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PathActMarker:an R package for inferring pathway activity of complex diseases

Frontiers of Computer Science 2025年第3期19卷 123-124页

作者： Xingyi LI Jun HAO Zhelin ZHAO Junming LI Xingyu LIAO Min LI Xuequn SHANG School of Computer Science Northwestern Polytechnical UniversityXi’an 710072China Research&Development Institute of Northwestern Polytechnical University in Shenzhen Shenzhen 518063China School of Software Northwestern Polytechnical UniversityXi’an 710072China Hunan Provincial Key Lab on Bioinformatics School of Computer Science and EngineeringCentral South UniversityChangsha 410083China

1 Introduction The process of complex diseases is closely linked to the disruption of key biological pathways,it is crucial to identify the dysfunctional pathways and quantify the degree of dysregulation at the indivi... 详细信息

关键词： pathway activity dysregulation complex diseases biological pathways disruption key biological pathwaysit identify dysfunctional pathways

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Characterization of six clinical drugs and dietary intervention in the nonobese CDAA-HFD mouse model of MASH and progressive fibrosis

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American Journal of Physiology - Gastrointestinal and Liver Physiology 2025年第1期328卷 G51-G71页

作者： Nielsen, Malte Hasle Nøhr-Meldgaard, Jacob Møllerhøj, Mathias Bonde Oró, Denise Pors, Susanne E. Andersen, Maja Worm Kamzolas, Ioannis Petsalaki, Evangelia Vacca, Michele Harder, Lea Mørch Perfield, James W. Veidal, Sanne Hansen, Henrik H. Feigh, Michael Gubra Hørsholm Denmark TVP Lab WT/MRC Institute of Metabolic Science University of Cambridge Cambridge United Kingdom European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Hinxton United Kingdom Interdisciplinary Department of Medicine University of Bari “Aldo Moro” Bari Italy Laboratory of Liver Metabolism and MASLD Roger Williams Institute of Hepatology London United Kingdom Research and Early Development Novo Nordisk A/S Måløv Denmark Lilly Research Laboratories Eli Lilly and Company Indianapolis IN United States

The choline-deficient L-amino acid defined-high-fat diet (CDAA-HFD) mouse model is widely used in preclinical metabolic dysfunction-associated steatohepatitis (MASH) research. To validate the CDAA-HFD mouse, we evaluated disease progression and responsiveness to dietary and pharmacological interventions with semaglutide, lanifibranor, elafibranor, obeticholic acid (OCA), firsocostat, and resmetirom. Disease phenotyping was performed in C57BL/6J mice fed CDAA-HFD for 3–20 wk and ranked using the MASLD Human Proximity Score (MHPS). Semaglutide, lanifibranor, elafibranor, OCA, firsocostat, or resmetirom were profiled as treatment intervention for 8 wk, starting after 6 wk of CDAA-HFD feeding. Semaglutide and lanifibranor were further evaluated as early (preventive) therapy for 9 wk, starting 3 wk after CDAA-HFD diet feeding. In addition, benefits of dietary intervention (chow reversal) for 8 wk were characterized following 6 wk of CDAA-HFD feeding. CDAA-HFD mice demonstrated a nonobese phenotype with fast onset and progression of MASH and fibrosis, high similarity to human MASH-fibrosis, and tumor development after 20 wk of diet-induction. Semaglutide and lanifibranor partially reversed fibrosis when administered as prevention but not as treatment intervention. Elafibranor was the only interventional drug therapy to improve fibrosis. In comparison, chow-reversal resulted in complete regression of steatosis with improved liver inflammation and fibrosis in CDAA-HFD mice. CDAA-HFD mice recapitulate histological hallmarks of advanced MASH with progressive severe fibrosis, however, in the absence of a clinical translational obese dysmetabolic phenotype. CDAA-HFD mice are suitable for profiling drug candidates directly targeting hepatic lipid metabolism, inflammation, and fibrosis. The timing of pharmacological intervention is critical for determining antifibrotic drug efficacy in the model. Copyright © 2025 The Authors.

关键词： CDAA-HFD mouse disease progression fibrosis metabolic dysfunction-associated steatohepatitis treatment intervention

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Invariant set theory for predicting potential failure of antibiotic cycling

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Infectious Disease Modelling 2025年第3期10卷 897-908页

作者： Anderson, Alejandro Kinahan, Matthew W. Gonzalez, Alejandro H. Udekwu, Klas Hernandez-Vargas, Esteban A. Department of Mathematics and Statistical Science University of Idaho Moscow ID United States Department of Biological Sciences Bioinformatics and Computational Biology University of Idaho Moscow ID United States University of Littoral (UNL) Institute of Technological Development for the Chemical Industry (INTEC) and National Scientific and Technical Research Council (CONICET) Santa Fe Argentina Institute for Modeling Collaboration and Innovation University of Idaho Moscow 83844–1103 ID United States

Collateral sensitivity, where resistance to one drug confers heightened sensitivity to another, offers a promising strategy for combating antimicrobial resistance, yet predicting resultant evolutionary dynamics remains a significant challenge. We propose here a mathematical model that integrates fitness trade-offs and adaptive landscapes to predict the evolution of collateral sensitivity pathways, providing insights into optimizing sequential drug therapies. Our approach embeds collateral information into a network of switched systems, allowing us to abstract the effects of sequential antibiotic exposure on antimicrobial resistance. We analyze the system stability at disease-free equilibrium and employ set-control theory to tailor therapeutic windows. Consequently, we propose a computational algorithm to identify effective sequential therapies to counter antibiotic resistance. By leveraging our theory with data on collateral sensivity interactions, we predict scenarios that may prevent bacterial escape for chronic Pseudomonas aeruginosa infections. © 2025 The Authors

关键词： Antibacterial resistance Collateral sensitivity Control invariant sets Switched systems

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The interictal transcriptomic map of migraine without aura

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Journal of Headache and Pain 2025年第1期26卷 1-17页

作者： Petschner, Peter Kumar, Sahel Nguyen, Duc A. Torok, Dora Gal, Zsofia Baksa, Daniel Gecse, Kinga Kokonyei, Gyongyi Mamitsuka, Hiroshi Juhasz, Gabriella Bioinformatics Center Institute of Chemical Research Kyoto University Uji Kyoto 611 - 0011 Japan Department of Pharmacodynamics Faculty of Pharmaceutical Sciences Semmelweis University Budapest 1089 Hungary Center of Pharmacology and Drug Research & Development Semmelweis University Budapest 1089 Hungary NAP3.0-SE Neuropsychopharmacology Research Group Hungarian Brain Research Program Semmelweis University Budapest 1089 Hungary Research Unit for Realization of Sustainable Society Kyoto University Uji Kyoto 611 - 0111 Japan Hanoi University of Science and Technology Hanoi 100000 Viet Nam Department of Personality and Clinical Psychology Institute of Psychology Pazmany Peter Catholic University Budapest 1088 Hungary Institute of Psychology ELTE Eötvös Loránd University Budapest 1064 Hungary

Background: The present study aimed to deliver a replicable transcriptomic map of migraine without aura (MO) and its comprehensive, genome- and drug discovery focused analysis to identify hypotheses for future research- and clinical attempts. Methods: We recruited 30 controls and 22 MO patients without serious chronic comorbidities/regular medication intake. RNA-sequencing was conducted interictally at two different time points to identify replicable differential gene expression and enriched pathways. Subsequent refining and functional analyses were performed, including: 1) testing additional patient factors, 2) running genetic association analysis on migraine in the UK Biobank (UKB) and our cohort, and 3) predicting drug binding with AutoDock Vina and machine learning to proteins of transcriptomic changes. Results: Difference in CYP26B1 was identified as key alteration in migraine. Gene set enrichment analysis identified 88 replicated, significant, exclusively downregulated core pathways, including metabolic, cardiovascular, and immune system-related gene sets and 69 leading genes, like CORIN. Logistic regression of leading genes’ and vitamin A pathway-related polymorphisms identified 11 significant polymorphisms in LRP1. Confirmatory analyses excluded a substantial impact of sex, allergy and different vitamin A/retinol intake. Binding simulations and predictions pointed to potential future drug molecules, like tetrandrine and probucol. Conclusion: The replicable transcriptomic map of MO and functional analyses: 1) identified pathomechanisms related to metabolic, cardiovascular and immune system related processes on a molecular level, 2) reported gene level hits, 3) proposed novel potential etiology, like LRP1-induced decreased retinoic acid signaling, and 4) delivered novel drug candidates for the disorder. © The Author(s) 2025.

关键词： Drug discovery Molecular pathophysiology Genomics Migraine without aura Transcriptomics

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Quantitative Reaction Systems

Quantitative Reaction Systems

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Innovative research in Applied Science, Engineering and Technology (IRASET),Conference on

作者： Victor Mitrana Mihaela Păun Ion Petre Ana-Maria Prelipcean Department of Information Systems Polytechnic University of Madrid Madrid Spain Department of Bioinformatics National Institute of Research and Development for Biological Sciences Bucharest Romania Department of Mathematics and Statistics University of Turku Turku Finland Department of Cellular and Molecular Biology National Institute of Research and Development for Biological Sciences Bucharest Romania

ISBN: (数字)9798331532970

ISBN: (纸本)9798331532987

We propose a new variant of reaction system that intends to take into account a few aspects of a biological reaction that have been considered at most partially in former works. These aspects are: (i) in the former variants, all the substances of the substrate completely vanish after identifying the set of reactants such that the result does not contain any former component of the substrate unless it is produced by the reaction, (ii) in any substrate, each element is either present in an arbitrary large number of copies, or it is not present at al, (iii) the effect of any inhibitor is the same but in biology the effect of inhibitors may be different due to their type. Our model considers multisets of reactants such that it is a more quantitative model than a qualitative one, inhibitors may be of different types such that their role may vary depending on the substrate, the substances that are not involved in the reaction remain in the substrate. We consider a parallel mode of enabling the reactions and prove that this mode may be simulated by sequential enabling. Later on, we define a computational model based on quantitative reaction systems and prove that their computation power equals that of multiset Turing machines.

关键词： Inhibitors Turing machines Biological system modeling Computational modeling Substrates

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The global burden of polycystic ovary syndrome, endometriosis, uterine fibroids, cervical cancer, uterine cancer, and ovarian cancer from 1990 to 2021

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BMC Public Health 2025年第1期25卷 1-20页

作者： Tang, Wei-Zhen Cai, Qin-Yu Huang, Kang-Jin Xu, Wei-Ze Li, Jia-Zheng Pan, Yun-Ren Xu, Hong-Yu Zhao, Yi-Fan Sheng, Ting-He Li, Zhi-Mou Liu, Tai-Hang Li, Ying-Bo Department of Bioinformatics School of Basic Medical Sciences Chongqing Medical University Chongqing 400016 China Institute of Neuroscience Department of Physiology School of Basic Medical Science Chongqing Medical University Chongqing 400016 China The Joint International Research Laboratory of Reproduction and Development Chongqing Medical University Chongqing 400016 China Chongqing Medical University Box 197 No.1 Yixueyuan Rd Chongqing 400016 China

Background: Globally, common gynecological disorders such as Polycystic Ovary Syndrome (PCOS), endometriosis, uterine fibroids (non-malignant gynecological diseases), as well as cervical cancer, uterine cancer, and ovarian cancer (gynecological cancers), profoundly impact women’s physical and mental health. The burden of these diseases exhibits significant geographical disparities across different countries and regions, making a comprehensive and precise assessment of the global burden of gynecological diseases particularly crucial. Such an assessment will facilitate the development of region-specific prevention and treatment strategies, contributing to a more effective response to these health challenges. Methods: Incidence, prevalence, mortality rates, and Disability-Adjusted Life Years (DALYs) data for the aforementioned gynecological conditions were obtained from the 2021 Global Burden of Disease (GBD) study and analyzed by age, location, and year. The burden associated with gynecological diseases was analyzed based on the Socio-demographic Index (SDI) and attributable risk factors. The Estimated Annual Percentage Change (EAPC) and its 95% Confidence Interval (CI) were used to assess temporal trends in burden. Results: In 2021, uterine fibroids were the leading non-malignant gynecological condition contributing to the highest Age-Standardized Incidence Rate (ASIR) and Age-Standardized Prevalence Rate (ASPR), with rates of 250.93 and 2841.07 per 100,000, respectively. Cervical cancer was the main contributor to the Age-Standardized Mortality Rate (ASMR) and Age-Standardized Disability Rate (ASDR) among the eight selected gynecological diseases, with rates of 6.62 and 226.28 per 100,000, respectively. From 1990 to 2021, the ASIR and ASPR for non-malignant gynecological conditions, such as PCOS and uterine fibroids, increased, while the ASDR for PCOS also rose. Among gynecological cancers, the ASIR for uterine cancer increased, while the ASPR for cervical cancer ro

关键词： Burden of disease Cervical cancer Disability-adjusted life-years (DALYs) Endometriosis Ovarian cancer Polycystic ovary syndrome Uterine cancer Uterine fibroids

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Digital Rupee Acceptance Dynamics Through the Lens of Theory of Planned Behaviour

Digital Rupee Acceptance Dynamics Through the Lens of Theory...

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IT Innovation and Knowledge Discovery (ITIKD), International Conference on

作者： Suraj Chandrakant Kamble Shikha Jain Rashmy Moray Jehad Al Dallal Institute of Management Development and Research IMDR® Pune India Symbiosis Institute of Management Studies (SIMS) Symbiosis International Deemed University (SIU) Pune India Center for Applied Mathematics and Bioinformatics Gulf University for Science and Technology Kuwait

ISBN: (数字)9798350355468

ISBN: (纸本)9798350355475

This study aimed to examine the acceptance of the digital rupee by assessing the relationship between users’ attitudes, subjective norms, and perceived behavioral control. The theory of planned behavior is used to analyze the influence of users’ intention to accept digital rupees for financial transactions, emphasizing motivations and barriers affecting users’ intention to use digital rupees. Following the stratified random sampling technique, the responses were collected through a structured questionnaire to represent diverse users. Statistical tools, including regression analysis, ANOVA, and t-test, were applied to achieve the research objectives. The study explored the impact of demographic variables in relation to behavior and identified that occupation significantly affects behavior among users. The findings reveal that positive attitudes, subjective norms, and perceived behavioral control significantly influence the acceptance of digital rupees. The research outcomes contribute to the theoretical frameworks of user behavior towards digital currencies, as well as practical insights into the adoption of digital rupees.

关键词： Technological innovation Attitude control Online banking Government Buildings Knowledge discovery Regression analysis Security Analysis of variance Lenses

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A review of sources for formulating dairy substitute: Highlights on cheese

Food and Humanity

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Food and Humanity 2025年 4卷

作者： Patel, Kajal S. Patil, Sonal Bhushette, Pravin Dabade, Ashish Sonawane, Sachin K. School of Biotechnology and Bioinformatics D. Y. Patil deemed to be University Sector 15 Plot No. 50 CBD Belapur Navi Mumbai 400614 India Institute of Management Development and Research Deccan Education Society Pune India

One of the most consumed parts of the diet is milk. With the increasing population, the demand for milk is also increasing, and it might be challenging to fulfill the requirements. People are changing their diet patterns due to various health and ethical aspects. This helps increase non-dairy sources such as soy, coconut, hemp, oat, etc. Plant-source milk can replace dairy milk entirely or partially in milk-based products, which can help to produce new products. Food Analogues will soon find an essential place in the market because of their versatility, wide variety, and availability. Cheese analogs have been one of these analogs that are available on the market. Cheese analogs are prepared by blending different vegetable source ingredients with partial or complete dairy milk replacement. The present review suggests coconut milk in dairy products because of its value. © 2025 Elsevier B.V.

关键词： Dairy analog Lactose intolerance Plant proteins

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Complete mitogenome of the critically endangered Asian king vulture (Sarcogyps calvus) (Aves, Accipitriformes, Accipitridae): evolutionary insights and comparative analysis

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ZooKeys 2025年第1234期1234卷 47-65页

作者： Buthasane, Wannapol Tangphatsornruang, Sithichoke Jenjaroenpun, Piroon Wongsurawat, Thidathip Sanannu, Saowaphang Shotelersuk, Vorasuk Suriyaphol, Gunnaporn Biochemistry Unit Department of Physiology Faculty of Veterinary Science Chulalongkorn University Bangkok 10330 Thailand National Omics Center National Center for Genetic Engineering and Biotechnology (BIOTEC) National Science and Technology Development Agency Pathum Thani 12120 Thailand Division of Medical Bioinformatics Research Department Faculty of Medicine Siriraj Hospital Mahidol University Bangkok 10700 Thailand Animal Conservation and Research Institute The Zoological Park Organization of Thailand Bangkok 10300 Thailand Center of Excellence for Medical Genomics Medical Genomics Cluster Department of Pediatrics Faculty of Medicine Chulalongkorn University Bangkok 10330 Thailand Excellence Center for Genomics and Precision Medicine King Chulalongkorn Memorial Hospital The Thai Red Cross Society Bangkok 10330 Thailand

The Asian king vulture (Sarcogyps calvus), also known as the red-headed vulture, is an Old World vulture (Gypini) facing severe population declines. This study aimed to assemble the complete mitogenome of S. calvus, explore its phylogenetic relationships, estimate divergence times, and examine genetic distances and amino acid substitutions. The mitogenome was de novo assembled from genomic DNA extracted from the blood of a female S. calvus. Phylogenetic and pairwise genetic distance analyses were conducted, comparing S. calvus with other members of Gypini, New World vultures (Cathartidae) and various other birds. The assembled mitogenome was 17,750 base pairs in length, comprising 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and two control regions. Most PCGs used the ATG start codon, except for cytochrome c oxidase subunit 1 (COX1), which employed GTG. Phylogenetic analysis revealed a close genetic relationship between S. calvus and other members of Gypini, with an estimated divergence time of 16.7 million years ago. Genetic distance analysis indicated that S. calvus was more closely related to other Gypini, as well as to Spilornis cheela and Circaetus pectoralis (Circaetini)), than to Cathartidae. Conserved amino acid substitutions between Gypini and Cathartidae were primarily observed in the NADH-ubiquinone oxidoreductase chain 1 (ND1) gene. This study provided the first complete mitogenome of S. calvus, offering new insights into its genomic structure, evolutionary history, and genetic relationships. © Wannapol Buthasane et al.

关键词： Asian king vulture comparative analysis evolution mitogenome Sarcogyps calvus

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OXidative Stress PREDictor: A Supervised Learning Approach for Annotating Cellular Oxidative Stress States in Inflammatory Cells

Advanced Intelligent Systems

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Advanced Intelligent Systems 2025年第3期7卷

作者： Chen, Po-Yuan Ko, Tai-Ming Institute of Bioinformatics and Systems Biology College of Engineering Bioscience National Yang Ming Chiao Tung University Hsinchu300 Taiwan Bioinformatics Program Institute of Statistical Science Taiwan International Graduate Program Academia Sinica Taipei115 Taiwan Institute of Biomedical Sciences Academia Sinica Taipei115 Taiwan Institute of Statistical Science Academia Sinica Taipei115 Taiwan Department of Biological Science and Technology College of Engineering Bioscience National Yang Ming Chiao Tung University Hsinchu300 Taiwan National Yang Ming Chiao Tung University Hsinchu300 Taiwan School of Pharmacy College of Pharmacy Drug Development and Value Creation Research Center Kaohsiung Medical University Kaohsiung807 Taiwan

Oxidative stress, characterized by an imbalance between reactive oxygen species (ROS) and antioxidants, plays a pivotal role in inflammatory responses associated with both chronic diseases and acute injuries. In this study, OXidative Stress PREDictor (OxSpred), a supervised learning model tailored to accurately annotate the oxidative stress state of innate immune cells at the single-cell level, is introduced. Compared to the traditional gene-set-variation-analysis-based enrichment method, OxSpred demonstrates superior accuracy with an area under the receiver operating characteristic curve of 0.89 and offers interpretable embeddings with significant biological relevance. Using the predicted ROS states, precise elucidation and interpretation of the roles of novel innate immune cell subtypes can be achieved. Overall, OxSpred enhances the utility of single-cell transcriptomic datasets by providing a robust in silico method for determining intracellular oxidative stress states, thereby enriching the understanding of innate immune cell functions during inflammation. © 2024 The Author(s). Advanced Intelligent Systems published by Wiley-VCH GmbH.

关键词： Cells

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