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- ItemAcesso aberto (Open Access)Evaluation of the Anti‑biofilm Efficacy of Kyotorphin Derivatives and Biosafety Assessment: In Vitro and In Vivo Investigations Targeting Bacterial and Fungal Pathogens(Springer, 2024) Carvalho, Isabel Chaves Silva [UNIFESP]; Simões, Fernanda da Silva Seiffert [UNIFESP]; de Andrade, Vitor Martins [UNIFESP]; Tada, Dayane Batista [UNIFESP]; Heras, Montserrat; Bardají, Eduard; Lopes-Ferreira, Mônica; Castanho, Miguel Augusto Rico Botas; Conceição, Katia [UNIFESP]; http://lattes.cnpq.br/5360223612968931Kyotorphin (KTP) dipeptide (l-Tyrosine-l-Arginine) and their derivatives possess a multitude of functions, qualifying them as "multifunctional peptides." Considering the escalating bacterial resistance to antibiotics, antimicrobial peptides offer a promising road, forming the central focus of this current investigation. The effectiveness of KTP derivatives, GABA-KTPNH2 and Indol-KTP-NH2, were assessed for biofilm inhibition in bacterial and fungal strains. The viability of these derivatives was tested in fibroblasts and B16-F10-Nex2 cells. In vivo toxicity was evaluated using the model organisms Galleria mellonella and Danio rerio. Notably, both GABA-KTP-NH2 and Indol-KTP-NH2 derivatives effectively hindered biofilm formation in E. coli, S. pneumoniae, and C. krusei. In the G. mellonella model, the derivatives exhibited significant larval survival rates in toxicity tests, while in infection tests, they demonstrated efficient treatment against the evaluated microorganisms. Conversely, zebrafish assays revealed that Indol-KTP-NH2 induced substantial mortality rates in embryos after 72 and 96 h of exposure. Similarly, the GABA-KTP-NH2 derivative exhibited heightened lethality, noticeable at the 100 μM concentration after the same exposure periods. Importantly, toxicity assessments unveiled a relatively lower toxicity profile, coupled with a reduced potential for inducing abnormalities. These results highlight the necessity of employing a comprehensive approach that integrates diverse techniques to thoroughly assess toxicity implications.
- ItemAcesso aberto (Open Access)Mechanistic insights on the antibacterial action of the kyotorphin peptide derivatives revealed by in vitro studies and Galleria mellonella proteomic analysis(Elsevier, 2024) Andrade, Vitor Martins de [UNIFESP]; Oliveira, Vitor D M [UNIFESP]; Barcick, Uilla [UNIFESP]; Ramu , Vasanthakumar G.; Heras, Montserrat; Bardají , Eduard R.; Castanho, Miguel A.R.B.; Zelanis, André [UNIFESP]; Capella, Aline [UNIFESP]; Junqueira, Juliana C.; Conceição, Katia [UNIFESP]; http://lattes.cnpq.br/5360223612968931Objectives: The selected kyotorphin derivatives were tested to improve their antimicrobial and antibiofilm activity. The antimicrobial screening of the KTP derivatives were ascertained in the representative strains of bacteria, including Streptococcus pneumoniae, Streptococcus pyogenes, Escherichia coli and Pseudomonas aeruginosa. Methods: Kyotorphin derivatives, KTP-NH2, KTP-NH2-DL, IbKTP, IbKTP-NH2, MetKTP-DL, MetKTP-LD, were designed and synthesized to improve lipophilicity and resistance to enzymatic degradation. Peptides were synthesized by standard solution or solid-phase peptide synthesis and purified using RP-HPLC, which resulted in >95 % purity, and were fully characterized by mass spectrometry and 1H NMR. The minimum inhibitory concentrations (MIC) determined for bacterial strains were between 20 and 419 μM. The direct effect of IbKTP-NH2 on bacterial cells was imaged using scanning electron microscopy. The absence of toxicity, high survival after infection and an increase in the hemocytes count was evaluated by injections of derivatives in Galleria mellonella larvae. Proteomics analyses of G. mellonella hemolymph were performed to investigate the underlying mechanism of antibacterial activity of IbKTP-NH2 at MIC. Results: IbKTP-NH2 induces morphological changes in bacterial cell, many differentially expressed proteins involved in DNA replication, synthesis of cell wall, and virulence were up-regulated after the treatment of G. mellonella with IbKTP-NH2. Conclusion: We suggest that this derivative, in addition to its physical activity on the bacterial membranes, can elicit a cellular and humoral immune response, therefore, it could be considered for biomedical applications.
- ItemAcesso aberto (Open Access)Um artigo sobre "Algoritmos de Lagrangiano aumentado para resolver o problema contínuo de alocação de recursos não linear".(Steffen Rebennack, 2023-08-20) Bueno, Luís Felipe [UNIFESP]; Haeser, Gabriel; Kolossoski, Oliver; http://lattes.cnpq.br/0017683968952439In the paper [Torrealba, E.M.R. et al. Augmented Lagrangian algorithms for solving the continuous nonlinear resource allocation problem. EJOR, 299(1) 46–59, 2021] an augmented Lagrangian algorithm was proposed for resource allocation problems with the intriguing characteristic that instead of solving the box-constrained augmented Lagrangian subproblem, they propose projecting the solution of the unconstrained subproblem onto such box. A global convergence result for the quadratic case was provided, however, this is somewhat counterintuitive, as in usual augmented Lagrangian theory, this strategy can fail in solving the augmented Lagrangian subproblems. In this note we investigate further this algorithm and we show that the proposed method may indeed fail when the Hessian of the quadratic is not a multiple of the identity. In the paper, it is not clear enough that two different projections are being used: one for obtaining their convergence results and other in their implementation. However, despite the lack of theoretical convergence, their strategy works remarkably well in some classes of problems; thus, we propose a hybrid method which uses their idea as a starting point heuristics, switching to a standard augmented Lagrangian method under certain conditions. Our contribution consists in presenting an efficient way of determining when the heuristics is failing to improve the KKT residual of the problem, suggesting that the heuristic procedure should be abandoned. Numerical results are provided showing that this strategy is successful in accelerating the standard method.
- ItemAcesso aberto (Open Access)Influence of periodic lift and drag on the orbit of rectangular parallelepiped satellites(Shahriar Afkhami, 2023-12-07) de Moraes, Rodolpho [UNIFESP]; Murcia-Piñeros, Jhonathan [UNIFESP]; Prado, A.F.B. de Almeida; http://lattes.cnpq.br/5577796502707425Satellites in Low Earth Orbits (LEO) are highly perturbed by the interaction with the atmosphere, the two components of this perturbation are lift and drag, which initially are a function of the satellite’s geometry, materials, atmosphere, and flow conditions. Due to the uncertainty in these values, the traditional model is to fix the coefficients along the orbit lifetime, without considering the changes in flow direction, product of the satellite attitude, and rotational dynamics. The purpose of the present paper is to analyse the influence of periodic variations of lift and drag on the satellite’s orbital elements, due to the satellite’s rotation at a constant angular velocity. Three parallelepiped solids were selected to model the satellite geometry, which is similar to the CubeSats standard. The aerodynamic coefficients are modelled using the panel method on free molecular flow, as a function of the angle of attack and the roll angle. The effects of periodic variations in drag result in secular perturbations in the orbital semi-major axis and eccentricity, with large differences at the lowest angular velocity. Lift, applied orthogonal to the plane orbit, affects the inclination at lower angular velocities because it keeps the magnitude and direction of this perturbation for a longer time. The novelty of the paper is the detection and quantification of the effects of periodic lift and drag in LEO on parallelepiped satellites.
- ItemEmbargoA parallel branch-and-cut and an adaptive metaheuristic to solve the family traveling salesman problem(Elsevier, 2023) Chaves, Antonio Augusto [UNIFESP]; Vianna, Barbara Lessa [UNIFESP]; Silva, Tiago Tibúrcio da [UNIFESP]; Schenekemberg, Cleder Marcos [UNIFESP]; http://lattes.cnpq.br/4973949421738244This paper addresses the Family Traveling Salesman Problem (FTSP), a variant of the Traveling Salesman Problem that group nodes into families. The goal is to select the best route by visiting only a subset of nodes from each family. We developed two methods to solve the FTSP: (i) a parallel branch- and-cut algorithm with an efficient local search procedure (P-B&C) to obtain an optimal solution, and (ii) an adaptive metaheuristic that combines the Biased Random-key Genetic Algorithm (BRKGA) with a reinforcement learning algorithm. In this case, the Q-Learning algorithm controls the parameters of the BRKGA during the evolutionary process. We perform computational experiments on a well-known benchmark dataset with 185 instances. Our P-B&C proves the optimal value for 179 instances, improving the best upper bounds in 19 open instances. The new local search component of the P-B&C finds the best upper bounds for 50% of instances. The BRKGA-QL finds the optimal solution in 131 instances, improving the best upper bounds in 21 open instances. Finally, we compare our results with the best results in the literature, and both methods show robustness and efficiency in solving the FTSP.