Redox homeostasis: The Golden Mean of healthy living

The notion that electrophiles serve as messengers in cell signaling is now widely accepted. Nonetheless, major issues restrain acceptance of redox homeostasis and redox signaling as components of main- tenance of a normal physiological steady state. The first is that redox signaling requires sudden switching on of oxidant production and bypassing of antioxidant mechanisms rather than a continuous process that, like other signaling mechanisms, can be smoothly turned up or down. The second is the mis- perception that reactions in redox signaling involve “reactive oxygen species” rather than reaction of specific electrophiles with specific protein thiolates. The third is that hormesis provides protection against oxidants by increasing cellular defense or repair mechanisms rather than by specifically ad- dressing the offset of redox homeostasis. Instead, we propose that both oxidant and antioxidant signaling are main features of redox homeostasis. As the redox shift is rapidly reversed by feedback reactions, homeostasis is maintained by continuous signaling for production and elimination of electrophiles and nucleophiles. Redox homeostasis, which is the maintenance of nucleophilic tone, accounts for a healthy physiological steady state. Electrophiles and nucleophiles are not intrinsically harmful or protective, and redox homeostasis is an essential feature of both the response to challenges and subsequent feedback. While the balance between oxidants and nucleophiles is preserved in redox homeostasis, oxidative stress provokes the establishment of a new radically altered redox steady state. The popular belief that scavenging free radicals by antioxidants has a beneficial effect is wishful thinking. We propose, instead, that continuous feedback preserves nucleophilic tone and that this is supported by redox active nutri- tional phytochemicals. These nonessential compounds, by activating Nrf2, mimic the effect of en- dogenously produced electrophiles (parahormesis). In summary, while hormesis, although globally protective, results in setting up of a new phenotype, parahormesis contributes to health by favoring maintenance of homeostasis

On the long-term correlations and multifractal properties of electric arc furnace time series

In this paper, we study long-term correlations and multifractal properties elaborated from time series of three-phase current signals coming from an industrial electric arc furnace plant. Implicit sinusoidal trends are suitably detected by considering the scaling of the fluctuation functions. Time series are then filtered via a Fourier-based analysis, removing hence such strong periodicities. In the filtered time series we detected long-term, positive correlations. The presence of positive correlations is in agreement with the typical V--I characteristic (hysteresis) of the electric arc furnace, providing thus a sound physical justification for the memory effects found in the current time series. The multifractal signature is strong enough in the filtered time series to be effectively classified as multifractal

Criticism of "Necessity of simultaneous co-existence of instantaneous and retarded interactions in classical electrodynamics" by Andrew E. Chubykalo and Stoyan J. Vlaev

The demonstration that the electromagnetic fields derived from the Lienard-Wiechert potentials do not satisfy the Maxwell equations is proved to be false. Errors were made in the computation of the derivatives of retarded quantities. The subsequent inference of the necessity of both instantaneous and retarded electromagnetic interactions cannot be made. Different choices of gauge can lead to a variety of forms for the scalar and vector potentials, always with the same retarded fields. Classical electromagnetic theory is complete as usually expressed. One may choose to work in the Lorenz gauge in which all quantities are retarded.Comment: pdf file, 5 pages, submitted to Int. J. Mod. Phy

Macroevolutionary patterns in cranial and lower jaw shape of ceratopsian dinosaurs (dinosauria, ornithischia). phylogeny, morphological integration, and evolutionary rates

Organisms: Ceratopsians were herbivorous, beaked dinosaurs, ranging from 1 m to 9 m in body length, usually four-footed, and with a bony frill that extended backwards from the cranium over the nape of the neck. Known from Asia, Europe, and North America, they appeared in the Late Jurassic and persisted until the end of the Late Cretaceous. Questions: Which evolutionary processes drive the phenotypic evolution of skulls and lower jaws within Ceratopsia? What is the degree of morphological integration between the skull and lower jaw, and between the snout and frill among clades? Finally, are there any morphological evolution rate shifts across the ceratopsian phylogeny? Data: Photographs from 121 ceratopsian skulls and 122 lower jaws in lateral view, both from original photos and published pictures. Fifty-five ceratopsian species are represented in the sample. Methods: We investigated cranial and lower jaw shape changes across ceratopsians applying two-dimensional geometric morphometrics. We also investigated the morphological variation of the snout and the frill. Using phylogenetic generalized least squares regression, we estimated the degree of phylogenetic signal in size and shape data, as well as in the shape-size relationship. We performed phenotypic evolutionary rate analysis on shape data to describe phenotypic shifts across the phylogeny. Using a rarefied version of Escoufier's RV coefficient, we tested morphological integration between skulls and lower jaws, and between snouts and frills. Finally, we explored the potential link between cranial and frill shape evolution in ceratopsians and the radiation of angiosperms using a linear regression model. Results: Skull, snout, and frill shapes differ among clades (with the exception of leptoceratopsids and protoceratopsids). Lower jaws show distinct morphologies among groups. Size and shape changes are phylogenetically structured. The frill drives the morphological variation of the skull, co-varying much more with the lower jaw than with the snout. The frill appears to evolve to co-vary better with the lower jaw in the more morphologically derived clades than in basal ones. A significant linear relationship does exist between cranial shape and angiosperm occurrences, suggesting the hypothesis that the frill evolved in response to changes in dietary compositions associated with the turnover between gymnosperms and angiosperms during the Cretaceous. Significant negative shifts in evolutionary rates characterize skull, snout, frill, and lower jaw shapes, corresponding to nodes where psittacosaurids diverge from other taxa. In contrast, a significant positive shift in skull and snout shape rate of evolution characterizes the clade Ceratopsoidea. Conclusion: The frill is the main driving force in the overall cranial shape within Ceratopsia and evolved secondarily to better co-vary with the lower jaw to produce a more efficient masticatory apparatus. The changes in frill shape are correlated with the angiosperm diversification that occurred in the Cretaceous and thus correlated with changes in diet. Ceratopsians exhibit a slowdown in the phenotypic evolutionary rate in the Early Cretaceous and an acceleration of the phenotypic rate in the Late Cretaceous

Males resemble females. re-evaluating sexual dimorphism in protoceratops andrewsi (neoceratopsia, protoceratopsidae)

BACKGROUND: Protoceratops andrewsi (Neoceratopsia, Protoceratopsidae) is a well-known dinosaur from the Upper Cretaceous of Mongolia. Some previous workers hypothesized sexual dimorphism in the cranial shape of this taxon, using qualitative and quantitative observations. In particular, width and height of the frill as well as the development of a nasal horn have been hypothesized as potentially sexually dimorphic. METHODOLOGY/PRINCIPAL FINDINGS: Here, we reassess potential sexual dimorphism in skulls of Protoceratops andrewsi by applying two-dimensional geometric morphometrics to 29 skulls in lateral and dorsal views. Principal Component Analyses and nonparametric MANOVAs recover no clear separation between hypothetical "males" and "females" within the overall morphospace. Males and females thus possess similar overall cranial morphologies. No differences in size between "males" and "females" are recovered using nonparametric ANOVAs. CONCLUSIONS/SIGNIFICANCE: Sexual dimorphism within Protoceratops andrewsi is not strongly supported by our results, as previously proposed by several authors. Anatomical traits such as height and width of the frill, and skull size thus may not be sexually dimorphic. Based on PCA for a data set focusing on the rostrum and associated ANOVA results, nasal horn height is the only feature with potential dimorphism. As a whole, most purported dimorphic variation is probably primarily the result of ontogenetic cranial shape changes as well as intraspecific cranial variation independent of sex

A generative model for protein contact networks

In this paper we present a generative model for protein contact networks. The soundness of the proposed model is investigated by focusing primarily on mesoscopic properties elaborated from the spectra of the graph Laplacian. To complement the analysis, we study also classical topological descriptors, such as statistics of the shortest paths and the important feature of modularity. Our experiments show that the proposed model results in a considerable improvement with respect to two suitably chosen generative mechanisms, mimicking with better approximation real protein contact networks in terms of diffusion properties elaborated from the Laplacian spectra. However, as well as the other considered models, it does not reproduce with sufficient accuracy the shortest paths structure. To compensate this drawback, we designed a second step involving a targeted edge reconfiguration process. The ensemble of reconfigured networks denotes improvements that are statistically significant. As a byproduct of our study, we demonstrate that modularity, a well-known property of proteins, does not entirely explain the actual network architecture characterizing protein contact networks. In fact, we conclude that modularity, intended as a quantification of an underlying community structure, should be considered as an emergent property of the structural organization of proteins. Interestingly, such a property is suitably optimized in protein contact networks together with the feature of path efficiency.Comment: 18 pages, 67 reference

Multifractal Characterization of Protein Contact Networks

The multifractal detrended fluctuation analysis of time series is able to reveal the presence of long-range correlations and, at the same time, to characterize the self-similarity of the series. The rich information derivable from the characteristic exponents and the multifractal spectrum can be further analyzed to discover important insights about the underlying dynamical process. In this paper, we employ multifractal analysis techniques in the study of protein contact networks. To this end, initially a network is mapped to three different time series, each of which is generated by a stationary unbiased random walk. To capture the peculiarities of the networks at different levels, we accordingly consider three observables at each vertex: the degree, the clustering coefficient, and the closeness centrality. To compare the results with suitable references, we consider also instances of three well-known network models and two typical time series with pure monofractal and multifractal properties. The first result of notable interest is that time series associated to proteins contact networks exhibit long-range correlations (strong persistence), which are consistent with signals in-between the typical monofractal and multifractal behavior. Successively, a suitable embedding of the multifractal spectra allows to focus on ensemble properties, which in turn gives us the possibility to make further observations regarding the considered networks. In particular, we highlight the different role that small and large fluctuations of the considered observables play in the characterization of the network topology

An Agent-Based Algorithm exploiting Multiple Local Dissimilarities for Clusters Mining and Knowledge Discovery

We propose a multi-agent algorithm able to automatically discover relevant regularities in a given dataset, determining at the same time the set of configurations of the adopted parametric dissimilarity measure yielding compact and separated clusters. Each agent operates independently by performing a Markovian random walk on a suitable weighted graph representation of the input dataset. Such a weighted graph representation is induced by the specific parameter configuration of the dissimilarity measure adopted by the agent, which searches and takes decisions autonomously for one cluster at a time. Results show that the algorithm is able to discover parameter configurations that yield a consistent and interpretable collection of clusters. Moreover, we demonstrate that our algorithm shows comparable performances with other similar state-of-the-art algorithms when facing specific clustering problems

Analysis of heat kernel highlights the strongly modular and heat-preserving structure of proteins

In this paper, we study the structure and dynamical properties of protein contact networks with respect to other biological networks, together with simulated archetypal models acting as probes. We consider both classical topological descriptors, such as the modularity and statistics of the shortest paths, and different interpretations in terms of diffusion provided by the discrete heat kernel, which is elaborated from the normalized graph Laplacians. A principal component analysis shows high discrimination among the network types, either by considering the topological and heat kernel based vector characterizations. Furthermore, a canonical correlation analysis demonstrates the strong agreement among those two characterizations, providing thus an important justification in terms of interpretability for the heat kernel. Finally, and most importantly, the focused analysis of the heat kernel provides a way to yield insights on the fact that proteins have to satisfy specific structural design constraints that the other considered networks do not need to obey. Notably, the heat trace decay of an ensemble of varying-size proteins denotes subdiffusion, a peculiar property of proteins