Analytical and numerical bifurcation analysis of a forest ecosystem model with human interaction

We perform both analytical and numerical bifurcation analysis of an alternating forest and grassland ecosystem model coupled with human interaction. The model consists of two nonlinear ordinary differential equations incorporating the human perception of the value of the forest. The system displays multiple steady states corresponding to different forest densities as well as regimes characterized by both stable and unstable limit cycles. We derive analytically the conditions with respect to the model parameters that give rise to various types of codimension-one criticalities such as transcritical, saddle-node, and Andronov-Hopf bifurcations and codimension-two criticalities such as cusp and Bogdanov-Takens bifurcations at which homoclinic orbits occur. We also perform a numerical continuation of the branches of limit cycles. By doing so, we reveal turning points of limit cycles marking the appearance/disappearance of sustained oscillations. Such critical points that cannot be detected analytically give rise to the abrupt loss of the sustained oscillations, thus leading to another mechanism of catastrophic shifts

Effective conductivity of inertial flows through porous media

We study two-dimensional incompressible inertial flows through porous media. At core (small) scale, we prove that the constitutive, nonlinear model can be rewritten into a linear one by means of a new parameter K* which encompasses all the inertial effects. In natural (large-scale) formations, K* is erratically changing, and we analytically compute its counterpart, which is coined generalized effective conductivity, by the self-consistent approach (SCA). In spite of its approximate nature, the SCA leads to simple results that are in good agreement with Monte Carlo simulations

Dose-dependent positive-to-negative shift of litter effects on seedling growth: a modelling study on 35 plant litter types

Modelling the inter-relationships between litter accumulation and plant–soil feedback is a major challenge to predict natural and agricultural ecosystem dynamics. At increasing levels of undecomposed plant litter, seedling growth tends to show a multi-faceted response trend, characterised by a peak of positive stimulation at lower dosage followed by inhibition at higher dosage. In this study, a new logistic model was developed to describe such trend and disentangle substrate-specific positive and negative effects of plant litter. The model was tested on 35 litter types applied to the common phytometer Lepidium sativum; all litter types were collected in Mediterranean shrublands of Campania region (southern Italy). Model fitting resulted to be generally higher relative to the widely used linear log response model, although in only half of the cases it also gave more parsimonious results in terms of minimising information loss. Positive and negative effects of plant litter resulted to be uncorrelated, showing that the overall trend is probably the result of the combined action of separate factors rather than the effect of a single factor behaving differently at the different doses. The results of this work provide new tools to finely tune the optimal doses in experiments on hormesis and litter phytotoxicity, through the identification of the most suited doses to centre the range of nearly linear response to litter concentration. A wide screening is also presented on the phytotoxicity profiles of a number of spontaneous plant species widely distributed in the Mediterranean area

Mathematical modelling and numerical bifurcation analysis of inbreeding and interdisciplinarity dynamics in academia

We address a mathematical model to approximate in a coarse qualitative the interaction between inbreeding-lobbying and interdisciplinarity in academia and perform a one and two-parameter numerical bifurcation analysis to analyse its dynamics. Disciplinary diversity is a necessary condition for the development of interdisciplinarity, which is being recognized today as the key to establish a vibrant academic environment with bigger potential for breakthroughs/innovation in research and technology. However, the interaction of several factors including institutional policies, and behavioural attitudes put significant barriers on advancing interdisciplinarity. A “cognitive rigidity” may rise due to reactive academic lobby behaviours favouring inbreeding. The proposed model consists of four coupled non-linear Ordinary Differential Equations simulating the interaction between certain types of academic behaviour and the rate of knowledge advancement which is related to the level of disciplinary diversity. The effect of a control policy that inhibits inbreeding-lobbying is also investigated. The numerical bifurcation analysis reveals a rich nonlinear behaviour including multistability, sustained oscillations, limit points of limit cycles, homoclinic bifurcations as well as codimension-two bifurcations and in particular Bogdanov–Takens and Bautin bifurcations

A General Process-Based Model for Describing the Metabolic Shift in Microbial Cell Cultures

The metabolic shift between respiration and fermentation at high glucose concentration is a widespread phenomenon in microbial world, and it is relevant for the biotechnological exploitation of microbial cell factories, affecting the achievement of high-cell-densities in bioreactors. Starting from a model already developed for the yeast Saccharomyces cerevisiae, based on the System Dynamics approach, a general process-based model for two prokaryotic species of biotechnological interest, such as Escherichia coli and Bacillus subtilis, is proposed. The model is based on the main assumption that glycolytic intermediates act as central catabolic hub regulating the shift between respiratory and fermentative pathways. Furthermore, the description of a mixed fermentation with secondary by-products, characteristic of bacterial metabolism, is explicitly considered. The model also represents the inhibitory effect on growth and metabolism of self-produced toxic compounds relevant in assessing the late phases of high-cell density culture. Model simulations reproduced data from experiments reported in the literature with different strains of non-recombinant and recombinant E. coli and B. subtilis cultured in both batch and fed-batch reactors. The proposed model, based on simple biological assumptions, is able to describe the main dynamics of two microbial species of relevant biotechnological interest. It demonstrates that a reductionist System Dynamics approach to formulate simplified macro-kinetic models can provide a robust representation of cell growth and accumulation in the medium of fermentation by-products

Spatial analysis of phylogenetic community structure: New version of a classical method

The increasing availability of phylogenetic information facilitates the use of evolutionary methods in community ecology to reveal the importance of evolution in the species assembly process. However, while several methods have been applied to a wide range of communities across different spatial scales with the purpose of detecting non-random phylogenetic patterns, the spatial aspects of phylogenetic community structure have received far less attention. Accordingly, the question for this study is: can point pattern analysis be used for revealing the phylogenetic structure of multi-species assemblages? We introduce a new individual-centered procedure for analyzing the scale-dependent phylogenetic structure of multi-species point patterns based on digitized field data. The method uses nested circular plots with increasing radii drawn around each individual plant and calculates the mean phylogenetic distance between the focal individual and all individuals located in the circular ring delimited by two successive radii. This scale-dependent value is then averaged over all individuals of the same species and the observed mean is compared to a null expectation with permutation procedures. The method detects particular radius values at which the point pattern of a single species exhibits maximum deviation from the expectation towards either phylogenetic aggregation or segregation. Its performance is illustrated using data from a grassland community in Hungary and simulated point patterns. The proposed method can be extended to virtually any distance function for species pairs, such as functional distances

Energy, forest, and indoor air pollution models for Sagarmatha National Park and Buffer Zone, Nepal

This paper presents the results of management-oriented research on energy, forest, and human health issues in a remote mountain area, the Sagarmatha National Park and Buffer Zone (SNPBZ), Nepal. The research was based on a broader, integrated participatory framework ultimately intended for use in adaptive management. The present study focused on the application of a participatory modeling framework to address problems related to energy demand and consumption, forest condition, and indoor air pollution, which were defined by the stakeholders as important issues to be addressed. The models were developed using a generalizing design that allows for user-friendly adaptation to other contexts (free download at http://hkkhpartnership.org). Moreover, we simulated management scenarios in collaboration with all modeling actors with the aim of building consensus on the understanding of the system as well as supporting decision-makers' capacity not only to respond to changes, but also to anticipate them. Importantly, the system dynamics assessment found that the SNPBZ forests are affected by an increasing demand for fuelwood (occurring due to tourism growth), as one of the main sources of energy. Selected forests show an average reduction of 38 in forest biomass from 1992 to 2008. This shows that the business-as-usual scenario is unlikely to result in the preservation of the current forest status; in fact, such preservation would require 75 of fuelwood to be replaced with alternative energy sources. At the same time, a 75 reduction of fuelwood use (and an 80 reduction of dung use) would reduce indoor carbon monoxide (CO) concentrations to the standard limits for CO exposure set by the World Health Organization

Targeting prolyl-isomerase Pin1 prevents mitochondrial oxidative stress and vascular dysfunction: insights in patients with diabetes

The present study demonstrates that Pin1 is a common activator of key pathways involved in diabetic vascular disease in different experimental settings including primary human endothelial cells, knockout mice, and diabetic patients. Gene silencing and genetic disruption of Pin1 prevent hyperglycaemia-induced mitochondrial oxidative stress, endothelial dysfunction, and vascular inflammation. Moreover, we have translated our findings to diabetic patients. In line with our experimental observations, Pin1 up-regulation is associated with impaired flow-mediated dilation, increased oxidative stress, and plasma levels of adhesion molecules. In perspective, these findings may provide the rationale for mechanism-based therapeutic strategies in patients with diabete

A comparison of Power Doppler with conventional sonographic imaging for the evaluation of renal artery stenosis

BACKGROUND: Power Doppler (PD) has improved diagnostic capabilities of vascular sonography, mainly because it is independent from the angle of insonation. We evaluated this technique in a prospective comparison with conventional imaging, consisting in Duplex and Color Doppler, for the evaluation of Renal Artery (RA) stenosis. METHODS: Sensitivity, specificity and predictive values of PD and conventional imaging were assessed in a blinded fashion on eighteen patients, 9 with angiographic evidence of unilateral RA stenosis (hypertensive patients) and 9 with angiographically normal arteries (control group). PD images were interpreted with an angiography-like criteria. RESULTS: In the control group both techniques allowed correct visualization of 16 out of the 18 normal arteries (93% specificity). Only in five hypertensive patients RA stenosis was correctly identified with conventional technique (56% sensitivity and 86% negative predictive value); PD was successful in all hypertensive patients (100% sensitivity and negative predictive value), since the operators could obtain in each case of RA stenosis a sharp color signal of the whole vessel with a clear "minus" at the point of narrowing of the lumen. All results were statistically significant (p < 0.01). CONCLUSIONS: This study demonstrates that PD is superior to conventional imaging, in terms of sensitivity and specificity, for the diagnosis of RA stenosis, because it allows a clear visualization of the whole stenotic vascular lumen. Especially if it is used in concert with the other sonographic techniques, PD can enable a more accurate imaging of renovascular disease with results that seem comparable to selective angiography