Sustainable scenarios in a plants-rhizobacteria-plant consumers system are in risk when biotic or abiotic factors change.

The ecological relationship among plants, rhizobacteria and plant consumers has attracted the attention of researchers due to its implications in field crops. It is known that, the rhizosphere is occupied not only by rhizobacteria which grant benefits to the plants but also by bacteria which are detrimental for them. In this work, we construct and analyze a plants-rhizobacteria-plant consumers system. In the modeling process, it is assumed that there is a conditioned interaction between plants and bacteria in the rhizosfera such that there is a mutualistic relationship at low densities of rhizobacteria and the relationship is parasitic or competitive at higher densities of them. Benefits granted by rhizobacteria include mechanisms that increase the plant growth and defense mechanisms against plant consumers. From the analysis of the model and its simplified version, we show that scenarios of coexistence of all populations can occur for a wide range of values of the parameters which describe biotic or abiotic factors; however, these scenarios are in risk since scenarios of exclusion of species can occur simultaneously due to the presence of bistability phenomena. The results obtained can be useful for the decision makers to design interventions strategies on field crops when plant growth-promoting rhizobacteria are used.

Reassessing the alternative ecosystem states proposition in the African savanna-forest domain.

Ecologists are being challenged to predict how ecosystems will respond to climate changes. According to the Multi-Colored World (MCW) hypothesis, climate impacts may not manifest because consumers such as fire and herbivory can override the influence of climate on ecosystem state. One MCW interpretation is that climate determinism fails because alternative ecosystem states (AES) are possible at some locations in climate space. We evaluated theoretical and empirical evidence for the proposition that forest and savanna are AES in Africa. We found that maps which infer where AES zones are located were contradictory. Moreover, data from longitudinal and experimental studies provide inconclusive evidence for AES. That is, although the forest-savanna AES proposition is theoretically sound, the existing evidence is not yet convincing. We conclude by making the case that the AES proposition has such fundamental consequences for designing management actions to mitigate and adapt to climate change in the savanna-forest domain that it needs a more robust evidence base before it is used to prescribe management actions.

Dynamics of a network mediated by IL-36 and involved in the pathogenesis of psoriasis.

The pathogenesis of the inflammatory, chronic, and common skin disease psoriasis involves immune cells, skin cells (keratinocytes), and the cytokines they secrete. Hyperproliferation and abnormal differentiation of keratinocytes are hallmarks of the disease. The roles of cytokines such as TNFα, IL-15, IL-17, and IL-23 in psoriasis have been studied through mathematical/computational models as well as experiments. However, the role of proinflammatory cytokine IL-36 in the onset and progression of psoriasis is still elusive. To explore the role of IL-36, we construct a network embodying indirect cell-cell interactions of a few immune and skin cells mediated by IL-36 based on existing knowledge. We also develop a mathematical model for the network and perform a global sensitivity analysis. Our results suggest that the model is most sensitive to a parameter that represents the level of cytokine IL-36. In addition, a steady-state analysis of the model suggests that an increase in the level of IL-36 could lead to the hyperproliferation of keratinocytes and, thus, psoriasis. Our analysis also highlights that the plaque formation and progression of psoriasis could occur through either a gradual or a switch-like increase in the keratinocyte population. We propose that the switch-like increase would be due to a bistable behavior of the network toward either a psoriatic or healthy state and could be used as a novel treatment strategy.

Consciousness and sleep.

Sleep is a universal, essential biological process. It is also an invaluable window on consciousness. It tells us that consciousness can be lost but also that it can be regained, in all its richness, when we are disconnected from the environment and unable to reflect. By considering the neurophysiological differences between dreaming and dreamless sleep, we can learn about the substrate of consciousness and understand why it vanishes. We also learn that the ongoing state of the substrate of consciousness determines the way each experience feels regardless of how it is triggered-endogenously or exogenously. Dreaming consciousness is also a window on sleep and its functions. Dreams tell us that the sleeping brain is remarkably lively, recombining intrinsic activation patterns from a vast repertoire, freed from the requirements of ongoing behavior and cognitive control.

Living in a noisy world-origins of gene expression noise and its impact on cellular decision-making.

The expression level of a gene can vary between genetically identical cells under the same environmental condition-a phenomenon referred to as gene expression noise. Several studies have now elucidated a central role of transcription factors in the generation of expression noise. Transcription factors, as the key components of gene regulatory networks, drive many important cellular decisions in response to cellular and environmental signals. Therefore, a very relevant question is how expression noise impacts gene regulation and influences cellular decision-making. In this Review, we summarize the current understanding of the molecular origins of expression noise, highlighting the role of transcription factors in this process, and discuss the ways in which noise can influence cellular decision-making. As advances in single-cell technologies open new avenues for studying expression noise as well as gene regulatory circuits, a better understanding of the influence of noise on cellular decisions will have important implications for many biological processes.

Analysis of long transients and detection of early warning signals of extinction in a class of predator-prey models exhibiting bistable behavior.

In this paper, we develop a method of analyzing long transient dynamics in a class of predator-prey models with two species of predators competing explicitly for their common prey, where the prey evolves on a faster timescale than the predators. In a parameter regime near a singular zero-Hopf bifurcation of the coexistence equilibrium state, we assume that the system under study exhibits bistability between a periodic attractor that bifurcates from the singular Hopf point and another attractor, which could be a periodic attractor or a point attractor, such that the invariant manifolds of the coexistence equilibrium point play central roles in organizing the dynamics. To find whether a solution that starts in a vicinity of the coexistence equilibrium approaches the periodic attractor or the other attractor, we reduce the equations to a suitable normal form, and examine the basin boundary near the singular Hopf point. A key component of our study includes an analysis of the long transient dynamics, characterized by their rapid oscillations with a slow variation in amplitude, by applying a moving average technique. We obtain a set of necessary and sufficient conditions on the initial values of a solution near the coexistence equilibrium to determine whether it lies in the basin of attraction of the periodic attractor. As a result of our analysis, we devise a method of identifying early warning signals, significantly in advance, of a future crisis that could lead to extinction of one of the predators. The analysis is applied to the predator-prey model considered in Sadhu (Discrete Contin Dyn Syst B 26:5251-5279, 2021) and we find that our theory is in good agreement with the numerical simulations carried out for this model.

Mathematical modeling of viral infection and the immune response controlled by the circadian clock.

Time of day affects how well the immune system responds to viral or bacterial infections. While it is well known that the immune system is regulated by the circadian clock, the dynamic origin of time-of-day-dependent immunity remains unclear. In this paper, we studied the circadian control of immune response upon infection of influenza A virus through mathematical modeling. Dynamic simulation analyses revealed that the time-of-day-dependent immunity was rooted in the relative phase between the circadian clock and the pulse of viral infection. The relative phase, which depends on the time the infection occurs, plays a crucial role in the immune response. It can drive the immune system to one of two distinct bistable states, a high inflammatory state with a higher mortality rate or a safe state characterized by low inflammation. The mechanism we found here also explained why the same species infected by different viruses has different time-of-day-dependent immunities. Further, the time-of-day-dependent immunity was found to be abolished when the immune system was regulated by an impaired circadian clock with decreased oscillation amplitude or without oscillations.

Advantages of Bistable Microwires in Digital Signal Processing.

The advantageous applications of magnetic bistable microwires have emerged during long-lasting research. They have a wide range of applications in the scientific sphere or technical practice. They can be used for various applications, including magnetic memories, biomedicine, and sensors. This manuscript is focused on the last-mentioned application of microwires-sensors-discussing various digital signal processing techniques used in practical applications. Thanks to the highly sensitive properties of microwires and their two stable states of magnetization, it is possible to perform precise measurements with less demanding digital processing. The manuscript presents four practical signal-processing methods of microwire response using three different experiments. These experiments are focused on detecting the signal in a simple environment without an external magnetic background, measuring with the external background of a ferromagnetic core, and measuring in harsh conditions with a strong magnetic background. The experiments aim to propose the best method under various conditions, emphasizing the quality and signal processing speed of the microwire signal.

The Design and Ground Test Verification of an Energy-Efficient Wireless System for the Fatigue Monitoring of Wind Turbine Blades Based on Bistable Piezoelectric Energy Harvesting.

A wireless monitoring system based on piezoelectric energy harvesting (PEH) is presented to provide fatigue data of wind turbine blades in operation. The system comprises three subsystems, each respectively providing the following functions: (i) the conversion of mechanical to electric energy by exploiting the bistable vibration of a composite beam with piezoelectric patches in post-buckling, (ii) harvesting the converted energy by means of a modified, commercial, off-the-shelf (COTS) circuit to feed a LiPo battery and (iii) the battery-powered acquisition and wireless transmission of sensory signals to the cloud to be elaborated upon by the end-user. The system was verified with ground tests under representative operation conditions, which demonstrated the fulfillment of the design requirements. The measurements indicated that the system provided 23% of the required power for fully autonomous operation when subjected to white noise base excitation of 1 g acceleration in the range of 1-20 Hz.

Neuronal synchrony and critical bistability: Mechanistic biomarkers for localizing the epileptogenic network.

OBJECTIVE: Postsurgical seizure freedom in drug-resistant epilepsy (DRE) patients varies from 30% to 80%, implying that in many cases the current approaches fail to fully map the epileptogenic zone (EZ). We aimed to advance a novel approach to better characterize epileptogenicity and investigate whether the EZ encompasses a broader epileptogenic network (EpiNet) beyond the seizure zone (SZ) that exhibits seizure activity. METHODS: We first used computational modeling to test putative complex systems-driven and systems neuroscience-driven mechanistic biomarkers for epileptogenicity. We then used these biomarkers to extract features from resting-state stereoelectroencephalograms recorded from DRE patients and trained supervised classifiers to localize the SZ against gold standard clinical localization. To further explore the prevalence of pathological features in an extended brain network outside of the clinically identified SZ, we also used unsupervised classification. RESULTS: Supervised SZ classification trained on individual features achieved accuracies of .6-.7 area under the receiver operating characteristic curve (AUC). Combining all criticality and synchrony features further improved the AUC to .85. Unsupervised classification discovered an EpiNet-like cluster of brain regions, in which 51% of brain regions were outside of the SZ. Brain regions in the EpiNet-like cluster engaged in interareal hypersynchrony and locally exhibited high-amplitude bistability and excessive inhibition, which was strikingly similar to the high seizure risk regime revealed by our computational modeling. SIGNIFICANCE: The finding that combining biomarkers improves SZ localization accuracy indicates that the novel mechanistic biomarkers for epileptogenicity employed here yield synergistic information. On the other hand, the discovery of SZ-like brain dynamics outside of the clinically defined SZ provides empirical evidence of an extended pathophysiological EpiNet.

Mechanism of Decision Making between Autophagy and Apoptosis Induction upon Endoplasmic Reticulum Stress.

Dynamic regulation of the cellular proteome is mainly controlled in the endoplasmic reticulum (ER). Accumulation of misfolded proteins due to ER stress leads to the activation of unfolded protein response (UPR). The primary role of UPR is to reduce the bulk of damages and try to drive back the system to the former or a new homeostatic state by autophagy, while an excessive level of stress results in apoptosis. It has already been proven that the proper order and characteristic features of both surviving and self-killing mechanisms are controlled by negative and positive feedback loops, respectively. The new results suggest that these feedback loops are found not only within but also between branches of the UPR, fine-tuning the response to ER stress. In this review, we summarize the recent knowledge of the dynamical characteristic of endoplasmic reticulum stress response mechanism by using both theoretical and molecular biological techniques. In addition, this review pays special attention to describing the mechanism of action of the dynamical features of the feedback loops controlling cellular life-and-death decision upon ER stress. Since ER stress appears in diseases that are common worldwide, a more detailed understanding of the behaviour of the stress response is of medical importance.

A machine-learning tool to identify bistable states from calcium imaging data.

Mapping neuronal activation using calcium imaging in vivo during behavioural tasks has advanced our understanding of nervous system function. In almost all of these studies, calcium imaging is used to infer spike probabilities because action potentials activate voltage-gated calcium channels and increase intracellular calcium levels. However, neurons not only fire action potentials, but also convey information via intrinsic dynamics such as by generating bistable membrane potential states. Although a number of tools for spike inference have been developed and are currently being used, no tool exists for converting calcium imaging signals to maps of cellular state in bistable neurons. Purkinje neurons in the larval zebrafish cerebellum exhibit membrane potential bistability, firing either tonically or in bursts. Several studies have implicated the role of a population code in cerebellar function, with bistability adding an extra layer of complexity to this code. In the present study, we develop a tool, CaMLSort, which uses convolutional recurrent neural networks to classify calcium imaging traces as arising from either tonic or bursting cells. We validate this classifier using a number of different methods and find that it performs well on simulated event rasters as well as real biological data that it had not previously seen. Moreover, we find that CaMLsort generalizes to other bistable neurons, such as dopaminergic neurons in the ventral tegmental area of mice. Thus, this tool offers a new way of analysing calcium imaging data from bistable neurons to understand how they participate in network computation and natural behaviours. KEY POINTS: Calcium imaging, compriising the gold standard of inferring neuronal activity, does not report cellular state in neurons that are bistable, such as Purkinje neurons in the cerebellum of larval zebrafish. We model the relationship between Purkinje neuron electrical activity and its corresponding calcium signal to compile a dataset of state-labelled simulated calcium signals. We apply machine-learning methods to this dataset to develop a tool that can classify the state of a Purkinje neuron using only its calcium signal, which works well on real data even though it was trained only on simulated data. CaMLsort (Calcium imaging and Machine Learning based tool to sort intracellular state) also generalizes well to bistable neurons in a different brain region (ventral tegmental area) in a different model organism (mouse). This tool can facilitate our understanding of how these neurons carry out their functions in a circuit.

Tunable optical bistability of two-dimensional tilted Dirac system.

We study the phenomenon of controlling the light by light known as the optical bistability for the two-dimensional tilted Dirac system. Using the Boltzmann approach under relaxation time approximation, we find that the optical bistability can be controlled by the nonlinear response of the system. For the prototype, we consider an inversion symmetry broken system. We find that the optical bistability associated with the nonlinear response is tunable with the strength of the tilt, gap and chemical potential. The resulting features suggest the inputs for the development of future-generation optical devices.

Network switches and their role in circadian clocks.

Circadian rhythms are generated by complex interactions among genes and proteins. Self-sustained ∼24 h oscillations require negative feedback loops and sufficiently strong nonlinearities that are the product of molecular and network switches. Here, we review common mechanisms to obtain switch-like behavior, including cooperativity, antagonistic enzymes, multisite phosphorylation, positive feedback, and sequestration. We discuss how network switches play a crucial role as essential components in cellular circadian clocks, serving as integral parts of transcription-translation feedback loops that form the basis of circadian rhythm generation. The design principles of network switches and circadian clocks are illustrated by representative mathematical models that include bistable systems and negative feedback loops combined with Hill functions. This work underscores the importance of negative feedback loops and network switches as essential design principles for biological oscillations, emphasizing how an understanding of theoretical concepts can provide insights into the mechanisms generating biological rhythms.

Order-of-Mutation Effects on Cancer Progression: Models for Myeloproliferative Neoplasm.

In some patients with myeloproliferative neoplasms (MPN), two genetic mutations are often found: JAK2 V617F and one in the TET2 gene. Whether one mutation is present influences how the other subsequent mutation will affect the regulation of gene expression. In other words, when a patient carries both mutations, the order of when they first arose has been shown to influence disease progression and prognosis. We propose a nonlinear ordinary differential equation, the Moran process, and Markov chain models to explain the non-additive and non-commutative mutation effects on recent clinical observations of gene expression patterns, proportions of cells with different mutations, and ages at diagnosis of MPN. Combined, these observations are used to shape our modeling framework. Our key proposal is that bistability in gene expression provides a natural explanation for many observed order-of-mutation effects. We also propose potential experimental measurements that can be used to confirm or refute predictions of our models.

Food-limited plant-herbivore model: Bifurcations, persistence, and stability.

This research paper delves into the two-dimensional discrete plant-herbivore model. In this model, herbivores are food-limited and affect the plants' density in their environment. Our analysis reveals that this system has equilibrium points of extinction, exclusion, and coexistence. We analyze the behavior of solutions near these points and prove that the extinction and exclusion equilibrium points are globally asymptotically stable in certain parameter regions. At the boundary equilibrium, we prove the existence of transcritical and period-doubling bifurcations with stable two-cycle. Transcritical bifurcation occurs when the plant's maximum growth rate or food-limited parameter reaches a specific boundary. This boundary serves as an invasion boundary for populations of plants or herbivores. At the interior equilibrium, we prove the occurrence of transcritical, Neimark-Sacker, and period-doubling bifurcations with an unstable two-cycle. Our research also establishes that the system is persistent in certain regions of the first quadrant. We demonstrate that the local asymptotic stability of the interior equilibrium does not guarantee the system's persistence. Bistability exists between boundary attractors (logistic dynamics) and interior equilibrium for specific parameters' regions. We conclude that changes to the food-limitation parameter can significantly alter the system's dynamic behavior. To validate our theoretical findings, we conduct numerical simulations.

Effect of size on expression of bistability in mouse spinal motoneurons.

Bistability in spinal motoneurons supports tonic spike activity in the absence of excitatory drive. Earlier work in adult preparations suggested that smaller motoneurons innervating slow antigravity muscle fibers are more likely to generate bistability for postural maintenance. However, whether large motoneurons innervating fast-fatigable muscle fibers display bistability is still controversial. To address this, we examined the relationship between soma size and bistability in lumbar (L4-L5) ventrolateral α-motoneurons of choline acetyltransferase (ChAT)-green fluorescent protein (GFP) and Hb9-GFP mice during the first 4 wk of life. We found that as neuron size increases, the prevalence of bistability rises. Smaller α-motoneurons lack bistability, whereas larger fast α-motoneurons [matrix metalloproteinase-9 (MMP-9)+/Hb9+] with a soma area ≥ 400 µm2 exhibit significantly higher bistability. Ionic currents associated with bistability, including the persistent Nav1.6 current, the thermosensitive Trpm5 Ca2+-activated Na+ current, and the slowly inactivating Kv1.2 current, also scale with cell size. Serotonin evokes full bistability in large motoneurons with partial bistable properties but not in small motoneurons. Our study provides important insights into the neural mechanisms underlying bistability and how motoneuron size correlates with bistability in mice.NEW & NOTEWORTHY Bistability is not a common feature of all mouse spinal motoneurons. It is absent in small, slow motoneurons but present in most large, fast motoneurons. This difference results from differential expression of ionic currents that enable bistability, which are highly expressed in large motoneurons but small or absent in small motoneurons. These results support a possible role for fast motoneurons in maintenance of tonic posture in addition to their known roles in fast movements.

Spontaneous Eye Blinks Map the Probability of Perceptual Reinterpretation During Visual and Auditory Ambiguity.

Spontaneous eye blinks are modulated around perceptual events. Our previous study, using a visual ambiguous stimulus, indicated that blink probability decreases before a reported perceptual switch. In the current study, we tested our hypothesis that an absence of blinks marks a time in which perceptual switches are facilitated in- and outside the visual domain. In three experiments, presenting either a visual motion quartet in light or darkness or a bistable auditory streaming stimulus, we found a co-occurrence of blink rate reduction with increased perceptual switch probability. In the visual domain, perceptual switches induced by a short interruption of visual input (blank) allowed an estimate of the timing of the perceptual event with respect to the motor response. This provided the first evidence that the blink reduction was not a consequence of the perceptual switch. Importantly, by showing that the time between switches and the previous blink was significantly longer than the inter-blink interval, our studies allowed to conclude that perceptual switches did not happen at random but followed a prolonged period of nonblinking. Correspondingly, blink rate and switch rate showed an inverse relationship. Our study supports the idea that the absence or presence of blinks maps perceptual processes independent of the sensory modality.

Hysteretic Room-Temperature Magnetic Bistability of the Crystalline 4,7-Difluoro-1,3,2-Benzodithiazolyl Radical.

The title radical R⋅, synthesized by reduction of the corresponding cation R+, is thermally stable up to ~380 K in the crystalline state under anaerobic conditions. With SQUID magnetometry, single-crystal and powder XRD, solid-state EPR and TG-DSC, reversible spin-Peierls transition between diamagnetic and paramagnetic states featuring ~10 K hysteretic loop is observed for R⋅ in the temperature range ~310-325 K; ΔH=~2.03 kJ mol-1 and ΔS=~6.23 J mol-1 K-1. The transition is accompanied by mechanical movement of the crystals, i. e., by thermosalient behavior. The low-temperature diamagnetic P-1 polymorph of R⋅ consists of R⋅2 π-dimers arranged in (…R⋅2…)n π-stacks; whereas the high-temperature paramagnetic P21/c polymorph, of uniform (…R⋅…)n π-stacks. With the XRD geometries, CASSCF and broken-symmetry DFT jointly suggest strong antiferromagnetic (AF) interactions within R⋅2 and weak between R⋅2 for the (…R⋅2…)n stacks; and moderate AF interactions between R⋅ for the (…R⋅…)n stacks. The fully hydrocarbon archetype of R⋅ does not reveal the aforementioned properties. Thus, the fluorinated 1,3,2-benzodithiazolyls pave a new pathway in the design and synthesis of metal-less magnetically-bistable materials.