Article
Biochemistry & Molecular Biology
Andrei Slabodkin, Maria Chernigovskaya, Ivana Mikocziova, Rahmad Akbar, Lonneke Scheffer, Milena Pavlovic, Habib Bashour, Igor Snapkov, Brij Bhushan Mehta, Cedric R. Weber, Jose Gutierrez-Marcos, Ludvig M. Sollid, Ingrid Hobaek Haff, Geir Kjetil Sandve, Philippe A. Robert, Victor Greiff
Summary: A study found that VDJ recombination rules may differ between individuals, leading to variations in the probability of generating (auto)antigen-specific Ig sequences. In addition to genetic factors, VDJ recombination is also influenced by non-genetic modulation.
Article
Biochemistry & Molecular Biology
Taciana Manso, Geraldine Folch, Veronique Giudicelli, Joumana Jabado-Michaloud, Anjana Kushwaha, Viviane Nguefack Ngoune, Maria Georga, Ariadni Papadaki, Chahrazed Debbagh, Perrine Pegorier, Morgane Bertignac, Saida Hadi-Saljoqi, Imene Chentli, Karima Cherouali, Safa Aouinti, Amar El Hamwi, Alexandre Albani, Merouane Elazami Elhassani, Benjamin Viart, Agathe Goret, Anna Tran, Gaoussou Sanou, Mael Rollin, Patrice Duroux, Sofia Kossida
Summary: IMGT (R) is an international immunogenetics information system with over 30 years of experience, providing databases and tools for the scientific community in the field of adaptive immune response. Its research and development focus on understanding the adaptive immune response, analyzing and exploring IG and TR repertoires, and studying amino acid changes and functions of antibody and TR engineering.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Computer Science, Theory & Methods
Bilal Ben Mahria, Ilham Chaker, Azeddine Zahi
Summary: This paper introduces a new lifecycle for learning ontology from relational databases based on software engineering requirements, as well as a new method for building ontology from relational databases based on a predefined lifecycle. Additionally, three new semantics extracted from relational databases are added, along with an evaluation process based on TBox and ABox metrics.
JOURNAL OF BIG DATA
(2021)
Review
Cardiac & Cardiovascular Systems
Doris A. Taylor, Lourdes Chacon-Alberty, Luiz C. Sampaio, Mariana Gonzalez Del Hierro, Emerson C. Perin, Fernanda C. P. Mesquita, Timothy D. Henry, Jay H. Traverse, Carl J. Pepine, Joshua M. Hare, Michael P. Murphy, Phillip C. Yang, Keith L. March, Rachel W. Vojvodic, Ray F. Ebert, Roberto Bolli
Summary: Cell-based therapy lacks standardized definitions and terminology, making comparisons across studies challenging. This article discusses the lack of consistency in descriptive terminology used in cell-based therapies and provides guidelines for standardizing nomenclature and definitions.
CARDIOVASCULAR RESEARCH
(2022)
Article
Fisheries
Susana Magadan, Stanislas Mondot, Yniv Palti, Guangtu Gao, Marie Paule Lefranc, Pierre Boudinot
Summary: High-throughput sequencing technologies have renewed interest in immune repertoires, including those of fish Ab and B cell repertoires. Comprehensive analysis of IGH genes in Atlantic salmon and rainbow trout have provided important insights into immune mechanisms and vaccine protection markers. This work establishes a resource for accurate annotation of Ig mRNA deep sequencing data.
DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY
(2021)
Article
Green & Sustainable Science & Technology
Caterina Pietra, Roberto De Lotto, Rakan Bahshwan
Summary: The concept of the healthy city has gained increasing relevance in recent decades, becoming well understood in various fields and by the general public. The authors discuss the complexity of elements and relationships in the concept of healthy cities from an ontological perspective, emphasizing the interdisciplinary nature of the concept. By utilizing basic formal ontology (BFO), the authors aim to establish an organizational definition for healthy cities and explore different types of ontological structures. Possible applications of the study and future research directions are also discussed.
Review
Clinical Neurology
Karen Gruetz, Christine Klein
Summary: Dystonia is a term that encompasses a variety of heterogeneous movement disorders, with clinical presentations ranging from isolated dystonia to multi-systemic disorders. Current classification of dystonia is based on two axes - clinical presentation and etiologic factors. Recent recommendations focus on terminology and nomenclature of inherited forms of dystonia and related syndromes.
JOURNAL OF NEURAL TRANSMISSION
(2021)
Article
Multidisciplinary Sciences
Barak Mizrahi, Roni Lotan, Nir Kalkstein, Asaf Peretz, Galit Perez, Amir Ben-Tov, Gabriel Chodick, Sivan Gazit, Tal Patalon
Summary: The study indicates preliminary evidence of waning vaccine effectiveness of BNT162b2 among all age groups above 16, with a higher incidence of infection in those vaccinated earlier in 2021. Further investigation into long-term protection against different strains is warranted.
NATURE COMMUNICATIONS
(2021)
Article
Medical Informatics
Xubing Hao, Rashmie Abeysinghe, Kirk Roberts, Licong Cui
Summary: This study presents a logical definition-based approach to identify potential missing concepts in SNOMED CT. The logical definitions of unrelated concepts are intersected to obtain potential missing concepts, and a text summarization model is used to predict their fully specified names. Validation results show that 10.04% of the identified potential missing concepts are valid.
BMC MEDICAL INFORMATICS AND DECISION MAKING
(2023)
Article
Biochemical Research Methods
Parnal Joshi, Sagnik Banerjee, Xiao Hu, Pranav M. Khade, Iddo Friedberg
Summary: With the rise in genomic data from sequencing technologies, the functions of many gene products remain unknown. High-throughput experiments are being conducted to address this gap, but the resulting annotations are biased towards less informative Gene Ontology terms. GOThresher, a Python tool, is introduced to identify and remove biases in protein function annotation databases, which is crucial for accurate understanding of protein function and training unbiased machine learning methods.
Review
Immunology
Ailing Zhao, Jiazheng Sun, Yipin Liu
Summary: Bacterial biofilms are complex microbial communities surrounded by extracellular polymeric substances. They are a significant problem in treating bacterial infections and can exhibit increased resistance to antibiotics, causing device-related and non-device infections and posing a serious threat to global health. Therefore, early detection and search for new treatments are essential. This paper systematically reviews the formation, infections, detection methods, and potential treatment strategies of bacterial biofilms, aiming to provide researchers with the latest progress in their detection and treatment.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Computer Science, Information Systems
Batool Lakzaei, Mehrnoush Shamsfard
Summary: The article presents a new approach to automatically creating an OWL ontology from a relational database by defining a set of rules to analyze and extract ontology elements.
INFORMATION SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Yuhao Ma, Meng Wu, Shuhui Li, Marcello Tonelli, Larry D. Unsworth
Summary: Protein carbamylation has been associated with diseases commonly seen in patients with reduced kidney function. A specific peptide sequence with high selectivity towards carbamylated human serum albumin (cHSA) was identified, showing the ability to bind cHSA at different levels of carbamylation and exhibiting specificity towards carbamylated fibrinogen. The study also suggests that the peptide may bind to homocitrulline residues in a manner similar to antibodies.
Review
Chemistry, Multidisciplinary
Aleksandar Kondinski, Jiaru Bai, Sebastian Mosbach, Jethro Akroyd, Markus Kraft
Summary: Knowledge engineering is the process of converting human knowledge into machine-readable form, which is the foundation of artificial intelligence and knowledge engineering. In the field of chemistry, knowledge engineering began with the development of expert systems that simulate the thinking process of chemists. With the help of tools like semantic webs, knowledge graphs, and cognitive software agents, more complex systems can now be represented, and new knowledge can be synthesized.
ACCOUNTS OF CHEMICAL RESEARCH
(2023)
Article
Medicine, Research & Experimental
Riti Biswas, Ed Belouski, Kevin Graham, Michelle Hortter, Marissa Mock, Christine E. Tinberg, Alan J. Russell
Summary: We are transitioning into an era where therapeutic proteins are constructed using building block-like strategies, but there is no standardized protocol for discussing these formats. Existing nomenclatures sacrifice readability for precision, causing confusion and complexity in drug discovery. To overcome this challenge, VERITAS is introduced as a flexible classification and naming scheme for antibodies, adaptable to various therapeutic formats. VERITAS names are user-friendly and directly reflect the structure of a format, making them valuable in scientific discourse and drug development algorithms.