Article
Ecology
Jinyun Tang, William J. Riley
Summary: The Liebig's law of the minimum is a crude approximation of the law of mass action, with other approximations such as the synthesizing unit model and additive model being more accurate. When growth is modeled as a function of substrate uptake, the LLM model restricts the organism's elemental stoichiometry, hindering its ability to resolve biological adaptation, ecological evolution, and community assembly. Further research is needed to evaluate the accuracy of different models and their impacts on long-term ecosystem dynamics.
ECOLOGICAL APPLICATIONS
(2021)
Article
Environmental Sciences
Bruno Ringeval, Marko Kvakic, Laurent Augusto, Philippe Ciais, Daniel S. Goll, Nathaniel D. Mueller, Christoph Mueller, Thomas Nesme, Nicolas Vuichard, Xuhui Wang, Sylvain Pellerin
Summary: By calculating the ratio between plant demand and soil supply, researchers conducted a theoretical analysis of nitrogen and phosphorus fertilization experiments to explore interaction formalisms between nutrients. The study revealed that synergistic co-limitation could occur even using Liebig's law of minimum under certain conditions, emphasizing the sensitivity of nutrient interaction categorization to mathematical formulation.
GLOBAL BIOGEOCHEMICAL CYCLES
(2021)
Article
Environmental Sciences
Elena A. Erofeeva
Summary: Hormetic trade-offs, characterized by low-dose stimulation and high-dose inhibition, can occur in various organisms and biological levels. These trade-offs can involve different functional traits or the same trait endpoints. The asynchronous responses of indicators to low-dose stressors are key factors leading to hormetic trade-offs. These trade-offs can have diverse effects on preconditioning, offspring, and population fitness. Additionally, they may contribute to evolutionary processes such as genotype selection and the assimilation of adaptive phenotypes through the Baldwin effect.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Review
Agronomy
Gudeta W. Sileshi
Summary: Optimisation of fertiliser use and site-specific nutrient management are increasingly critical in balancing agricultural productivity with the growing demand for food and environmental concerns. Trials in sub-Saharan Africa have focused on developing economically optimum rates (EORs) for crops, but estimation of nutrient-response parameters and EORs is challenging. Recommendations include using factorial designs and response surface models, using a minimum of six nutrient levels, and considering Reference Soil Groups and cropping history for site-specific EORs.
EXPERIMENTAL AGRICULTURE
(2021)
Article
Marine & Freshwater Biology
Han Zhu, Zhi-Yu Huang, Shan Jiang, Ling Pan, Yi-Long Xi
Summary: This study investigates the adaptability of Brachionus dorcas populations to oxytetracycline (OTC) selection through selection experiments and common garden experiments. The results show that populations exposed to OTC experience increased growth rate but decreased mictic ratio, suggesting a trade-off between asexual and sexual reproduction. The significantly increased tolerance and fitness costs and gains indicate the importance of considering past exposures to pollutants when evaluating the effects of current stressors on natural populations.
AQUATIC TOXICOLOGY
(2022)
Article
Physics, Multidisciplinary
Shamreen Iram, Emily Dolson, Joshua Chiel, Julia Pelesko, Nikhil Krishnan, Ozenc Gungor, Benjamin Kuznets-Speck, Sebastian Deffner, Efe Ilker, Jacob G. Scott, Michael Hinczewski
Summary: The study proposes using quantum methods to control potential evolutionary outcomes to address the unpredictability of evolution. By manipulating the speed and trajectories of evolution, this approach has diverse applications in disease treatment, climate change adaptation, agriculture, and bioengineering.
Article
Multidisciplinary Sciences
Pallavi Kakade, Shabnam Sircaik, Corinne Maufrais, Iuliana V. Ene, Richard J. Bennett
Summary: Aneuploidy, a common phenomenon in fungi, can alter gene expression and promote adaptation to environmental cues. In a study on Candida albicans, a fungal pathogen, researchers found that a strain with a trisomy of chromosome 7 exhibited increased fitness during colonization and infection. The presence of this trisomy resulted in decreased filamentation, and the NRG1 gene on chromosome 7 played a role in inhibiting filamentation. These findings highlight how aneuploidy enables C. albicans to adapt to its host through gene dosage-dependent regulation of morphology.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Immunology
Zuoqiang Wang, Siqi Zhu, Congcong Li, Lin Lyu, Jingchen Yu, Danni Wang, Zhihong Xu, Jinjing Ni, Beile Gao, Jie Lu, Yu-Feng Yao
Summary: This study systematically dissected the gene essentiality profiling of Salmonella under different stress conditions during infection. The essentiality of genes varied in different host niches. Some genes were identified as essential in all stress conditions, and a novel essential fitness gene was discovered. Additionally, an unknown sRNA was found to be essential for resistance to a specific protein.
EMERGING MICROBES & INFECTIONS
(2022)
Article
Multidisciplinary Sciences
Olivier Cotto, Troy Daya
Summary: This study reveals that inferring the underlying genotype-fitness map from observed DFEs is challenging, as many different maps can produce the same DFE. The research also suggests that a random genotype-fitness map would result in the DFE with the largest information entropy, which matches empirical DFEs well.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Multidisciplinary
Tin Phan, James J. Elser, Yang Kuang
Summary: Organism growth is determined by multiple resources interdependently, but traditional growth models based on the Droop cell quota framework only consider single-resource limitations. To overcome this limitation, we propose a multiple-resource limitation growth function and incorporate it into an existing producer-grazer model. Our proposed model captures various experimental observations and provides bounds on the expected growth of an organism. It is also more mathematically tractable compared to other stoichiometric models.
APPLIED SCIENCES-BASEL
(2023)
Article
Evolutionary Biology
Erik Svensson, Mads F. Schou, Julian Melgar, John Waller, Anel Engelbrecht, Zanell Brand, Schalk Cloete, Charlie K. Cornwallis
Summary: This study investigates the thermoregulatory capacity of ostriches and finds that females with better regulation of head temperatures have higher egg-laying rates under hotter conditions. The study also reveals that thermoregulatory capacity is heritable and shows signs of local adaptation to temperature fluctuations. These findings suggest that thermoregulation in ostriches has evolved in response to past climatic conditions and is currently under selection through its effect on reproduction.
Article
Ecology
Genki Sahashi, Kentaro Morita
Summary: This study used long-term mass-marking program data from Japan to evaluate the effects of wild genes on the survival of captive-bred populations. The results showed that increasing the percentage of wild genes can improve the survival rate of captive-bred offspring in the wild.
FRONTIERS IN ECOLOGY AND THE ENVIRONMENT
(2022)
Article
Biology
James A. deMayo, Reid S. Brennan, Melissa H. Pespeni, Michael Finiguerra, Lydia Norton, Gihong Park, Hannes Baumann, Hans G. Dam
Summary: Phenotypic plasticity and evolutionary adaptation can help populations cope with global change, but the limits and costs of adaptation under multiple stressors are not well understood. This study found that a copepod species, Acartia hudsonica, initially experienced a decline in fitness under the combined effects of ocean warming and acidification, but fully recovered within four generations, indicating an adaptive response and synergy between stressors. However, in the long term, the fitness of the adapted lineage was lower compared to the ambient conditions, suggesting a cost to producing phenotypes adapted to both warming and acidification. The study also found sustained phenotypic plasticity in the adapted lineage, even when exposed to different environments.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biology
Gautam Reddy, Michael M. Desai
Summary: Recent research shows that consistent patterns of fitness increase in microbial evolution experiments are mainly driven by diminishing-returns and increasing-costs epistasis. Although the origin of this global epistasis remains unknown, it is found to emerge as a consequence of widespread microscopic epistasis. The specific quantitative relationship between the magnitude of global epistasis and the stochastic effects of microscopic epistasis predicts a universal form of fitness effects distribution when epistasis is prevalent.
Article
Evolutionary Biology
Rama P. Bhatia, Hande Acar Kirit, Cecil M. Lewis Jr, Krithivasan Sankaranarayanan, Jonathan P. Bollback
Summary: Horizontal gene transfer is a powerful evolutionary force in bacterial adaptation, but it is constrained by environmental factors and gene characteristics. This study examines the fitness effects of 44 genes transferred from Escherichia coli to Salmonella enterica in infection-relevant environments, and finds that dosage-dependent effects and gene length are important barriers to HGT. Most transferred genes have deleterious effects, with longer genes having stronger negative fitness consequences. Additionally, the fitness effects of transferred genes vary in different environments. Overall, HGT incurs significant fitness costs on the recipient, with gene characteristics and the environment acting as evolutionary barriers.
Editorial Material
Pediatrics
Damian Roland, Neslihan Suzen, Timothy J. Coats, Jeremy Levesley, Alexander N. Gorban, Evgeny M. Mirkes
PEDIATRIC RESEARCH
(2021)
Article
Engineering, Chemical
Alexander N. Gorban, Denis Constales, Gregory S. Yablonsky
Summary: The concept of Conservatively Perturbed Equilibrium involves perturbing a chemical system from its equilibrium state while maintaining temperature and total amount of elements constant. The unperturbed species in the system will reach at least one extreme concentration value during the transient evolution. The optimization of maximal concentration during transition is presented for reversible first-order reactions, simplifying the overall optimization problem.
CHEMICAL ENGINEERING SCIENCE
(2021)
Article
Materials Science, Multidisciplinary
A. N. Gorban
Summary: This work demonstrates how avoiding the partial equilibrium assumption modifies the reaction rates, resulting in an effective 'entanglement' of reaction rates which become linear combinations of different MAL expressions.
RESULTS IN PHYSICS
(2021)
Review
Biology
A. N. Gorban, T. A. Tyukina, L. Pokidysheva, E. Smirnova
Summary: The concept of biological adaptation has been closely linked to mathematical, engineering, and physical ideas. Selye introduced the notion of adaptation energy in 1938, which sparked debate. Research has found that in systems adapting to environmental factors, correlation and variance tend to increase.
PHYSICS OF LIFE REVIEWS
(2021)
Article
Physics, Multidisciplinary
Jonathan Bac, Evgeny M. Mirkes, Alexander N. Gorban, Ivan Tyukin, Andrei Zinovyev
Summary: This technical note introduces an open-source Python package called scikit-dimension for intrinsic dimension estimation. The package provides a uniform implementation of various known ID estimators based on scikit-learn API, allowing evaluation of global and local intrinsic dimension as well as generating synthetic datasets. It is developed with tools to assess code quality, coverage, unit testing and continuous integration.
Article
Geochemistry & Geophysics
Nataliya Rybnikova, Boris A. Portnov, Evgeny M. Mirkes, Andrei Zinovyev, Anna Brook, Alexander N. Gorban
Summary: In this article, machine learning techniques were used to transform panchromatic night light images into RGB images. The analysis showed that model-estimated RGB images demonstrated a high degree of correspondence with the original RGB images. Linear, kernel, and random forest regressions provided better correlations, contrast similarity, and lower WMSEs levels, while RGB images generated using the elastic map approach provided higher consistency of predictions.
IEEE TRANSACTIONS ON GEOSCIENCE AND REMOTE SENSING
(2022)
Article
Computer Science, Artificial Intelligence
Yuliya Tsybina, Innokentiy Kastalskiy, Mikhail Krivonosov, Alexey Zaikin, Victor Kazantsev, Alexander N. Gorban, Susanna Gordleeva
Summary: Modeling the neuronal processes underlying short-term working memory in neuroscience remains a major focus, and this paper proposes a mathematical model of a spiking neural network that demonstrates how information fragments are maintained and disappear through the activation of astrocytes. The astrocytes exhibit calcium transients on a scale of seconds, modulating synaptic transmission efficiency and neuronal firing rates. The study illustrates how these transients encode neuronal discharge frequencies and provide robust short-term storage of information.
NEURAL COMPUTING & APPLICATIONS
(2022)
Editorial Material
Biology
A. N. Gorban, T. A. Tyukina, L. I. Pokidysheva, E. V. Smirnova
PHYSICS OF LIFE REVIEWS
(2022)
Article
Chemistry, Analytical
Nataliya Rybnikova, Evgeny M. Mirkes, Alexander N. Gorban
Summary: Data on artificial night-time light emitted from areas and captured by satellites are available globally in panchromatic format. Spectral properties of NTL provide more information for analysis, but are only available locally or commercially. Machine learning techniques were used to convert panchromatic NTL images into colored ones, with convolutional neural networks showing better predictive power for models, especially for testing datasets, compared to other methods.
Article
Multidisciplinary Sciences
Innokentiy A. Kastalskiy, Evgeniya Pankratova, Evgeny M. Mirkes, Victor B. Kazantsev, Alexander N. Gorban
Summary: The dynamics of epidemics are influenced by shifts in people's behavior during outbreaks. Combining social stress dynamics with classical epidemic models can accurately describe statistical data and aid in the development of tailored management strategies for different societies.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Andrei Zinovyev, Michail Sadovsky, Laurence Calzone, Aziz Fouche, Clarice S. Groeneveld, Alexander Chervov, Emmanuel Barillot, Alexander N. Gorban
Summary: Cell cycle is a vital process in biology, and mathematical modeling has been used to describe its molecular mechanisms. Recent advancements in transcriptomic and proteomic profiling have allowed researchers to study the cell cycle at the single-cell level. This has increased the need for simplified and semi-phenomenological models to understand the underlying processes. In this study, a modeling framework is proposed to recapitulate the essential properties of the cell cycle and analyze experimental data.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Physics, Multidisciplinary
Evgeny M. Mirkes, Jonathan Bac, Aziz Fouche, Sergey V. Stasenko, Andrei Zinovyev, Alexander N. Gorban
Summary: Domain adaptation is a popular paradigm in machine learning that addresses the divergence between labeled and unlabeled datasets. We propose a method called DAPCA which uses principal component analysis to find a reduced data representation for domain adaptation. DAPCA is an iterative algorithm that solves a quadratic optimization problem and has guaranteed convergence.
Editorial Material
Computer Science, Artificial Intelligence
Witali Dunin-Barkowski, Alexander Gorban
FRONTIERS IN NEUROROBOTICS
(2023)
Proceedings Paper
Computer Science, Artificial Intelligence
Qinghua Zhou, Alexander N. Gorban, Evgeny M. Mirkes, Jonathan Bac, Andrei Zinovyev, Ivan Y. Tyukin
Summary: The study suggests a correlation between the accuracies of trained networks and values of easily computable measures defined on randomly initialised networks, raising the question of exploring other, more principled measures. The dimensionality and quasi-orthogonality of neural networks' feature space may jointly serve as discriminants of network performance.
2022 INTERNATIONAL JOINT CONFERENCE ON NEURAL NETWORKS (IJCNN)
(2022)