Article
Computer Science, Information Systems
Leo Besancon, Catarina Ferreira Da Silva, Parisa Ghodous, Jean-Patrick Gelas
Summary: Decentralized Applications (DApps) provide distributed trusted applications that utilize blockchain technology. This article proposes a blockchain ontology focused on DApps to formalize their development and improve interoperability. By using Semantic Web Rule Language and an inference engine, constraints and properties of a defined DApp can be inferred, as demonstrated with Ethereum and Polygon.
Article
Business
Linda Elmhadhbi, Mohamed-Hedi Karray, Bernard Archimede, J. Neil Otte, Barry Smith
Summary: Disaster response is a collaborative and critical process that involves multiple emergency responders. However, inadequate communication and interoperability issues can hinder the effectiveness of disaster response efforts. This article presents a scenario-based terrorism case study and proposes a semantics-based common operational command system to enhance information flow among emergency responders.
IEEE TRANSACTIONS ON ENGINEERING MANAGEMENT
(2022)
Article
Multidisciplinary Sciences
Vinicius Costa Lima, Rui Pedro Charters Lopes Rijo, Filipe Andrade Bernardi, Marcio Eloi Colombo Filho, Francisco Barbosa-Junior, Felipe Carvalho Pellison, Rafael Mello Galliez, Afranio Lineu Kritski, Domingos Alves
Summary: Clinical research outcomes rely on the accurate definition of research protocols, data collection strategies, and data management plans. Electronic Data Capture Systems mitigate resource challenges and provide a reliable environment for health research, promoting result dissemination and data reusability.
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Fernando Zhapa-Camacho, Maxat Kulmanov, Robert Hoehndorf
Summary: Motivation: This research developed a Python library called mOWL for machine learning with ontologies formalized in the Web Ontology Language (OWL). MOWL implements ontology embedding methods to map information in formal knowledge bases and ontologies into vector spaces, preserving properties and relations in ontologies. It also provides methods for similarity computation, deductive inference, and zero-shot learning. The library was demonstrated on knowledge-based predictions of protein-protein interactions using the gene ontology and gene-disease associations using phenotype ontologies.
Review
Computer Science, Information Systems
Allan Mazimwe, Imed Hammouda, Anthony Gidudu
Summary: The level of knowledge sharing and reuse in the field of disaster management does not align well with FAIR recommendations, leading to challenges. Research reveals potential opportunities for evaluating the maturity of sharing, discovery, and integration of disaster management ontologies using FAIR indicators.
ISPRS INTERNATIONAL JOURNAL OF GEO-INFORMATION
(2021)
Article
Materials Science, Ceramics
Mahdis Noori, Masoud Atapour, Fakhreddin Ashrafizadeh, Hassan Elmkhah, Giovanna Gautier di Confiengo, Sara Ferraris, Sergio Perero, Marilena Cardu, Silvia Spriano
Summary: Titanium alloys have poor resistance to friction, which negatively affects their corrosion behavior and osseointegration. Nanostructured PVD coatings with biocompatibility, anti-wear, and anti-corrosion characteristics are highly sought after in biomedical applications. In this study, TiN, ZrN, CrN/TiN, and CrN/ZrN thin films were coated on a Ti6Al4V substrate, and their physical-chemical properties, surface topography, wettability, hardness, adhesion strength, apatite-forming ability, and corrosion performance were investigated. The findings show that the multilayer coatings have higher hardness and scratch resistance. The CrN/ZrN multilayer coating exhibits the best corrosion resistance and hydroxyapatite precipitation, making it a potential candidate for orthopedic and dental implants.
CERAMICS INTERNATIONAL
(2023)
Article
Automation & Control Systems
Yameng An, Feiwei Qin, Baiping Chen, Rene Simon, Huifeng Wu
Summary: This article presents an approach using the OntoPLC semantic model to enable automatic porting of PLC projects between development environments and prevent information loss during the translation process. The method improves programming efficiency, encourages code exchange, and promotes software reuse.
IEEE TRANSACTIONS ON INDUSTRIAL INFORMATICS
(2021)
Article
Computer Science, Information Systems
Alfonso Castro, Victor A. Villagra, Paula Garcia, Diego Rivera, David Toledo
Summary: In today's world, data is considered a principal asset for companies and official bodies to make strategic decisions, with advances in big data technology leading to increased complexity in data management. Data governance is crucial in simplifying this complexity, with an approach based on ontological reasoning proposed in this paper showing feasibility in reducing the complexity of managing big data environments through testing.
Review
Chemistry, Applied
Biao Hu, Yuchun Guo, Houbin Li, Xinghai Liu, Yuanyu Fu, Fuyuan Ding
Summary: In recent years, chitosan-based biomaterials produced by layer-by-layer assembly have been extensively researched and applied in various fields such as antimicrobial applications, drug delivery, wound dressings, and tissue engineering. The driving forces of layer-by-layer assembly, including electrostatic interactions, hydrogen bonds, and Schiff base linkages, have been discussed in detail. Various forms of chitosan-based layer-by-layer materials, such as films/coatings, capsules, and fibers, have been reviewed in terms of their applications and advancements.
CARBOHYDRATE POLYMERS
(2021)
Article
Mathematical & Computational Biology
Nicolas Matentzoglu, Damien Goutte-Gattat, Shawn Zheng Kai Tan, James P. Balhoff, Seth Carbon, Anita R. Caron, William D. Duncan, Joe E. Flack, Melissa Haendel, Nomi L. Harris, William R. Hogan, Charles Tapley Hoyt, Rebecca C. Jackson, HyeongSik Kim, Huseyin Kir, Martin Larralde, Julie A. McMurry, James A. Overton, Bjoern Peters, Clare Pilgrim, Ray Stefancsik, Sofia M. C. Robb, Sabrina Toro, Nicole A. Vasilevsky, Ramona Walls, Christopher J. Mungall, David Osumi-Sutherland
Summary: This article discusses the complex workflows involved in managing the ontology life cycle and the diverse set of tools required for this process. Standardizing release practices and quality standards are crucial in the biomedical domain to enable interoperability. The article also provides an overview of the Ontology Development Kit (ODK) and its practical applications.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2022)
Article
Computer Science, Information Systems
Ricardo Gacitua, Hernan Astudillo, Bernhard Hitpass, Mariutsi Osorio-Sanabria, Carla Taramasco
Summary: Many governments around the world are engaging in digital transformation initiatives to improve efficiency, effectiveness, cost, and transparency. Research has found that current approaches to modeling collaborative e-government processes primarily use frameworks and general models, with a shift in focus from technology and organization towards citizens, and from open participation towards data transparency in collaborative studies.
Article
Computer Science, Artificial Intelligence
Samira Babalou, Alsayed Algergawy, Birgitta Koenig-Ries
Summary: Computing the semantic similarity between pairs of terms is crucial for various shared data applications. One way to determine term similarity is to assess their word similarity using knowledge resources like ontologies or corpora. Information-theoretic approaches have shown promise by computing concept information content from ontologies. Choosing a suitable subsumer, called Consensus Common Subsumer (CCS), among common ancestors of two concepts can impact the quality of term similarity assessment.
DATA & KNOWLEDGE ENGINEERING
(2023)
Article
Computer Science, Information Systems
Diana Sousa, Francisco M. Couto
Summary: Biomedical Relation Extraction systems enhance our understanding of biological and medical processes by identifying and classifying relations between entities. Integrating Knowledge Graph-based recommendation models expands the system's capabilities and improves the identification of true relations.
IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS
(2022)
Article
Chemistry, Applied
Xiao Ma, Guomin Wu, Fangfang Dai, Dan Li, Hao Li, Li Zhang, Hongbing Deng
Summary: In this study, chitosan (CS) and polydopamine (PDA) were introduced into electrospun nanofibrous SF mats through layer-by-layer self-assembly (LBL) to enhance antibacterial ability and cytocompatibility. With the successful deposition confirmed, the mats showed increased tensile modulus and better hydrophilicity performance. Moreover, the structured mats exhibited significantly improved antibacterial ability and biocompatibility, showcasing the potential for expanded biomedical applications of SF.
CARBOHYDRATE POLYMERS
(2021)
Article
Computer Science, Information Systems
Xiaofei Zhao, Fanzhang Li, Hongji Yang
Summary: This study proposes an approach for extracting modules from OWL RL ontologies to improve the efficiency of concept satisfiability checking, by simplifying ontologies through deleting irrelevant elements. Experimental results show that the method can effectively reduce reasoning time, with efficiency increased by 1.15 to 9.08 times.
Review
Oncology
Hulya Yilmaz Temel, Oznur Kaymak, Seren Kaplan, Basak Bahcivanci, Georgios V. Gkoutos, Animesh Acharjee
Summary: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive and deadly disease, with the gut microbiome and its metabolic regulation playing a critical role. The complex process of gut metabolic regulation involves the microbiome and microbiome-derived short-chain fatty acids (SCFAs). SCFAs regulate inflammation, lipid, and glucose metabolism through different pathways. This review summarizes recent advancements in understanding the associations between PDAC and gut and oral microbiota, as well as their interactions with SCFAs. Additionally, potential therapeutic applications of microbiota in PDAC are discussed.
Article
Biochemical Research Methods
Fernando Zhapa-Camacho, Maxat Kulmanov, Robert Hoehndorf
Summary: Motivation: This research developed a Python library called mOWL for machine learning with ontologies formalized in the Web Ontology Language (OWL). MOWL implements ontology embedding methods to map information in formal knowledge bases and ontologies into vector spaces, preserving properties and relations in ontologies. It also provides methods for similarity computation, deductive inference, and zero-shot learning. The library was demonstrated on knowledge-based predictions of protein-protein interactions using the gene ontology and gene-disease associations using phenotype ontologies.
Article
Biology
Luke T. Slater, John A. Williams, Paul N. Schofield, Sophie Russell, Samantha C. Pendleton, Andreas Karwath, Hilary Fanning, Simon Ball, Robert Hoehndorf, Georgios V. Gkoutos
Summary: Annotation of biomedical entities with ontology classes facilitates semantic analysis and utilization of background knowledge. We have developed a new tool called Klarigi, which introduces multiple scoring heuristics to identify compositional and discriminatory classes for annotated entity groups. Klarigi utilizes semantic inference, classification, and significance testing to provide characteristic and explanatory explanations for biomedical datasets, offering a distinct perspective compared to traditional enrichment methods.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Review
Cardiac & Cardiovascular Systems
Simrat K. Gill, Andreas Karwath, Hae-Won Uh, Victor Roth Cardoso, Zhujie Gu, Andrey Barsky, Luke Slater, Animesh Acharjee, Jinming Duan, Lorenzo Dall'Olio, Said El Bouhaddani, Saisakul Chernbumroong, Mary Stanbury, Sandra Haynes, Folkert W. Asselbergs, Diederick E. Grobbee, Marinus J. C. Eijkemans, Georgios Gkoutos, Dipak Kotecha
Summary: Artificial intelligence (AI) is increasingly being used in healthcare, particularly in cardiovascular disease management. This article outlines a step-by-step approach to implementing high-value AI in healthcare, starting with data selection and pre-processing, followed by algorithmic and data validation, and performance evaluation. It emphasizes the need for further education and addressing issues related to data access and security. The application of AI in healthcare offers the opportunity for personalized medical care by considering confounders and interactions.
EUROPEAN HEART JOURNAL
(2023)
Article
Biology
Bruno F. E. Matarese, Hassan Rahmoune, Nguyen T. K. Vo, Colin B. Seymour, Paul N. Schofield, Carmel Mothersill
Summary: This study characterizes the emission of acoustic waves from cultured cells exposed to X-ray photon radiation. Acoustic signals were recorded using an ultrasound transducer before, during, and after irradiation. The results show that radiation dose rate and cell viability affect the acoustic signal characteristics. Live and dead cells exhibit different acoustic signal patterns.
INTERNATIONAL JOURNAL OF RADIATION BIOLOGY
(2023)
Review
Surgery
Bilal Gani Taib, A. Karwath, K. Wensley, L. Minku, G. Gkoutos, N. Moiemen
Summary: Artificial Intelligence (AI) has shown successful application in burns care and can assist in interpreting various aspects of burns care. This systematic review and diagnostic test accuracy meta-analyses aim to evaluate and summarize the current research direction in this field. The results focus on burn depth, burn segmentation, and burn-related mortality, with neural networks being the most common machine learning algorithm utilized.
JOURNAL OF PLASTIC RECONSTRUCTIVE AND AESTHETIC SURGERY
(2023)
Article
Cardiac & Cardiovascular Systems
Jannis Dickow, Shinwan Kany, Victor Roth Cardoso, Patrick T. Ellinor, Georgios V. Gkoutos, Holly K. Van Houten, Paulus Kirchhof, Andreas Metzner, Peter A. Noseworthy, Xiaoxi Yao, Andreas Rillig
Summary: A recent study suggests that early rhythm control is more beneficial for patients with atrial fibrillation and a high comorbidity burden. This study analyzed a large database and found that early rhythm control can reduce the risk of death, stroke, heart failure, or myocardial infarction in patients with a high comorbidity burden.
CIRCULATION-ARRHYTHMIA AND ELECTROPHYSIOLOGY
(2023)
Review
Oncology
Janine Dretzke, Ava Lorenc, Ada Adriano, Clare Herd, Hisham Mehanna, Paul Nankivell, David J. Moore
Summary: The current follow-up models in cancer are seen as unsustainable and inflexible. Patient-initiated follow-up (PIFU) is gaining interest as an alternative model, and it is important to determine its acceptability to patients and healthcare professionals (HCPs). The findings show that most women treated for breast or endometrial cancer and HCPs support PIFU, but further research is needed.
Article
Chemistry, Multidisciplinary
Sherin Abdelrahman, Rui Ge, Hepi H. Susapto, Yang Liu, Faris Samkari, Manola Moretti, Xinzhi Liu, Robert Hoehndorf, Abdul-Hamid Emwas, Mariusz Jaremko, Ranim H. H. Rawas, Charlotte A. E. Hauser
Summary: Cells' interactions with their microenvironment influence their morphological features and regulate crucial cellular functions. Most biological data available are based on inadequate in vitro two-dimensional cellular models. In this study, ultrashort self-assembling peptide sequences were used to create efficient three-dimensional in vitro models of human dermal fibroblast cells. The results showed distinct metabolic and transcriptomic profiles of 2D and 3D cultured cells, indicating the importance of utilizing 3D models to study complex mechanisms.
Article
Biochemical Research Methods
Senay Kafkas, Marwa Abdelhakim, Mahmut Uludag, Azza Althagafi, Malak Alghamdi, Robert Hoehndorf
Summary: TARVar is an automated tool that ranks variants based on patient symptoms and clinical signs using evidence from literature and genomes. It improves upon existing tools by allowing flexible expression of patient symptoms in free-text format.
BMC BIOINFORMATICS
(2023)
Review
Biochemistry & Molecular Biology
Olalekan Lee Aiyegbusi, Christel McMullan, Sarah Hughes, Grace Turner, Anuradhaa Subramanian, Richard Hotham, Elin Haf Davies, Chris K. Frost, Yvonne J. Alder, Lisa Agyen, Lewis Buckland, Jennifer Camaradou, Amy V. Chong, Felicity J. Jeyes, Sumita M. Kumar, Karen Matthews, Patricia Moore, Jane Ormerod, Gary Price, Michael Saint-Cricq, David Stanton, Anita Walker, Shamil Haroon, Alastair C. Denniston, Melanie Calvert, TLC Study Grp, Kirsty Brown, Joht Singh Chandan, Georgios V. Gkoutos, Louise J. Jackson, Janet M. Lord, Tom Marshall, Steven Marwaha, Puja Myles, Krishnarajah Nirantharakumar, Samantha Cruz Rivera, Elizabeth Sapey, Nikita Simms-Williams, Tim Williams, David C. Wraith
Summary: The authors present a checklist for patient and public involvement and engagement in future research based on the lessons learned from the TLC study. Patient and public involvement can offer valuable insights into the experiences of those affected by a disease. Inclusive collaboration between patients, the public, and researchers can lead to productive relationships and address patient needs in health research.
Correction
Multidisciplinary Sciences
Dominic Russ, John A. Williams, Victor Roth Cardoso, Laura Bravo-Merodio, Samantha C. Pendleton, Furqan Aziz, Animesh Acharjee, Georgios V. Gkoutos
Article
Multidisciplinary Sciences
Furqan Aziz, Luke T. Slater, Laura Bravo-Merodio, Animesh Acharjee, Georgios V. Gkoutos
Summary: Link prediction in complex networks is of great significance in identifying missing links and studying network evolution. This paper proposes a method that combines parametrised matrix forest index with local similarity index to predict missing links with higher accuracy.
SCIENTIFIC REPORTS
(2023)