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STEATOSIS AND FIBROSIS PREDICTIVE SCORES IN PATIENTS WITH TYPE 2 DIABETES

Ultrasound in medicine & Biology 2022年 48卷 S11-S12页

作者： Mare, Ruxandra - Georgeta Lupusoru, Raluca Sporea, Ioan Popescu, Alina Sima, Alexandra Timar, Romulus Sirli, Roxana Department of Internal Medicine II Division of Gastroenterology and Hepatology Center for Advanced Research in Gastroenterology and Hepatology "Victor Babes" University of Medicine and Pharmacy Timisoara Romania Center for Advanced Hepatology Research of the Academy of Medical Sciences Timisoara Romania Center for Modeling Biological Systems and Data Analysis Department of Functional Sciences “Victor Babes” University of Medicine and Pharmacy Timisoara Romania Gastroenterology and Hepatology Timisoara Romania Department of Internal Medicine II Division of Diabetes and Metabolic Disorders "Victor Babes" University of Medicine and Pharmacy Timisoara Romania

ObjectivesThe prevalence of non-alcoholic fatty liver disease (NAFLD) is increasing in patients with type 2 diabetes (T2D), as a result, a systematic screening in this population should be performed. The aim of this study was to identify risk factors associated with moderate steatosis (S2) and advanced fibrosis (F≥3) and to develop a score that could be used in daily practice. MaterialsA prospective study on 534 patients with T2D was conducted using Vibration Controlled Transient Elastography (VCTE) to assess fibrosis severity and Controlled Attenuation Parameter (CAP) to assess steatosis severity. We stratified our cohort into study cohort (348 patients) and validation cohort (186 patients). We aimed for 10 valid CAP and liver stiffness measurements (LSM) with an IQR/Median <30%. A cut-off value of 290 dB/m was used to define S2 while for F≥3 a cut-off of 9.7 kPa [1]. For developing a score for stratifying the risk of moderate steatosis, and of advanced fibrosis, we used univariate and multivariate logistic regression analysis. ResultsOut of 534 patients, 62.7% had at least S2 and 19.2% had at least F≥3 by VCTE. In univariate analysis, BMI (p< 0.0001), waist circumference -WC (p< 0.0001), elevated levels of ALT (p=0.001), total cholesterol -TC (p=0.03), triglycerides-TG (p=0.01), fasting blood glucose (p=0.004) and presence of hypertension-HTA (p=0.04) were associated with at least moderate steatosis. The steatosis score is composed of: 0.5 points for high BMI (>32.1 kg/m2), TC (> 235 mg/dl), TG (>165 mg/dl), glycemia (> 200 mg/dl), ALT (> 40 U/L) and WC (> 100 cm) and 1 point for the presence of HTA. In univariate analysis, BMI (p< 0.0001), WC (p< 0.0001), elevated levels of AST (p=0.001), liver steatosis (p=0.03) were associated with at least F≥3. The fibrosis score is composed of: 0.5 points for high BMI (>32.4 kg/m2), AST (> 42 U/L), WC (> 110 cm) and for the presence of steatosis. The derived steatosis and fibrosis cut-offs for identifying patients with T2D we

关键词： fibrosis steatosis type 2 diabetes

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Game theory of pandemic control: Can collaborative vaccine allocation strategies lead to better outcomes?

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IJID Regions 2025年 14卷 100535-100535页

作者： Yiwen Wang Yang Ye Xiaoyi Su Qingpeng Zhang Hsiang-Yu Yuan Department of Computer Science and Engineering The Chinese University of Hong Kong Hong Kong China Center for Infectious Disease Modeling and Analysis Yale School of Public Health New Haven CT 06520 Department of Biostatistics City University of Hong Kong Hong Kong China HKU Musketeers Foundation Institute of Data Science and Department of Pharmacology and Pharmacy The University of Hong Kong Hong Kong China Department of Biomedical Sciences Jockey Club College of Veterinary Medicine and Life Sciences City University of Hong Kong Hong Kong China Centre for Applied One Health Research and Policy Advice Jockey Club College of Veterinary Medicine and Life Sciences City University of Hong Kong Hong Kong China

Introduction Increasing vaccine uptake is an effective way to prevent COVID-19 infection in individual countries after the relaxation of social distancing. However, under the limited vaccine resources, vaccine inequality between high- and low-income countries can also produce more infection and cost. Reducing such inequality relies on a more cooperative (unselfish) strategy, such as vaccine donation from high-income countries, which may initially increase their cost. The study aims to analyze the impact of vaccine inequality on cooperative decision-making between two populations. The results provide important insights on achieving global control of infectious disease outbreaks. Material and Methods We developed a transmission model incorporating virus evolution under different vaccine-induced natural selection and the migration to allow a long-term repeated outbreak. Vaccine allocation strategies were implemented between two populations the high vaccine coverage population (HC) and the low coverage population (LC). A game theory approach was employed to explore whether pursuing minimum cost for both sides (cooperative strategy) or itself (non-cooperative strategy) for each population. We estimated the effect of each strategy on the total cost (i.e. the sum of vaccine, hospitalization and labor costs). The Nash equilibrium was obtained by minimizing their own cost for individual countries under different vaccine inequality scenarios (from low to high inequality). Results Under low inequality, both populations achieved the same optimal cost with both cooperative and non-cooperative strategies. Under medium or high inequality, both populations reached a Nash equilibrium with non-cooperative strategies and could not reach global optimum. When inequality was high, HC tended towards vaccine donation even though non-cooperative strategies were adopted. Discussion When inequality is high, although cooperative decisions can obtain global optimal outcomes, populations tend to

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Corrigendum to "Risk factors of early spontaneous preterm birth despite carrying a cervical pessary in singleton pregnancies with a short cervix: Development of a risk prediction model" [Eur J Obstet Gynecol Reprod Biol X 22 (2024) 100305]

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European journal of obstetrics & gynecology and reproductive biology: X 2024年 23卷 100325页

作者： Carme Merced Laia Pratcorona Teresa Higueras Mireia Vargas Esther Del Barco Judit Solà Elena Carreras Maria Goya Department of Obstetrics Hospital Universitari de Vic Consorci Hospitalari de Vic Barcelona Spain. Department of Obstetrics Hospital Germans Trias I Pujol Universitat Autònoma de Barcelona Barcelona Spain. Maternal Fetal Medicine Unit Department of Obstetrics Hospital Universitari Vall d'Hebron Universitat Autònoma de Barcelona Barcelona Spain. Department of Obstetrics Althaia Xarxa Assistencial Universitària de Manresa Barcelona Spain. Data Analysis and Modeling Research Group Universitat de Vic-Universitat Central de Catalunya Vic Barcelona Spain.

[This corrects the article DOI: 10.1016/***.2024.100305.].

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CSIG-11. TUMOR-CELL INTRINSIC CALCIUM OSCILLATIONS DRIVE BRAIN METASTASIS

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Neuro-Oncology 2024年第SUPPLEMENT_8期26卷 viii65–viii66页

作者： Hebach, Nils R Olshausen, Niels Schlag, Joana S Bang, Severin Kraft, Theresa Mayer, Chanté Linke, Zoe Westphal, Dana Seifert, Michael Timmer, Jens Wick, Wolfgang Winkler, Frank Karreman, Matthia A Clinical Cooperation Unit Neurooncology German Cancer Research Center Heidelberg Germany Neurology Clinic and National Center for Tumor Diseases Heidelberg Germany Institute of Physics University of Freiburg Freiburg Germany Freiburg Center for Data Analysis and Modeling (FDM) Freiburg Germany Institute for Medical Informatics and Biometry (IMB) Carl Gustav Carus Faculty of Medicine Dresden Germany National Center for Tumor Diseases (NCT) Dresden Germany Department of Dermatology Medical Faculty and University Hospital Carl Gustav Carus Dresden Germany

Calcium is a ubiquitous secondary messenger which regulates many cellular processes. Recently, we have shown that a subpopulation of glioblastoma cells can intrinsically generate calcium oscillations which drive proliferative signalling. Here, we set out to investigate whether such cancer cell autonomous oscillations are also present in secondary brain tumours. Employing longitudinal intravital two-photon microscopy in awake mice, we demonstrate that brain metastases of melanoma and lung cancer exhibit spontaneous calcium oscillationsin vivoalong the metastatic cascade. These oscillations are already observed during intravascular arrest and inin vitromonocultures, suggesting a tumour-cell intrinsic origin. We developed a fully automatic image analysis pipeline to accurately quantify calcium oscillations bothin vivoandin vitro. Mathematical modelling of cytosolic and ER calcium stores can predict stable calcium oscillations with similar frequency and peak characteristics as those experimentally observed. We discovered that these oscillations are tightly regulated by an interplay of calcium-induced calcium release and store-operated calcium entry (SOCE). Similarly, SOCE-related ion channels are enriched in tissue from human melanoma brain metastases compared to healthy brain controls and calcium activity can also be observedex vivoin patient-derived brain metastasis resections. Finally, by correlating calcium activity and EdU incorporation we discovered that the presence of calcium oscillations predicts their proliferative potentialin vitro. Importantly, by intravital two-photon microscopy we show that calcium activity correlates with metastasis size in preclinical models, suggesting a potential new therapeutic angle from which to target brain metastases.

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MO831: Hepatitis Virus Infection in End-Stage Kidney Disease Patients Treated by Haemodialysis in Romania After 5 Years of Active Antiviral Therapy, Revisited

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Nephrology Dialysis Transplantation 2022年第SUPPLEMENT_3期37卷

作者： Marc, Luciana Lupusoru, Raluca Schiller, Oana-Marina Mihaescu, Adelina Bob, Flaviu Chisavu, Lazar Schiller, Adalbert Department of Internal Medicine II—Division of Nephrology `Victor Babeș’ University of Medicine and Pharmacy Timisoara Romania Faculty of Medicine Nephrology Clinic County Emergency Hospital `Pius Brinzeu’ Timisoara Romania `Victor Babeș’ University of Medicine and Pharmacy Centre for Molecular Research in Nephrology and Vascular Disease Timisoara Romania Department of Internal Medicine II—Division of Gastroenterology and Hepatology `Victor Babeș’ University of Medicine and Pharmacy Timisoara Romania Department of Functional Sciences `Victor Babeș’ University of Medicine and Pharmacy Center for Modeling Biological Systems and Data Analysis Timisoara Romania County Emergency Hospital `Pius Brinzeu’ Gastroenterology and Hepatology Clinic Timisoara Romania `Avitum’ Hemodialysis Center Timisoara Romania

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A systematic review of challenges and proposed solutions in modeling multimodal data

arXiv

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arXiv 2025年

作者： Farhadizadeh, Maryam Weymann, Maria Blaß, Michael Kraus, Johann Gundler, Christopher Walter, Sebastian Hempen, Noah Binder, Harald Binder, Nadine Institute of General Practice/Family Medicine Faculty of Medicine Medical Center University of Freiburg Elsässer Straße 2M Freiburg79110 Germany Freiburg Center for Data Analysis Modeling and AI University of Freiburg Ernst-Zermelo-Str. 1 Freiburg79104 Germany Institute of Medical Biometry and Statistics Faculty of Medicine Medical Center University of Freiburg Stefan-Meier-Straße 26 Freiburg79104 Germany Institute for Applied Medical Informatics University Medical Center Hamburg-Eppendorf Martinistraße 52 Hamburg20251 Germany Institute of Medical Systems Biology Ulm University Helmholtzstraße 16 Ulm89081 Germany Department of Computer Science Faculty of Engineering University of Freiburg Georges-Köhler-Allee 051 Freiburg79110 Germany

Multimodal data modeling has emerged as a powerful approach in clinical research, enabling the integration of diverse data types such as imaging, genomics, wearable sensors, and electronic health records. Despite its potential to improve diagnostic accuracy and support personalized care, modeling such heterogeneous data presents significant technical challenges. This systematic review synthesizes findings from 69 studies to identify common obstacles, including missing modalities, limited sample sizes, dimensionality imbalance, interpretability issues, and finding the optimal fusion techniques. We highlight recent methodological advances, such as transfer learning, generative models, attention mechanisms, and neural architecture search that offer promising solutions. By mapping current trends and innovations, this review provides a comprehensive overview of the field and offers practical insights to guide future research and development in multimodal modeling for medical applications. © 2025, CC BY.

关键词： Clinical research

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MO481: Novel Predictors of CKD in Metabolic Fatty Liver Disease Patients: Steatosis Vs Fibrosis. A Prospective Study Using Transient Elastography With Controlled Attenuation Parameter

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Nephrology Dialysis Transplantation 2022年第SUPPLEMENT_3期37卷

作者： Marc, Luciana Mihaescu, Adelina Lupusoru, Raluca Bob, Flaviu Chisavu, Lazar Timar, Bogdan Timar, Romulus Schiller, Adalbert Department of Internal Medicine II—Division of Nephrology `Victor Babeș’ University of Medicine and Pharmacy Timisoara Romania Centre for Molecular Research in Nephrology and Vascular Disease Faculty of Medicine `Victor Babeș’ University of Medicine and Pharmacy Timisoara Nephrology Clinic County Emergency Hospital `Pius Brinzeu’ Timisoara Romania Department of Internal Medicine II—Division of Gastroenterology and Hepatology `Victor Babes’ University of Medicine and Pharmacy Timisoara Romania Center for Modeling Biological Systems and Data Analysis Department of Functional Sciences `Victor Babes’ University of Medicine and Pharmacy Timisoara Romania County Emergency Hospital `Pius Brinzeu’ Gastroenterology and Hepatology Clinic Timisoara Romania Department of Internal Medicine II—Division of Diabetes and Nutritional Disease `Victor Babeș’ University of Medicine and Pharmacy Timisoara Romania Diabetes and Nutrition Disease Clinic County Emergency Hospital `Pius Brinzeu’Timisoara Romania

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Recent advances in T-cell receptor repertoire analysis: Bridging the gap with multimodal single-cell RNA sequencing

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ImmunoInformatics 2022年 5卷

作者： Sebastiaan Valkiers Nicky de Vrij Sofie Gielis Sara Verbandt Benson Ogunjimi Kris Laukens Pieter Meysman Adrem Data Lab Department of Computer Science University of Antwerp Antwerp Belgium Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS) University of Antwerp Antwerp Belgium Clinical Immunology Unit Department of Clinical Sciences Institute of Tropical Medicine Antwerp Belgium Molecular Digestive Oncology Department of Oncology Katholieke Universiteit Leuven Leuven Belgium Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID) Vaccine & Infectious Disease Institute (VAXINFECTIO) University of Antwerp Antwerp Belgium Antwerp Center for Translational Immunology and Virology (ACTIV) Vaccine and Infectious Disease Institute (VAXINFECTIO) University of Antwerp Antwerp Belgium Department of Paediatrics Antwerp University Hospital Antwerp Belgium

T cells exercise a multitude of functions such as cytotoxicity, secretion of immunomodulating cytokines or regulation of tolerance, collectively resulting in an effective control of immune-related disease. Through the unique mechanism of V(D)J recombination, T cells express a highly specific receptor complex known as the T-cell receptor (TCR). Single-cell sequencing technologies have paved the road for interrogating the transcriptome and the paired αβ TCR repertoire of a single T cell in tandem. In contrast, conventional bulk methods are restricted to only one layer of information. This combination of transcriptomic- and repertoire information can provide novel insight into the functional character of T cell immunity. Recently, single-cell technologies have gained in popularity due to improvements in throughput, decrease in cost and the ability for multimodal experiments that integrate different information layers. Consequently, this prompts the need for the development of novel computational tools that integrate transcriptomic profiles and corresponding features of the TCR repertoire. Here we discuss the current progress in the field of single-cell T cell sequencing, with a focus on the multimodality of new approaches that allow the paired profiling of cellular phenotype and clonotype information. In addition, this review provides detailed descriptions of recent computational developments for analyzing single-cell TCR sequencing data in an integrative manner using novel computational approaches. Finally, we present an overview of the available software tools that can be used to perform integrative analysis of gene expression and TCR profiles.

关键词： Single-cell sequencing Single-cell immune profiling Single-cell gene expression T-cell receptor repertoire Multi-omics

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Extracellular vesicles present in bone, blood and extracellular matrix have distinctive characteristics and biologic roles

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Journal of Immunology and Regenerative medicine 2022年 18卷

作者： Madeline C. Cramer William A. D'Angelo Marley J. Dewey Allison M. Manuel Steven J. Mullett Stacy G. Wendell Dobrawa Napierala Peng Jiang Stephen F. Badylak Department of Surgery University of Pittsburgh Pittsburgh PA USA McGowan Institute for Regenerative Medicine University of Pittsburgh Pittsburgh PA USA Department of Bioengineering University of Pittsburgh Pittsburgh PA USA Health Sciences Metabolomics and Lipidomics Core University of Pittsburgh Pittsburgh PA USA Department of Pharmacology and Chemical Biology University of Pittsburgh Pittsburgh PA USA Center for Craniofacial Regeneration Department of Oral Biology University of Pittsburgh School of Dental Medicine Pittsburgh PA USA Center for Gene Regulation in Health and Disease Cleveland State University Cleveland OH USA Center for Applied Data Analysis and Modeling Cleveland State University Cleveland OH USA Department of Biological Geological and Environmental Sciences Cleveland State University Cleveland OH USA

Introduction Extracellular vesicles (EV) have long been recognized as an important means of cell to cell communication, but current metrics to delineate various subpopulations of EV are limited. Recently, a distinctive subpopulation of EV embedded within the extracellular matrix of soft tissues, termed matrix-bound nanovesicles (MBV), has been described. Although the lipid membrane composition and intravesicular cargo of MBV clearly differ from liquid phase EV (i.e. exosomes), a more comprehensive characterization of the physical and biologic properties of MBV vs. exosomes and those of a separate subpopulation of EV, specifically bone matrix vesicles, would contribute to our understanding of the biogenesis and physiologic role of these three EV subpopulations. Results The physical characteristics, protein and miRNA cargo profiling, vesicle membrane lipidomics, and immunomodulatory activity were used to compare skeletal muscle-derived MBV, liquid phase plasma exosomes, and mineralization-competent matrix vesicles of provisional bone matrix. We show that despite similar physical characteristics, these three preparations of EV represent distinct entities with different biologic activity. Conclusion These results inform metrics for the categorization of EV and provide tools for the isolation of EV for potential diagnostic and therapeutic applications.

关键词： Extracellular vesicles Matrix bound nanovesicles Exosomes Calcifying matrix vesicles Immunomodulation

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From FAIR to CURE: Guidelines for Computational Models of Biological Systems

arXiv

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arXiv 2025年

作者： Sauro, Herbert M. Agmon, Eran Blinov, Michael L. Gennari, John H. Hellerstein, Joe Heydarabadipour, Adel Hunter, Peter Jardine, Bartholomew E. May, Elebeoba Nickerson, David P. Smith, Lucian P. Bader, Gary D. Bergmann, Frank Boyle, Patrick M. Dräger, Andreas Faeder, James R. Feng, Song Freire, Juliana Fröhlich, Fabian Glazier, James A. Gorochowski, Thomas E. Helikar, Tomas Hoops, Stefan Imoukhuede, Princess Keating, Sarah M. Konig, Matthias Laubenbacher, Reinhard Loew, Leslie M. Lopez, Carlos F. Lytton, William W. McCulloch, Andrew Mendes, Pedro Myers, Chris J. Myers, Jerry G. Mulugeta, Lealem Niarakis, Anna van Niekerk, David D. Olivier, Brett G. Patrie, Alexander A. Quardokus, Ellen M. Radde, Nicole Rohwer, Johann M. Sahle, Sven Schaff, James C. Sego, T.J. Shin, Janis Snoep, Jacky L. Vadigepalli, Rajanikanth Wiley, H. Steve Waltemath, Dagmar Moraru, Ion Department of Bioengineering University of Washington SeattleWA98195-5061 United States Intelligent Systems Engineering and Biocomplexity Institute Indiana University Street BloomingtonIN47408 United States Center for Cardiovascular Biology University of Washington SeattleWA98195-5061 United States eScience Institute University of Washington SeattleWA98195-5061 United States Institute for Stem Cell and Regenerative Medicine University of Washington SeattleWA98195-5061 United States School of Biological Sciences University of Bristol 24 Tyndall Avenue BristolBS8 1TQ United Kingdom Departments of Physiology & Pharmacology Neurology Downstate Health Science University BrooklynNY11203 United States Department of Neurology Kings County Hospital BrooklynNY11203 United States NASA-John H. Glenn Research Center MS 110-3 21000 Brookpark Road ClevelandOH44135 United States Center for Cell Analysis and Modeling UConn Health 263 Farmington Avenue FarmingtonCT06030-6406 United States Amsterdam Institute for Life and Environment Vrije Universiteit Amsterdam De Boelelaan 1108 Amsterdam1081 HZ Netherlands Department of Pathology and Genomic Medicine Thomas Jefferson University 1020 Locust St PhiladelphiaPA19107 United States Biological Sciences Division Pacific Northwest National Laboratory 902 Battelle Blvd RichlandWA99354 United States Auckland Bioengineering Institute University of Auckland Auckland1010 New Zealand Center of Integrative Biology University of Toulouse III-Paul Sabatier 165 Rue Marianne Grunberg-Manago Toulouse31400 France Lifeware Group Inria Building Alan Turing 1 Rue Honoré d’Estienne d’Orves Palaiseau91120 France Multiscale Modeling Group Altos Labs Redwood CityCA94065 United States partner site Tübingen Tübingen Germany Ottfried-Müller-Str. 37 Tübingen72076 Germany 06120 Germany Department of Computer Science Center for Data Science New York University New YorkNY11201 United States Department of Bi

Guidelines for managing scientific data have been established under the FAIR principles requiring that data be Findable, Accessible, Interoperable, and Reusable. In many scientific disciplines, especially computational biology, both data and models are key to progress. For this reason, and recognizing that such models are a very special type of "data", we argue that computational models, especially mechanistic models prevalent in medicine, physiology and systems biology, deserve a complementary set of guidelines. We propose the CURE principles, emphasizing that models should be Credible, Understandable, Reproducible, and Extensible. We delve into each principle, discussing verification, validation, and uncertainty quantification for model credibility;the clarity of model descriptions and annotations for understandability;adherence to standards and open science practices for reproducibility;and the use of open standards and modular code for extensibility and reuse. We outline recommended and baseline requirements for each aspect of CURE, aiming to enhance the impact and trustworthiness of computational models, particularly in biomedical applications where credibility is paramount. Our perspective underscores the need for a more disciplined approach to modeling, aligning with emerging trends such as Digital Twins and emphasizing the importance of data and modeling standards for interoperability and reuse. Finally, we emphasize that given the non-trivial effort required to implement the guidelines, the community moves to automate as many of the guidelines as possible. © 2025, CC BY.

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