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This work aims to produce hybrid materials with potential applications in dye photodegradation. Therefore, hybrid films were obtained by incorporating cobalt (II, III) oxide (Co3O4) or cobalt ferrite (CoFe2O4) nanoparticles (NPs) with 18 ± 1.6 nm and 26 ± 1.3 nm, respectively, into a poly 3-hydroxybutyrate (P3HB) polymeric matrix. The Co3O4@P3HB and CoFe2O4@P3HB hybrid films were fabricated by solvent casting in a ratio of 85 mg to 15 mg (P3HB-NPs). Different spectroscopic and microscopy techniques characterized the Co3O4 and CoFe2O4 NPs and the P3HB, Co3O4@P3HB and CoFe2O4@P3HB films. The optical band gap for Co3O4 and CoFe2O4 NPs was estimated from their diffuse reflectance spectra (DRS) around 2.5 eV. X-ray diffraction (XRD) of the hybrid films revealed that the nanometric sizes of the Co3O4 and CoFe2O4 nanoparticles incorporated into the P3HB are preserved. The magnetic hysteresis curve of CoFe2O4 nanoparticles and CoFe2O4@P3HB film showed a ferromagnetic behaviour at 300 K. Transmission electron microscopy (TEM) confirmed the formation of nanocrystals, and scanning electron microscopy (SEM) provided evidence for the successful incorporation of the NPs into the P3HB matrix. The surface roughness and hydrophilicity of the hybrid films are increased compared to the P3HB film. The impact of the nanoparticles and the hybrid films on the photodegradation of methyl orange (MO) in its acidic form was studied. The photodegradation tests were carried out by direct sunlight exposure. The CoFe2O4@P3HB hybrid film achieved 85% photodegradation efficiency of a methyl orange solution of 20 ppm after 15 minutes of exposure to sunlight. After 30 minutes of exposure to sunlight, the nanoparticles and the hybrid films reached about 90% of the MO degradation. The results suggest that combining nanoparticles with the polymer significantly enhances photodegradation compared to isolated nanoparticles., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Bernal-Sánchez et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

In this paper, we explore different methods to detect patterns in the activity of bus rapid transit (BRT) systems focusing on two aspects of transit: infrastructure and the movement of vehicles. To this end, we analyze records of velocity and position of each active vehicle in nine BRT systems located in the Americas. We detect collective patterns that characterize each BRT system obtained from the statistical analysis of velocities in the entire system (global scale) and at specific zones (local scale). We analyze the velocity records at the local scale applying the Kullback-Leibler divergence to compare the vehicular activity between zones. This information is organized in a similarity matrix that can be represented as a network of zones. The resulting structure for each system is analyzed using network science methods. In particular, by implementing community detection algorithms on networks, we obtain different groups of zones characterized by similarities in the movement of vehicles. Our findings show that the representation of the dataset with information of vehicles as a network is a useful tool to characterize at different scales the activity of BRT systems when geolocalized records of vehicular movement are available. This general approach can be implemented in the analysis of other public transportation systems., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Martínez-González et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Pauli channels are fundamental in the context of quantum computing as they model the simplest kind of noise in quantum devices. We propose a quantum algorithm for simulating Pauli channels and extend it to encompass Pauli dynamical maps (parametrized Pauli channels). A parametrized quantum circuit is employed to accommodate for dynamical maps. We also establish the mathematical conditions for an N-qubit transformation to be achievable using a parametrized circuit where only one single-qubit operation depends on the parameter. The implementation of the proposed circuit is demonstrated using IBM's quantum computers for the case of one qubit, and the fidelity of this implementation is reported., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Basile, Pineda. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Positron Emission Mammography (PEM) is a valuable molecular imaging technique for breast studies using pharmaceuticals labeled with positron emitters and dual-panel detectors. PEM scanners normally use large scintillation crystals coupled to sensitive photodetectors. Multiple interactions of the 511 keV annihilation photons in the crystals can result in event mispositioning leading to a negative impact in radiopharmaceutical uptake quantification. In this work, we report the study of crystal scatter effects of a large-area dual-panel PEM system designed with either monolithic or pixelated lutetium yttrium orthosilicate (LYSO) crystals using the Monte Carlo simulation platform GATE. The results show that only a relatively small fraction of coincidences (~20%) arise from events where both coincidence photons undergo single interactions (mostly through photoelectric absorption) in the crystals. Most of the coincidences are events where at least one of the annihilation photons undergoes a chain of Compton scatterings: approximately 79% end up in photoelectric absorption while the rest (<1%) escape the detector. Mean positioning errors, calculated as the distance between first hit and energy weighted (assigned) positions of interaction, were 1.70 mm and 1.92 mm for the monolithic and pixelated crystals, respectively. Reconstructed spatial resolution quantification with a miniDerenzo phantom and a list mode iterative reconstruction algorithm shows that, for both crystal types, 2 mm diameter hot rods were resolved, indicating a relatively small effect in spatial resolution. A drastic reduction in peak-to-valley ratios for the same hot-rod diameters was observed, up to a factor of 14 for the monolithic crystals and 7.5 for the pixelated ones., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Saaidi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Although friendship networks have been extensively studied, few models and studies are available to understand the reciprocity of friendship and foes. Here a model is presented to explain the directed friendship and foes network formation observed in experiments of Mexican and Hungarian schools. Within the presented model, each agent has a private opinion and a public one that shares to the group. There are two kinds of interactions between agents. The first kind represent interactions with the neighbors while the other represents the attitude of an agent to the overall public available information. Links between agents evolve as a combination of the public and private information available. Friendship is defined using a fitness function according to the strength of the agent's bonds, clustering coefficient, betweenness centrality and degree. Enmity is defined as very negative links. The model allows us to reproduce the distribution of mentions for friends and foes observed in the experiments, as well as the topology of the directed networks., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 García-Rodríguez et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

One of the first steps in protein sequence analysis is comparing sequences to look for similarities. We propose an information theoretical distance to compare cellular automata representing protein sequences, and determine similarities. Our approach relies in a stationary Hamming distance for the evolution of the automata according to a properly chosen rule, and to build a pairwise similarity matrix and determine common ancestors among different species in a simpler and less computationally demanding computer codes when compared to other methods., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 F. Souza et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

We introduce a general framework for empirically detecting interactions in communities of entities characterized by different features. This approach is inspired by ideas and methods coming from ecology and finance and is applied to a large dataset extracted from the cryptocurrency market. The inter-species interaction network is constructed using a similarity measure based on the log-growth rate of the capitalizations of the cryptocurrency market. The detected relevant interactions are only of the cooperative type, and the network presents a well-defined clustered structure, with two practically disjointed communities. The first one is made up of highly capitalized cryptocurrencies that are tightly connected, and the second one is made up of small-cap cryptocurrencies that are loosely linked. This approach based on the log-growth rate, instead of the conventional price returns, seems to enhance the discriminative potential of the network representation, highlighting a modular structure with compact communities and a rich hierarchy that can be ascribed to different functional groups. In fact, inside the community of the more capitalized coins, we can distinguish between clusters composed of some of the more popular first-generation cryptocurrencies, and clusters made up of second-generation cryptocurrencies. Alternatively, we construct the network of directed interactions by using the partial correlations of the log-growth rate. This network displays the important centrality of Bitcoin, discloses a core cluster containing a branch with the most capitalized first-generation cryptocurrencies, and emphasizes interesting correspondences between the detected direct pair interactions and specific features of the related currencies. As risk strongly depends on the interaction structure of the cryptocurrency system, these results can be useful for assisting in hedging risks. The inferred network topology suggests fewer probable widespread contagions. Moreover, as the riskier coins do not strongly interact with the others, it is more difficult that they can drive the market to more fragile states., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Brigatti et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Neuronal interactions give rise to complex dynamics in cortical networks, often described in terms of the diversity of activity patterns observed in a neural signal. Interestingly, the complexity of spontaneous electroencephalographic signals decreases during slow-wave sleep (SWS); however, the underlying neural mechanisms remain elusive. Here, we analyse in-vivo recordings from neocortical and hippocampal neuronal populations in rats and show that the complexity decrease is due to the emergence of synchronous neuronal DOWN states. Namely, we find that DOWN states during SWS force the population activity to be more recurrent, deterministic, and less random than during REM sleep or wakefulness, which, in turn, leads to less complex field recordings. Importantly, when we exclude DOWN states from the analysis, the recordings during wakefulness and sleep become indistinguishable: the spiking activity in all the states collapses to a common scaling. We complement these results by implementing a critical branching model of the cortex, which shows that inducing DOWN states to only a percentage of neurons is enough to generate a decrease in complexity that replicates SWS., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 González et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

In contrast with robust systems that resist noise or fragile systems that break with noise, antifragility is defined as a property of complex systems that benefit from noise or disorder. Here we define and test a simple measure of antifragility for complex dynamical systems. In this work we use our antifragility measure to analyze real data from return prices in the stock and cryptocurrency markets. Our definition of antifragility is the product of the return price and a perturbation. We explore different types of perturbations that typically arise from within the system. Our results suggest that for both the stock market and the cryptocurrency market, the tendency among the 'top performers' is to be robust rather than antifragile. It would be important to explore other possible definitions of antifragility to understand its role in financial markets and in complex dynamical systems in general., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Alatorre et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The aim of this work was to analyze the influence of sex hormones and anatomical details (trabeculations and false tendons) on the electrophysiology of healthy human hearts. Additionally, sex- and anatomy-dependent effects of ventricular tachycardia (VT) inducibility are presented. To this end, four anatomically normal, human, biventricular geometries (two male, two female), with identifiable trabeculations, were obtained from high-resolution, ex-vivo MRI and represented by detailed and smoothed geometrical models (with and without the trabeculations). Additionally one model was augmented by a scar. The electrophysiology finite element model (FEM) simulations were carried out, using O'Hara-Rudy human myocyte model with sex phenotypes of Yang and Clancy. A systematic comparison between detailed vs smooth anatomies, male vs female normal hearts was carried out. The heart with a myocardial infarction was subjected to a programmed stimulus protocol to identify the effects of sex and anatomical detail on ventricular tachycardia inducibility. All female hearts presented QT-interval prolongation however the prolongation interval in comparison to the male phenotypes was anatomy-dependent and was not correlated to the size of the heart. Detailed geometries showed QRS fractionation and increased T-wave magnitude in comparison to the corresponding smoothed geometries. A variety of sustained VTs were obtained in the detailed and smoothed male geometries at different pacing locations, which provide evidence of the geometry-dependent differences regarding the prediction of the locations of reentry channels. In the female phenotype, sustained VTs were induced in both detailed and smooth geometries with RV apex pacing, however no consistent reentry channels were identified. Anatomical and physiological cardiac features play an important role defining risk in cardiac disease. These are often excluded from cardiac electrophysiology simulations. The assumption that the cardiac endocardium is smooth may produce inaccurate predictions towards the location of reentry channels in in-silico tachycardia inducibility studies., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Gonzalez-Martin et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The consideration of an existing stochastic approach for the reproduction of ranked data pointed at a formal equivalence between its key mathematical expression and that for trajectories at the tangent bifurcation. This fact led to a nonlinear dynamical approach for rank distributions that shows similarities with universality classes in critical phenomena. The renormalization group (RG) fixed-point map f*(x) for a tangent bifurcation of arbitrary nonlinearity z > 1 has proved to be a powerful tool into which the formalism can be couched. The source distribution P(N) of the stochastic approach can be linked to f*(x) while the size-rank N(k) and frequency-rank F(k') distributions are obtained, respectively, from the map trajectories xt and the sums of its positions. We provide now an extension to Number Theory as we obtain from the trajectories xt of f*(x) the numbers, or asymptotic approximations of them, for the Factorial, Natural, Prime and Fibonacci sets. A measure of the advance of these numbers towards infinity is given by sums of positions that represent their reciprocals. We specify rank distribution universality classes, already associated with real data, to these number sets. We find that the convergence of the series of number reciprocals occurs first at nonlinearity z = 2, that which corresponds to the classical Zipf law, and link this transition edge to the action of the attractor when it first reduces the fractal dimension of trajectory positions to zero. Furthermore, the search of logarithmic corrections common to borderline dimensions provides a link to the Prime numbers set. Finally, we find corroborating evidence of these logarithmic corrections from the analysis of large data sets for ranked earthquake magnitudes. The formalism links all types of ranked distributions to a generalized extensive entropy., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2022 Velarde, Robledo. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The COVID-19 pandemic abruptly changed the classroom context and presented enormous challenges for all actors in the educational process, who had to overcome multiple difficulties and incorporate new strategies and tools to construct new knowledge. In this work we analyze how student performance was affected, for a particular case of higher education in La Plata, Argentina. We developed an analytical model for the knowledge acquisition process, based on a series of surveys and information on academic performance in both contexts: face-to-face (before the onset of the pandemic) and virtual (during confinement) with 173 students during 2019 and 2020. The information collected allowed us to construct an adequate representation of the process that takes into account the main contributions common to all individuals. We analyzed the significance of the model by means of Artificial Neural Networks and a Multiple Linear Regression Method. We found that the virtual context produced a decrease in motivation to learn. Moreover, the emerging network of contacts built from the interaction between peers reveals different structures in both contexts. In all cases, interaction with teachers turned out to be of the utmost importance in the process of acquiring knowledge. Our results indicate that this process was also strongly influenced by the availability of resources of each student. This reflects the reality of a developing country, which experienced prolonged isolation, giving way to a particular learning context in which we were able to identify key factors that could guide the design of strategies in similar scenarios., Competing Interests: The authors have declared that no competing interests exist.

Background: Despite lipid-lowering and antiplatelet therapy, the pattern of residual lipoproteins seems relevant to long-term cardiovascular outcomes. This study aims to evaluate the effects of combined therapies, commonly used in subjects with acute myocardial infarction, in the quality of low-density lipoprotein (LDL) particles., Methods: Prospective, open-label trial, included patients with acute myocardial infarction. Patients were randomized to antiplatelet treatment (ticagrelor or clopidogrel) and subsequently to lipid-lowering therapy (rosuvastatin or simvastatin/ezetimibe) and were followed up for six months. Nonlinear optical properties of LDL samples were examined by Gaussian laser beam (Z-scan) to verify the oxidative state of these lipoproteins, small angle X-ray scattering (SAXS) to analyze structural changes on these particles, dynamic light scattering (DLS) to estimate the particle size distribution, ultra violet (UV)-visible spectroscopy to evaluate the absorbance at wavelength 484 nm (typical from carotenoids), and polyacrylamide gel electrophoresis (Lipoprint) to analyze the LDL subfractions., Results: Simvastatin/ezetimibe with either clopidogrel or ticagrelor was associated with less oxidized LDL, and simvastatin/ezetimibe with ticagrelor to lower cholesterol content in the atherogenic subfractions of LDL, while rosuvastatin with ticagrelor was the only combination associated with increase in LDL size., Conclusions: The quality of LDL particles was influenced by the antiplatelet/lipid-lowering strategy, with ticagrelor being associated with the best performance with both lipid-lowering therapies. Trial registration: NCT02428374., Competing Interests: I confirm that this does not alter our adherence to PLOS ONE policies on sharing data and materials. The study design, data collection, statistical analysis, or publications were not influenced by the sponsors and are the exclusive responsibility of the investigators.

Escherichia coli as water-borne bacteria exists in the recirculation water of coal flotation and affects the recovery of coal flotation. In order to study the effect of Escherichia coli on coal flotation, we changed the concentration of Escherichia coli and pH in the coal flotation system and found that Escherichia coli had an adverse effect on coal flotation. The concentration of Escherichia coli was negatively correlated with the recovery of coal. When the concentration of Escherichia coli reached 5.0 × 109 cells/ml, the recovery of coal flotation was 50.25%, and the change of pH basically did not affect the adverse effect of Escherichia coli on coal flotation. The mechanism was studied through Zeta potential, Fourier transform infrared spectroscopy, Scanning electron microscopy and Contact angle measurements. The results revealed that Escherichia coli could be adsorbed to the coal surface by hydrogen bonding, which changed the hydrophobicity of the coal surface and then reduced the recovery of coal flotation., Competing Interests: The authors have declared that no competing interests exist.

Cities are characterized by the presence of a dense population with a high potential for interactions between individuals of diverse backgrounds. They appear in parallel to the Neolithic revolution a few millennia ago. The advantages brought in terms of agglomeration for economy, innovation, social and cultural advancements have kept them as a major landmark in recent human history. There are many different aspects to study in urban systems from a scientific point of view, one can concentrate in demography and population evolution, mobility, economic output, land use and urban planning, home accessibility and real estate market, energy and water consumption, waste processing, health, education, integration of minorities, just to name a few. In the last decade, the introduction of communication and information technologies have enormously facilitated the collection of datasets on these and other questions, making possible a more quantitative approach to city science. All these topics have been addressed in many works in the literature, and we do not intend to offer here a systematic review. Instead, we will only provide a brief taste of some of these above-mentioned aspects, which could serve as an introduction to the collection 'Cities as Complex Systems'. Such a non-systematic view will lead us to leave outside many relevant papers, and for this we must apologise., Competing Interests: The authors have declared that no competing interests exist.

Scientists and astronomers have attached great importance to the task of discovering new exoplanets, even more so if they are in the habitable zone. To date, more than 4300 exoplanets have been confirmed by NASA, using various discovery techniques, including planetary transits, in addition to the use of various databases provided by space and ground-based telescopes. This article proposes the development of a deep learning system for detecting planetary transits in Kepler Telescope light curves. The approach is based on related work from the literature and enhanced to validation with real light curves. A CNN classification model is trained from a mixture of real and synthetic data. The model is then validated only with unknown real data. The best ratio of synthetic data is determined by the performance of an optimisation technique and a sensitivity analysis. The precision, accuracy and true positive rate of the best model obtained are determined and compared with other similar works. The results demonstrate that the use of synthetic data on the training stage can improve the transit detection performance on real light curves., Competing Interests: The authors have declared that no competing interests exist.

Citrus canker is one of the main bacterial diseases that affect citrus crops and is caused by Xanthomonas citri which affects all citrus species worldwide. New strategies to control citrus canker are necessary and the use of bacteriophages as biocontrol agent could be an alternative. Phages that infect Xanthomonas species have been studied, such as XacN1, a myovirus that infects X. citri. Here we report the isolation and characterization of a new jumbo phage, vb&#95;XciM&#95;LucasX, which infects X. citri and X. fuscans. Transmission electron microscopy allowed classification of LucasX in the Myoviridae family, which was corroborated by its genomic sequencing, annotation, and proteome clustering. LucasX has a 305,651 bp-long dsDNA genome. ORF prediction and annotation revealed 157 genes encoding putative structural proteins such as capsid and tail related proteins and phage assembly associated proteins, however, for most of the structural proteins it was not possible assign specific functions. Its genome encodes several proteins related to DNA replication and nucleotide metabolism, five putative RNA polymerases, at least one homing endonuclease mobile element, a terminase large subunit (TerL), an endolysin and many proteins classified as beneficial to the host. Proteome clustering and phylogeny analyses showed that LucasX is a new jumbo phage having as its closest neighbor the Xanthomonas jumbo phage Xoo-sp14. LucasX presented a burst size of 40 PFU/infected cell of X. citri 306, was completely inactivated at temperatures above 50°C, presented survival lower than 25% after 80 s of exposition to artificial UV light and had practically no tolerance to concentrations above 2.5 g/L NaCl or 40% ethanol. LucasX presented optimum pH at 7 and a broad range of Xanthomonas hosts, infecting twenty-one of the twenty-three strains tested. Finally, the LucasX yield was dependent on the host strain utilized, resulting one order of magnitude higher in X. fuscans C 752 than in X. citri 306, which points out to the possibility of phage yield improvement, an usual challenge for biocontrol purposes., Competing Interests: The authors have declared that no competing interests exist.

We report strong evidence of the importance of contact hubs (or superspreaders) in mitigating the current COVID-19 pandemic. Contact hubs have a much larger number of contacts than the average in the population, and play a key role on the effectiveness of vaccination strategies. By using an age-structures compartmental SEIAHRV (Susceptible, Exposed, Infected symptomatic, Asymptomatic, Hospitalized, Recovered, Vaccinated) model, calibrated from available demographic and COVID-19 incidence, and considering separately those individuals with a much greater number of contacts than the average in the population, we show that carefully choosing who will compose the first group to be vaccinated can impact positively the total death toll and the demand for health services. This is even more relevant in countries with a lack of basic resources for proper vaccination and a significant reduction in social isolation. In order to demonstrate our approach we show the effect of hypothetical vaccination scenarios in two countries of very different scales and mitigation policies, Brazil and Portugal., Competing Interests: The authors have declared that no competing interests exist.

To understand airline transportation networks (ATN) systems we can effectively represent them as multilayer networks, where layers capture different airline companies, the nodes correspond to the airports and the edges to the routes between the airports. We focus our study on the importance of leveraging synthetic generative multilayer models to support the analysis of meaningful patterns in these routes, capturing an ATN's evolution with an emphasis on measuring its resilience to random or targeted attacks and considering deliberate locations of airports. By resorting to the European ATN and the United States ATN as exemplary references, in this work, we provide a systematic analysis of major existing synthetic generation models for ATNs, specifically ANGEL, STARGEN and BINBALL. Besides a thorough study of the topological aspects of the ATNs created by the three models, our major contribution lays on an unprecedented investigation of their spectral characteristics based on Random Matrix Theory and on their resilience analysis based on both site and bond percolation approaches. Results have shown that ANGEL outperforms STARGEN and BINBALL to better capture the complexity of real-world ATNs by featuring the unique properties of building a multiplex ATN layer by layer and of replicating layers with point-to-point structures alongside hub-spoke formations., Competing Interests: The authors have declared that no competing interests exist.

Scale-free networks constitute a fast-developing field that has already provided us with important tools to understand natural and social phenomena. From biological systems to environmental modifications, from quantum fields to high energy collisions, or from the number of contacts one person has, on average, to the flux of vehicles in the streets of urban centres, all these complex, non-linear problems are better understood under the light of the scale-free network's properties. A few mechanisms have been found to explain the emergence of scale invariance in complex networks, and here we discuss a mechanism based on the way information is locally spread among agents in a scale-free network. We show that the correct description of the information dynamics is given in terms of the q-exponential function, with the power-law behaviour arising in the asymptotic limit. This result shows that the best statistical approach to the information dynamics is given by Tsallis Statistics. We discuss the main properties of the information spreading process in the network and analyse the role and behaviour of some of the parameters as the number of agents increases. The different mechanisms for optimization of the information spread are discussed., Competing Interests: The authors have declared that no competing interests exist.

The vast majority of plant viruses are unenveloped, i.e., they lack a lipid bilayer that is characteristic of most animal viruses. The interactions between plant viruses, and between viruses and surfaces, properties that are essential for understanding their infectivity and to their use as bionanomaterials, are largely controlled by their surface charge, which depends on pH and ionic strength. They may also depend on the charge of their contents, i.e., of their genes or-in the instance of virus-like particles-encapsidated cargo such as nucleic acid molecules, nanoparticles or drugs. In the case of enveloped viruses, the surface charge of the capsid is equally important for controlling its interaction with the lipid bilayer that it acquires and loses upon leaving and entering host cells. We have previously investigated the charge on the unenveloped plant virus Cowpea Chlorotic Mottle Virus (CCMV) by measurements of its electrophoretic mobility. Here we examine the electrophoretic properties of a structurally and genetically closely related bromovirus, Brome Mosaic Virus (BMV), of its capsid protein, and of its empty viral shells, as functions of pH and ionic strength, and compare them with those of CCMV. From measurements of both solution and gel electrophoretic mobilities (EMs) we find that the isoelectric point (pI) of BMV (5.2) is significantly higher than that of CCMV (3.7), that virion EMs are essentially the same as those of the corresponding empty capsids, and that the same is true for the pIs of the virions and of their cleaved protein subunits. We discuss these results in terms of current theories of charged colloidal particles and relate them to biological processes and the role of surface charge in the design of new classes of drug and gene delivery systems., Competing Interests: The authors have declared that no competing interests exist.

Although traditional models of epidemic spreading focus on the number of infected, susceptible and recovered individuals, a lot of attention has been devoted to integrate epidemic models with population genetics. Here we develop an individual-based model for epidemic spreading on networks in which viruses are explicitly represented by finite chains of nucleotides that can mutate inside the host. Under the hypothesis of neutral evolution we compute analytically the average pairwise genetic distance between all infecting viruses over time. We also derive a mean-field version of this equation that can be added directly to compartmental models such as SIR or SEIR to estimate the genetic evolution. We compare our results with the inferred genetic evolution of SARS-CoV-2 at the beginning of the epidemic in China and found good agreement with the analytical solution of our model. Finally, using genetic distance as a proxy for different strains, we use numerical simulations to show that the lower the connectivity between communities, e.g., cities, the higher the probability of reinfection., Competing Interests: The authors have declared that no competing interests exist.

Cells exert traction forces on the extracellular matrix to which they are adhered through the formation of focal adhesions. Spatial-temporal regulation of traction forces is crucial in cell adhesion, migration, cellular division, and remodeling of the extracellular matrix. By cultivating cells on polyacrylamide hydrogels of different stiffness we were able to investigate the effects of substrate stiffness on the generation of cellular traction forces by Traction Force Microscopy (TFM), and characterize the molecular dynamics of the focal adhesion protein zyxin by Fluorescence Correlation Spectroscopy (FCS) and Fluorescence Recovery After Photobleaching (FRAP). As the rigidity of the substrate increases, we observed an increment of both, cellular traction generation and zyxin residence time at the focal adhesions, while its diffusion would not be altered. Moreover, we found a positive correlation between the traction forces exerted by cells and the residence time of zyxin at the substrate elasticities studied. We found that this correlation persists at the subcellular level, even if there is no variation in substrate stiffness, revealing that focal adhesions that exert greater traction present longer residence time for zyxin, i.e., zyxin protein has less probability to dissociate from the focal adhesion., Competing Interests: The authors have declared that no competing interests exist.

Cooperation is crucial to overcome some of the most pressing social challenges of our times, such as the spreading of infectious diseases, corruption and environmental conservation. Yet, how cooperation emerges and persists is still a puzzle for social scientists. Since human cooperation is individually costly, cooperative attitudes should have been eliminated by natural selection in favour of selfishness. Yet, cooperation is common in human societies, so there must be some features which make it evolutionarily advantageous. Using a cognitive inspired model of human cooperation, recent work Realpe-Gómez (2018) has reported signatures of criticality in human cooperative groups. Theoretical evidence suggests that being poised at a critical point provides evolutionary advantages to groups by enhancing responsiveness of these systems to external attacks. After showing that signatures of criticality can be detected in human cooperative groups composed by Moody Conditional Cooperators, in this work we show that being poised close to a turning point enhances the fitness and make individuals more resistant to invasions by free riders., Competing Interests: The authors have declared that no competing interests exist.

The paradigm for compartment models in epidemiology assumes exponentially distributed incubation and removal times, which is not realistic in actual populations. Commonly used variations with multiple exponentially distributed variables are more flexible, yet do not allow for arbitrary distributions. We present a new formulation, focussing on the SEIR concept that allows to include general distributions of incubation and removal times. We compare the solution to two types of agent-based model simulations, a spatially homogeneous one where infection occurs by proximity, and a model on a scale-free network with varying clustering properties, where the infection between any two agents occurs via their link if it exists. We find good agreement in both cases. Furthermore a family of asymptotic solutions of the equations is found in terms of a logistic curve, which after a non-universal time shift, fits extremely well all the microdynamical simulations. The formulation allows for a simple numerical approach; software in Julia and Python is provided., Competing Interests: The authors have declared that no competing interests exist.

Dealing with traffic congestion is one of the most pressing challenges for cities. Transport authorities have implemented several strategies to reduce traffic jams with varying degrees of success. The use of reversible lanes is a common approach to improve traffic congestion during rush hours. A reversible lane can change its direction during a time interval to the more congested direction. This strategy can improve traffic congestion in specific scenarios. Most reversible lanes in urban roads are fixed in time and number; however, traffic patterns in cities are highly variable and unpredictable due to this phenomenon's complex nature. Therefore, reversible lanes may not improve traffic flow under certain circumstances; moreover, they could worsen it because of traffic fluctuations. In this paper, we use cellular automata to model adaptive reversible lanes(aka dynamic reversible lanes). Adaptive reversible lanes can change their direction using real-time information to respond to traffic demand fluctuations. Using real traffic data, our model shows that adaptive reversible lanes can improve traffic flow up to 40% compared to conventional reversible lanes. Our results show that there are significant fluctuations in traffic flow even during rush hours, and thus cities would benefit from implementing adaptive reversible lanes., Competing Interests: The authors have declared that no competing interests exist.

Adoption of a new technology depends on many factors. Marketing, advertising, social interactions, and personal convictions are relevant features when deciding to adopt, or not, a new technology. Thus, it is very important to determine the relative weight of these factors when introducing a new technology. Here we discuss an agent based model to investigate the behavior of agents exposed to advertising and social contacts. Agents may follow the social pressure, or maybe contrarians, acting against the majority, to decide if they adopt or not a new technology. First, we solve analytically the model that relies on the above quoted factors. Then, we compare the theoretical results with empirical data concerning the adoption of innovations by American households during the 20th century. The analysis of the diffusion dynamics process is done either for the whole period, or by periods based on the so-called technical-economic paradigms, according to Freeman and Perez. Three different periods are considered: before 1920, from 1920 to 1970, and after 1970. We study the evolution of the model parameters for each technical-economic period. Finally, by adjusting the key parameters we are able to collapse all the data into a universal curve that describes all the adoption processes., Competing Interests: The authors have declared that no competing interests exist.

Automatic monitoring of biodiversity by acoustic sensors has become an indispensable tool to assess environmental stress at an early stage. Due to the difficulty in recognizing the Amazon's high acoustic diversity and the large amounts of raw audio data recorded by the sensors, the labeling and manual inspection of this data is not feasible. Therefore, we propose an ecoacoustic index that allows us to quantify the complexity of an audio segment and correlate this measure with the biodiversity of the soundscape. The approach uses unsupervised methods to avoid the problem of labeling each species individually. The proposed index, named the Ecoacoustic Global Complexity Index (EGCI), makes use of Entropy, Divergence and Statistical Complexity. A distinguishing feature of this index is the mapping of each audio segment, including those of varied lengths, as a single point in a 2D-plane, supporting us in understanding the ecoacoustic dynamics of the rainforest. The main results show a regularity in the ecoacoustic richness of a floodplain, considering different temporal granularities, be it between hours of the day or between consecutive days of the monitoring program. We observed that this regularity does a good job of characterizing the soundscape of the environmental protection area of Mamirauá, in the Amazon, differentiating between species richness and environmental phenomena., Competing Interests: The authors have declared that no competing interests exist.

Loss of retinoblastoma (RB) function in the cone cells during retina development is necessary but not sufficient for retinoblastoma development. It has been reported that in the absence of RB activity, a retinoma is generated, and the onset of retina cancer occurs until the p53 pathway is altered. Unlike other types of cancer, in retinoblastoma the p53 tumour suppressor is mostly wild type, although its two primary regulators, MDMX and MDM2, are commonly dysregulated. A mutated RB form is inherited in around 35% of the cases, but normally two, somatic mutations are needed to alter the RB function. Here we investigated the mRNA levels of RB, p53, MDMX and MDM2 in peripheral blood samples of retinoblastoma patients to monitor the pathway status of p53 in somatic cells. We sought to investigate the involvement of these genes in the development of retina cancer, with the aim of identifying biomarkers for early diagnosis of this disease., Competing Interests: The authors have declared that no competing interests exist.

Human visual-motor coordination is an essential function of movement control, which requires interactions of multiple brain regions. Understanding the cortical-motor coordination is important for improving physical therapy for motor disabilities. However, its underlying transient neural dynamics is still largely unknown. In this study, we applied an eigenvector-based dynamical network analysis method to investigate the functional connectivity calculated from electroencephalography (EEG) signals under visual-motor coordination task and to identify its meta-stable states dynamics. We first tested this signal processing on a simulated network to evaluate it in comparison with other dynamical methods, demonstrating that the eigenvector-based dynamical network analysis was able to correctly extract the dynamical features of the evolving networks. Subsequently, the eigenvector-based analysis was applied to EEG data collected under a visual-motor coordination experiment. In the EEG study with participants, the results of both topological analysis and the eigenvector-based dynamical analysis were able to distinguish different experimental conditions of visual tracking task. With the dynamical analysis, we showed that different visual-motor coordination states can be distinguished by investigating the meta-stable states dynamics of the functional connectivity., Competing Interests: No authors have competing interests.

Monitoring migration flows is crucial to respond to humanitarian crisis and to design efficient policies. This information usually comes from surveys and border controls, but timely accessibility and methodological concerns reduce its usefulness. Here, we propose a method to detect migration flows worldwide using geolocated Twitter data. We focus on the migration crisis in Venezuela and show that the calculated flows are consistent with official statistics at country level. Our method is versatile and far-reaching, as it can be used to study different features of migration as preferred routes, settlement areas, mobility through several countries, spatial integration in cities, etc. It provides finer geographical and temporal resolutions, allowing the exploration of issues not contemplated in official records. It is our hope that these new sources of information can complement official ones, helping authorities and humanitarian organizations to better assess when and where to intervene on the ground., Competing Interests: The authors have declared that no competing interests exist.

The co-circulation of different arboviruses in the same time and space poses a significant threat to public health given their rapid geographic dispersion and serious health, social, and economic impact. Therefore, it is crucial to have high quality of case registration to estimate the real impact of each arboviruses in the population. In this work, a Vector Autoregressive (VAR) model was developed to investigate the interrelationships between discarded and confirmed cases of dengue, chikungunya, and Zika in Brazil. We used data from the Brazilian National Notifiable Diseases Information System (SINAN) from 2010 to 2017. There were three peaks in the series of dengue notification in this period occurring in 2013, 2015 and in 2016. The series of reported cases of both Zika and chikungunya reached their peak in late 2015 and early 2016. The VAR model shows that the Zika series have a significant impact on the dengue series and vice versa, suggesting that several discarded and confirmed cases of dengue could actually have been cases of Zika. The model also suggests that the series of confirmed and discarded chikungunya cases are almost independent of the cases of Zika, however, affecting the series of dengue. In conclusion, co-circulation of arboviruses with similar symptoms could have lead to misdiagnosed diseases in the surveillance system. We argue that the routinely use of mathematical and statistical models in association with traditional symptom-surveillance could help to decrease such errors and to provide early indication of possible future outbreaks. These findings address the challenges regarding notification biases and shed new light on how to handle reported cases based only in clinical-epidemiological criteria when multiples arboviruses co-circulate in the same population., Competing Interests: The authors have declared that no competing interests exist.

We study the time evolution of the shape of a vesicle membrane under time-dependent spontaneous curvature by means of phase-field model. We introduce the variation in time of the spontaneous curvature via a second field which represents the concentration of a substance that anchors with the lipid bilayer thus changing the local curvature and producing constriction. This constriction is mediated by the action on the membrane of an structure resembling the role of a Z ring. Our phase-field model is able to reproduce a number of different shapes that have been experimentally observed. Different shapes are associated with different constraints imposed upon the model regarding conservation of membrane area. In particular, we show that if area is conserved our model reproduces the so-called L-form shape. By contrast, if the area of the membrane is allowed to grow, our model reproduces the formation of a septum in the vicinity of the constriction. Furthermore, we propose a new term in the free energy which allows the membrane to evolve towards eventual pinching., Competing Interests: The authors have declared that no competing interests exist.

Introduction: This study explores the possibility of a relationship between the sphericity degree of a target volume with the dose distribution. This relationship is evaluated based on the ratio isodose volume / target volume (IV/TV) and the metrics coverage, i.e., selectivity, gradient index, conformity index and mean dose when planning radiosurgery for vestibular schwannoma., Methods: Sphericity degree (φ) was calculated for each target volume (TV) of 64 patients who underwent stereotactic radiosurgery (SRS) for vestibular schwannoma. The calculation of this parameter was developed using the theoretical definition for operational sphericity φ = VP/VCS. The values found are evaluated considering the following metrics:-Coverage (C), selectivity (S), gradient index (GI), Paddick conformity index (CIPaddick) and dose distribution (IV/TV). The planning was also carried out considering a spherical target volume defined in a spherical phantom. The spherical volume is the same as the target used in the treatment plan. The planning of the spherical target was considered as a reference plan to evaluate the dose distribution inside and outside the volume., Results: It was possible to observe that the majority of target volumes has (ϕ) around 0,66-0,77, corresponding to 54,7% of the total. Considering the mean values for metrics, the results are: C = 0,98, S = 0,78, GI = 3,11 and CI = 0,81. The dose distribution was equivalent for treatment plans and reference plans. Quantitative analysis for IV/TV shows that these values are higher than 30% for treatment plans where shot density is large., Conclusion: This study demonstrates that de sphericity degree (φ) can be related to the dose distribution (IV/TV). Therefore the sphericity degree is a good parameter to evaluate the dose distribution of a plan for vestibular schwannoma treatment, considering the reference plan as being a spherical target using a leksell gamma knife® perfexion (LGKP). This study shows that the sphericity degree offers important information of the dose distribution outside and inside the target volume. This is not evaluated by the other parameters already implemented as metric to analyzing the GKP plans., Competing Interests: The authors have declared that no competing interests exist.

Protracted conflict is one of the largest human challenges that have persistently undermined economic and social progress. In recent years, there has been increased emphasis on using statistical and physical science models to better understand both the universal patterns and the underlying mechanics of conflict. Whilst macroscopic power-law fractal patterns have been shown for death-toll in wars and self-excitation models have been shown for roadside ambush attacks, very few works deal with the challenge of complex dynamics between gangs at the intra-city scale. Here, based on contributions to the historical memory of the conflict in Colombia, Medellin's gang-confrontation-network is presented. It is shown that socio-economic and violence indexes are moderate to highly correlated to the structure of the network. Specifically, the death-toll of conflict is strongly influenced by the leading eigenvalues of the gangs' conflict adjacency matrix, which serves a proxy for unstable self-excitation from revenge attacks. The distribution of links based on the geographic distance between gangs in confrontation leads to the confirmation that territorial control is a main catalyst of violence and retaliation among gangs. As a first attempt to explore the time evolution of the confrontation network, the Boltzmann-Lotka-Volterra (BLV) dynamic interaction network analysis is applied to quantify the spatial embeddedness of the dynamic relationship between conflicting gangs in Medellin. However, the non-stationary character of the violence in Medellin during the observation period restricts the application of the BLV model and results suggest that more involved and comprehensive models are needed to described the dynamics of Medellin's armed conflict., Competing Interests: The authors have read the journal’s policy and the authors of this manuscript have the following competing interests: LAP is a paid employee of Guane Enterprises. This does not alter our adherence to PLOS ONE policies on sharing data and materials. There are no patents, products in development or marketed products to declare.

The reaction-diffusion equation serves to model systems in the diffusion regime with sources. Specific applications include diffusion processes in chemical reactions, as well as the propagation of species, diseases, and populations in general. In some of these applications the location of an outbreak, for instance, the source point of a disease or the nest of a vector spreading a virus is important. Also important are the environmental parameters of the domain where the process diffuses, namely the space-dependent diffusion coefficient and the proliferation parameter of the process. Determining both, the location of a source and the environmental parameters, define an inverse problem that in turn, involves a partial differential equation. In this paper we classify the values of these parameters using Support Vector Machines (SVM) trained with numerical solutions of the reaction-diffusion problem. Our set up has accuracy of classifying the outbreak location above 90% and 77% of classifying both, the location and the environmental parameters. The approach presented in our analysis can be directly implemented by measuring the population under study at specific locations in the spatial domain as function of time., Competing Interests: The authors have declared that no competing interests exist.

Optical tweezers have enabled the exploration of picoNewton forces and dynamics in single-molecule systems such as DNA and molecular motors. In this work, we used optical tweezers to study the folding/unfolding dynamics of the APTSTX1-aptamer, a single-stranded DNA molecule with high affinity for saxitoxin (STX), a lethal neurotoxin. By measuring the transition force during (un)folding processes, we were able to characterize and distinguish the conformational changes of this aptamer in the presence of magnesium ions and toxin. This work was supported by molecular dynamics (MD) simulations to propose an unfolding mechanism of the aptamer-Mg+2 complex. Our results are a step towards the development of new aptamer-based STX sensors that are potentially cheaper and more sensitive than current alternatives., Competing Interests: The authors have declared that no competing interests exist.

A recent work (Hernández, et al., 2018) introduced a networked voting rule supported by a trust-based social network, where indications of possible representatives were based on individuals opinions. Individual contributions went beyond a simple vote-counting and were based on proxy voting. This mechanism selects committees with high levels of representativeness, weakening the possibility of patronage relations. By incorporating the integrity of individuals and its perception, we here address the question of the resulting committee's trustability. Our results show that this voting rule provides sufficiently small committees with high levels of representativeness and integrity. Furthermore, the voting system displays robustness to strategic and untruthful application of the voting algorithm., Competing Interests: The authors have declared that no competing interests exist.

In this work we analyze potential environmental drivers of malaria cases in Northwestern Argentina. We inspect causal links between malaria and climatic variables by means of the convergent cross mapping technique, which provides a causality criterion from the theory of dynamic systems. Analysis is based on 12 years of weekly malaria P. vivax cases in Tartagal, Salta, Argentina-at the southern fringe of malaria incidence in the Americas-together with humidity and temperature time-series spanning the same period. Our results show that there are causal links between malaria cases and both maximum temperature, with a delay of five weeks, and minimum temperature, with delays of zero and twenty two weeks. Humidity is also a driver of malaria cases, with thirteen weeks delay between cause and effect. Furthermore we also determined the sign and strength of the effects. Temperature has always a positive non-linear effect on cases, with maximum temperature effects more pronounced above 25°C and minimum above 17°C, while effects of humidity are more intricate: maximum humidity above 85% has a negative effect, whereas minimum humidity has a positive effect on cases. These results might be signaling processes operating at short (below 5 weeks) and long (over 12 weeks) time delays, corresponding to effects related to parasite cycle and mosquito population dynamics respectively. The non-linearities found for the strength of the effect of temperature on malaria cases make warmer areas more prone to higher increases in the disease incidence. Moreover, our results indicate that an increase of extreme weather events could enhance the risks of malaria spreading and re-emergence beyond the current distribution. Both situations, warmer climate and increase of extreme events, will be remarkably increased by the end of the century in this hot spot of climate change., Competing Interests: The authors have declared that no competing interests exist.

This study presents multiwall and bamboo-like carbon nanotubes found in samples from the Allende carbonaceous chondrite using high-resolution transmission electron microscopy (HRTEM). A highly disordered lattice observed in this material suggests the presence of chiral domains in it. Our results also show amorphous and poorly-graphitized carbon, nanodiamonds, and onion-like fullerenes. The presence of multiwall and bamboo-like carbon nanotubes have important implications for hypotheses that explain how a probable source of asymmetry in carbonaceous chondrites might have contributed to the enantiomeric excess in soluble organics under extraterrestrial scenarios. This is the first study proving the existence of carbon nanotubes in carbonaceous chondrites., Competing Interests: The authors have declared that no competing interests exist.

The understanding of human mobility patterns in different transportation modes is an interdisciplinary research field with a direct impact in aspects as varied as urban planning, traffic optimization, sustainability, the reduction of operating costs as well as the mitigation of pollution in urban areas. In this paper, we study the global activity of users in bike-sharing systems operating in the cities of Chicago and New York. For this transportation mode, we explore the temporal and spatial characteristics of the mobility of cyclists. In particular, through the analysis of origin-destination matrices, we characterize the spatial structure of the displacements of users. We apply a mobility model for the global activity of the system that classifies the displacements between stations in local and non-local transitions. In local transitions, cyclists move in a region around each station whereas, in the non-local case, bike users travel with long-range displacements in a similar way to Lévy flights. We reproduce the spatial dynamics by using Monte Carlo simulations. The obtained results are similar to the observed in real data and reveal that the model implemented captures important characteristics of the global spatial dynamics in the systems analyzed., Competing Interests: The authors have declared that no competing interests exist.

We present an equivalence between stochastic and deterministic variable approaches to represent ranked data and find the expressions obtained to be suggestive of statistical-mechanical meanings. We first reproduce size-rank distributions N(k) from real data sets by straightforward considerations based on the assumed knowledge of the background probability distribution P(N) that generates samples of random variable values similar to real data. The choice of different functional expressions for P(N): power law, exponential, Gaussian, etc., leads to different classes of distributions N(k) for which we find examples in nature. Then we show that all of these types of functions can be alternatively obtained from deterministic dynamical systems. These correspond to one-dimensional nonlinear iterated maps near a tangent bifurcation whose trajectories are proved to be precise analogues of the N(k). We provide explicit expressions for the maps and their trajectories and find they operate under conditions of vanishing or small Lyapunov exponent, therefore at or near a transition to or out of chaos. We give explicit examples ranging from exponential to logarithmic behavior, including Zipf's law. Adoption of the nonlinear map as the formalism central character is a useful viewpoint, as variation of its few parameters, that modify its tangency property, translate into the different classes for N(k)., Competing Interests: The authors have declared that no competing interest exist.

Citrus canker is a plant disease caused by the bacteria Xanthomonas citri subsp. citri that affects all domestic varieties of citrus. Some annotated genes from the X. citri subsp. citri genome are assigned to an interesting class named "pathogenicity, virulence and adaptation". Amongst these is sodM, which encodes for the gene product XcSOD, one of four superoxide dismutase homologs predicted from the genome. SODs are widespread enzymes that play roles in the oxidative stress response, catalyzing the degradation of the deleterious superoxide radical. In Xanthomonas, SOD has been associated with pathogenesis as a counter measure against the plant defense response. In this work we initially present the 1.8 Å crystal structure of XcSOD, a manganese containing superoxide dismutase from Xanthomonas citri subsp. citri. The structure bears all the hallmarks of a dimeric member of the MnSOD family, including the conserved hydrogen-bonding network residues. Despite the apparent gene redundancy, several attempts to obtain a sodM deletion mutant were unsuccessful, suggesting the encoded protein to be essential for bacterial survival. This intriguing observation led us to extend our structural studies to the remaining three SOD homologs, for which comparative models were built. The models imply that X. citri subsp. citri produces an iron-containing SOD which is unlikely to be catalytically active along with two conventional Cu,ZnSODs. Although the latter are expected to possess catalytic activity, we propose they may not be able to replace XcSOD for reasons such as distinct subcellular compartmentalization or differential gene expression in pathogenicity-inducing conditions., Competing Interests: The authors have declared that no competing interests exist.

Acidithiobacillus thiooxidans is an acidophilic chemolithoautotrophic bacterium widely used in the mining industry due to its metabolic sulfur-oxidizing capability. The biooxidation of sulfide minerals is enhanced through the attachment of At. thiooxidans cells to the mineral surface. The Type IV pili (TfP) of At. thiooxidans may play an important role in the bacteria attachment since TfP play a key adhesive role in the attachment and colonization of different surfaces. In this work, we report for the first time the mRNA sequence of three TfP proteins from At. thiooxidans, the adhesin protein PilY1 and the TfP pilins PilW and PilV. The nucleotide sequences of these TfP proteins show changes in some nucleotide positions with respect to the corresponding annotated sequences. The bioinformatic analyses and 3D-modeling of protein structures sustain their classification as TfP proteins, as structural homologs of the corresponding proteins of Ps. aeruginosa, results that sustain the role of PilY1, PilW and PilV in pili assembly. Also, that PilY1 comprises the conserved Neisseria-PilC (superfamily) domain of the tip-associated adhesin, while PilW of the superfamily of putative TfP assembly proteins and PilV belongs to the superfamily of TfP assembly protein. In addition, the analyses suggested the presence of specific functional domains involved in adhesion, energy transduction and signaling functions. The phylogenetic analysis indicated that the PilY1 of Acidithiobacillus genus forms a cohesive group linked with iron- and/or sulfur-oxidizing microorganisms from acid mine drainage or mine tailings., Competing Interests: The authors have declared that no competing interests exist.

Purine nucleoside phosphorylases (PNPs) play an important role in the blood fluke parasite Schistosoma mansoni as a key enzyme of the purine salvage pathway. Here we present the structural and kinetic characterization of a new PNP isoform from S. mansoni, SmPNP2. Thermofluorescence screening of different ligands suggested cytidine and cytosine are potential ligands. The binding of cytosine and cytidine were confirmed by isothermal titration calorimetry, with a KD of 27 μM for cytosine, and a KM of 76.3 μM for cytidine. SmPNP2 also displays catalytic activity against inosine and adenosine, making it the first described PNP with robust catalytic activity towards both pyrimidines and purines. Crystal structures of SmPNP2 with different ligands were obtained and comparison of these structures with the previously described S. mansoni PNP (SmPNP1) provided clues for the unique capacity of SmPNP2 to bind pyrimidines. When compared with the structure of SmPNP1, substitutions in the vicinity of SmPNP2 active site alter the architecture of the nucleoside base binding site thus permitting an alternative binding mode for nucleosides, with a 180° rotation from the canonical binding mode. The remarkable plasticity of this binding site enhances our understanding of the correlation between structure and nucleotide selectivity, thus suggesting new ways to analyse PNP activity., Competing Interests: The authors have declared that no competing interests exist.

Here we discuss the formation of phyllotactic patterns in the shoot apical meristem (SAM) of plants, where the spatial distribution of the phytohormone auxin determines phyllotaxis in a domain that is growing and changing in time. We assume that the concentration of auxin modifies the mechanical properties of the domain and that the mechanical stress field in the SAM orients the flux of auxin. To study this problem we propose a mechanism for pattern formation in growing domains with variable curvature. The dynamics of chemicals is modeled by a reaction-diffusion system that produces a three dimensional pattern of chemical concentrations that changes the stress field in the domain while growing. The growth process is modeled by a phase-field order parameter which determines the location of the boundaries of the domain. This field is coupled to the chemical concentration through a curvature term that affects the local mechanical stress in the domain. The local stress changes in turn modify the chemical patterns. Our model constitutes a useful and novel approach in theoretical biology, as many developmental processes in organisms seem to be affected by the changes of curvature, size, mechanical stress and other physical aspects. Several patterns seen in many plants are reproduced under certain conditions by our model., Competing Interests: The authors have declared that no competing interests exist.

The primary objective of this study is to monitor tumor growth by using image techniques and behavioral testing through general and specific motor activities (spontaneous movements and gait). Our sample includes male Wistar rats, 2 months old and weighing 250-300 g, that is categorized into three groups: control, sham, and experimental. The experimental group was anesthetized; the C6 cells with luciferase expression that were suspended in a culture medium were implanted into the right frontoparietal cortex of the rats. The sham group received implant only with culture medium without cells. Images and behavioral tests were evaluated at base time and at 7, 14, 21, and 28 days after induced tumor growth analysis. The tumor volume measured by magnetic resonance imaging (MRI) and quantitative bioluminescence imaging (BLI) signal showed a correlation coefficient of r = 0.96. The MRI showed that the mean tumor volume increased by approximately 10, 26, and 49 times according to a comparison of tumor volume on the seventh day with 14, 21, and 28 days, respectively. The quantification of the BLI signal was (4.12 ± 2.01) x 10(8), (8.33 ± 3.12) x 10(8), (28.43 ± 6.32) x 10(8), and (63.02 ± 10.53) x 10(8) photons/s at the seventh, fourteenth, twenty-first, and twenty-eighth day, respectively. After 14 days of tumor induction, both behavioral tests showed significant differences between tumor and sham or control groups. Our study showed a high correlation between MRI and BLI for tumor growth monitoring with complement aspects analysis in tumor volume. In addition, functional behavioral analysis displayed sensitivity to monitor tumor growth, as well as to detect early significant changes between groups, primarily in the tumor group. The results of gait analysis were more sensitive than general motor analysis., Competing Interests: The authors have declared that no competing interests exist.