Article
Physics, Fluids & Plasmas
Ayan Biswas
Summary: In this study, a biochemical assay was used to convert fan-in networks into feed-forward loops (FFLs). The researchers discovered that redundant information about the output gene product can be broken down into finer components mediated by the constituent pathways. They found that variance-based information within the linear noise regime played a role in quantifying these submodular redundancies. Contrary to conventional wisdom, they found that information redundancy depended nontrivially on inter-regulator correlation.
Article
Cell Biology
Hui Hu, Wei Huang, Hong Zhang, Jianye Li, Qiong Zhang, Ya-Ru Miao, Fei-Fei Hu, Lu Gan, Zhenhong Su, Xiangliang Yang, An-Yuan Guo
Summary: The miR-9-5p/FOXO1/CPEB3 feed-forward loop was identified and found to play a critical role in the progression of hepatocellular carcinoma (HCC). This regulatory module could potentially serve as a new therapeutic target for HCC treatment.
Article
Biochemical Research Methods
Pascal A. Pieters, Bryan L. Nathalia, Ardjan J. van der Linden, Peng Yin, Jongmin Kim, Wilhelm T. S. Huck, Tom F. A. de Greef
Summary: Regulatory pathways in living cells use feed-forward architectures to process and interpret signals, with the ability to reduce noise and detect fold changes. Experimental study in bacterial cells using post-transcriptional regulation has implemented a synthetic feed-forward loop, showing effective repression of background activity but limited potential as a temporal filter.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Carrie Easter, Ellouise Leadbeater, Matthew J. Hasenjager
Summary: This study uses an agent-based model to investigate how individual variation in activity and movement shapes the production of feed-forward loops in a simulated insect colony. The findings suggest that individual variation in activity drives the over-representation of feed-forward loops by determining the directionality of interactions. However, activity variation does not promote faster or more efficient information flow. On the other hand, individual variation in movement trajectory, although not involved in generating feed-forward loops, promotes fast and efficient information flow by linking otherwise unconnected regions.
ROYAL SOCIETY OPEN SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Zhengze Lu, Yang Long, Jiaxin Li, Kebai Ren, Wei Zhao, Xuhui Wang, Chunyu Xia, Yashi Wang, Man Li, Zhirong Zhang, Qin He
Summary: The developed LA/DOX NP can inhibit inflammatory cell recruitment in the liver and lungs through multiple mechanisms, block NF-kappa B and STAT3 signaling pathways, thereby shutting down inflammatory feed-forward loops, providing a new therapeutic strategy for breast cancer and its metastasis.
JOURNAL OF CONTROLLED RELEASE
(2021)
Article
Multidisciplinary Sciences
Xiaowei Guo, Zhuojie Li, Xiaojie Zhu, Meixiao Zhan, Chenxi Wu, Xiang Ding, Kai Peng, Wenzhe Li, Xianjue Ma, Zhongwei Lv, Ligong Lu, Lei Xue
Summary: Autophagy is a degradation process that regulates various physiological and pathological activities. SNAI2, a crucial factor in cancer progression, has been identified as a regulator of autophagy. The binding of DNA targets is critical for FOXO3 to regulate protein nuclear localization, and SNAI2 expression is mediated by FOXO3. These findings reveal a new regulatory loop for inducing autophagy gene expression under energy stress.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Endocrinology & Metabolism
James C. Lech, Sophia Dorfsman, Zoltan Repas, Tjaart P. J. Kruger, Ingrid Melinda Gyalai, Laszlo G. Boros
Summary: This review examines the metabolic diversities in cattle after grain feeding, highlighting the impact of grain feeding on animal and human health, and the significance of deuterium in metabolic processes.
Article
Mechanics
Tuhin Subhra Roy, Mintu Nandi, Pinaki Chaudhury, Sudip Chattopadhyay, Suman K. Banik
Summary: In this study, we propose a stochastic framework to analyze fluctuation propagation in classes of coherent feed-forward loops. We consider the contributions of direct and indirect pathways as well as additive and multiplicative integration mechanisms. The analysis of output fluctuations reveals the contributions of different fluctuation terms to the overall output fluctuations.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2023)
Article
Biochemistry & Molecular Biology
Young Koung Lee, Sunita Kumari, Andrew Olson, Felix Hauser, Doreen Ware
Summary: Zinc finger homeodomain (ZF-HD) transcription factors have important roles in the growth, development, and architecture regulation of plants. In Arabidopsis, ZF-HD TFs negatively regulate miR157 and positively regulate SPL10, creating a feed-forward loop that constitutes a miRNA regulatory module.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Energy & Fuels
Qingyi Wang, Binlei Ju, Yudi Lei, Dan Zhou, Shuai Yin, Danyun Li
Summary: This paper proposes a fractional full feed-forward method to address the issue of harmonic disturbance in the design of grid-connected inverters. Through analysis of the mathematical model and implementation process, this method not only improves harmonic suppression performance, but also reduces the order of the mathematical model's differential term.
CSEE JOURNAL OF POWER AND ENERGY SYSTEMS
(2023)
Article
Humanities, Multidisciplinary
Satyaki Roy, Ahmad F. Al Musawi, Preetam Ghosh
Summary: Complex networks are abstract mathematical representations of real-world systems, and predicting unknown interactions in these networks is of great interest in various fields. Network motifs, which are recurring subnetworks, play a crucial role. In the realm of social science, link prediction models are used to understand various phenomena. This study proposes a new metric, based on a specific network motif called feed-forward loop, which outperforms existing methods on multiple datasets. The authors also discuss the potential applications of this metric in dynamic network inference and the design of combined metrics using different network motifs.
HUMANITIES & SOCIAL SCIENCES COMMUNICATIONS
(2023)
Article
Engineering, Electrical & Electronic
Gang Liu, Haifeng Zhang, Xinda Song
Summary: This article investigates the position-estimation deviation issue of sensorless drive method based on SMO and PLL, and proposes a technology combining phase self-compensation SMO and feed-forward PLL to effectively address the problem.
IEEE JOURNAL OF EMERGING AND SELECTED TOPICS IN POWER ELECTRONICS
(2021)
Article
Genetics & Heredity
Anna Terebus, Farid Manuchehrfar, Youfang Cao, Jie Liang
Summary: The study provides comprehensive characterizations of the stochastic multimodality of feed-forward loops (FFLs), including how switching between different network phenotypes is controlled and the topological sensitivity of the multimodality of the landscapes to regulation intensities. Results show that slow binding and unbinding dynamics of transcription factor to promoter result in strong stochastic behavior of FFLs different from deterministic models, and strong input intensity may lead to up to 6 stable phenotypes.
FRONTIERS IN GENETICS
(2021)
Article
Biology
Edmundo G. Vides, Ayan Adhikari, Claire Y. Chiang, Pawel Lis, Elena Purlyte, Charles Limouse, Justin L. Shumate, Elena Spinola-Lasso, Herschel S. Dhekne, Dario R. Alessi, Suzanne R. Pfeffer
Summary: Activating mutations in LRRK2 can phosphorylate a subset of Rab GTPases. LRRK2 can be recruited by Rab29 to the surface of the Golgi and phosphorylate itself and Rab substrates. The study also found that LRRK2 can bind to Rab8A and Rab10, and identified specific binding regions. Washout experiments showed that the rapid recovery of kinase activity in cells depends on the association between LRRK2 and phosphorylated Rab proteins.
Article
Chemistry, Analytical
Minseong Kim, Hyun-Chul Choi
Summary: This paper presents a new style transfer method called total style transfer, which resolves the limitation of existing methods that cannot fully transfer the scale-across style pattern of a style image into a content image by utilizing intra/inter-scale statistics of multi-scaled feature maps. The method achieves lower memory consumption, faster feed-forwarding speed, and the lowest style loss compared to recent cascade schemes and other style transfer methods.
Article
Biochemical Research Methods
Salva Duran-Nebreda, Jordi Pla, Blai Vidiella, Jordi Pinero, Nuria Conde-Pueyo, Ricard Sole
Summary: This article discusses the characteristics of multicellular entities and their spatial patterns related to functions, as well as the repeating distributions in biological structures. It introduces patterning modules and synthetic gene circuits, along with the phenomenon of symmetry-breaking demonstrated through experimental results.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biology
Ricard Sole, Guim Aguade-Gorgorio
Summary: Differentiation therapy (DTH) is a promising approach to cancer treatment, showing success in specific types of cancer. Mathematical framework and ecological models provide insights for therapy design, but challenges remain in its application to solid tumors.
JOURNAL OF THEORETICAL BIOLOGY
(2021)
Article
Green & Sustainable Science & Technology
Josep M. Anto, Jose Luis Marti, Jaume Casals, Paul Bou-Habib, Paula Casal, Marc Fleurbaey, Howard Frumkin, Manel Jimenez-Morales, Jacint Jordana, Carla Lancelotti, Humberto Llavador, Lela Melon, Ricard Sole, Francesc Subirada, Andrew Williams
Summary: We are living in a time that requires massive and novel coordinated scientific and societal efforts to address pressing challenges threatening catastrophic change to the natural environment. Universities and academic institutions have the opportunity and responsibility to take a leading role in this era. The Planetary Wellbeing Initiative aims to promote the highest attainable standard of wellbeing for both human and non-human beings, requiring collaboration across various fields to tackle the challenges of global complexity, interdisciplinarity, and urgency.
Article
Respiratory System
Martin L. Watzenboeck, Anna-Dorothea Gorki, Federica Quattrone, Riem Gawish, Stefan Schwarz, Christopher Lambers, Peter Jaksch, Karin Lakovits, Sophie Zahalka, Nina Rahimi, Philipp Starkl, Doerte Symmank, Tyler Artner, Celine Pattaroni, Nikolaus Fortelny, Kristaps Klavins, Florian Frommlet, Benjamin J. Marsland, Konrad Hoetzenecker, Stefanie Widder, Sylvia Knapp
Summary: Lung transplantation is the ultimate treatment option for patients with end-stage respiratory diseases, but the mortality rate is high due to chronic lung allograft dysfunction (CLAD). The mechanisms leading to CLAD are not well understood due to insufficient understanding of post-transplant adaptation processes. This study analyzed bronchoalveolar lavage samples from lung recipients and donors, and found that recipient-specific and environmental factors shape the long-term lung microbiome. Certain bacterial strains were found to be correlated with underlying lung diseases even after transplantation. Machine learning techniques accurately predicted future changes in lung function, with the microbial profiles showing high predictive power. The study highlights the importance of understanding lung adaptation processes and the role of microbiome in predicting allograft function.
EUROPEAN RESPIRATORY JOURNAL
(2022)
Article
Multidisciplinary Sciences
Blai Vidiella, Antoni Guillamon, Josep Sardanyes, Victor Maull, Jordi Pla, Nuria Conde, Ricard Sole
Summary: This paper presents an engineered gene network that displays self-organized criticality (SOC) behavior in living cells, poising them close to a critical state. The authors discuss the potential implications of this state on cellular dynamics and behavior.
NATURE COMMUNICATIONS
(2021)
Correction
Multidisciplinary Sciences
Blai Vidiella, Antoni Guillamon, Josep Sardanyes, Victor Maull, Jordi Pla, Nuria Conde, Ricard Sole
NATURE COMMUNICATIONS
(2021)
Article
Biology
Guim Aguade-Gorgorio, Stuart Kauffman, Ricard Sole
Summary: Phenotypic switching in cancer cells is a common phenomenon across tumor types and plays a crucial role in tumor evolution and therapy resistance. A mathematical framework has been developed to understand the dynamics of phenotypic switching, which provides insights for the success of combination therapies targeting both replication and phenotypic transitions.
BULLETIN OF MATHEMATICAL BIOLOGY
(2022)
Article
Ecology
Miguel Berdugo, Blai Vidiella, Ricard V. Sole, Fernando T. Maestre
Summary: With ongoing climate change, the probability of exceeding aridity thresholds in drylands and experiencing abrupt ecosystem changes is higher than ever. By identifying different mechanisms causing aridity thresholds and potential amplification mechanisms, we can develop specific hypotheses to bridge knowledge gaps and focus on monitoring and adapting to abrupt ecosystem changes in global drylands.
FUNCTIONAL ECOLOGY
(2022)
Article
Ecology
Stefanie Widder, Jiangchao Zhao, Lisa A. Carmody, Qingyang Zhang, Linda M. Kalikin, Patrick D. Schloss, John J. LiPuma
Summary: In this study, bacterial communities in the airways of cystic fibrosis patients were analyzed, leading to the identification of different pulmotypes which show temporal sequence patterns and significant correlations with patient clinical status. By constructing pulmotype-specific metabolic activity profiles, it was found that microbial communities within pulmotypes drive distinct community functions.
Review
Physics, Multidisciplinary
Ricard Sole, Josep Sardanyes, Santiago F. Elena
Summary: Viruses have complex relationships with other organisms, sometimes parasitizing them and causing diseases, while also playing a pivotal role in the evolution of their hosts.
REPORTS ON PROGRESS IN PHYSICS
(2021)
Article
Ecology
Patrick Fraser, Ricard Sole, Gemma de las Cuevas
Summary: The article discusses why the brain can understand self-reference and introduces the "Strange Loop Model" to explain this phenomenon. This model involves causal feedback between two brain modules to avoid paradoxes of self-reference and negation. It also suggests that the brain's metastable dynamics can limit endless reasoning. Finally, the representation of logical inconsistencies in the model leads to causal incongruence between brain subsystems.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Article
Microbiology
Stefanie Widder, Irene Goerzer, Benjamin Friedel, Nina Rahimi, Stefan Schwarz, Peter Jaksch, Sylvia Knapp, Elisabeth Puchhammer-Stoeckl
Summary: This study provides a detailed analysis of virome dynamics after lung transplantation, revealing host, body compartment, and time-specific dependency patterns among viruses. The results also suggest genetic adaptation to the host microenvironment at the level of the virome and support the hypothesis of functional complementarity between Anellovirus groups and other persistent viruses.
Correction
Microbiology
Stefanie Widder, Irene Goerzer, Benjamin Friedel, Nina Rahimi, Stefan Schwarz, Peter Jaksch, Sylvia Knapp, Elisabeth Puchhammer-Stoeckl
Meeting Abstract
Cardiac & Cardiovascular Systems
S. Widder, R. Gawish, M. Watzenboeck, A. Gorki, F. Quattrone, S. Schwarz, C. Lambers, P. Jaksch, K. Lakovits, S. Zahalka, N. Rahimi, P. Starkl, D. Symmank, T. Artner, K. Hoetzenecker, S. Knapp
JOURNAL OF HEART AND LUNG TRANSPLANTATION
(2021)
Meeting Abstract
Medicine, General & Internal
Martin L. Watzenboeck, Anna-Dorothea Gorki, Federica Quattrone, Riem Gawish, Stefan Schwarz, Christopher Lambers, Peter Jaksch, Karin Lakovits, Sophie Zahalka, Nina Rahimi, Philipp Starkl, Doerte Symmank, Tyler Artner, Celine Pattaroni, Nikolaus Fortelny, Kristaps Klavins, Benjamin J. Marsland, Konrad Hoetzenecker, Stefanie Widder, Sylvia Knapp
WIENER KLINISCHE WOCHENSCHRIFT
(2020)
