One of the lasting controversies in phylogenetic inference is the degree to which specific evolutionary models should influence the choice of methods. Model‐based approaches to phylogenetic inference ...(likelihood, Bayesian) are defended on the premise that without explicit statistical models there is no science, and parsimony is defended on the grounds that it provides the best rationalization of the data, while refraining from assigning specific probabilities to trees or character‐state reconstructions. Authors who favour model‐based approaches often focus on the statistical properties of the methods and models themselves, but this is of only limited use in deciding the best method for phylogenetic inference—such decision also requires considering the conditions of evolution that prevail in nature. Another approach is to compare the performance of parsimony and model‐based methods in simulations, which traditionally have been used to defend the use of models of evolution for DNA sequences. Some recent papers, however, have promoted the use of model‐based approaches to phylogenetic inference for discrete morphological data as well. These papers simulated data under models already known to be unfavourable to parsimony, and modelled morphological evolution as if it evolved just like DNA, with probabilities of change for all characters changing in concert along tree branches. The present paper discusses these issues, showing that under reasonable and less restrictive models of evolution for discrete characters, equally weighted parsimony performs as well or better than model‐based methods, and that parsimony under implied weights clearly outperforms all other methods.
Classic chemotherapy his little or no specificity for cancer cells, normally resulting in low accumulation at the tumor region (inefficacy), and in severe side effects (toxicity). This challenge has ...resulted in the development of several deliver strategies for chemotherapy agents to improve their concentration at the tumor site, simultaneously increasing their anticancer efficacy, while reducing the associated adverse systemic effects. In this work, the potential of drug delivery strategies involving the use of nanocarriers for controlling the biodistribution of antitumor drugs is deeply revised: passive targeting (through the enhanced permeability and retention effect, EPR effect) and active targeting (including stimuli-sensitive carriers and ligand-mediated delivery). Special attention will be also focussed on the recent approaches for overcoming multi-drug resistence. Finally, a general view of the problem of "nanotoxicity" in cancer treatment is also given.
Mangrove forests are one of the world's most threatened tropical ecosystems with global loss exceeding 35% (ref. 1). Juvenile coral reef fish often inhabit mangroves, but the importance of these ...nurseries to reef fish population dynamics has not been quantified. Indeed, mangroves might be expected to have negligible influence on reef fish communities: juvenile fish can inhabit alternative habitats and fish populations may be regulated by other limiting factors such as larval supply or fishing. Here we show that mangroves are unexpectedly important, serving as an intermediate nursery habitat that may increase the survivorship of young fish. Mangroves in the Caribbean strongly influence the community structure of fish on neighbouring coral reefs. In addition, the biomass of several commercially important species is more than doubled when adult habitat is connected to mangroves. The largest herbivorous fish in the Atlantic, Scarus guacamaia, has a functional dependency on mangroves and has suffered local extinction after mangrove removal. Current rates of mangrove deforestation are likely to have severe deleterious consequences for the ecosystem function, fisheries productivity and resilience of reefs. Conservation efforts should protect connected corridors of mangroves, seagrass beds and coral reefs.
Abstract
Information theory and Thermodynamics have developed closer in the last years, with a growing application palette in which the formal equivalence between the Shannon and Gibbs entropies is ...exploited. The main barrier to connect both disciplines is the fact that information does not imply a dynamics, whereas thermodynamic systems unfold with time, often away from equilibrium. Here, we analyze chain-like systems comprising linear sequences of physical objects carrying symbolic meaning. We show that, after defining a reading direction, both reversible and irreversible informations emerge naturally from the principle of microscopic reversibility in the evolution of the chains driven by a protocol. We find fluctuation equalities that relate entropy, the relevant concept in communication, and energy, the thermodynamically significant quantity, examined along sequences whose content evolves under writing and revision protocols. Our results are applicable to nanoscale chains, where information transfer is subject to thermal noise, and extendable to virtually any communication system.
Aim To develop and implement a method for phylogenetic biogeography that is both event based and geographically explicit, that is, that uses the geographical ranges observed in the terminals instead ...of 'predefined areas.' Methods The method, GEM (Geographically explicit Event Model), attributes vicariance, sympatry (range copying), point sympatry (subset sympatry) or founder events, to the internal nodes of the tree. The cost of a reconstruction is calculated as the event cost plus the amount of range changes along a branch, and the best reconstruction is the combination of the event and range assignments that minimize the cost. Results The approach was implemented in a computer program, EVS, using a geographical data model (a raster) in which range changes were measured by pixel counts. The program can be used in real-sized datasets, using an heuristic to find reasonable solutions in short times. Main conclusion GEM provides a method for direct analysis of joint data on phylogeny and explicit distribution ranges, and proposes both the ancestral ranges and the biogeographical events connected with cladogenesis.
In the marine realm, the tropics host an extraordinary diversity of taxa but the drivers underlying the global distribution of marine organisms are still under scrutiny and we still lack an accurate ...global predictive model. Using a spatial database for 6336 tropical reef fishes, we attempted to predict species richness according to geometric, biogeographical and environmental explanatory variables. In particular, we aimed to evaluate and disentangle the predictive performances of temperature, habitat area, connectivity, mid-domain effect and biogeographical region on reef fish species richness. We used boosted regression trees, a flexible machine-learning technique, to build our predictive model and structural equation modeling to test for potential ‘mediation effects’ among predictors. Our model proved to be accurate, explaining 80% of the total deviance in fish richness using a cross-validated procedure. Coral reef area and biogeographical region were the primary predictors of reef fish species richness, followed by coast length, connectivity, mid-domain effect and sea surface temperature, with interactions between the region and other predictors. Important indirect effects of water temperature on reef fish richness, mediated by coral reef area, were also identified. The relationship between environmental predictors and species richness varied markedly among biogeographical regions. Our analysis revealed that a few easily accessible variables can accurately predict reef fish species richness. They also highlight concerns regarding ongoing environmental declines, with region-specific responses to variation in environmental conditions predicting a variable response to anthropogenic impacts.
A likelihood method that approximates the behaviour of implied weighting is described. This approach provides a likelihood perspective on several aspects of implied weighting, such as guidance for ...the choice of concavity values, a justification to use different concavities for different numbers of taxa, and a natural basis for extended implied weighting. In this approach, the number of free parameters in the estimation depends on C, the number of characters (in contrast to the standard Mk model, which estimates 2T–3 parameters for T taxa). Depending on the characteristics of the dataset, the likelihood obtained with this approach may in some cases be similar or superior to that of the Mk model, but with fewer parameters being adjusted. Because of that tradeoff, testing against the Mk model by means of the Akaike information criterion on a set of 182 morphological datasets indicated many cases (36) in which the likelihood approximation to implied weighting is the best method, from an information‐theoretic point of view. Given that it is expected to produce (almost) the same results as this maximum‐likelihood approximation, implied weighting can therefore be seen as a valid alternative to the Mk model often used for morphological datasets, on the basis of a criterion for model fit widely advocated by likelihoodists.
We analyzed a quantitative multiscale model that describes the epigenetic dynamics during the growth and evolution of an avascular tumor. A gene regulatory network (GRN) formed by a set of ten genes ...that are believed to play an important role in breast cancer development was kinetically coupled to the microenvironmental agents: glucose, estrogens, and oxygen. The dynamics of spontaneous mutations was described by a Yule-Furry master equation whose solution represents the probability that a given cell in the tissue undergoes a certain number of mutations at a given time. We assumed that the mutation rate is modified by a spatial gradient of nutrients. The tumor mass was simulated by means of cellular automata supplemented with a set of reaction diffusion equations that described the transport of microenvironmental agents. By analyzing the epigenetic state space described by the GRN dynamics, we found three attractors that were identified with cellular epigenetic states: normal, precancer and cancer. For two-dimensional (2D) and three-dimensional (3D) tumors we calculated the spatial distribution of the following quantities: (i) number of mutations, (ii) mutation of each gene and, (iii) phenotypes. Using estrogen as the principal microenvironmental agent that regulates cell proliferation process, we obtained tumor shapes for different values of estrogen consumption and supply rates. It was found that he majority of mutations occurred in cells that were located close to the 2D tumor perimeter or close to the 3D tumor surface. Also, it was found that the occurrence of different phenotypes in the tumor are controlled by estrogen concentration levels since they can change the individual cell threshold and gene expression levels. All results were consistently observed for 2D and 3D tumors.
For a bio-economy establishment, understanding the energy consumption needs to produce solid biofuels is a key point. Herein, olive tree pruning was treated by both dry (pyrolysis and torrefaction) ...and wet (hydrothermal carbonization) thermal treatments. Product yield, solid quality and energy consumption were assessed. The solids were characterized by means of chemical and thermogravimetric analysis. For all treatments, coal-like solid products were obtained, with higher heating values (HHV) of almost 30 MJ kg−1 in most of the conditions evaluated. Chars from pyrolysis presented the greater carbon content (between 76 and 85 wt%) but also the higher ash content (ranging from 6 to 9 wt%). From an energy consumption perspective, torrefaction registered the lowest energy consumption (between 5.85 and 20.76 MJ kg−1 char). The highest energy contents per kilogram of char produced were also reflected in torrefaction samples, with values around 11 MJ kg−1 char. Although the obtained HHVs were greater for pyrolysis chars the higher mass yields obtained in torrefaction makes it more profitable. The least severe conditions allowed to obtain a positive energy balance only with the solid phase considered. Nonetheless, further room for improvement is possible since the gas and liquid phases may also be valorised.
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•Pyrolysis, torrefaction and HTC were assessed regarding yield, quality and energy consumption.•From both wet and dry treatments, products with HHV of ca. 30 MJ kg−1 were obtained.•Pyrolysis concentrates the carbon content in the char to a greater extent (80 wt%).•The highest energy content per kg of char were reflected in torrefaction samples.•Torrefaction registered the lowest energy consumption from ca. 5–20 MJ kg−1 char.
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