6,139 research outputs found

    Heterogeneity of the attractor of the Lorenz '96 model: Lyapunov analysis, unstable periodic orbits, and shadowing properties

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    It is well known that the predictability of weather and climate is strongly state-dependent. Special, easily recognisable, and extremely relevant atmospheric states like blockings are associated with anomalous instability. This reflects the general property that the attractors of chaotic dynamical systems can feature considerable heterogeneity in terms of dynamical properties, and specifically, of their instability. The attractor of a chaotic dynamical systems is densely populated by unstable periodic orbits that can be used to approximate any forward trajectory through the so-called shadowing. Dynamical heterogeneity can lead to the presence of unstable periodic orbits with different number of unstable dimensions. This phenomenon - unstable dimensions variability - has considerable implications in terms of the structural stability of the system and of the possibility to model accurately its behaviour through numerical models. As a step in the direction of better understanding the properties of high-dimensional chaotic systems, here we provide an extensive numerical investigation of the variability of the dynamical properties across the attractor of the much studied Lorenz '96 model. By combining the Lyapunov analysis of the tangent space with the study of the shadowing of the chaotic trajectory performed by a very large set of unstable periodic orbits, we show that the observed variability in the number of unstable dimensions, which is a serious breakdown of hyperbolicity, is associated with the presence of a substantial number of finite-time Lyapunov exponents that fluctuate about zero also when very long averaging times are considered. The transition between regions of the attractor with different degrees of instability is associated with a significant drop of the quality of the shadowing. By performing a coarse graining based on the shadowing unstable periodic orbits, we are able to characterise the slow fluctuations of the system between regions featuring, on the average, anomalously high and anomalously low instability. In turn, such regions are associated, respectively, with states of anomalously high and low energy, thus providing a clear link between the microscopic and thermodynamical properties of the system

    Linear Amplification in Nonequilibrium Turbulent Boundary Layers

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    Resolvent analysis is applied to nonequilibrium incompressible adverse pressure gradient (APG) turbulent boundary layers (TBL) and hypersonic boundary layers with high temperature real gas effects, including chemical nonequilibrium. Resolvent analysis is an equation-based, scale-dependent decomposition of the Navier Stokes equations, linearized about a known mean flow field. The decomposition identifies the optimal response and forcing modes, ranked by their linear amplification. To treat the nonequilibrium APG TBL, a biglobal resolvent analysis approach is used to account for the streamwise and wall-normal inhomogeneities in the streamwise developing flow. For the hypersonic boundary layer in chemical nonequilibrium, the resolvent analysis is constructed using a parallel flow assumption, incorporating N₂, O₂, NO, N, and O as a mixture of chemically reacting gases. Biglobal resolvent analysis is first applied to the zero pressure gradient (ZPG) TBL. Scaling relationships are determined for the spanwise wavenumber and temporal frequency that admit self-similar resolvent modes in the inner layer, mesolayer, and outer layer regions of the ZPG TBL. The APG effects on the inner scaling of the biglobal modes are shown to diminish as their self-similarity improves with increased Reynolds number. An increase in APG strength is shown to increase the linear amplification of the large-scale biglobal modes in the outer region, similar to the energization of large scale modes observed in simulation. The linear amplification of these modes grows linearly with the APG history, measured as the streamwise averaged APG strength, and relates to a novel pressure-based velocity scale. Resolvent analysis is then used to identify the length scales most affected by the high-temperature gas effects in hypersonic TBLs. It is shown that the high-temperature gas effects primarily affect modes localized near the peak mean temperature. Due to the chemical nonequilibrium effects, the modes can be linearly amplified through changes in chemical concentration, which have non-negligible effects on the higher order modes. Correlations in the components of the small-scale resolvent modes agree qualitatively with similar correlations in simulation data. Finally, efficient strategies for resolvent analysis are presented. These include an algorithm to autonomously sample the large amplification regions using a Bayesian Optimization-like approach and a projection-based method to approximate resolvent analysis through a reduced eigenvalue problem, derived from calculus of variations.</p

    Neuromodulatory effects on early visual signal processing

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    Understanding how the brain processes information and generates simple to complex behavior constitutes one of the core objectives in systems neuroscience. However, when studying different neural circuits, their dynamics and interactions researchers often assume fixed connectivity, overlooking a crucial factor - the effect of neuromodulators. Neuromodulators can modulate circuit activity depending on several aspects, such as different brain states or sensory contexts. Therefore, considering the modulatory effects of neuromodulators on the functionality of neural circuits is an indispensable step towards a more complete picture of the brain’s ability to process information. Generally, this issue affects all neural systems; hence this thesis tries to address this with an experimental and computational approach to resolve neuromodulatory effects on cell type-level in a well-define system, the mouse retina. In the first study, we established and applied a machine-learning-based classification algorithm to identify individual functional retinal ganglion cell types, which enabled detailed cell type-resolved analyses. We applied the classifier to newly acquired data of light-evoked retinal ganglion cell responses and successfully identified their functional types. Here, the cell type-resolved analysis revealed that a particular principle of efficient coding applies to all types in a similar way. In a second study, we focused on the issue of inter-experimental variability that can occur during the process of pooling datasets. As a result, further downstream analyses may be complicated by the subtle variations between the individual datasets. To tackle this, we proposed a theoretical framework based on an adversarial autoencoder with the objective to remove inter-experimental variability from the pooled dataset, while preserving the underlying biological signal of interest. In the last study of this thesis, we investigated the functional effects of the neuromodulator nitric oxide on the retinal output signal. To this end, we used our previously developed retinal ganglion cell type classifier to unravel type-specific effects and established a paired recording protocol to account for type-specific time-dependent effects. We found that certain retinal ganglion cell types showed adaptational type-specific changes and that nitric oxide had a distinct modulation of a particular group of retinal ganglion cells. In summary, I first present several experimental and computational methods that allow to study functional neuromodulatory effects on the retinal output signal in a cell type-resolved manner and, second, use these tools to demonstrate their feasibility to study the neuromodulator nitric oxide

    High-resolution spatial patterns and drivers of terrestrial ecosystem carbon dioxide, methane, and nitrous oxide fluxes in the tundra

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    Arctic terrestrial greenhouse gas (GHG) fluxes of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) play an important role in the global GHG budget. However, these GHG fluxes are rarely studied simultaneously, and our understanding of the conditions controlling them across spatial gradients is limited. Here, we explore the magnitudes and drivers of GHG fluxes across fine-scale terrestrial gradients during the peak growing season (July) in sub-Arctic Finland. We measured chamber-derived GHG fluxes and soil temperature, soil moisture, soil organic carbon and nitrogen stocks, soil pH, soil carbon-to-nitrogen (C/N) ratio, soil dissolved organic carbon content, vascular plant biomass, and vegetation type from 101 plots scattered across a heterogeneous tundra landscape (5 km2). We used these field data together with high-resolution remote sensing data to develop machine learning models for predicting (i.e., upscaling) daytime GHG fluxes across the landscape at 2 m resolution. Our results show that this region was on average a daytime net GHG sink during the growing season. Although our results suggest that this sink was driven by CO2 uptake, it also revealed small but widespread CH4 uptake in upland vegetation types, almost surpassing the high wetland CH4 emissions at the landscape scale. Average N2O fluxes were negligible. CO2 fluxes were controlled primarily by annual average soil temperature and biomass (both increase net sink) and vegetation type, CH4 fluxes by soil moisture (increases net emissions) and vegetation type, and N2O fluxes by soil C/N (lower C/N increases net source). These results demonstrate the potential of high spatial resolution modeling of GHG fluxes in the Arctic. They also reveal the dominant role of CO2 fluxes across the tundra landscape but suggest that CH4 uptake in dry upland soils might play a significant role in the regional GHG budget.</p

    Shifting patterns of dengue three years after Zika virus emergence in Brazil

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    This is the final version. Available from Nature Research via the DOI in this record. Data availability: Counts of probable dengue virus cases and hospitalizations for individual states and the city of Salvador, Bahia, were obtained from the Brazilian Information System for Notifiable Diseases (SINAN, https://datasus.saude.gov.br/acesso-a-informacao/doencas-e-agravos-de-notificacao-2001-a-2006-sinan and https://datasus.saude.gov.br/acesso-a-informacao/doencas-e-agravos-de-notificacao-de-2007-em-diante-sinan) and Unified Health System (SUS) through the DATASUS (https://datasus.saude.gov.br/acesso-a-informacao/morbidade-hospitalar-do-sus-sih-sus). Population size estimates were obtained from DATASUS (https://datasus.saude.gov.br/populacao-residente). Weekly DENV and ZIKV notified cases (clinically suspected and confirmed) in the Bahian city of Feira de Santana were obtained directly from the Secretaria Municipal de SaĂșde of the city (https://www.feiradesantana.ba.gov.br/servicos.asp?id=14&link=sms/vigilancia_saude/vigilancia_epidemiologica.asp). All relevant data used in Figs. 1–3 and Supplementary Fig. 1-8,14,16 are available in the GitHub repository https://github.com/francescopinotti92/dengue_and_zika_brazil.n 2015, the Zika virus (ZIKV) emerged in Brazil, leading to widespread outbreaks in Latin America. Following this, many countries in these regions reported a significant drop in the circulation of dengue virus (DENV), which resurged in 2018-2019. We examine age-specific incidence data to investigate changes in DENV epidemiology before and after the emergence of ZIKV. We observe that incidence of DENV was concentrated in younger individuals during resurgence compared to 2013-2015. This trend was more pronounced in Brazilian states that had experienced larger ZIKV outbreaks. Using a mathematical model, we show that ZIKV-induced cross-protection alone, often invoked to explain DENV decline across Latin America, cannot explain the observed age-shift without also assuming some form of disease enhancement. Our results suggest that a sudden accumulation of population-level immunity to ZIKV could suppress DENV and reduce the mean age of DENV incidence via both protective and disease-enhancing interactions.UK Research and InnovationHuman Frontiers Science ProgrammePON ‘Ricerca e Innovazione’ 2014-202

    Single-cell time-series analysis of metabolic rhythms in yeast

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    The yeast metabolic cycle (YMC) is a biological rhythm in budding yeast (Saccharomyces cerevisiae). It entails oscillations in the concentrations and redox states of intracellular metabolites, oscillations in transcript levels, temporal partitioning of biosynthesis, and, in chemostats, oscillations in oxygen consumption. Most studies on the YMC have been based on chemostat experiments, and it is unclear whether YMCs arise from interactions between cells or are generated independently by each cell. This thesis aims at characterising the YMC in single cells and its response to nutrient and genetic perturbations. Specifically, I use microfluidics to trap and separate yeast cells, then record the time-dependent intensity of flavin autofluorescence, which is a component of the YMC. Single-cell microfluidics produces a large amount of time series data. Noisy and short time series produced from biological experiments restrict the computational tools that are useful for analysis. I developed a method to filter time series, a machine learning model to classify whether time series are oscillatory, and an autocorrelation method to examine the periodicity of time series data. My experimental results show that yeast cells show oscillations in the fluorescence of flavins. Specifically, I show that in high glucose conditions, cells generate flavin oscillations asynchronously within a population, and these flavin oscillations couple with the cell division cycle. I show that cells can individually reset the phase of their flavin oscillations in response to abrupt nutrient changes, independently of the cell division cycle. I also show that deletion strains generate flavin oscillations that exhibit different behaviour from dissolved oxygen oscillations from chemostat conditions. Finally, I use flux balance analysis to address whether proteomic constraints in cellular metabolism mean that temporal partitioning of biosynthesis is advantageous for the yeast cell, and whether such partitioning explains the timing of the metabolic cycle. My results show that under proteomic constraints, it is advantageous for the cell to sequentially synthesise biomass components because doing so shortens the timescale of biomass synthesis. However, the degree of advantage of sequential over parallel biosynthesis is lower when both carbon and nitrogen sources are limiting. This thesis thus confirms autonomous generation of flavin oscillations, and suggests a model in which the YMC responds to nutrient conditions and subsequently entrains the cell division cycle. It also emphasises the possibility that subpopulations in the culture explain chemostat-based observations of the YMC. Furthermore, this thesis paves the way for using computational methods to analyse large datasets of oscillatory time series, which is useful for various fields of study beyond the YMC

    Evolutionary ecology of obligate fungal and microsporidian invertebrate pathogens

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    The interactions between hosts and their parasites and pathogens are omnipresent in the natural world. These symbioses are not only key players in ecosystem functioning, but also drive genetic diversity through co-evolutionary adaptations. Within the speciose invertebrates, a plethora of interactions with obligate fungal and microsporidian pathogens exist, however the known interactions is likely only a fraction of the true diversity. Obligate invertebrate fungal and microsporidian pathogen require a host to continue their life cycle, some of which have specialised in certain host species and require host death to transmit to new hosts. Due to their requirement to kill a host to spread to a new one, obligate fungal and microsporidian pathogens regulate invertebrate host populations. Pathogen specialisation to a single or very few hosts has led to some fungi evolving the ability to manipulate their host’s behaviour to maximise transmission. The entomopathogenic fungus, Entomophthora muscae, infects houseflies (Musca domestica) over a week-long proliferation cycle, resulting in flies climbing to elevated positions, gluing their mouthparts to the substrate surface, and raising their wings to allow for a clear exit from fungal conidia through the host abdomen. These sequential behaviours are all timed to occur within a few hours of sunset. The E. muscae mechanisms used in controlling the mind of the fly remain relatively unknown, and whether other fitness costs ensue from an infection are understudied.European Commissio

    Effect of boreal forest disturbance due to logging at different spatial scales on migratory songbirds

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    Boreal birds have experienced population declines that may be related to alteration of the forest at a range of scales. Understanding how resource extraction may affect the distribution and abundance of species is critical to address conservation policy in the boreal forest region. This study aims to understand how habitat alteration by logging influences the abundance and habitat choices of a migratory songbird, the Canada Warbler (CAWA; Cardellina canadensis) in its Canadian breeding range and more specifically within the northwestern region of Ontario, where there is little information about this species at risk. I assess whether there exists a different response in the abundance of upland migratory songbirds to logging disturbance at different scales. Also, I assessed the “habitat compensation hypothesis,” which states that some species can substitute their primary habitat for other alternative and less preferred habitats on the landscape. I conduct a meta-analysis of 21 studies to identify the effects of habitat alteration on a relative abundance index (RAI) of 21 upland songbird species, comparing logged to unlogged sites along the southern border of Canadian boreal forest. Using generalized linear mixed models (GLMM), I model the RAI incorporating two scales (local- and landscape-scale effects), time since logging, and forest type. Several species, including CAWA, are reported in decline in Canada. They occasionally have a higher mean RAI comparing logged areas at landscape scale than comparing at the finer local scale, suggesting that they occupy lower quality habitats in disturbed areas. The results are consistent with other findings: birds associated with old-growth forests are most sensitive to logging, as well as birds that nest on trees and those more associated with a coniferous forest. I then assess how time since logging affects CAWA occurrence and distribution in Northwestern Ontario. I use Maxent software to develop a predictive highresolution (30 m) field-validated species distribution model (SDM). [...
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