity role directionality.

    Purpose of the Study:

    • To enrich the BioRED corpus with essential entity role directionality annotations.
    • To develop a novel multi-task language model for joint identification of relationships, findings, and entity roles.
    • To improve the accuracy of biological relation extraction from biomedical literature.

    Main Methods:

    • Manual annotation of entity roles (subject/object) for relationships within the BioRED corpus.
    • Development of a novel multi-task language model incorporating soft-prompt learning.
    • Jointly training the model to identify relationships, novel findings, and entity roles.

    Main Results:

    • Creation of an enriched BioRED corpus with 10,864 directionality annotations.
    • The proposed multi-task model demonstrated superior performance compared to state-of-the-art models like GPT-4 and Llama-3.
    • Successful joint identification of relationships, novel findings, and entity roles.

    Conclusions:

    • The addition of directionality to BioRED significantly enhances its utility for biological network analysis.
    • The novel multi-task language model provides a powerful tool for accurate biological relation extraction.
    • This work advances automated knowledge discovery in the biomedical domain.