Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements.

In the SARS-CoV-2 lineage, RNA elements essential for its viral life cycle, including genome replication and gene expression, have been identified. Still, the precise structures and functions of these RNA regions in coronaviruses remain poorly understood. This lack of knowledge points out the need for further research to better understand these crucial aspects of viral biology and, in time, prepare for future outbreaks. In this research, the in silico analysis of the cis RNA structures that act in the alpha-, beta-, gamma-, and deltacoronavirus genera has provided a detailed view of the presence and adaptation of the structures of these elements in coronaviruses. The results emphasize the importance of these cis elements in viral biology and their variability between different viral variants. Some coronavirus variants in some groups, depending on the cis element (stem-loop1 and -2; pseudoknot stem-loop1 and -2, and s2m), exhibited functional adaptation. Additionally, the conformation flexibility of the s2m element in the SARS variants was determined, suggesting a coevolution of this element in this viral group. The variability in secondary structures suggests genomic adaptations that may be related to replication processes, genetic regulation, as well as the specific pathogenicity of each variant. The results suggest that RNA structures in coronaviruses can adapt and evolve toward different viral variants, which has important implications for viral adaptation, pathogenicity, and future therapeutic strategies.

Linear mixed-effect models for correlated response to process electroencephalogram recordings.

A data set of clinical studies of electroencephalogram recordings (EEG) following data acquisition protocols in control individuals (Eyes Closed Wakefulness - Eyes Open Wakefulness, Hyperventilation, and Optostimulation) are quantified with information theory metrics, namely permutation Shanon entropy and permutation Lempel Ziv complexity, to identify functional changes. This work implement Linear mixed-effects models (LMEMs) for confirmatory hypothesis testing. The results show that EEGs have high variability for both metrics and there is a positive correlation between them. The mean of permutation Lempel-Ziv complexity and permutation Shanon entropy used simultaneously for each of the four states are distinguishable from each other. However, used separately, the differences between permutation Lempel-Ziv complexity or permutation Shanon entropy of some states were not statistically significant. This shows that the joint use of both metrics provides more information than the separate use of each of them. Despite their wide use in medicine, LMEMs have not been commonly applied to simultaneously model metrics that quantify EEG signals. Modeling EEGs using a model that characterizes more than one response variable and their possible correlations represents a new way of analyzing EEG data in neuroscience.

Nanoparticles of Betalain-Gelatin with Antioxidant Properties by Coaxial Electrospraying: Preparation and Characterization.

Betalains are bioactive compounds with attractive antioxidant properties for the food industry, endowing them with potential application in food coatings to maintain quality and extend shelf life. However, they have low stability to factors such as light, temperature, and humidity. An alternative to protect bioactive compounds is nanoencapsulation; one of the most used techniques to produce an encapsulation is coaxial electrospraying. In this research, the preparation and characterization of gelatin-betalain nanoparticles were carried out using the coaxial electrospray technique. Betalains were extracted from pitaya (Stenocereus thurberi) and encapsulated in gelatin. The obtained material was evaluated by SEM, FTIR, TGA, and DSC techniques and for its antioxidant capacity. By SEM, nanoparticles with spherical and monodisperse morphologies were observed, with betalain concentrations of 1 and 3% w/v and average diameters of 864 and 832 µm, respectively. By FTIR, the interaction between betalain and gelatin was observed through amino groups and hydrogen bonds. Likewise, the antioxidant activity of the betalains was maintained at the time of encapsulation, increasing the antioxidant activity as the concentration increased. The results of the DPPH, ABTS, and total phenols methods were 645.4592 µM T/g, 832.8863 ± 0.0110 µM T/g, and 59.8642 ± 0.0279 mg GAE/g for coaxial nanoparticles with 3% betalains, respectively. Therefore, the coaxial electrospray technique was useful for obtaining nanoparticles with good antioxidant properties, and due to the origin of its components and since the use of toxic solvents is not necessary in the technique, the material obtained can be considered food grade with potential application as a coating on functional foods.

Roughening of the anharmonic elastic interface in correlated random media.

We study the roughening properties of the anharmonic elastic interface in the presence of temporally correlated noise. The model can be seen as a generalization of the anharmonic Larkin model, recently introduced by Purrello, Iguain, and Kolton [Phys. Rev. E 99, 032105 (2019)2470-004510.1103/PhysRevE.99.032105], to investigate the effect of higher-order corrections to linear elasticity in the fate of interfaces. We find analytical expressions for the critical exponents as a function of the anharmonicity index n, the noise correlator range θ∈[0,1/2], and dimension d. In d=1 we find that the interface becomes faceted and exhibits anomalous scaling for θ>1/4 for any degree of anharmonicity n>1. Analytical expressions for the anomalous exponents α_{loc} and κ are obtained and compared with a numerical integration of the model. Our theoretical results show that anomalous roughening cannot exist for this model in dimensions d>1.

NMR-based leaf metabolic profiling of V. planifolia and three endemic Vanilla species from the Peruvian Amazon.

The fruit of Vanilla planifolia is broadly preferred by the agroindustry and gourmet markets due to its refined flavor and aroma. Peruvian Vanilla has been proposed as a possible source for genetic improvement of existing Vanilla cultivars, but, little has been done to facilitate comprehensive studies of these and other Vanilla. Here, a nuclear magnetic resonance (NMR) metabolomic platform was developed to profile for the first time the leaves - organ known to accumulate vanillin putative precursors - of V. planifolia and those of Peruvian V. pompona, V. palmarum, and V. ribeiroi, with the aim to determine metabolic differences among them. Analysis of the NMR spectra allowed the identification of thirty-six metabolites, twenty-five of which were quantified. One-way ANOVA and post-hoc Tukey test revealed that these metabolites changed significantly among species, whilst multivariate-analyses allowed the identification of malic and homocitric acids, together with two vanillin precursors, as relevant metabolic markers for species differentiation.

Efficient harmonic oscillator chain energy harvester driven by colored noise.

We study the performance of an electromechanical harmonic oscillator chain as an energy harvester to extract power from finite-bandwidth ambient random vibrations, which are modelled by colored noise. The proposed device is numerically simulated and its performance assessed by means of the net electrical power generated and its efficiency in converting the external noise-supplied power into electrical power. Our main result is a much enhanced performance, both in the net electrical power delivered and in efficiency, of the harmonic chain with respect to the popular single oscillator resonator. Our numerical findings are explained by means of an analytical approximation, in excellent agreement with numerics.

Morphological and metabolic profiling of a tropical-adapted potato association panel subjected to water recovery treatment reveals new insights into plant vigor.

Potato (Solanum tuberosum L.) is one of the world's most important crops, but it is facing major challenges due to climatic changes. To investigate the effects of intermittent drought on the natural variability of plant morphology and tuber metabolism in a novel potato association panel comprising 258 varieties we performed an augmented block design field study under normal irrigation and under water-deficit and recovery conditions in Ica, Peru. All potato genotypes were profiled for 45 morphological traits and 42 central metabolites via nuclear magnetic resonance. Statistical tests and norm of reaction analysis revealed that the observed variations were trait specific, that is, genotypic versus environmental. Principal component analysis showed a separation of samples as a result of conditional changes. To explore the relational ties between morphological traits and metabolites, correlation-based network analysis was employed, constructing one network for normal irrigation and one network for water-recovery samples. Community detection and difference network analysis highlighted the differences between the two networks, revealing a significant correlational link between fumarate and plant vigor. A genome-wide association study was performed for each metabolic trait. Eleven single nucleotide polymorphism (SNP) markers were associated with fumarate. Gene Ontology analysis of quantitative trait loci regions associated with fumarate revealed an enrichment of genes regulating metabolic processes. Three of the 11 SNPs were located within genes, coding for a protein of unknown function, a RING domain protein and a zinc finger protein ZAT2. Our findings have important implications for future potato breeding regimes, especially in countries suffering from climate change.

Faceted patterns and anomalous surface roughening driven by long-range temporally correlated noise.

We investigate Kardar-Parisi-Zhang (KPZ) surface growth in the presence of power-law temporally correlated noise. By means of extensive numerical simulations of models in the KPZ universality class we find that, as the noise correlator index increases above some threshold value, the surface exhibits anomalous kinetic roughening of the type described by the generic scaling theory of Ramasco et al. [Phys. Rev. Lett. 84, 2199 (2000)PRLTAO0031-900710.1103/PhysRevLett.84.2199]. Remarkably, as the driving noise temporal correlations increase, the surface develops a characteristic pattern of macroscopic facets that completely dominates the dynamics in the long time limit. We argue that standard scaling fails to capture the behavior of KPZ subject to long-range temporally correlated noise. These phenomena are not not described by the existing theoretical approaches, including renormalization group and self-consistent approaches.

Ultra-Clean Pure Shift 1H-NMR applied to metabolomics profiling.

Even though Pure Shift NMR methods have conveniently been used in the assessment of crowded spectra, they are not commonly applied to the analysis of metabolomics data. This paper exploits the recently published SAPPHIRE-PSYCHE methodology in the context of plant metabolome. We compare single pulse, PSYCHE, and SAPPHIRE-PSYCHE spectra obtained from aqueous extracts of Physalis peruviana fruits. STOCSY analysis with simplified SAPPHIRE-PSYCHE spectra of six types of Cape gooseberry was carried out and the results attained compared with classical STOCSY data. PLS coefficients analysis combined with 1D-STOCSY was performed in an effort to simplify biomarker identification. Several of the most compromised proton NMR signals associated with critical constituents of the plant mixture, such as amino acids, organic acids, and sugars, were more cleanly depicted and their inter and intra correlation better reveled by the Pure Shift methods. The simplified data allowed the identification of glutamic acid, a metabolite not observed in previous studies of Cape gooseberry due to heavy overlap of its NMR signals. Overall, the results attained indicated that Ultra-Clean Pure Shift spectra increase the performance of metabolomics data analysis such as STOCSY and multivariate coefficients analysis, and therefore represent a feasible and convenient additional tool available to metabolomics.

Backbone chemical shift assignment of macrophage infectivity potentiator virulence factor of Trypanosoma cruzi.

Chagas disease is a trypanosomiasis disease inflicted by Trypanosoma cruzi parasite. In Latin America, at least 10 million people are infected and annually, 10,000 casualties are deplored. Macrophage infectivity potentiator protein is one of the major virulence factors secreted by T. cruzi (TcMIP) in order to infect its host but little is known about its mechanism of action. Studies confer TcMIP an important role in the extracellular matrix transmigration and basal lamina penetration. Here, we report the backbone 1H, 13C, and 15N resonance assignment of TcMIP and the comparison of the secondary structure obtained against reported X-ray crystallography data.

NMR-based metabolic study of fruits of Physalis peruviana L. grown in eight different Peruvian ecosystems.

The berry of Physalis peruviana L. (Solanaceae) represents an important socio-economical commodity for Latin America. The absence of a clear phenotype renders it difficult to trace its place of origin. In this study, Cape gooseberries from eight different regions within the Peruvian Andes were profiled for their metabolism implementing a NMR platform. Twenty-four compounds could be unequivocally identified and sixteen quantified. One-way ANOVA and post-hoc Tukey test revealed that all of the quantified metabolites changed significantly among regions: Bambamarca I showed the most accumulated significant differences. The coefficient of variation demonstrated high phenotypic plasticity for amino acids, while sugars displayed low phenotypic plasticity. Correlation analysis highlighted the closely coordinated behavior of the amino acid profile. Finally, PLS-DA revealed a clear separation among the regions based on their metabolic profiles, accentuating the discriminatory capacity of NMR in establishing significant phytochemical differences between producing regions of the fruit of P. peruviana L.

Thermal rectification in mass-graded next-nearest-neighbor Fermi-Pasta-Ulam lattices.

We study the thermal rectification efficiency, i.e., quantification of asymmetric heat flow, of a one-dimensional mass-graded anharmonic oscillator Fermi-Pasta-Ulam lattice both with nearest-neighbor (NN) and next-nearest-neighbor (NNN) interactions. The system presents a maximum rectification efficiency for a very precise value of the parameter that controls the coupling strength of the NNN interactions, which also optimizes the rectification figure when its dependence on mass asymmetry and temperature differences is considered. The origin of the enhanced rectification is the asymmetric local heat flow response as the heat reservoirs are swapped when a finely tuned NNN contribution is taken into account. A simple theoretical analysis gives an estimate of the optimal NNN coupling in excellent agreement with our simulation results.

Changes in the Bacterial Community Structure of Remediated Anthracene-Contaminated Soils.

Mixing soil or adding earthworms (Eisenia fetida (Savigny, 1826)) accelerated the removal of anthracene, a polycyclic aromatic hydrocarbon, from a pasture and an arable soil, while a non-ionic surfactant (Surfynol® 485) inhibited the removal of the contaminant compared to the untreated soil. It was unclear if the treatments affected the soil bacterial community and consequently the removal of anthracene. Therefore, the bacterial community structure was monitored by means of 454 pyrosequencing of the 16S rRNA gene in the pasture and arable soil mixed weekly, amended with Surfynol® 485, E. fetida or organic material that served as food for the earthworms for 56 days. In both soils, the removal of anthracene was in the order: mixing soil weekly (100%) > earthworms applied (92%) > organic material applied (77%) > untreated soil (57%) > surfactant applied (34%) after 56 days. There was no clear link between removal of anthracene from soil and changes in the bacterial community structure. On the one hand, application of earthworms removed most of the contaminant from the arable soil and had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of the Acidobacteria, Chloroflexi and Gemmatimonadetes, and an increase in that of the Proteobacteria compared to the unamended soil. Mixing the soil weekly removed all anthracene from the arable soil, but had little or no effect on the bacterial community structure. On the other hand, application of the surfactant inhibited the removal of anthracene from the arable soil compared to the untreated soil, but had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of Cytophagia (Bacteroidetes), Chloroflexi, Gemmatimonadetes and Planctomycetes and an increase in that of the Flavobacteria (Bacteroidetes) and Proteobacteria. Additionally, the removal of anthracene was similar in the different treatments of both the arable and pasture soil, but the effect of application of carrot residue, earthworms or the surfactant on the bacterial community structure was more accentuated in the arable soil than in the pasture soil. It was found that removal of anthracene was not linked to changes in the bacterial community structure.

Bacterial colonization of a fumigated alkaline saline soil.

After chloroform fumigating an arable soil, the relative abundance of phylotypes belonging to only two phyla (Actinobacteria and Firmicutes) and two orders [Actinomycetales and Bacillales (mostly Bacillus)] increased in a subsequent aerobic incubation, while it decreased for a wide range of bacterial groups. It remained to be seen if similar bacterial groups were affected when an extreme alkaline saline soil was fumigated. Soil with electrolytic conductivity between 139 and 157 dS m(-1), and pH 10.0 and 10.3 was fumigated and the bacterial community structure determined after 0, 1, 5 and 10 days by analysis of the 16S rRNA gene, while an unfumigated soil served as control. The relative abundance of the Firmicutes increased in the fumigated soil (52.8%) compared to the unfumigated soil (34.2%), while that of the Bacteroidetes decreased from 16.2% in the unfumigated soil to 8.8% in the fumigated soil. Fumigation increased the relative abundance of the genus Bacillus from 14.7% in the unfumigated soil to 25.7%. It was found that phylotypes belonging to the Firmicutes, mostly of the genus Bacillus, were dominant in colonizing the fumigated alkaline saline as found in the arable soil, while the relative abundance of a wide range of bacterial groups decreased.

Hearing loss, auditory neuropathy, and neurological co-morbidity in children with birthweight <750 g.

BACKGROUND AND AIMS: The current literature considers a birthweight <1,500 g as a risk factor for sensorineural hearing loss (SNHL, hearing threshold >25 decibels), auditory neuropathy (AN), and several neurological sequelae. The aim of the study was to determine the frequency and risk factors associated with SNHL, AN, and neurological morbidity in a group of children with birthweights of <750 g treated at a neonatal care unit and recruited into a long-term follow-up program. METHODS: A case-control study was carried out. Inclusion criteria were birthweight <750 g and born between the years 2000 and 2010. We performed brainstem auditory-evoked potentials (BAEP), evoked otoacoustic emissions (EOAE) and free-field audiometry (FFA) in this population. Neonatal variables and procedures were compared between children with SNHL and children with normal bilateral hearing (NBH). RESULTS: A total of 93 children with a mean age of 4 years were included in the follow-up. Six children (6.4%) had SNHL and 87 had NBH. We were unable to identify AN in the sample. Mean weight for this sample was 673 ± 68 g and gestational age 27.5 ± 2 weeks. Variables reflecting differences between groups included days under mechanical ventilation, furosemide treatment, and bronchopulmonary dysplasia. In the SNHL group, three patients had periventricular leukomalacia, two had hydrocephalus, and one patient had cerebral palsy. CONCLUSIONS: Frequency of SNHL in children with birthweights <750 g was higher than in other premature infants and was related with mechanical ventilation, furosemide application, and bronchopulmonary dysplasia. Association with other neurological morbidities was frequent. Early diagnosis and intervention are required.

Covariant hydrodynamic Lyapunov modes and strong stochasticity threshold in Hamiltonian lattices.

We scrutinize the reliability of covariant and Gram-Schmidt Lyapunov vectors for capturing hydrodynamic Lyapunov modes (HLMs) in one-dimensional Hamiltonian lattices. We show that, in contrast with previous claims, HLMs do exist for any energy density, so that strong chaos is not essential for the appearance of genuine (covariant) HLMs. In contrast, Gram-Schmidt Lyapunov vectors lead to misleading results concerning the existence of HLMs in the case of weak chaos.

Structure of characteristic Lyapunov vectors in anharmonic Hamiltonian lattices.

In this work we perform a detailed study of the scaling properties of Lyapunov vectors (LVs) for two different one-dimensional Hamiltonian lattices: the Fermi-Pasta-Ulam and Φ^{4} models. In this case, characteristic (also called covariant) LVs exhibit qualitative similarities with those of dissipative lattices but the scaling exponents are different and seemingly nonuniversal. In contrast, backward LVs (obtained via Gram-Schmidt orthonormalizations) present approximately the same scaling exponent in all cases, suggesting it is an artificial exponent produced by the imposed orthogonality of these vectors. We are able to compute characteristic LVs in large systems thanks to a "bit reversible" algorithm, which completely obviates computer memory limitations.

Efecto del tratamiento combinado con metformina/glimepirida sobre la función endotelial en pacientes con diabetes mellitus tipo 2 evaluados mediante PET / Effects of the combined treatment with Metformin/Glimepiride on endothelial function of patients with type 2 diabetes mellitus: a positron emission tomography (PET) evaluation study

The purpose of this study was to determine the effect of treatment, with Metformin alone or with the combination of Glimepiride/Metformin, on coronary endothelial function in asymptomatic patients with recently diagnosed type 2 diabetes mellitus (DM) Methods: 16 asymptomatic patients with type DM2 and 15 healthy controls (HC) were studied. At baseline and after treatment, myocardial blood flow (MBF) was measured with 13N-ammonia Possitron Emission Tomography (PET) at rest, during cold pressor testing (CPT) and during pharmacologic stress with adenosine. The endothelial dependent vasodilation index (EDVI), myocardial flow reserve (MFR) and the percentage of the change between rest MBF and CPT MBF (%deltaMBF) were calculated as markers of endothelial function. MBF was normalized to the rate pressure product (RPP). RESULTS: EDVI and %deltaMBF were significantly lower in diabetic patients before treatment in comparison with HC demonstrating endothelial dysfunction in the former. Treatment with Glimepiride/Metformin significantly increased EDVI and %deltaMBF in diabetic patients from baseline, thus showing an improvement in coronary endothelial function.

[Effects of the combined treatment with Metformin/Glimepiride on endothelial function of patients with type 2 diabetes mellitus. A positron emission tomography (PET) evaluation study]. / Efecto del tratamiento combinado con metformina/glimepirida sobre la función endotelial en pacientes con diabetes mellitus tipo 2 evaluados mediante PET.

UNLABELLED: The purpose of this study was to determine the effect of treatment, with Metformin alone or with the combination of Glimepiride/Metformin, on coronary endothelial function in asymptomatic patients with recently diagnosed type 2 diabetes mellitus (DM) Methods: 16 asymptomatic patients with type DM2 and 15 healthy controls (HC) were studied. At baseline and after treatment, myocardial blood flow (MBF) was measured with 13N-ammonia Possitron Emission Tomography (PET) at rest, during cold pressor testing (CPT) and during pharmacologic stress with adenosine. The endothelial dependent vasodilation index (EDVI), myocardial flow reserve (MFR) and the percentage of the change between rest MBF and CPT MBF (%deltaMBF) were calculated as markers of endothelial function. MBF was normalized to the rate pressure product (RPP). RESULTS: EDVI and %deltaMBF were significantly lower in diabetic patients before treatment in comparison with HC demonstrating endothelial dysfunction in the former. Treatment with Glimepiride/Metformin significantly increased EDVI and %deltaMBF in diabetic patients from baseline, thus showing an improvement in coronary endothelial function.