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PublicationMapping the Evolutionary Space of SARS-CoV-2 Variants to Anticipate Emergence of Subvariants Resistant to COVID-19 Therapeutics( 2024)New sublineages of SARS-CoV-2 variants-of-concern (VOCs) continuously emerge with mutations in the spike glycoprotein. In most cases, the sublineage-defining mutations vary between the VOCs. It is unclear whether these differences reflect lineage-specific likelihoods for mutations at each spike position or the stochastic nature of their appearance. Here we show that SARS-CoV-2 lineages have distinct evolutionary spaces (a probabilistic definition of the sequence states that can be occupied by expanding virus subpopulations). This space can be accurately inferred from the patterns of amino acid variability at the whole-protein level. Robust networks of co-variable sites identify the highest-likelihood mutations in new VOC sublineages and predict remarkably well the emergence of subvariants with resistance mutations to COVID-19 therapeutics. Our studies reveal the contribution of low frequency variant patterns at heterologous sites across the protein to accurate prediction of the changes at each position of interest.We describe a systematic approach to identify "clues" that can predict the mutational profiles of SARS-CoV-2 subvariants at early stages after emergence of their parental lineages. We found that the likelihood for mutations at each position of spike is lineage-specific, and is estimated well by the mutational patterns at all positions of the protein. As examples, we apply the model to forecast emergence of resistance to the antibody therapeutics Bebtelovimab and Cilgavimab, which appeared in sublineages of VOCs BA.5 and BA.4, respectively. Emergence of these subvariants required changes in treatment protocols of COVID-19 patients. In both cases, the escape mutations were predicted well by the mutational profiles at all positions of spike at early time points after emergence of the parental VOCs. Accurate estimations of the imminent changes in SARS-CoV-2 lineages can contribute to design and selection of therapeutics that maintain their efficacy against future forms of this virus.
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PublicationExploring the adjustment to parasite pressure hypothesis: differences in uropygial gland volume and haemosporidian infection in palearctic and neotropical birds( 2021)Parasites are globally widespread pathogenic organisms, which impose important selective forces upon their hosts. Thus, in accordance with the Adjustment to parasite pressure hypothesis, it is expected that defenses among hosts vary relative to the selective pressure imposed by parasites. According to the latitudinal gradient in diversity, species richness and abundance of parasites peak near the equator. The uropygial gland is an important defensive exocrine gland against pathogens in birds. Size of the uropygial gland has been proposed to vary among species of birds because of divergent selection by pathogens on their hosts. Therefore, we should expect that bird species from the tropics should have relatively larger uropygial glands for their body size than species from higher latitudes. However, this hypothesis has not yet been explored. Here, we analyze the size of the uropygial gland of 1719 individual birds belonging to 36 bird species from 3 Neotropical (Peru) and 3 temperate areas (Spain). Relative uropygial gland volume was 12.52% larger in bird species from the tropics than from temperate areas. This finding is consistent with the relative size of this defensive organ being driven by selective pressures imposed by parasites. We also explored the potential role of this gland as a means of avoiding haemosporidian infection, showing that species with large uropygial glands for their body size tend to have lower mean prevalence of haemosporidian infection, regardless of their geographical origin. This result provides additional support for the assumption that secretions from the uropygial gland reduce the likelihood of becoming infected with haemosporidians.
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PublicationTechno-Economic Energy Optimization of the Off-Grid Electrical System with Power to Gas Storage Technology( 2023-01-01)Renewable energy sources (RESs) have undeniable advantages over the recent years not only to supply electrical demand but also electrical demand. However, maximum use of the RES’s power has always been challenging as high penetration of the RESs as well as their intermittent nature might compromise the distribution networks power flow constraints. This paper proposes optimal energy operation of the off-grid distribution network (DN) with participation of the power-to-gas (PtG) storage system. In this regard, PtG system is considered as an energy supplier in the DN. The natural gas generated by using PtG is applied to backup diesel generators for meeting demand at peak times. The objective functions in the system are modeled based on technical and economic modeling including minimize the operation cost and maximize the system reliability. The optimal energy operation in the two case studies is assumed considering non-participation and participation of the PtG system. To solving of the energy optimization, particle swarm optimization algorithm is proposed. Finally, proposed case studies under numerical simulation are implemented for validation of the participation of the PtG system.
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PublicationDesign and validation of a peruvian food exchange list for meal planning( 2022-01-01)Objective: The purpose of the study was to design and validate a Peruvian food portions exchange list (LIA) for the preparation of diets and menu planning. Methodology: The methodology for designing exchange lists described in previous studies was used as a basis, developed in six phases carried out in multiple laboratory interventions, where 273 foods were evaluated and studied through a qualitative descriptive analysis. A validation was performed with 12 nutritionists who elaborated a nutritional plan and then the nutritional composition obtained using the Peruvian table of food composition 2017 (TPCA) was compared with the nutritional composition applying LIA. For the comparison of methods, the Wilcoxon test was applied. Results: A Peruvian food exchange list (LIA) was developed that included 273 foods categorized into seven exchange groups. The mean energy and macronutrient intake for each exchange group was estimated and a photographic album was compiled with the exchange portions. Regarding the validation of the LIA, in the comparison of the amount of energy, carbohydrates, proteins and fats of the meal plans using TPCA versus LIA no significant differences were found. Conclusion: A valid LIA was obtained that allows the preparation and planning of diets in an efficient way, within an adequate margin of error, new studies incorporating other more specific populations and new foods are recommended.
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PublicationEffect of Coturnix japonica (quail) egg yolk in ethanol damage-induced mice( 2023-01-01)Introduction: The high prevalence of neurodegenerative diseases in the older adult population requires research focused on functional foods with regulatory properties on redox state and with antioxidant potential. Quail egg yolk is a food with a great diversity of antioxidant compounds with neuroprotective activity. Objective: To evaluate the effect of Coturnix japonica egg yolk administration on the nervous tissue of mice against ethanol damage induction. Methodology: 35 mice received the following treatment via orogastric for five days: groups I and II water (10 mL/kg), group III egg yolk (5 mL/kg), group IV egg yolk (10 mL/kg) and group V egg yolk (15 mL/kg). On the fifth day, 99% ethanol was administered subcutaneously (5 g/kg) to groups II-V. After four hours, the mice were decapitated to obtain the brain and cerebellum and subsequently perform biochemical tests and histopathological analysis. Results: Group IV presented neuronal proliferation phenomenon and Purkinje cells pluristratification in the brain and cerebellum respectively and additionally presented a better GSH/GSSG ratio (p<0.05) in comparison to group II. There was no statistically significant difference between protein levels or protein sulfhydryl groups in any of the groups. Conclusions: Coturnix japonica egg yolk administration resulted in better preservation of the brain and cerebellum’s cytoarchitecture and increased GSH profile.