Article
Genetics & Heredity
Zeyu Zhang, Yaning Yang, Yinsheng Zhou, Hongyan Fang, Min Yuan, Kate Sasser, Hisham Hamadeh, Xu Steven Xu
Summary: Mutual exclusivity analyses are effective in identifying driver genes for cancer studies, but controlling false positives and improving accuracy is challenging. A forward selection algorithm (FSME) proposed in this study for identifying mutually exclusive gene sets shows higher precision and recall rates compared to other approaches such as CoMEt, WExT, and MEGSA. Application to TCGA real datasets confirms FSME's utility in discovering cancer driver genes.
JOURNAL OF HUMAN GENETICS
(2021)
Article
Multidisciplinary Sciences
Ami G. Sangster, Robert J. Gooding, Andrew Garven, Hamid Ghaedi, David M. Berman, Scott K. Davey
Summary: Muscle invasive bladder cancer is characterized by abundant mutations, particularly in DNA damage response and chromatin modification genes. The significance of these mutations and their interactions in the development and progression of the disease have been explored through the identification of mutually exclusive mutation patterns. The discovery of these patterns sheds light on the mechanisms underlying muscle invasive bladder cancer and may guide therapeutic development.
Review
Cell Biology
Francesca Florini, Joseph E. Visone, Kirk W. Deitsch
Summary: Cellular decision-making at the level of gene expression is crucial for the development and evolution of organisms, leading to phenotypic diversity and adaptive subpopulations. Organisms and parasites have evolved different strategies to choose one gene from a large family for expression.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Computer Science, Information Systems
Huimin Zhang, Yi Shi, Wu Xie
Summary: In multi-agent systems, coordinating and controlling each agent to complete tasks on mutually exclusive resources is a basic mission due to the high cost of some hardware and software in reality. However, when applying supervisory control theory (SCT) to MAS, the size of the plant model increases exponentially with the number of agents, leading to a state explosion problem. To address this issue, a synchronous product with constraints and a framework for computing the supremal supervisor for the entire MAS are proposed. Experimental studies show the effectiveness of the proposed approach. The research contributes to mitigating the state explosion problem in supervisory control of MAS and eliminates the need for an additional coordinator compared to decentralized or distributed control.
Article
Pharmacology & Pharmacy
Yongyi Bai, Haishen Yao, Xuehan Jiang, Suyan Bian, Jinghui Zhou, Xingzhi Sun, Gang Hu, Lan Sun, Guotong Xie, Kunlun He
Summary: This study proposes a method to construct a nonmutually exclusive decision tree for medication recommendations for complicated diseases such as HF, and applies it in a CDSS. Our framework is universal for most diseases and could be generally applied in developing the CDSS for treatment.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Alfy Benny, Remya Ramakrishnan, Mahesh Hariharan
Summary: The study reveals that the Greek cross (+) stacked orientation exhibits mutually exclusive hole and electron transfer couplings in any molecular candidate, independent of the nature of the monomer. Additionally, the Greek cross (+) stacks of the considered acene candidates exhibit selective charge carrier mobility in the hopping regime of charge transport.
Article
Multidisciplinary Sciences
Xuan Liu, Wanru Du, Xiaoyin Wang, Ruiqun Li, Pengcheng Sun, Xiaochuan Jing
Summary: This paper proposes a mutually exclusive Binary Cross Tagging (BCT) scheme and develops an end-to-end BCT framework to jointly extract overlapping entities and triples. The proposed framework achieves encouraging performance in F1 scores on multiple datasets, especially when the overlapping problem becomes complex.
Article
Engineering, Marine
H. C. Seyffert
Summary: This study develops a non-linear Design Loads Generator process to examine extreme responses of marine systems by linking wave profiles with a probabilistic framework. Analysis of rare wave groups results in an ensemble of short wave profiles to excite converged extreme value statistics of defined responses.
Article
Biochemistry & Molecular Biology
Xue-Ling Mao, Zi-Han Li, Meng-Han Huang, Jin-Tao Wang, Jing-Bo Zhou, Qing-Run Li, Hong Xu, Xi-Jin Wang, Xiao-Long Zhou
Summary: This study revealed the presence of METTL2A and METTL2B in vivo, and successfully demonstrated their m(3)C32 modification activity on tRNA(Thr) and tRNA(ser)(GCU) in vitro. The research also found that G35 and t(6)A37 are essential for tRNA(Thr) m(3)C32 formation, while the anticodon loop and long arm are crucial for tRNA(ser)(GCU) m(3)C32 biogenesis.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Pediatrics
Enza D'Auria, Martina Minutoli, Alessandra Colombo, Marco Ugo Andrea Sartorio, Fiammetta Zunica, Gianvincenzo Zuccotti, Vassilios Lougaris
Summary: In recent decades, there has been a simultaneous increase in the prevalence of atopic and autoimmune disorders in pediatric population. While the Th1-Th2 paradigm suggests separate immune responses for autoimmune diseases and hypersensitivity reactions, recent evidence indicates that these diseases may share common pathogenic pathways.
FRONTIERS IN PEDIATRICS
(2023)
Article
Genetics & Heredity
Haiyang Dong, Lei Li, Xiaohua Zhu, Jilong Shi, Ying Fu, Shixin Zhang, Yang Shi, Bingbing Xu, Jian Zhang, Feng Shi, Yongfeng Jin
Summary: Our study identified evidence of evolutionarily conserved RNA base pairings mediating mutually exclusive splicing in the exon 4 cluster of Dscam1 in Coleoptera species. In contrast to fly species, most exon 6 selector sequences are partially located in the variable exon region in Coleoptera species. Additionally, bidirectional RNA-RNA interactions were predicted to regulate mutually exclusive splicing of variable exon 9 of Dscam1.
FRONTIERS IN GENETICS
(2021)
Review
Food Science & Technology
Iain J. Gordon, Adrian D. Manning, Laetitia M. Navarro, Julia Rouet-Leduc
Summary: Rewilding is a relatively new approach to nature conservation, aiming to restore ecosystems to a natural state with trophic complexity and ecological processes, but faces challenges and limitations in practice that need to be carefully considered to meet broader societal conservation needs.
FRONTIERS IN SUSTAINABLE FOOD SYSTEMS
(2021)
Article
Engineering, Biomedical
Suyoung Lee, Seohyun Byun, Changhon Lee, Sun Hee Park, Dipayan Rudra, Yoichiro Iwakura, You Jeong Lee, Sin-Hyeog Im, Dong Soo Hwang
Summary: This study reveals the impact of bending stiffness on the immune regulatory properties of chitosan, indicating the potential of low molecular weight chitosan as a pharmaceutical ingredient for treating various inflammatory disorders.
ADVANCED HEALTHCARE MATERIALS
(2022)
Article
Computer Science, Information Systems
Taegeun Moon, Hyoungshick Kim, Sangwon Hyun
Summary: To counter compression side-channel attacks (CSCA), researchers propose Mutexion, a highly efficient CSCA mitigation system that allows full compression of web pages, including secret data, by excluding certain subsequences. They develop automated annotation techniques to trace secret and user-controlled data in web pages. Evaluation results demonstrate that Mutexion effectively prevents CSCA while achieving a similar compression ratio as vulnerable zlib.
ACM TRANSACTIONS ON THE WEB
(2022)
Article
Chemistry, Physical
Manmatha Mahato, Jong-Nam Kim, Rassoul Tabassian, Araz Rajabi-Abhari, Ji-Seok Kim, Sanghee Nam, Hyunjoon Yoo, Il-Kwon Oh
Summary: A mutually exclusive ytterbium and nitrogen-co-doped mesoporous titania-carbon (YbNTiO2@C) is reported as a positive electrode material for self-cleaning functionality and high-power triboelectric nanogenerators. The nano-porous structures of YbNTiO2@C provide a larger platform for atom-to-atom contacts and increase the charge density of the tribolayer, resulting in significant enhancement of TENG performances and self-cleaning function under sunlight.
Article
Oncology
Magdalena Keller, Katharina Rohlf, Annika Glotzbach, Gregor Leonhardt, Simon Lueke, Katharina Derksen, Oezlem Demirci, Defne Goecener, Mohammad AlWahsh, Joerg Lambert, Cecilia Lindskog, Marcus Schmidt, Walburgis Brenner, Matthias Baumann, Eldar Zent, Mia-Lisa Zischinsky, Birte Hellwig, Katrin Madjar, Joerg Rahnenfuehrer, Nina Overbeck, Joerg Reinders, Cristina Cadenas, Jan. G. G. Hengstler, Karolina Edlund, Rosemarie Marchan
Summary: This study found that EDI3 is highly expressed in ER-HER2+ breast tumors, and its expression and activity are also highest in ER-HER2+ breast cancer cell lines. Silencing HER2 and inhibiting HER2 signaling can decrease EDI3 expression. Silencing EDI3 can selectively decrease cell viability in ER-HER2+ cells. Therefore, EDI3 may be a potential therapeutic target in patients with HER2-targeted therapy-resistant ER-HER2+ breast cancer.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2023)
Review
Health Care Sciences & Services
Sarah Friedrich, Andreas Groll, Katja Ickstadt, Thomas Kneib, Markus Pauly, Joerg Rahnenfuhrer, Tim Friede
Summary: This article reviews regularization approaches in data science for overcoming overfitting and improving prediction, and discusses their limited application in medical research. The authors suggest increased use of regularization approaches in medicine, despite the added complexity they bring to analyses. Proper investments in computing facilities and educational resources can help overcome these challenges.
STATISTICAL METHODS IN MEDICAL RESEARCH
(2023)
Article
Psychiatry
Johannes C. S. Zang, Caroline May, Birte Hellwig, Dirk Moser, Jan G. Hengstler, Steve Cole, Markus Heinrichs, Joerg Rahnenfuehrer, Katrin Marcus, Robert Kumsta
Summary: The experience of childhood adversity has been linked to poor health outcomes in adulthood. Previous research focused on DNA methylation and transcriptomic profiles, while neglecting the level of proteins. Using mass spectrometry, this study examined the proteome of CD14(+) monocytes in adults with childhood adversity before and after psychosocial stress exposure. The results indicated upregulation of specific proteins related to immune processes, protein metabolism, and mitochondrial biology, especially in females.
TRANSLATIONAL PSYCHIATRY
(2023)
Article
Biochemistry & Molecular Biology
Ilinca Suciu, Johannes Delp, Simon Gutbier, Anna-Katharina Ueckert, Anna-Sophie Spreng, Philipp Eberhard, Christiaan Karreman, Falk Schreiber, Katrin Madjar, Joerg Rahnenfuehrer, Ivana Celardo, Ivano Amelio, Marcel Leist
Summary: Proteasome inhibition is related to parkinsonian pathology and dopaminergic neuron degeneration. In this study, the metabolome and transcriptome regulations of human LUHMES neurons exposed to MG-132 were investigated, revealing compromised energy metabolism and activation of stress response pathways. These findings provide insights into the cellular responses to proteasome dysfunction and potential therapeutic interventions for Parkinson's disease.
Article
Medicine, General & Internal
Joerg Rahnenfuehrer, Riccardo De Bin, Axel Benner, Federico Ambrogi, Lara Lusa, Anne-Laure Boulesteix, Eugenia Migliavacca, Harald Binder, Stefan Michiels, Willi Sauerbrei, Lisa McShane
Summary: This review provides an overview of key aspects and methods for analyzing high-dimensional data in biomedical research. It addresses the challenges and opportunities of analyzing high-dimensional data, and offers solutions and references for researchers.
Article
Gastroenterology & Hepatology
Huan Su, Madhuri Haque, Svea Becker, Karolina Edlund, Julia Duda, Qingbi Wang, Johanna Reissing, Hanns-Ulrich Marschall, Lena S. Candels, Mohamed Mohamed, Wilhelm Sjoland, Lijun Liao, Stephan A. Drexler, Till Strowig, Joerg Rahnenfuehrer, Jan G. Hengstler, Maximilian Hatting, Christian Trautwein
Summary: This study used a mouse model to investigate the impact of the PNPLA3 I148M polymorphism on the progression of NAFLD. It was found that mice with the PNPLA3 I148M genotype showed exacerbated NAFLD, which was associated with changes in microbiota composition and liver gene expression, leading to a stronger inflammatory response and enhanced liver fibrosis progression.
LIVER INTERNATIONAL
(2023)
Article
Oncology
Katrin Almstedt, Lisa Krauthauser, Franziska Kappenberg, Daniel-Christoph Wagner, Anne-Sophie Heimes, Marco J. J. Battista, Katharina Anic, Slavomir Krajnak, Antje Lebrecht, Roxana Schwab, Walburgis Brenner, Wolfgang Weikel, Joerg Rahnenfuehrer, Jan G. G. Hengstler, Wilfried Roth, Annette Hasenburg, Kathrin Stewen, Marcus Schmidt
Summary: This study investigated the differences in HER2 expression levels between primary tumors and distant metastases in HER2-negative breast cancer patients. The results showed relevant discordance of HER2-low status between primary tumors and their corresponding distant metastases. Significant HER2 discordance rates were observed between different metastatic sites and molecular subtypes. These findings highlight the importance of evaluating potentially therapy-relevant discordance rates between a primary tumor and corresponding distant metastases.
Review
Toxicology
Franziska Kappenberg, Julia C. C. Duda, Leonie Schuermeyer, Onur Guel, Tim Brecklinghaus, Jan G. G. Hengstler, Kirsten Schorning, Joerg Rahnenfuehrer
Summary: The analysis of dose-response, concentration-response, and time-response relationships is a crucial aspect of toxicological research. Researchers must decide whether to solely consider measured concentrations or use a parametric model for extrapolation. This study examines the current state of statistical analysis in the toxicological literature through a comprehensive review of dose-response analyses published in three major journals in 2021. The review covers biological considerations, statistical design elements, and analysis aspects, providing concrete guidance for statistical planning, execution, and analysis of dose-response studies.
ARCHIVES OF TOXICOLOGY
(2023)
Article
Biochemical Research Methods
Leonie Schuermeyer, Kirsten Schorning, Joerg Rahnenfuehrer
Summary: An important problem in toxicology is the simultaneous inference of concentration-response relationships in gene expression data. The choice of experimental design and the set of concentrations used for observations greatly affect the quality of inference. In this study, we propose efficient designs for simultaneous inference and use D-optimality criterion and K-means procedure for clustering support points.
BMC BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Florian Seidel, Franziska Kappenberg, Susann Fayyaz, Andreas Scholtz-Illigens, Anna Cherianidou, Katharina Derksen, Patrick Nell, Rosemarie Marchan, Karolina Edlund, Marcel Leist, Agapios Sachinidis, Jorg Rahnenfuehrer, Reinhard Kreiling, Jan G. Hengstler
Summary: The study conducted a comparison of the four currently approved parabens and found that cytotoxicity and gene expression changes only occurred at high concentrations. It suggests that the results of in vivo DART with ethylparaben are similar to the methyl- or propyl derivates.
CHEMICO-BIOLOGICAL INTERACTIONS
(2023)
Article
Multidisciplinary Sciences
Franziska Kappenberg, Joerg Rahnenfuehrer
Summary: In toxicological concentration-response studies, determining the alert concentration is a common goal. High-throughput gene expression experiments provide concentration-response profiles for thousands of genes simultaneously. We propose an empirical Bayes approach for information sharing across genes, which improves the estimation accuracy for most genes but may lead to increased errors for some genes that cannot be mitigated with more sophisticated prior distributions.
Article
Cell Biology
Anna Cherianidou, Franziska Kappenberg, Florian Seidel, Aviseka Acharya, Panagiota Papazoglou, Sureshkumar Perumal Srinivasan, Juergen Hescheler, Luying Peng, Marcel Leist, Jan G. Hengstler, Joerg Rahnenfuehrer, Agapios Sachinidis
Summary: Animal studies for embryotoxicity evaluation are limited in their relevance to humans due to species differences. This study used human induced pluripotent stem cells (hiPSCs) to recapitulate cardiomyogenesis and identify key genes and processes affected by potential teratogens. We found that certain retinoids completely blocked cardiomyogenesis in hiPSCs and established a Developmental Cardiotoxicity Index that accurately differentiates teratogens from non-teratogens.
CELL DEATH DISCOVERY
(2023)
Article
Toxicology
Marieke Stolte, Wiebke Albrecht, Tim Brecklinghaus, Lisa Gruendler, Peng Chen, Jan G. Hengstler, Franziska Kappenberg, Jorg Rahnenfuehrer
Summary: This article explores the use of dimension reduction methods and advanced statistical learning algorithms for classifying compounds based on hepatotoxic risk. The research shows that combining data from cytotoxicity assays and gene expression variables leads to better prediction accuracy than using these variables individually. Different strategies for summarizing gene expression data also contribute to improved prediction quality.
COMPUTATIONAL TOXICOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Paulina Szymczak, Ewa Szczurek
Summary: Antimicrobial peptides (AMPs) are promising agents against antimicrobial resistance, and their discovery and generation can be enhanced through discrimination and generation approaches. Recent achievements in AI-driven AMP discovery are reviewed, highlighting exciting directions.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Health Care Sciences & Services
Thomas Czypionka, Emil N. Iftekhar, Barbara Prainsack, Viola Priesemann, Simon Bauer, Andre Calero Valdez, Sarah Cuschieri, Enrico Glaab, Eva Grill, Jenny Krutzinna, Christos Lionis, Helena Machado, Carlos Martins, George N. Pavlakis, Matjaz Perc, Elena Petelos, Martyn Pickersgill, Alexander Skupin, Eva Schernhammer, Ewa Szczurek, Sotirios Tsiodras, Peter Willeit, Paul Wilmes
Summary: In the summer of 2021, European governments lifted most NPIs due to prolonged waves of COVID-19. However, without achieving high enough vaccination rates, the virus re-emerged. Different countries have adopted various public health strategies for autumn and winter, either aiming for low incidence through re-introducing NPIs or accepting high incidence levels. The study argues that a coordinated low incidence strategy is necessary, built on open communication and trust.
LANCET REGIONAL HEALTH-EUROPE
(2022)