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Modeling Bacterial Species: Using Sequence Similarity with Clustering Techniques

Computers, Materials & Continua 2021年第8期68卷 1661-1672页

作者： Miguel-Angel Sicilia Elena garc.a-Barriocanal Marçal Mora-Cantallops Salvador Sánchez-Alonso lino González University of Alcalá Alcaláde Henares(Madrid)28871Spain Camilo JoséCela University Madrid28007Spain

Existing studies have challenged the current definition of named bacterial species,especially in the case of highly recombinogenic *** has led to considering the use of computational procedures to examine potential bacterial clusters that are not identified by species *** paper describes the use of sequence data obtained from MLST databases as input for a k-means algorithm extended to deal with housekeeping gene sequences as a metric of similarity for the clustering *** implementation of the k-means algorithm has been developed based on an existing source code implementation,and it has been evaluated against MLST *** point out to potential bacterial clusters that are close to more than one different named species and thus may become candidates for alternative classifications accounting for genotypic *** use of hierarchical clustering with sequence comparison as similarity metric has the potential to find clusters different from named species by using a more informed cluster formation strategy than a conventional nominal variant of the algorithm.

关键词： Clustering bacterial species k-means sequence alignment

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Serum levels of chemokines in adolescents with major depression treated with fluoxetine

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World Journal of Psychiatry 2020年第8期10卷 175-186页

作者： Francisco Rafael de la Peña Carlos Cruz-Fuentes lino Palacios Manuel Iván Girón-Pérez Emilio Medina-Rivero Maria Dolores Ponce-Regalado Samantha Alvarez-Herrera Gilberto Pérez-Sánchez Enrique Becerril-Villanueva JoséLuis Maldonado-garc.a María C Jiménez-Martínez Lenin Pavón Adolescent Clinic Clinical ServicesNational Institute of Psychiatry“Ramón de la Fuente”Mexico City 14370Mexico Department of Psychiatric Genetics Clinical Research BranchNational Institute of Psychiatry“Ramón de la Fuente”Mexico City 14370Mexico Universidad Autónoma de Nayarit Laboratorio de InmunotoxicologíaBoulevard Tepic-Xalisco s/nCd de la Cultura Amado NervoTepic 63000Mexico Centro Nayarita de Innovación y Transferencia de Tecnología A.C.Laboratorio Nacional para la Investigación en Inocuidad Alimentaria-Unidad Nayarit Calle Tres s/n.Cd IndustrialTepic 63000NayaritMexico Unidad de Desarrollo e Investigación en Bioprocesos Escuela Nacional de Ciencias BiológicasInstituto Politécnico NacionalUnidad Profesional Lázaro CárdenasMexico City 11340Mexico Departamento de Ciencias de Salud Centro Universitario de los AltosUniversidad de Guadalajara Av Rafael Casillas Aceves No.1200Tepatitlán de MorelosJalisco47610Mexico Laboratory of Psychoimmunology National Institute of Psychiatry“Ramón de la Fuente”Mexico City 14370Mexico Department of Immunology and Research Unit Institute of Ophthalmology“Conde de Valenciana Foundation”Mexico City 06800Mexico Department of Biochemistry Faculty of MedicineNational Autonomous University of MexicoMexico City 04510Mexico

BACKGROUND Major depressive disorder(MDD)is a global health issue that affects 350 million people of all *** between 2%and 5.6%of affected individuals are adolescents,research on young patients is *** inflammatory response contributes to the onset of depression,and in adult MDD patients,symptom severity has been linked to chemokine *** To determine the differences in circulatory levels of chemokines in healthy volunteers(HVs)and adolescents with MDD,and assess the changes induced by fluoxetine *** The 22 adolescents with MDD were monitored during the first 8 wk of clinical follow-up and clinical psychiatric evaluation was done using the Hamilton depresión rating scale(HDRS).The serum levels of monocyte chemoattractant protein-1(MCP-1),macrophage inflammatory protein(MIP)-1α,MIP-1β,interleukin(IL)-8,interferon gamma-induced protein(IP)-10,and eotaxin were measured in patients and *** In all cases,significant differences were detected in circulating chemokine levels between patients before treatment and HVs(P<0.0001).All chemokines decreased at 4 wk,but only MCP-1 and IL-8 significantly differed(P<0.05)between 0 wk and 4 *** the patients,all chemokines rose to their initial concentrations by 8 wk vs 0 wk,but only IP-10 did so significantly(P<0.05).All patients experienced a significant decrease in HDRS scores at 4 wk(P<0.0001)and 8 wk(P<0.0001)compared with 0 *** Despite the consumption of fluoxetine,patients had significantly higher chemokine levels,even after considering the improvement in HDRS *** high levels of eotaxin,IP-10,and IL-8 partially explain certain aspects that are affected in MDD such as cognition,memory,and learning.

关键词： Adolescents Major depression Chemokine Fluoxetine Interferon gammainduced protein-10

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