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Cobo-Lopez, S.

Publications and source records attributed to Cobo-Lopez, S..

2 recordsLinked to original sources

Emerging dynamic regimes and tipping points from finite empirical principles

The dynamics of biogeochemical, ecological, and astronomical systems are transient. Yet, predicting the occurrence of dynamical shifts remains a challenge due to inferential uncertainties from datasets and the limitations of asymptotic-dependent theories. To address this problem, we developed a theoretical framework that builds on the finite nature of observations. This framework assesses the relative importance of processes, defined as the mechanisms that contribute to the rate of change of the systems dynamic variables, and it predicts the critical values that would trigger a shift into a new regime. The number of observable dynamic regimes within the framework increases exponentially with the number of processes. Observers, however, only experience dynamic regimes associated with relevant processes-- those exceeding a tipping point--within their reference framework. A case study of the framework was tested for a classic predator-prey system with four processes parameterized for bacteria (prey) and lytic bacteriophages (predator). The analysis recovered the sixteen dynamic regimes predicted by the framework, including two non-trivial quasi-equilibrium dynamics. An adaptive Boolean model, which used only relevant observable processes, validated the accuracy of the framework, recovering the dynamics of the full model. The observational framework introduced here provides a strategy for identifying the processes and conditions that lead to tipping points, representing a conceptual paradigm shift in transient dynamics, placing the focus on the specific, finite context of the observer, rather than the intrinsic, asymptotic states of the system. SIGNIFICANCESudden shifts in ecological, climate, and biological systems--so-called tipping points or critical transitions--are notoriously difficult to predict. This study introduces a mathematical framework that redefines these transitions as outcomes shaped by the observers empirical limits. By accounting for finite observation time and resolution, the framework uncovers a rich spectrum of dynamic regimes that classical theories overlook. Its conceptual rigor and practical value are demonstrated in a predator-prey system. This new approach reframes how to forecast regime shifts in complex systems and offers a tool with broad relevance, from microbial ecosystems to planetary climate.

ecology↗

Gut Microbiome Wellness Index 2 for Enhanced Health Status Prediction from Gut Microbiome Taxonomic Profiles

Recent advancements in human gut microbiome research have revealed its crucial role in shaping innovative predictive healthcare applications. We introduce Gut Microbiome Wellness Index 2 (GMWI2), an advanced iteration of our original GMWI prototype, designed as a robust, disease-agnostic health status indicator based on gut microbiome taxonomic profiles. Our analysis involved pooling existing 8069 stool shotgun metagenome data across a global demographic landscape to effectively capture biological signals linking gut taxonomies to health. GMWI2 achieves a cross-validation balanced accuracy of 80% in distinguishing healthy (no disease) from non-healthy (diseased) individuals and surpasses 90% accuracy for samples with higher confidence (i.e., outside the "reject option"). The enhanced classification accuracy of GMWI2 outperforms both the original GMWI model and traditional species-level -diversity indices, suggesting a more reliable tool for differentiating between healthy and non-healthy phenotypes using gut microbiome data. Furthermore, by reevaluating and reinterpreting previously published data, GMWI2 provides fresh insights into the established understanding of how diet, antibiotic exposure, and fecal microbiota transplantation influence gut health. Looking ahead, GMWI2 represents a timely pivotal tool for evaluating health based on an individuals unique gut microbial composition, paving the way for the early screening of adverse gut health shifts. GMWI2 is offered as an open-source command-line tool, ensuring it is both accessible to and adaptable for researchers interested in the translational applications of human gut microbiome science.

bioinformatics↗