Article
Construction & Building Technology
Kris McGlinn, Rob Brennan, Christophe Debruyne, Alan Meehan, Lorraine McNerney, Eamonn Clinton, Philip Kelly, Declan O'Sullivan
Summary: BIM is crucial for integrating building data within the building life cycle, supporting various use cases related to automation, energy efficiency, and sustainability. Open building data faces challenges in standardization, data interdependency, access, security, and intellectual property protection. In Ireland, OSi maintains a large dataset called Prime2, including building GIS data and building specific data, supporting the development of a national geospatial identifier infrastructure based on an OSi building ontology.
AUTOMATION IN CONSTRUCTION
(2021)
Article
Green & Sustainable Science & Technology
Marco Medici, Damion Dooley, Maurizio Canavari
Summary: Current global regulations concerning pesticide use lack stringency, leading to opaque information and insufficient disclosure of hazards. The creation of the PestOn ontology aims to enhance accessibility of pesticide product information and improve information flow in the food value chain.
Article
Microbiology
Sunmyoung Lee, Tamiko Ono, Kiyoko Aoki-Kinoshita
Summary: Researchers utilize Semantic Web techniques to standardize data exchange formats for better integration and sharing of glycomics data. By describing the E.coli O-antigen biosynthesis pathway and applying it to the BioPAX ontology, researchers provide a method for biologists to more easily understand and share glycan information.
Article
Multidisciplinary Sciences
Heidi Kleven, Thomas H. Gillespie, Lyuba Zehl, Timo Dickscheid, Jan G. Bjaalie, Maryann E. Martone, Trygve B. Leergaard
Summary: Brain atlases are crucial for accurate anatomical description of neuroscience data, but the lack of standardized description hinders their use in analytic tools and data registration. To address this issue, we developed an Atlas Ontology Model (AtOM) that provides a standardized framework for communication and use of brain atlases. By applying AtOM to different species' brain atlases, we demonstrate its potential in facilitating data integration and complying with FAIR guiding principles.
Article
Computer Science, Artificial Intelligence
Maryam Daneshfar, Timo Hartmann, Jochen Rabe
Summary: This study aims to establish a common framework for the surrounding data required in building renovation. It has practical implications for engineers by providing a shared knowledge framework, and for software developers by providing a foundation for integrating BIM and GIS data for renovation purposes.
ADVANCED ENGINEERING INFORMATICS
(2022)
Article
Computer Science, Interdisciplinary Applications
R. Thirumahal, G. SudhaSadasivam
Summary: Heterogeneous database integration is the process of merging data from multiple databases. The challenges of semantic, syntactic, and structural heterogeneity make solving the heterogeneity problem difficult. This research study proposes a Semantic Integration of Heterogeneous Healthcare Data based on Hybrid Root Linked Health Record (LHR) Ontology to overcome these challenges. The approach uses semantic web technologies to connect healthcare data from multiple devices and introduces a hybrid root LHR ontology to model the health data from various databases. SPARQL queries are used for database searching, enabling the discovery of semantically comparable records.
EARTH SCIENCE INFORMATICS
(2023)
Article
Clinical Neurology
Yana A. Wilson, Hayley Smithers-Sheedy, Katarina Ostojic, Emma Waight, Michael C. Kruer, Michael C. Fahey, Gareth Baynam, Jozef Gecz, Nadia Badawi, Sarah McIntyre
Summary: This study defines clinical common data elements (CDEs) and a mandatory minimum data set (MDS) for genomic studies of cerebral palsy (CP) through an online Delphi survey, providing a standardized foundation for phenotype data in CP genomic studies and facilitating international collaborations and data pooling.
DEVELOPMENTAL MEDICINE AND CHILD NEUROLOGY
(2022)
Article
Computer Science, Artificial Intelligence
Eyosias Dawit Guyo, Timo Hartmann, Sean Snyders
Summary: Firefighters need accurate and timely information about a building and its environment to perform their duty safely and successfully during a fire emergency. This paper proposes an ontology-based solution that defines the required building and environmental data. The proposed ontology has been validated and published online.
ADVANCED ENGINEERING INFORMATICS
(2023)
Article
Multidisciplinary Sciences
Alishah Mawji, Edmond Li, Arjun Chandna, Teresa Kortz, Samuel Akech, Matthew O. Wiens, Niranjan Kissoon, Mark Ansermino
Summary: Standardized collection of pediatric sepsis predictors can improve data compatibility across research studies. A set of common data elements was developed, including standardized prompts, response values, and prioritization, to facilitate efficient data collection methods. The routine use of these common data elements in future studies can enhance data sharing and support the development of risk prediction algorithms.
Article
Computer Science, Artificial Intelligence
David Payares-Garcia, Jorge Mateu, Wiebke Schick
Summary: This paper introduces NeuroNorm, a robust and reproducible preprocessing pipeline for structural MRI data that automatically adapts to input datasets and produces high-quality results.
Article
Gastroenterology & Hepatology
Christopher Ma, Rocio Sedano, Ahmed Almradi, Niels Vande Casteele, Claire E. Parker, Leonardo Guizzetti, David F. Schaeffer, Robert H. Riddell, Reetesh K. Pai, Robert Battat, Bruce E. Sands, Christophe Rosty, Marla C. Dubinsky, Florian Rieder, Noam Harpaz, Maria T. Abreu, Robert Bryant, Gregory Y. Lauwers, Richard Kirsch, Mark A. Valasek, Eileen Crowley, William J. Sandborn, Brian G. Feagan, Rish K. Pai, Vipul Jairath
Summary: The study aimed to standardize histologic measurements in UC clinical trials, including appropriate biopsy strategies, evaluative indices, and thresholds for disease activity. Multiple biopsy strategies are acceptable, such as segmental biopsies based on endoscopic appearance. Baseline histologic activity should be required for enrollment, with recognition of operational implications.
Article
Multidisciplinary Sciences
Maulik R. Kamdar, Mark A. Musen
Summary: Despite the efforts to create Life Sciences Linked Open Data (LSLOD) cloud, there are still semantic heterogeneity issues across biomedical linked open data sources. Some sources are standalone, lack inter-linkage, and use unpublished schemas with minimal reuse or mappings. The LSLOD schema graph analysis in this research provides assistance to researchers querying and integrating data from multiple biomedical sources simultaneously on the Web.
Article
Biochemistry & Molecular Biology
Tim Beck, Thomas Rowlands, Tom Shorter, Anthony J. Brookes
Summary: The GWAS Central resource is a valuable tool for researchers, offering comprehensive GWAS data and user-friendly website tools. It has recently integrated mouse disease model data to support the study of human genetic variation. The updated interfaces and browser provide enhanced functionality for data analysis and visualization.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Clinical Neurology
Jordi Pegueroles, Victor Montal, Alexandre Bejanin, Eduard Vilaplana, Mateus Aranha, Miguel Angel Santos-Santos, Daniel Alcolea, Ignasi Carrio, Valle Camacho, Rafael Blesa, Alberto Lleo, Juan Fortea
Summary: The AMYQ index is a new MRI-independent measure for standardizing and quantifying amyloid burden, with high agreement with the Centiloid scale and excellent diagnostic performance for discriminating patients with Alzheimer's disease from controls.
ALZHEIMERS & DEMENTIA
(2021)
Article
Multidisciplinary Sciences
April E. Hebert, Usha S. Kreaden, Ana Yankovsky, Dongjing Guo, Yang Li, Shih-Hao Lee, Yuki Liu, Angela B. Soito, Samira Massachi, April E. Slee
Summary: Survival analysis after oncological treatments requires specific analysis techniques. This paper proposes a hierarchical utilization method to extract or estimate hazard ratios and standardize time-to-event outcomes, maximizing the inclusion of studies in meta-analyses.
Article
Biochemistry & Molecular Biology
Asmaa Abdullah, Yoshitaka Hayashi, Naoko Morimura, Akhilesh Kumar, Kazuhiro Ikenaka, Akira Togayachi, Hisashi Narimatsu, Seiji Hitoshi
Summary: In this study, the expression of Fut9 and Lewis X in the brain and retina was investigated. Fut9 was found to be expressed in cortical neurons and corticothalamic projection neurons. The loss of Fut9 resulted in a reduction in the number of neurons in the cortex and retina, indicating the significant roles of Fut9 in the differentiation, migration, and maturation of neural precursor cells.
NEUROCHEMICAL RESEARCH
(2022)
Article
Urology & Nephrology
Masayuki Tasaki, Hiroaki Tateno, Takashi Sato, Hisashi Narimatsu, Kazuhide Saito, Yuki Nakagawa, Toshinari Aoki, Masami Kamimura, Takashi Ushiki, Kota Takahashi, Yoshihiko Tomita
Summary: The study investigated the reactivity of anti-ABO antibodies detected after ABO-incompatible kidney transplantation with stable graft function to the renal graft endothelial cells, and found that the antibody reactivity was low.
CLINICAL AND EXPERIMENTAL NEPHROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Eric W. Deutsch, Nuno Bandeira, Yasset Perez-Riverol, Vagisha Sharma, Jeremy J. Carver, Luis Mendoza, Deepti J. Kundu, Shengbo Wang, Chakradhar Bandla, Selvakumar Kamatchinathan, Suresh Hewapathirana, Benjamin S. Pullman, Julie Wertz, Zhi Sun, Shin Kawano, Shujiro Okuda, Yu Watanabe, Brendan MacLean, Michael J. MacCoss, Yunping Zhu, Yasushi Ishihama, Juan Antonio Vizcaino
Summary: This article describes the recent developments in the ProteomeXchange (PX) consortium, which aims to standardize data submission and dissemination of MS proteomics data. The article highlights the increase in the number of datasets submitted to PX resources and the growing data re-use activities.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Xia Zou, Jishun Lu, Yao Deng, Qiannan Liu, Xialin Yan, Yalu Cui, Xiao Xiao, Meng Fang, Fang Yang, Hiromichi Sawaki, Takashi Sato, Binbin Tan, Xiaoyan Lu, Bo Feng, Atsushi Kuno, Hisashi Narimatsu, Chunfang Gao, Yan Zhang
Summary: This study revealed that ST6GAL1 and alpha 2,6 sialylation are negatively correlated with HCC cell metastasis. ST6GAL1 overexpression inhibits HCC cell migration and invasion in vitro and suppresses HCC metastasis in vivo, possibly through regulating MCAM expression.
Review
Biochemistry & Molecular Biology
Nobuaki Miura, Shujiro Okuda
Summary: Metaproteomics is a promising field with the potential to contribute to disease research by understanding the communication between the human host and the microbiome. However, its analytical strategies are limited by the constraints of proteomics. This review demonstrates the usefulness of metaproteomics in disease research and discusses the challenges and potential solutions for applying it to conventional proteomics analysis methods.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Microbiology
Hideto Shirasawa, Chisato Nishiyama, Rika Hirano, Takashi Koyanagi, Shujiro Okuda, Hiroki Takagi, Shin Kurihara
Summary: A recent study has shown that bacteria found in fermented foods can produce high concentrations of polyamines, which are beneficial for human nutrition.
BIOSCIENCE OF MICROBIOTA FOOD AND HEALTH
(2023)
Article
Gastroenterology & Hepatology
Kazuki Natsui, Atsunori Tsuchiya, Risa Imamiya, Mayuko Osada-Oka, Yui Ishii, Yohei Koseki, Nobutaka Takeda, Kei Tomiyoshi, Fusako Yamazaki, Yuki Yoshida, Riuko Ohashi, Yiwei Ling, Koji Ueda, Nobuko Moritoki, Kazuhiro Sato, Takahiro Nakajima, Yoshinori Hasegawa, Shujiro Okuda, Shinsuke Shibata, Shuji Terai
Summary: This study investigated the role of outer-membrane vesicles (OMVs) in the pathogenesis of cirrhosis. OMVs derived from Escherichia coli induced inflammation, fibrosis, and suppression of albumin production, exacerbating liver inflammation and fibrosis. These findings have important implications for the prevention and treatment of cirrhosis.
LIVER INTERNATIONAL
(2023)
Article
Oncology
Masayuki Nagahashi, YiWei Ling, Chie Toshikawa, Tetsu Hayashida, Yuko Kitagawa, Manabu Futamura, Takashi Kuwayama, Seigo Nakamura, Hideko Yamauchi, Teruo Yamauchi, Koji Kaneko, Chizuko Kanbayashi, Nobuaki Sato, Junko Tsuchida, Kazuki Moro, Masato Nakajima, Yoshifumi Shimada, Hiroshi Ichikawa, Stephen Lyle, Yasuo Miyoshi, Kazuaki Takabe, Shujiro Okuda, Toshifumi Wakai
Summary: This study aimed to clarify the clinical significance of genomic profiling data, including copy number alterations (CNA) and tumor mutation burden (TMB), in TNBC patients. The results showed that CNA, but not TMB, was significantly associated with DFS and OS in TNBC patients. Additionally, the combination of CNA-high and TP53 alterations was identified as a promising biomarker for identifying a subgroup of TNBC patients with significantly worse prognosis.
Article
Multidisciplinary Sciences
Koichi Arakawa, Tamiko Ono, Kiyoko F. Aoki-Kinoshita, Yasunori Yamamoto
Summary: The study constructed a foundation for discovering glycan and virus interaction data using Semantic Web technologies. An ontology was created to encapsulate the semantics of virus-glycan interactions, and RDF was used to represent the data obtained from non-RDF related databases and literature. The data has been made publicly available as open data and a service for free searches using SPARQL is provided.
Article
Emergency Medicine
Kentaro Omatsu, Mieko Uchiyama, Utako Shimizu, Yiwei Ling, Shujiro Okuda, Yu Koyama
Summary: Based on a nationwide study of out-of-hospital cardiac arrest patients, it was found that EMS response interval was longer during heavy snowfall periods, and the survival rate in winter was lower, both in heavy snowfall areas and other areas. However, heavy snowfall had little effect on neurologically-favorable outcomes at one month.
PREHOSPITAL AND DISASTER MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Amanda L. Lewis, Philip Toukach, Evan Bolton, Xi Chen, Martin Frank, Thomas Luetteke, Yuriy Knirel, Ian Schoenhofen, Ajit Varki, Evgeny Vinogradov, Robert J. Woods, Natasha Zachara, Jian Zhang, Johannis P. Kamerling, Sriram Neelamegham
Summary: Nonulosonic acids, also known as NulOs, are a group of 2-ketoaldonic acids with a 9-carbon backbone. They occur in two forms in nature, namely the 3-deoxy sialic acids in deuterostomes like vertebrates and their pathogens, and the 3,9-dideoxy sialic-acid-like molecules found in bacteria and archaea. NulOs play significant roles in evolution, biology, and disease, and their diversity is reflected in over 90 sialic acid forms and 50 sialic-acid-like variants.
Article
Biochemistry & Molecular Biology
Tiejun Cheng, Tamiko Ono, Masaaki Shiota, Issaku Yamada, Kiyoko F. Aoki-Kinoshita, Evan E. Bolton
Summary: The GlyCosmos Glycoscience Portal and PubChem are two major portals for glycoscience and chemistry, respectively. They have made efforts to integrate their complementary data, allowing users to easily access and utilize glycan-related information. This integration provides improved awareness and enhanced access to glycan-related information for life science researchers.
Article
Biochemistry & Molecular Biology
Philip Toukach
Summary: In this study, the Carbohydrate Structure Database is linked to the Immune Epitope Database, allowing users to explore glycan structures and associated epitopes. By starting with an epitope, users can find glycans from other organisms that share the same structural determinant and retrieve additional taxonomical, medical, and other data. This database mapping demonstrates the advantages of integrating immunological and glycomic databases.
