Testing Theories of the Glass Transition with the Same Liquid but Many Kinetic Rules.

We study the glass transition by exploring a broad class of kinetic rules that can significantly modify the normal dynamics of supercooled liquids while maintaining thermal equilibrium. Beyond the usual dynamics of liquids, this class includes dynamics in which a fraction (1-f_{R}) of the particles can perform pairwise exchange or "swap moves," while a fraction f_{P} of the particles can move only along restricted directions. We find that (i) the location of the glass transition varies greatly but smoothly as f_{P} and f_{R} change and (ii) it is governed by a linear combination of f_{P} and f_{R}. (iii) Dynamical heterogeneities (DHs) are not governed by the static structure of the material; their magnitude correlates instead with the relaxation time. (iv) We show that a recent theory for temporal growth of DHs based on thermal avalanches holds quantitatively throughout the (f_{R},f_{P}) diagram. These observations are negative items for some existing theories of the glass transition, particularly those reliant on growing thermodynamic order or locally favored structure, and open new avenues to test other approaches, as we illustrate.

Hierarchical structured surfaces enhance the contact angle of the hydrophobic (meta-stable) state.

The relation between wetting properties and geometric parameters of fractal surfaces are widely discussed on the literature and, however, there are still divergences on this topic. Here we propose a simple theoretical model to describe the wetting properties of a droplet of water placed on a hierarchical structured surface and test the predictions of the model and the dependence of the droplet wetting state on the initial conditions using simulation of the 3-spin Potts model. We show that increasing the auto-similarity level of the hierarchy - called n - does not affect considerably the stable wetting state of the droplet but increases its contact angle. Simulations also explicit the existence of metastable states on this type of surfaces and shows that, when n increases, the metastability becomes more pronounced. Finally we show that the fractal dimension of the surface is not a good predictor of the contact angle of the droplet.

A genetic variant in the TRAF1/C5 gene lead susceptibility to active pulmonary tuberculosis by decreased TNF-α levels.

Host genetics are important to consider in the role of resistance or susceptibility for developing active pulmonary tuberculosis (TB). Several association studies have reported the role of variants in STAT4 and TRAF1/C5 as risk factors to autoimmune diseases. Nevertheless, more data is needed to elucidate the role of these gene variants in infectious disease. Our data reports for the first time, variant rs10818488 in the TRAF1/C5 gene (found 47% of the population worldwide), is associated with susceptibility (OR = 1.51) to development TB. Multivariate analysis evidenced association between rs10818488 TRAF1/C5 and risk to multibacillary TB (OR = 4.18), confers increased bacteria load in the lung, indicates a decreased ability to control pathogen levels in the lung, and spread of the pathogen to new hosts. We showed that the "loss-of-function" variant in TRAF1/C5 led to susceptibility for TB by decreased production of TNF-α. Our results suggest the role of variant TRAF1/C5 in susceptibility to TB as well as in clinical presentation of multibacillary TB.

Direct coupling analysis of epistasis in allosteric materials.

In allosteric proteins, the binding of a ligand modifies function at a distant active site. Such allosteric pathways can be used as target for drug design, generating considerable interest in inferring them from sequence alignment data. Currently, different methods lead to conflicting results, in particular on the existence of long-range evolutionary couplings between distant amino-acids mediating allostery. Here we propose a resolution of this conundrum, by studying epistasis and its inference in models where an allosteric material is evolved in silico to perform a mechanical task. We find in our model the four types of epistasis (Synergistic, Sign, Antagonistic, Saturation), which can be both short or long-range and have a simple mechanical interpretation. We perform a Direct Coupling Analysis (DCA) and find that DCA predicts well the cost of point mutations but is a rather poor generative model. Strikingly, it can predict short-range epistasis but fails to capture long-range epistasis, in consistence with empirical findings. We propose that such failure is generic when function requires subparts to work in concert. We illustrate this idea with a simple model, which suggests that other methods may be better suited to capture long-range effects.

Modeling oil-water separation with controlled wetting properties.

Several oil-water separation techniques have been proposed to improve the capacity of cleaning water. With the technological possibility of producing materials with antagonist wetting behavior, for example, a substrate that repels water and absorbs oil, the understanding of the properties that control this selective capacity has increased with the goal of being used as the mechanism to separate mixed liquids. Besides the experimental advance in this field, less is known from the theoretical side. In this work, we propose a theoretical model to predict the wetting properties of a given substrate and introduce simulations with a four-spin cellular Potts model to study its efficiency in separating water from oil. Our results show that the efficiency of the substrates depends both on the interaction between the liquids and on the wetting behavior of the substrates itself. The water behavior of the droplet composed of both liquids is roughly controlled by the hydrophobicity of the substrate. Predicting the oil behavior, however, is more complex because the substrate being oleophilic does not guarantee that the total amount of oil present on the droplet will be absorbed by the substrate. For both types of substrates considered in this work, pillared and porous with a reservoir, there is always an amount of reminiscent oil on the droplet, which is not absorbed by the substrate due to the interaction with the water and the gas. Both theoretical and numerical models can be easily modified to analyze other types of substrates and liquids.

Universality of jamming of nonspherical particles.

Amorphous packings of nonspherical particles such as ellipsoids and spherocylinders are known to be hypostatic: The number of mechanical contacts between particles is smaller than the number of degrees of freedom, thus violating Maxwell's mechanical stability criterion. In this work, we propose a general theory of hypostatic amorphous packings and the associated jamming transition. First, we show that many systems fall into a same universality class. As an example, we explicitly map ellipsoids into a system of "breathing" particles. We show by using a marginal stability argument that in both cases jammed packings are hypostatic and that the critical exponents related to the contact number and the vibrational density of states are the same. Furthermore, we introduce a generalized perceptron model which can be solved analytically by the replica method. The analytical solution predicts critical exponents in the same hypostatic jamming universality class. Our analysis further reveals that the force and gap distributions of hypostatic jamming do not show power-law behavior, in marked contrast to the isostatic jamming of spherical particles. Finally, we confirm our theoretical predictions by numerical simulations.

Jamming with Tunable Roughness.

We introduce a new model to study the effect of surface roughness on the jamming transition. By performing numerical simulations, we show that for a smooth surface, the jamming transition density and the contact number at the transition point both increase upon increasing asphericity, as for ellipsoids and spherocylinders. Conversely, for a rough surface, both quantities decrease, in quantitative agreement with the behavior of frictional particles. Furthermore, in the limit corresponding to the Coulomb friction law, the model satisfies a generalized isostaticity criterion proposed in previous studies. We introduce a counting argument that justifies this criterion and interprets it geometrically. Finally, we propose a simple theory to predict the contact number at finite friction from the knowledge of the force distribution in the infinite friction limit.

Architecture and coevolution of allosteric materials.

We introduce a numerical scheme to evolve functional elastic materials that can accomplish a specified mechanical task. In this scheme, the number of solutions, their spatial architectures, and the correlations among them can be computed. As an example, we consider an "allosteric" task, which requires the material to respond specifically to a stimulus at a distant active site. We find that functioning materials evolve a less-constrained trumpet-shaped region connecting the stimulus and active sites, and that the amplitude of the elastic response varies nonmonotonically along the trumpet. As previously shown for some proteins, we find that correlations appearing during evolution alone are sufficient to identify key aspects of this design. Finally, we show that the success of this architecture stems from the emergence of soft edge modes recently found to appear near the surface of marginally connected materials. Overall, our in silico evolution experiment offers a window to study the relationship between structure, function, and correlations emerging during evolution.

Mechanics of Allostery: Contrasting the Induced Fit and Population Shift Scenarios.

In allosteric proteins, binding a ligand can affect function at a distant location, for example, by changing the binding affinity of a substrate at the active site. The induced fit and population shift models, which differ by the assumed number of stable configurations, explain such cooperative binding from a thermodynamic viewpoint. Yet, understanding what mechanical principles constrain these models remains a challenge. Here, we provide an empirical study on 34 proteins supporting the idea that allosteric conformational change generally occurs along a soft elastic mode presenting extended regions of high shear. We argue, based on a detailed analysis of how the energy profile along such a mode depends on binding, that in the induced fit scenario, there is an optimal stiffness ka∗ ∼ 1/N for cooperative binding, where N is the number of residues. We find that the population shift scenario is more robust to mutations affecting stiffness because binding becomes more and more cooperative with stiffness up to the same characteristic value ka∗, beyond which cooperativity saturates instead of decaying. We numerically confirm these findings in a nonlinear mechanical model. Dynamical considerations suggest that a stiffness of order ka∗ is favorable in that scenario as well, supporting that for proper function, proteins must evolve a functional elastic mode that is softer as their size increases. In consistency with this view, we find a fair anticorrelation between the stiffness of the allosteric response and protein size in our data set.

Principles for Optimal Cooperativity in Allosteric Materials.

Allosteric proteins transmit a mechanical signal induced by binding a ligand. However, understanding the nature of the information transmitted and the architectures optimizing such transmission remains a challenge. Here we show, using an in silico evolution scheme and theoretical arguments, that architectures optimized to be cooperative, which efficiently propagate energy, qualitatively differ from previously investigated materials optimized to propagate strain. Although we observe a large diversity of functioning cooperative architectures (including shear, hinge, and twist designs), they all obey the same principle of displaying a mechanism, i.e., an extended soft mode. We show that its optimal frequency decreases with the spatial extension L of the system as L-d/2, where d is the spatial dimension. For these optimal designs, cooperativity decays logarithmically with L for d = 2 and does not decay for d = 3. Overall, our approach leads to a natural explanation for several observations in allosteric proteins and indicates an experimental path to test if allosteric proteins lie close to optimality.

Geographic and Gender Diversity in the Brazilian Academy of Sciences.

Recent studies have shown that diversity in race and gender is important to improve competitiveness, creativity and innovation. However, many studies have shown that the universe of science is not diverse in none of these criteria. In this work, we quantify the gender and geographic diversity in the Brazilian science. We study in detail the profile of the titular members of the most prestigious academic institution of Brazil, the Brazilian Academy of Sciences (ABC). Our analysis shows that the members of the ABC concentrates 80% in the Southeast region and that the overwhelming majority is composed by men. We show that female and male researchers have roughly the same amount of publication per year but women produce more human resources. Using the Brazilian Researchers' Fellowship databank we show that the gender and diversity both in gender and in geography decreases along the researchers' career.

Wettability of Reentrant Surfaces: A Global Energy Approach.

In this work, we consider two possible wetting states for a droplet when placed on a substrate: the Fakir configuration of a Cassie-Baxter (CB) state with a droplet residing on top of roughness grooves and the one characterized by the homogeneous wetting of the surface, referred as the Wenzel (W) state. We extend a theoretical model based on the global interfacial energies for both states CB and W to study the wetting behavior of simple and double reentrant surfaces. Due to the minimization of the energies associated with each wetting state, we predict the thermodynamic wetting state of the droplet for a given surface texture and obtain its contact angle θC. We first use this model to find the geometries for pillared, simple and double reentrant surfaces that most enhances θC and conclude that the repellent behavior of these surfaces is governed by the relation between the height and width of the reentrances. We compare our results with recent experiments and discuss the limitations of this thermodynamic approach. To address one of these limitations, we implement Monte Carlo simulations of the cellular Potts Model in three dimensions, which allow us to investigate the dependency of the wetting state on the initial state of the droplet. We find that when the droplet is initialized in a CB state, it gets trapped in a local minimum and stays in the repellent behavior irrespective of the theoretical prediction. When the initial state is W, simulations show a good agreement with theory for pillared surfaces for all geometries, but for reentrant surfaces the agreement only happens in few cases: for most simulated geometries the contact angle reached by the droplet in simulations is higher than θC predicted by the model. Moreover, we find that the contact angle of the simulated droplet is higher when placed on the reentrant surfaces than for a pillared surfaces with the same height, width and pillar distance.

Force distribution affects vibrational properties in hard-sphere glasses.

We theoretically and numerically study the elastic properties of hard-sphere glasses and provide a real-space description of their mechanical stability. In contrast to repulsive particles at zero temperature, we argue that the presence of certain pairs of particles interacting with a small force f soften elastic properties. This softening affects the exponents characterizing elasticity at high pressure, leading to experimentally testable predictions. Denoting P(f) ~ f(θ(e)), the force distribution of such pairs and ϕ(c) the packing fraction at which pressure diverges, we predict that (i) the density of states has a low-frequency peak at a scale ω*, rising up to it as D(ω) ~ ω(2+a), and decaying above ω* as D(ω) ~ ω(-a) where a = (1 - θ(e))/(3 + θ(e)) and ω is the frequency, (ii) shear modulus and mean-squared displacement are inversely proportional with ⟨δR²⟩ ~ 1/µ ~ (ϕ(c) - ϕ)(κ), where κ = 2 - 2/(3 + θ(e)), and (iii) continuum elasticity breaks down on a scale ℓ(c) ~ 1/√(δz) ~ (ϕ(c) - ϕ)(-b), where b = (1 + θ(e))/(6 + 2θ(e)) and δz = z - 2d, where z is the coordination and d the spatial dimension. We numerically test (i) and provide data supporting that θ(e) ≈ 0.41 in our bidisperse system, independently of system preparation in two and three dimensions, leading to κ ≈ 1.41, a ≈ 0.17, and b ≈ 0.21. Our results for the mean-square displacement are consistent with a recent exact replica computation for d = ∞, whereas some observations differ, as rationalized by the present approach.

Modeling of Droplet Evaporation on Superhydrophobic Surfaces.

When a drop of water is placed on a rough surface, there are two possible extreme regimes of wetting: the one called Cassie-Baxter (CB) with air pockets trapped underneath the droplet and the one called the Wenzel (W) state characterized by the homogeneous wetting of the surface. A way to investigate the transition between these two states is by means of evaporation experiments, in which the droplet starts in a CB state and, as its volume decreases, penetrates the surface's grooves, reaching a W state. Here we present a theoretical model based on the global interfacial energies for CB and W states that allows us to predict the thermodynamic wetting state of the droplet for a given volume and surface texture. We first analyze the influence of the surface geometric parameters on the droplet's final wetting state with constant volume and show that it depends strongly on the surface texture. We then vary the volume of the droplet, keeping the geometric surface parameters fixed to mimic evaporation and show that the drop experiences a transition from the CB to the W state when its volume reduces, as observed in experiments. To investigate the dependency of the wetting state on the initial state of the droplet, we implement a cellular Potts model in three dimensions. Simulations show very good agreement with theory when the initial state is W, but it disagrees when the droplet is initialized in a CB state, in accordance with previous observations which show that the CB state is metastable in many cases. Both simulations and the theoretical model can be modified to study other types of surfaces.

TRPV1 antagonism by capsazepine modulates innate immune response in mice infected with Plasmodium berghei ANKA.

Thousands of people suffer from severe malaria every year. The innate immune response plays a determinant role in host's defence to malaria. Transient receptor potential vanilloid 1 (TRPV1) modulates macrophage-mediated responses in sepsis, but its role in other pathogenic diseases has never been addressed. We investigated the effects of capsazepine, a TRPV1 antagonist, in malaria. C57BL/6 mice received 10(5) red blood cells infected with Plasmodium berghei ANKA intraperitoneally. Noninfected mice were used as controls. Capsazepine or vehicle was given intraperitoneally for 6 days. Mice were culled on day 7 after infection and blood and spleen cell phenotype and activation were evaluated. Capsazepine decreased circulating but not spleen F4/80(+)Ly6G(+) cell numbers as well as activation of both F4/80(+)and F4/80(+)Ly6G(+) cells in infected animals. In addition, capsazepine increased circulating but not spleen GR1(+) and natural killer (NK) population, without interfering with natural killer T (NKT) cell numbers and blood NK and NKT activation. However, capsazepine diminished CD69 expression in spleen NKT but not NK cells. Infection increased lipid peroxidation and the release of TNFα and IFNγ, although capsazepine-treated group exhibited lower levels of lipid peroxidation and TNFα. Capsazepine treatment did not affect parasitaemia. Overall, TRPV1 antagonism modulates the innate immune response to malaria.

A clinical report of an oral lichen planus associated to epidermoid carcinoma in contact with metallic restorations.

The aim of this study was to relate the clinical case of a patient with oral lichen planus (OLP) and a history of epidermoid carcinoma associated with metallic restorations. The etiology of OLP is a mucocutaneous disease, which is poorly understood. Studies point to the potential of malignant transformation of OLP and its association with metallic restorations. The metallic restorations were replaced by crowns with a ceramic covering associated and osseointegrated implants in the edentulous areas. About 1 year later, it was observed a bilateral regression of the tongue lesions. The replacement of metallic restorations can contribute to improvement of OLP.

Between invisibility and resistance: indigenous health and demography during the Brazilian military dictatorship. / Entre invisibilidade e resistência: saúde e demografia indígenas durante a ditadura militar brasileira.

This article aims to systematize and analyze, from a historical perspective, the discussions that permeated the topic of indigenous health in interface with the demography of these populations, based on the political dimension that the quantification of indigenous peoples assumed during the military dictatorship in Brazil. Covering an extensive period that extends from the establishment of the Indian Protection Service in 1910 until the end of the 1980s, this article offers a comprehensive view of the topic. The analysis focuses primarily on the 1970s, highlighting the actors involved in this debate: indigenous leaders, indigenists, academics, health professionals, and missionaries.

Este artigo tem por objetivo sistematizar e analisar em perspectiva histórica as discussões que permearam o tema da saúde indígena em interface com a demografia dessas populações, partindo da dimensão política que a quantificação dos povos indígenas assumiu durante a ditadura militar no Brasil. Abrangendo um extenso período que se estende do estabelecimento do Serviço de Proteção aos Índios em 1910 até o fim dos anos 1980, busca-se oferecer uma visão ampliada sobre o tema. O foco da análise recai especialmente nos anos 1970, destacando os atores envolvidos neste debate: lideranças indígenas, indigenistas, acadêmicos, profissionais de saúde e missionários.

Epigenetics Regulation in Responses to Abiotic Factors in Plant Species: A Systematic Review.

Plants have several mechanisms to adapt or acclimate to environmental stress. Morphological, physiological, or genetic changes are examples of complex plant responses. In recent years, our understanding of the role of epigenetic regulation, which encompasses changes that do not alter the DNA sequence, as an adaptive mechanism in response to stressful conditions has advanced significantly. Some studies elucidated and synthesized epigenetic mechanisms and their relationships with environmental change, while others explored the interplay between epigenetic modifications and environmental shifts, aiming to deepen our understanding of these complex processes. In this study, we performed a systematic review of the literature to analyze the progression of epigenetics studies on plant species' responses to abiotic factors. We also aimed to identify the most studied species, the type of abiotic factor studied, and the epigenetic technique most used in the scientific literature. For this, a search for articles in databases was carried out, and after analyzing them using pre-established inclusion criteria, a total of 401 studies were found. The most studied species were Arabidopsis thaliana and Oryza sativa, highlighting the gap in studies of non-economic and tropical plant species. Methylome DNA sequencing is the main technique used for the detection of epigenetic interactions in published studies. Furthermore, most studies sought to understand the plant responses to abiotic changes in temperature, water, and salinity. It is worth emphasizing further research is necessary to establish a correlation between epigenetic responses and abiotic factors, such as extreme temperatures and light, associated with climate change.