Critical and Near-Critical Branching Processes

Scale-free dynamics in physical and biological systems can arise from a variety of causes. Here, we explore a branching process which leads to such dynamics. We find conditions for the appearance of power laws and study quantitatively what happens to these power laws when such conditions are violated. From a branching process model, we predict the behavior of two systems which seem to exhibit near scale-free behavior--rank-frequency distributions of number of subtaxa in biology, and abundance distributions of genotypes in an artificial life system. In the light of these, we discuss distributions of avalanche sizes in the Bak-Tang-Wiesenfeld sandpile model.Comment: 9 pages LaTex with 10 PS figures. v.1 of this paper contains results from non-critical sandpile simulations that were excised from the published versio

Fractal geometry of spin-glass models

Stability and diversity are two key properties that living entities share with spin glasses, where they are manifested through the breaking of the phase space into many valleys or local minima connected by saddle points. The topology of the phase space can be conveniently condensed into a tree structure, akin to the biological phylogenetic trees, whose tips are the local minima and internal nodes are the lowest-energy saddles connecting those minima. For the infinite-range Ising spin glass with p-spin interactions, we show that the average size-frequency distribution of saddles obeys a power law $\sim w^{-D}$, where w=w(s) is the number of minima that can be connected through saddle s, and D is the fractal dimension of the phase space

Loop analysis of blood pressure/volume homeostasis

We performed a mathematical analysis of the dynamic control loops regulating the vasomotor tone of vascular smooth muscle, blood volume, and mean arterial pressure, which involve the arginine vasopressin (AVP) system, the atrial natriuretic peptide system (ANP), and the renin-angiotensin-aldosterone system (RAAS). Our loop analysis of the AVP-ANP-RAAS system revealed the concurrent presence of two different regulatory mechanisms, which perform the same qualitative function: one affects blood pressure by regulating vasoconstriction, the other by regulating blood volume. Both the systems are candidate oscillators consisting of the negative-feedback loop of a monotone system: they admit a single equilibrium that can either be stable or give rise to oscillatory instability. Also a subsystem, which includes ANP and AVP stimulation of vascular smooth muscle cells, turns out to be a candidate oscillator composed of a monotone system with multiple negative feedback loops, and we show that its oscillatory potential is higher when the delays along all feedback loops are comparable. Our results give insight into the physiological mechanisms ruling long-term homeostasis of blood hydraulic parameters, which operate based on dynamical loops of interactions

Scaling properties of protein family phylogenies

One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of balance) of a large set of protein phylogenies with a set of species phylogenies. The comparative analysis shows that both sets of phylogenies share remarkably similar scaling behavior, suggesting the universality of branching rules and of the evolutionary processes that drive biological diversification from gene to species level. In order to explain such generality, we propose a simple model which allows us to estimate the proportion of evolvability/robustness needed to approximate the scaling behavior observed in the phylogenies, highlighting the relevance of the robustness of a biological system (species or protein) in the scaling properties of the phylogenetic trees. Thus, the rules that govern the incapability of a biological system to diversify are equally relevant both at the gene and at the species level.Comment: Replaced with final published versio

A probabilistic sediment cascade model of sediment transfer in the Illgraben

We present a probabilistic sediment cascade model to simulate sediment transfer in a mountain basin (Illgraben, Switzerland) where sediment is produced by hillslope landslides and rockfalls and exported out of the basin by debris flows and floods. The model conceptualizes the fluvial system as a spatially lumped cascade of connected reservoirs representing hillslope and channel storages where sediment goes through cycles of storage and remobilization by surface runoff. The model includes all relevant hydrological processes that lead to runoff formation in an Alpine basin, such as precipitation, snow accumulation, snowmelt, evapotranspiration, and soil water storage. Although the processes of sediment transfer and debris flow generation are described in a simplified manner, the model produces complex sediment discharge behavior which is driven by the availability of sediment and antecedent wetness conditions (system memory) as well as the triggering potential (climatic forcing). The observed probability distribution of debris flow volumes and their seasonality in 2000–2009 are reproduced. The stochasticity of hillslope sediment input is important for reproducing realistic sediment storage variability, although many details of the hillslope landslide triggering procedures are filtered out by the sediment transfer system. The model allows us to explicitly quantify the division into transport and supply-limited sediment discharge events. We show that debris flows may be generated for a wide range of rainfall intensities because of variable antecedent basin wetness and snowmelt contribution to runoff, which helps to understand the limitations of methods based on a single rainfall threshold for debris flow initiation in Alpine basins

Why honey is effective as a medicine. 1. Its use in modern medicine

Honey has been used as a medicine for thousands of years and its curative properties are well documented. However, modern medicine turned its back on honey and it is only now, with the advent of multi-resistant bacteria, that the antibiotic properties of honey are being rediscovered

Aging Skin: Nourishing from Out-In. Lessons from Wound Healing

Skin lesion therapy, peculiarly in the elderly, cannot be isolated from understanding that the skin is an important organ consisting of different tissues. Furthermore, dermis health is fundamental for epidermis integrity, and so adequate nourishment is mandatory in maintaining skin integrity. The dermis nourishes the epidermis, and a healthy epidermis protects the dermis from the environment, so nourishing the dermis through the epidermal barrier is a technical problem yet to be resolved. This is also a consequence of the laws and regulations restricting cosmetics, which cannot have properties that pass the epidermal layer. There is higher investment in cosmetics than in the pharmaceutical industry dealing with skin therapies, because the costs of drug registration are enormous and the field is unprofitable. Still, wound healing may be seen as an opportunity to “feed” the dermis directly. It could also verify whether providing substrates could promote efficient healing and test optimal skin integrity maintenance, if not skin rejuvenation, in an ever aging population

Local-scale forcing effects on wind flows in an urban environment: Impact of geometrical simplifications

Wind flow in urban areas is strongly affected by the urban geometry. In the last decades most of the geometries used to reproduce urban areas, both in wind-tunnel (WT) tests and Computational Fluid Dynamics (CFD) simulations, were simplified compared to reality in order to limit experimental effort and computational costs. However, it is unclear to which extent these geometrical simplifications can affect the reliability of the numerical and experimental results. The goal of this paper is to quantify the deviations caused by geometrical simplifications. The case under study is the district of Livorno city (Italy), called \ue2\u80\u9cQuartiere La Venezia\ue2\u80\u9d. The 3D steady Reynolds-averaged Navier-Stokes (RANS) simulations are solved, first for a single block of the district, then for the whole district. The CFD simulations are validated with WT tests at scale 1:300. Comparisons are made of mean wind velocity profiles between WT tests and CFD simulations, and the agreement is quantified using four validation metrics (FB, NMSE, R and FAC1.3). The results show that the most detailed geometry provides improved performance, especially for wind direction \uce\ub1 = 240\uc2\ub0 (22% difference in terms of FAC1.3)

Polyphenol characterization and skin-preserving properties of hydroalcoholic flower extract from Himantoglossum robertianum (Orchidaceae)

Himantoglossum robertianum (Loisel.) P. Delforge is a Mediterranean orchid whose propagation in vitro has been achieved, making it eligible as a source of bioactive substances. Flowers were analyzed by light and SEM microscopy and used to obtain a polyphenol-rich, hydroalcoholic flower extract (HFE). HFE was characterized for total phenols, flavonoids and proanthocyanidins, and for polyphenol profile by RP-LC-DAD. Antioxidant assays, in vitro collagenase and elastase inhibition, and MTT and cell motility assays on HaCaT keratinocytes were done. Microscopy showed epidermal cells containing anthocyanins in the flower labellum. Flavonoids (flavones and flavan-3-ols) represented the most abundant compounds (42.91%), followed by scopoletin (33.79%), and phenolic acids (23.3%). Antioxidant assays showed strong activities, rating ORAC > FRAP > TEAC > \u3b2-carotene bleaching > DPPH > iron-chelation. Biological assays showed elastase and collagenase inhibition (up to 42% and 78%, respectively), improvement of HaCaT cell viability after treatment with 500 \u3bcM H2O2 (from 30% to 84% of control), and stimulation of cell migration rate up to 210% of control. In summary, HFE counteracted different free radicals, while protective properties were shown by cell-free and cell-based bioassays, suggesting the possible use of H. robertianum flowers for skin-preserving, repair, and anti-aging applications

A multistationary loop model of ALS unveils critical molecular interactions involving mitochondria and glucose metabolism

Amyotrophic lateral sclerosis (ALS) is a poor-prognosis disease with puzzling pathogenesis and inconclusive treatments. We develop a mathematical model of ALS based on a system of interactive feedback loops, focusing on the mutant SOD1G93A mouse. Misfolded mutant SOD1 aggregates in motor neuron (MN) mitochondria and triggers a first loop characterized by oxidative phosphorylation impairment, AMP kinase over-activation, 6-phosphofructo-2-kinase (PFK3) rise, glucose metabolism shift from pentose phosphate pathway (PPP) to glycolysis, cell redox unbalance, and further worsening of mitochondrial dysfunction. Oxidative stress then triggers a second loop, involving the excitotoxic glutamatergic cascade, with cytosolic Ca2+ overload, increase of PFK3 expression, and further metabolic shift from PPP to glycolysis. Finally, cytosolic Ca2+ rise is also detrimental to mitochondria and oxidative phosphorylation, thus closing a third loop. These three loops are overlapped and positive (including an even number of inhibitory steps), hence they form a candidate multistationary (bistable) system. To describe the system dynamics, we model the interactions among the functional agents with differential equations. The system turns out to admit two stable equilibria: the healthy state, with high oxidative phosphorylation and preferential PPP, and the pathological state, with AMP kinase activation, PFK3 over expression, oxidative stress, excitotoxicity and MN degeneration. We demonstrate that the loop system is monotone: all functional agents consistently act toward the healthy or pathological condition, depending on low or high mutant SOD1 input. We also highlight that molecular interactions involving PFK3 are crucial, as their deletion disrupts the system\u2019s bistability leading to a single healthy equilibrium point. Hence, our mathematical model unveils that promising ALS management strategies should be targeted to mechanisms that keep low PFK3 expression and activity within MNs