Article
Multidisciplinary Sciences
Morad M. Mokhtar, Achraf El Allali, Mohamed-Elamir F. Hegazy, Mohamed A. M. Atia
Summary: PlantPathMarks database is a comprehensive, user-friendly pathway-based gene marker database that provides interactive visualization tools for pathway markers in plant genomes.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
David S. Wishart, Ray Kruger, Aadhavya Sivakumaran, Karxena Harford, Selena Sanford, Rahil Doshi, Nitya Kehrtarpal, Omolola Fatokun, Daphnee Doucet, Ashley Zubkowski, Hayley Jackson, Gina Sykes, Miguel Ramirez-Gaona, Ana Marcu, Carin Li, Kristen Yee, Christiana Garros, Dorsa Yahya Rayat, Jeanne Coleongco, Tharuni Nandyala, Vasuk Gautam, Eponine Oler
Summary: PathBank is a database that provides comprehensive metabolite pathway information. With the latest update of PathBank 2.0, there have been significant improvements in the number, quality, and functionality of pathways, making it more useful for interpreting metabolomics data.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Agriculture, Dairy & Animal Science
Jiaojiao Xu, Jiadi Liang, Wenjun Chen, Xin Wen, Na Zhang, Baohua Ma, Yongde Zou, Jiandui Mi, Yan Wang, Xindi Liao, Yinbao Wu
Summary: In this study, the effect of therapeutic doxycycline on the pig intestinal bacterial community was examined. It was found that doxycycline did not affect the diversity of the microbial community structure, but it did affect bacterial interactions and metabolic pathways. This study provides insight into the impact of doxycycline on the pig intestinal microbiota in pig breeding.
Article
Multidisciplinary Sciences
Petri Vanni, Mysore Tejesvi, Sofia Ainonen, Marjo Renko, Katja Korpela, Jarmo Salo, Niko Paalanne, Terhi Tapiainen
Summary: The study found that both Caesarean section and perinatal antibiotics significantly influence the predicted metabolic profiles of the gut microbiome in children at the age of 1 year. The functional profiles of the gut microbiome differed according to delivery mode and antibiotic exposure, with specific pathways showing distinct variations.
SCIENTIFIC REPORTS
(2021)
Article
Horticulture
Ru Li, Min Tian, Shanshan Nie, Lugang Zhang
Summary: Heterosis, an important genetic improvement technique, is widely used to enhance the productive traits of hybrid progeny. In this study, heterosis performance and alternative splicing (AS) events were analyzed in 16 hybrids and their parents. Significant heterosis was observed in these hybrids, with a wide range of mid-parent heterosis values (MPV). There were various AS events in each combination, with intron retention being the most common type. Differential AS genes (DASGs) were identified between the parents and the hybrids, and were significantly enriched in metabolic pathways. DASGs in amino acid metabolism were found to be associated with strong heterosis combinations and plant gross weight (PGW).
Article
Multidisciplinary Sciences
Eduard Ocana-Pallares, Tom A. Williams, David Lopez-Escardo, Alicia S. Arroyo, Jananan S. Pathmanathan, Eric Bapteste, Denis Tikhonenkov, Patrick J. Keeling, Gergely J. Szollosi, Inaki Ruiz-Trillo
Summary: Animals and fungi have distinct morphologies and genetic changes. Animals gained important genes from pre-metazoan ancestors, while fungi experienced net losses in functional categories. Fungal genomes have more metabolic genes and show less divergence from the Opisthokonta ancestor compared to animals. Gene fusions are more prevalent in animals, while horizontal gene transfers are more common in fungi and protists.
Article
Biochemical Research Methods
Thomas Sauter, Tamara Bintener, Ali Kishk, Luana Presta, Tessy Prohaska, Daniel Guignard, Ni Zeng, Claudia Cipriani, Sundas Arshad, Thomas Pfau, Patricia Martins Conde, Maria Pires Pacheco
Summary: This article introduces a long-standing project-based learning course within the Master in Integrated Systems Biology program at the University of Luxembourg, which aims to cultivate students' ability to solve real-life problems and promote engagement and critical thinking. The article provides a detailed description of the course schedule and content, showcases student projects, and reflects on the outcomes and lessons learned.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Microbiology
Tadashi Maeda, Hiroaki Zai, Yuto Fukui, Yoshifumi Kato, Eri Kumade, Toshiyasu Watanabe, Norihiro Furusyo, Hitoshi Nakajima, Kazuho Arai, Yoshikazu Ishii, Kazuhiro Tateda, Yoshihisa Urita
Summary: Helicobacter pylori infection altered the composition and functions of duodenal microbiota, leading to changes in the relative abundance of certain bacterial taxa and metabolic pathways. These disruptions may contribute to the development of diseases associated with H. pylori infection.
Article
Biochemistry & Molecular Biology
Simone Filardo, Marisa Di Pietro, Marta De Angelis, Gabriella Brandolino, Maria Grazia Porpora, Rosa Sessa
Summary: High-throughput technologies, such as 16s rDNA sequencing, have enhanced our understanding of the microbiota composition in the genital tract during infections like Chlamydia trachomatis. In this study, the predicted metabolic pathways of the cervicovaginal microbiota associated with C. trachomatis genital infection were investigated using PICRUSt2 analysis. The results showed diverse metabolic pathways in women with a CST-IV microbiota, regardless of infection status. C. trachomatis infection altered the metabolic profiles, leading to an increased prevalence of certain pathways. This study provides insights for future metabolomic studies on the metabolic pathways characterizing C. trachomatis genital infection in the cervicovaginal microenvironment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Karuna Yadav, Devender Arora, Indu Jatain, Kashyap Kumar Dubey, Namrata Dhaka, Inderjeet Kaur, Nidhi Adlakha
Summary: This study provides a comprehensive understanding of the biosynthetic pathway of CoQ(10) in A. tumefaciens, including the roles of key precursors and enzymes. Pathway inhibitors were found to decrease CoQ(10) production, while enhancers increased CoQ(10) production.
JOURNAL OF APPLIED MICROBIOLOGY
(2023)
Article
Biochemical Research Methods
Nirvana Nursimulu, Alan M. Moses, John Parkinson
Summary: Constraint-based modeling is a powerful framework for studying cellular metabolism. In this paper, the authors introduce Architect, a pipeline for automatic metabolic model reconstruction from protein sequences. Their method shows improved precision and recall compared to existing tools, and the resulting metabolic model is of high quality. Given the importance of metabolic models in various applications, this work contributes to the field and provides a valuable tool for researchers.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Oncology
Ece Gumusoglu-Acar, Tuba Gunel, Mohammad Kazem Hosseini, Berkcan Dogan, Efnan Elif Tekarslan, Berk Gurdamar, Nazife Cevik, Ugur Sezerman, Samet Topuz, Kilic Aydinli
Summary: This study sought to identify novel circulating microRNAs as potential biomarkers for the prediction and early diagnosis of EOC. Microarray analysis revealed 31 dysregulated miRNAs in serum and three miRNAs in tissue, which were further validated using reverse transcription-quantitative PCR. Pathway analysis indicated that these validated miRNAs were involved in several important pathways, supporting their potential as biomarkers and treatment targets for EOC.
Article
Biochemistry & Molecular Biology
George Minadakis, Kyproula Christodoulou, George Tsouloupas, George M. Spyrou
Summary: PathIN is a web-service that enables the rapid creation of pathway-based networks at multiple biological levels and is supported by a database repository of reference pathway networks. It offers five different methodologies for generating networks and is expected to be a valuable tool for understanding molecular mechanism networks related to specific diseases.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Engineering, Environmental
Jing Zhu, Hong You, Zhipeng Li, Binghan Xie, Weirun Li, Shaojie Qi, Rui Wang, Hongying Chen, Binyu Ma, Yi Ding, Haili Tan, Feng Liu, How Yong Ng
Summary: Photogranules have advantages in treating high saline wastewater, but their formation mechanism needs further investigation. This study explores the impact of SMP and EPS on photogranulation and reveals different formation mechanisms in different types of reactors based on the analysis of pollutant removal efficiencies, microbial communities, and SMP and EPS compositions.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Computer Science, Artificial Intelligence
Odin Zhang, Jintu Zhang, Jieyu Jin, Xujun Zhang, Renling Hu, Chao Shen, Hanqun Cao, Hongyan Du, Yu Kang, Yafeng Deng, Furui Liu, Guangyong Chen, Chang-Yu Hsieh, Tingjun Hou
Summary: This article introduces a three-dimensional molecular generative model called ResGen, which is conditioned on protein pockets and can design organic molecules inside a given target. The ResGen model has a higher success rate in generating novel molecules that bind more tightly to unseen targets than existing approaches. It also successfully generates drug-like molecules with lower binding energy and higher diversity than state-of-the-art methods in real-world scenarios.
NATURE MACHINE INTELLIGENCE
(2023)
Article
Engineering, Multidisciplinary
Dimitris K. Iakovidis, Melanie Ooi, Ye Chow Kuang, Serge Demidenko, Alexandr Shestakov, Vladimir Sinitsin, Manus Henry, Andrea Sciacchitano, Stefano Discetti, Silvano Donati, Michele Norgia, Andreas Menychtas, Ilias Maglogiannis, Selina C. Wriessnegger, Luis Alberto Barradas Chacon, George Dimas, Dimitris Filos, Anthony H. Aletras, Johannes Toger, Feng Dong, Shangjie Ren, Andreas Uhl, Jacek Paziewski, Jianghui Geng, Francesco Fioranelli, Ram M. Narayanan, Carlos Fernandez, Christoph Stiller, Konstantina Malamousi, Spyros Kamnis, Konstantinos Delibasis, Dong Wang, Jianjing Zhang, Robert X. Gao
Summary: Signal processing plays a crucial role in sensor-enabled systems and has various applications. The advancement in artificial intelligence and machine learning has shifted research focus towards intelligent, data-driven signal processing. This roadmap provides a critical overview of current methods and applications, aiming to identify future challenges and research opportunities for next generation measurement systems.
MEASUREMENT SCIENCE AND TECHNOLOGY
(2022)
Article
Plant Sciences
Maria G. Savvidou, Angelo Ferraro, Petros Schinas, Diomi Mamma, Dimitris Kekos, Evangelos Hristoforou, Fragiskos N. Kolisis
Summary: This study presents a method of cell immobilization using microalgae carrying magnetic properties. By enzymatic and mechanical treatments, cell walls are destroyed and protoplasts are generated, which can then be transformed with magnetic nanoparticles. The regeneration of transformed protoplasts is optimized using various supplements. The transformed protoplasts are immobilized and grown on a magnetic surface without any supplement.
Article
Chemistry, Analytical
Dionysios Koulouris, Andreas Menychtas, Ilias Maglogiannis
Summary: Augmented reality (AR) and Internet of Things (IoT) are core technological elements in modern information systems and applications, with extensive applications in healthcare. This work presents a prototype platform that combines AR and IoT for the development of serious games in the healthcare domain. The platform aims to promote user physical activities and monitor their health and cognitive statuses through challenges and quests in virtual and real world environments.
Article
Biochemistry & Molecular Biology
Botle Precious Setlai, Rodney Hull, Meshack Bida, Chrisna Durandt, Thanyani Victor Mulaudzi, Aristotelis Chatziioannou, Zodwa Dlamini
Summary: Immune response is crucial for patient prognosis and response to cancer treatment. Tumors evade immune surveillance by altering antigen processing pathways and the tumor microenvironment. This review highlights the molecular signaling pathways involved in immune suppression and how cancer cells manipulate antigen processing to escape immune surveillance. Additionally, the review explores the potential use of these pathways in precision medicine and understanding drug resistance.
Article
Computer Science, Artificial Intelligence
Panagiotis Mavrogiannis, Ilias Maglogiannis
Summary: In recent years, there has been a growing interest in visual sports analytics, particularly in the field of football, involving player and ball detection, action recognition, and camera pose estimation. This paper proposes a low-cost methodology using computer vision techniques to extract football analytics from simple TV broadcasts. It discusses the state of the art in this field and presents an integrated pipeline for player localization and insights extraction, along with technical details and post-analytic results. The paper also suggests potential future expansions for the proposed pipeline.
NEURAL COMPUTING & APPLICATIONS
(2022)
Article
Chemistry, Analytical
Athanasia Zlatintsi, Panagiotis P. Filntisis, Christos Garoufis, Niki Efthymiou, Petros Maragos, Andreas Menychtas, Ilias Maglogiannis, Panayiotis Tsanakas, Thomas Sounapoglou, Emmanouil Kalisperakis, Thomas Karantinos, Marina Lazaridi, Vasiliki Garyfalli, Asimakis Mantas, Leonidas Mantonakis, Nikolaos Smyrnis
Summary: This paper presents an innovative integrated system called e-Prevention, which utilizes wearable technologies and digital phenotyping to effectively monitor and prevent relapse in patients with mental disorders. By applying machine learning and deep learning techniques to the collected data, it is possible to detect and predict relapses.
Article
Health Care Sciences & Services
Maria V. V. Vasileiou, Ilias G. G. Maglogiannis
Summary: The Health Bot is an intelligent system that utilizes NLP technology to support telemedicine services and enhance patient interactions with the healthcare system. It can predict the probability of specific diseases based on symptoms analysis and provide alerts and medical assessments accordingly.
JOURNAL OF HEALTHCARE ENGINEERING
(2022)
Article
Health Care Sciences & Services
Paris Amerikanos, Ilias Maglogiannis
Summary: This study presents recent advancements in machine learning and computer vision algorithms for the detection of regions of interest (ROIs) in whole slide images (WSIs) in a clinical pathology setting. A state-of-the-art deep learning framework (Detectron2) is trained for object detection and instance segmentation tasks, and the predictions are evaluated against competing models.
JOURNAL OF PERSONALIZED MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Klaus G. Petry, Eleftherios Pilalis, Aristotelis Chatziioannou
Summary: Phage-displayed peptide selections generate complex repertoires of several hundred thousand peptides. In repeated selections, only a very small number of common peptides are found, indicating the difficulty of distinguishing between specific peptide binders and background noise. This study compares the NGS data of three peptide repertoires obtained under identical conditions and confirms the reproducibility of phage-displayed peptide selections through peptide-to-peptide mappings.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Oncology
Georgia Kontogianni, Konstantinos Voutetakis, Georgia Piroti, Katerina Kypreou, Irene Stefanaki, Efstathios Iason Vlachavas, Eleftherios Pilalis, Alexander Stratigos, Aristotelis Chatziioannou, Olga Papadodima
Summary: This study aimed to characterize patients with primary cutaneous melanoma (CM) by analyzing both germline and somatic variations as well as alterations at the gene expression level. Oncogenic alterations were identified and phenotypic cell states were inferred from transcriptomic data. Integrating mutational and transcriptomic data could provide insights into genes and pathways involved in the maintenance of phenotypic states in primary melanomas.
Article
Chemistry, Inorganic & Nuclear
Georgios Banis, Maria Savvidou, Antonios Georgas, Athanasios Batagiannis, Fragiskos Kolisis, Angelo Ferraro, Evangelos Hristoforou
Summary: Electroporation is a technique that temporarily disrupts the plasma membrane of living cells using high-voltage electric current, allowing the introduction of small molecules and nucleic acids. This study presents a continuous-flow cuvette design and testing for efficient cell transformation.
Article
Computer Science, Artificial Intelligence
Athanasios Kallipolitis, Panayiotis Yfantis, Ilias Maglogiannis
Summary: Explaining the predictions of neural networks for medical image classification is important. This study proposes a segmentation-based explainability scheme that focuses on the visual characteristics of each segment in an image to provide enhanced visualizations. Results show that the proposed methodology improves the performance of the Grad-CAM technique by 4% to 9%.
NEURAL COMPUTING & APPLICATIONS
(2023)
Article
Psychiatry
Emmanouil Kalisperakis, Thomas Karantinos, Marina Lazaridi, Vasiliki Garyfalli, Panagiotis P. Filntisis, Athanasia Zlatintsi, Niki Efthymiou, Asimakis Mantas, Leonidas Mantonakis, Theodoros Mougiakos, Ilias Maglogiannis, Panayotis Tsanakas, Petros Maragos, Nikolaos Smyrnis
Summary: Monitoring biometric data using smartwatches provides a new approach for quantifying behavior in patients with psychiatric disorders. This study found that digital phenotypes derived from smartwatches can predict changes in psychopathology of patients with psychotic disorders.
FRONTIERS IN PSYCHIATRY
(2023)
Proceedings Paper
Computer Science, Information Systems
Dionysios Koulouris, Antonios Pardos, Parisis Gallos, Andreas Menychtas, Ilias Maglogiannis
Summary: By blending real world information with data from digital environments using modern visualizations empowered with augmented reality features, more comprehensive and attractive software solutions can be created, contributing to the adoption of new, disrupting solutions in the fields of health and urban planning.
2022 18TH INTERNATIONAL CONFERENCE ON WIRELESS AND MOBILE COMPUTING, NETWORKING AND COMMUNICATIONS (WIMOB)
(2022)
Proceedings Paper
Computer Science, Artificial Intelligence
Konstantinos Moutselos, Ilias Maglogiannis
Summary: The study demonstrates the stability of a classifier trained in the ISIC 2019 dataset in different scenarios and highlights the challenges of transferring and using classifiers from a competitive to a clinical setting.
ARTIFICIAL INTELLIGENCE APPLICATIONS AND INNOVATIONS. AIAI 2022 IFIP WG 12.5 INTERNATIONAL WORKSHOPS
(2022)
