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Optimization of a Classical Algorithm for the Alignment of Genomic Sequences with Artificial Bee Colony

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Journal of Mechanics Engineering and Automation 2022年第2期12卷 57-63页

作者： Raul Magdaleno Peñaloza Andrea Magadan Salazar gerardo reyes salgado Department of Computer Science Centro de Investigacion y Desarrollo TecnologicoCuernavaca Morelos 62490Mexico

This article shows genomic alignment methods using the classic“Needleman”and“Smith-Waterman”algorithms,the latter they were optimized by the ABC(artificial bee colony)*** the genomic alignment,a goal state is not presented,the experiments that are carried out show alternative alignments by ABC were *** types of alignments could exist within the classical algorithm,based on a horizontal,vertical,diagonal and inverse search mechanism on a match value *** ABC-Smith Waterman algorithm was generated from the genomic sequences written in rows and columns for the search for similarities that will provide values that ABC uses to process and provide more results of alignments that can be used by scientists for their experiments and research.

关键词： Algorithm genomic alignment ABC Needleman Smith-Waterman

HP0953-hypothetical virulence factor overexpresion and localization during Helicobacter pylori infection of gastric epithelium

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World Journal of Gastroenterology 2022年第29期28卷 3886-3902页

作者： Nancy K Arteaga-Resendiz gerardo E Rodea Rosa María Ribas-Aparicio Alma L Olivares-Cervantes Juan Arturo Castelán-Vega Joséde Jesús Olivares-Trejo Sandra Mendoza-Elizalde Edgar O López-Villegas Christian Colín Pamela Aguilar-Rodea Alfonso reyes-López Marcela Salazar García Norma Velázquez-Guadarrama Laboratorio de Investigación en Enfermedades Infecciosas Hospital Infantil de México Federico GómezMexico City 06720Mexico Posgrado en Biomedicina y Biotecnología Molecular Laboratorio de Producción y Control de BiológicosEscuela Nacional de Ciencias BiológicasInstituto Politécnico NacionalMexico City 11340Mexico Laboratorio de Adquisición de Hierro Universidad Autónoma de la Ciudad MéxicoPosgrado Ciencias GenómicaMexico City 03100Mexico Laboratorio Central de Microscopía Escuela Nacional de Ciencias BiológicasInstituto Politécnico NacionalMexico City 11340Mexico Centro de estudios económicos y sociales en salud Hospital Infantil de México Federico GómezMexico City 06720Mexico Laboratorio de Investigación en Biología del Desarrollo y Teratogénesis Experimental Hospital Infantil de México Federico GómezMexico City 06720Mexico

BACKGROUND The high prevalence and persistence of Helicobacter pylori(H. pylori) infection, as well as the diversity of pathologies related to it, suggest that the virulence factors used by this microorganism are varied. Moreover, as its proteome contains 340hypothetical proteins, it is important to investigate them to completely understand the mechanisms of its virulence and survival. We have previously reported that the hypothetical protein HP0953 is overexpressed during the first hours of adhesion to inert surfaces, under stress conditions, suggesting its role in the environmental survival of this bacterium and perhaps as a virulence *** To investigate the expression and localization of HP0953 during adhesion to an inert surface and against gastric(AGS) *** Expression analysis was performed for HP0953 during H. pylori adhesion. HP0953 expression at 0,3, 12, 24, and 48 h was evaluated and compared using the Kruskal-Wallis equality-of-populations rank test. Recombinant protein was produced and used to obtain polyclonal antibodies for immunolocalization. Immunogold technique was performed on bacterial sections during adherence to inert surfaces and AGS cells, which was analyzed by transmission electron microscopy. HP0953 protein sequence was analyzed to predict the presence of a signal peptide and transmembrane helices, both provided by the ExPASy platform, and using the GLYCOPP platform for glycosylation sites. Different programs, via, I-TASSER, RaptorX, and HHalign-Kbest, were used to perform three-dimensional *** HP0953 exhibited its maximum expression at 12 h of infection in gastric epithelium *** technique revealed HP0953 localization in the cytoplasm and accumulation in some peripheral areas of the bacterial body, with greater expression when it is close to AGS *** analysis revealed the presence of a signal peptide that interacts with the transmembrane region and then allows the release of the protein

关键词： Hypothetical protein HP0953 Adherence Helicobacter pylori Glycocalyx Virulence factor Persistence

Application of a new reagent for analysis of oxygen presence in a lowcarbon steel wire rod

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Journal of Iron and Steel Research(International) 2021年第6期28卷 729-738页

作者： M.I.Dávila-Pérez H.J.Vergara-Hernández O.Vázquez-Gómez F.reyes-Calderón E.López-Martínez J.M.salgado-López National Technology of Mexico/T.I.of Morelia Morelia 58120MichoacanMexico National Council for Science and Technology CONACYT Mexico City 03940Mexico Isthmus University Santo Domingo TehuantepecOaxaca 70760Mexico Engineering and Industrial Development Center CIDESI Santiago de Queretaro 76125QueretaroMexico

A microstructural analysis was performed to determine the presence of oxygen in a wire rod section of AISI 1008 steel with a surface mechanical failure produced during wire *** failure zone was analyzed by comparison using three different attack reagents:alkaline sodium chromate(ASC),ASC with hydrogen peroxide and amyl alcohol,and a solution of nitric acid in ethyl *** reagents were applied in samples in the failure zone,showing different types of zones in regions with internal and superficial defects such as carbides,pores,cracks,deformation,and detachment zones,indicating the possible presence of *** areas identified were observed by means of an optical microscope and were correlated with the content of elements that were present in the region using a scanning electron microscope and a scattered X-ray energy spectrometer,which determined that the areas identified by chromate sodium correspond to regions with a high concentration of oxygen and slag-forming elements such as silicon,aluminum,and iron;this is associated with the presence of oxygen in the oxide *** was also observed that the ASC and the modified ASC solution with hydrogen peroxide and amyl alcohol could identify areas with a high presence of oxides,while the nitric acid solution only identified the steel *** modified ASC solution is an alternative to identify the presence of chemical variants of oxygen because the conventional formulation is unstable and has a too short shelf life,and therefore,its application must be carried out at the time of preparation.

关键词： Etching Alkaline sodium chromate Oxide presence Internal defect

The Relative Importance of Natural Disturbances and Local Site Factors on Woody Vegetation Regeneration Diversity across a Large, Contiguous Forest Region

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Open Journal of Forestry 2013年第3期3卷 88-98页

作者： gerardo P. reyes Daniel Kneeshaw Louis de Grandpré Department of Biological Sciences Centre for Forest Research University of Quebec in Montreal Montreal Canada Department of Biological Sciences Centre for Forest Research University of Quebec in Montreal Montreal Canada Faculty of Interdisciplinary Studies Lakehead University Orillia Canada Department of Biological Sciences Centre for Forest Research University of Quebec in Montreal Montreal Canada Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre Ste-Foy Canada

Stand-level diversity after natural disturbance can potentially differ across a large, contiguous forest region despite being dominated by the same canopy species throughout as differences in disturbance types and local site conditions can regulate species distribution. Our main objective was to examine the relative importance of natural disturbances (spruce budworm (Choristoneura fumiferana) outbreak, windthrow, and their interaction) and local site factors (climate, physiography, and stand structure and composition variables) on woody vegetation diversity among three, physiographically distinct locations across a large, contiguous forest region. Seventy-six Abies balsamea-Betula spp. stands affected by natural disturbance were compared and analysed using canonical ordination methods, diversity indices, and ANOVA. Different combinations of factors were important for vegetation re-establishment at each location. Differences in alpha (α), beta (β), gamma (γ), Shannon’s H’, and evenness (J) diversity indices were observed among locations across the study region. Our findings indicate that while certain processes are important for maintaining canopy dominance by Abies balsamea and Betula spp. throughout the region, different combinations of factors were important for creating variation in woody species diversity among locations that resulted in greater woody species diversity at the regional scale.

关键词： Regeneration Natural Disturbance Environmental Factors Species Diversity Eastern Boreal Mixedwood Region

Safety and Efficacy of Oral Mirodenafil in Mexican with Erectile Dysfunction

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International Journal of Clinical Medicine 2016年第9期7卷 628-638页

作者： Juan gerardo reyes-García Noemí Santos-Caballero Francisco Javier Flores-Murrieta Sección de Estudios de Posgrado e Investigación Escuela Superior de Medicina Instituto Politécnico Nacional Ciudad de México Mexico Landsteiner Scientific S.A. de C.V. Ciudad de México Mexico Unidad de Investigación en Farmacología Instituto Nacional de Enfermedades Respiratorias “Ismael Cosio Villegas” Ciudad de México Mexico

Erectile dysfunction is treated with 5-phospodiesterase inhibitors as Mirodenafil, which has shown its efficacy and safety in Koreans, however;no information in other populations is available. An open clinical trial study was designed to evaluate the efficacy and safety in real life of a fixed-dose of Mirodenafil in Mexican patients with erectile dysfunction. Forty-seven male patients received a 100 mg tablet of Mirodenafil, during 12 weeks. Primary outcome efficacy measure was the percentage of male patients with successful intercourse. Secondary outcomes measures included patient satisfaction, mood and self-esteem level. Safety assessments included laboratory tests, vital signs, physical examination, 12-lead electrocardiogram recordings, and incidence of adverse events by patients. Oral administration of Mirodenafil improved in an 80% - 90% the number of successful intercourses from 7 to 84 days of treatment. Moreover, patients reported a significant increment in their sexual satisfaction, mood and self-esteem. Mirodenafil treatment did not modify vital signs nor anthropometric parameters during 84 days. Mild headache was the most frequent adverse event (17.0%) and there were no severe adverse events during pharmacological treatment. Data suggest that oral Mirodenafil is safety, well tolerated and effective in the Mexican population with erectile dysfunction.

关键词： Efficacy Erectile Dysfunction Mexicans Mirodenafil Safety

Higher cardiovascular risk scores and liver fibrosis risk estimated by biomarkers in patients with metabolic-dysfunction-associated fatty liver disease

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World Journal of Hepatology 2022年第8期14卷 1633-1642页

作者： Giovanni Alejandro salgado Alvarez Samanta Mayanin Pinto Galvez Uriel Garcia Mora Ana Delfina Cano Contreras Cristina Durán Rosas Bryan Adrián Priego-Parra Arturo Triana Romero Mercedes Amieva Balmori Federico Roesch Dietlen Sophia Eugenia Martinez Vazquez Ines Osvely Mendez Guerrero Luis Alberto Chi-Cervera Raúl Bernal reyes Leonardo Alberto Martinez Roriguez Maria Eugenia Icaza Chavez Jose Maria Remes Troche Instituto de Investigaciones Médico-biologicas Universidad VeracruzanaVeracruz 91700VeracruzMexico Department of Gastroenterología Instituto Nacional de Ciencias Médicas y Nutrición Salvador ZubiránMéxico 14080MéxicoMexico Clínica de Especialidades Gastrointestinales y Hepáticas Hospital Star MedicaMerida 97133YucatanMexico Department of Gastroenterologia Sociedad Española de BeneficenciaPachuca 42000HidalgoMexico Department of Gastroenterologia Clínica de Rehabilitación Metabólica Digestiva y HepáticaMexico 14080MexicoMexico Department of Gastroenterologia Hospital Star Médica de MéridaMerida 97133YucatanMexico

BACKGROUND The definition of metabolic-dysfunction-associated fatty liver disease(MAFLD)allows identification of metabolically complicated *** risk scores are related to cardiovascular risk(CVR)scores and could be useful for the identification of patients at risk of systemic *** To evaluate the relationship between MAFLD and CVR using the Framingham risk score in a group of Mexican *** Cross-sectional,observational and descriptive study carried out in a cohort of 585 volunteers in the state of Veracruz with MAFLD *** risk of liver fibrosis was calculated with aspartate aminotransferase-to-platelet ratio index,nonalcoholic fatty liver disease score and fibrosis-4,as well as with transient hepatic elastography with Fibroscan~?.The CVR was determined by the Framingham *** One hundred and twenty-five participants(21.4%)with MAFLD criteria were evaluated,average age 54.4 years,63.2%were women,body mass index 32.3 kg/m~*** Framingham CVR was high in 43 patients(33.9%).Transient elastography was performed in 55.2%of volunteers;39.1%with high CVR and predominance in advanced fibrosis(F3–F4).The logistic regression analysis showed that liver fibrosis,diabetes and hypertension independently increased *** One of every three patients with MAFLD had a high CVR,and in those with high fibrosis risk,the CVR risk was even greater.

关键词： Fatty liver Cardiovascular risk Hepatic steatosis Fibrosis Liver disease

Early transmission dynamics of COVID-19 in a southern hemisphere setting:Lima-Peru:February 29^(th)-March 30^(th),2020

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Infectious Disease Modelling 2020年第1期5卷 338-345页

作者： César V.Munayco Amna Tariq Richard Rothenberg Gabriela G.Soto-Cabezas Mary F.reyes Andree Valle Leonardo Rojas-Mezarina César Cabezas Manuel Loayza gerardo Chowell 无 Centro Nacional de Epidemiología Prevencion y Control de EnfermedadesPeruvian Ministry of HealthLimaPeru Department of Population Health Sciences School of Public HealthGeorgia State UniversityAtlantaGAUSA Instituto Nacional de Salud Peruvian Ministry of HealthLimaPeru Peru COVID-19 working group

The COVID-19 pandemic that emerged in Wuhan China has generated substantial morbidity and mortality impact around the world during the last four *** daily trend in reported cases has been rapidly rising in Latin America since March 2020 with the great majority of the cases reported in Brazil followed by Peru as of April 15th,*** Peru implemented a range of social distancing measures soon after the confirmation of its first case on March 6th,2020,the daily number of new COVID-19 cases continues to accumulate in this *** assessed the early COVID-19 transmission dynamics and the effect of social distancing interventions in Lima,*** estimated the reproduction number,R,during the early transmission phase in Lima from the daily series of imported and autochthonous cases by the date of symptoms onset as of March 30th,*** also assessed the effect of social distancing interventions in Lima by generating short-term forecasts grounded on the early transmission dynamics before interventions were put in *** to the implementation of the social distancing measures in Lima,the local incidence curve by the date of symptoms onset displays near exponential growth dynamics with the mean scaling of growth parameter,p,estimated at 0.96(95%CI:0.87,1.0)and the reproduction number at 2.3(95%CI:2.0,2.5).Our analysis indicates that school closures and other social distancing interventions have helped slow down the spread of the novel coronavirus,with the nearly exponential growth trend shifting to an approximately linear growth trend soon after the broad scale social distancing interventions were put in place by the *** the interventions appear to have slowed the transmission rate in Lima,the number of new COVID-19 cases continue to accumulate,highlighting the need to strengthen social distancing and active case finding efforts to mitigate disease transmission in the region.

关键词： COVID-19 SARS-CoV-2 Transmission potential Short-term forecast Reproduction number Generalized growth model

Molecular Microbial Diagnostic in Lung Transplant Recipients

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Journal of Cancer Therapy 2012年第5期3卷 511-520页

作者： Sebastián Méndez-álvarez gerardo Pulido-reyes Javier Donate-Correa Arturo Soriano Benítez de Lugo General Surgery Service Hospital Universitario Ntra. Sra. de Candelaria Santa Cruz de Tenerife Spain. Research Unit Hospital Universitario Ntra. Sra. de Candelaria Santa Cruz de Tenerife Spain

The appearing of microbial lineages carrying multiple dangerous loci are results from the extensive use of antibiotics and has brought a huge increase in the infections-derived morbidity and mortality, which is critical in the hospital setting. Etiologic agents of these non easily tractable infections include bacteria, such as the genus Staphylococcus, but also fungi and virus. Alterations in the immune system allow these organisms to invade and affect the functionality of any tissue, organ or system of the human being. Pulmonary infection occurs as result of deficient lung systemic defence mechanisms which could be altered by medical treatments or by environmental factors. The infective agents commonly gain access to the lung by air, but also by blood or lymphatic system. Staphylococcus aureus strains that share antibiotic resistance and virulence factors represent the aetiological agent responsible of many cases of bacterial pneumonia, thoracic surgery postoperative infections, and diverse tissue infections, resulting in significant disease and morbidity in recipient patients after lung transplantation. The control and treatment of Staphylococcus infections, especially methicillin resistant strains, need for developing reliable and rapid methods of detection and characterization of these microorganisms. Nowadays, new insights into the diagnostic and epidemiology of MRSA and other pathogenic staphylococci have been developed employing molecular methods. This has meant an important advance in the diagnostic and treatment plans of such infective bacteria.

关键词： Molecular Microbial Diagnostic Lung Transplant Recipients

Comparison between Classical and Intelligent Identification Systems for Classification of Gait Events

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Journal of Control Science and Engineering 2015年第1期3卷 21-34页

作者： Carlos Galvan-Duque Ricardo Zavala-yoe gerardo Rodriguez-reyes Felipe Mendoza-Cruz MichelinAlvarez-Camacho Ricardo Ramirez-Mendoza Orthotics and Prosthetics Laboratory lnstituto Nacional de Rehabilitacion Mexico City Mexico School of Engineering and Architecture Graduate Studies Tecnologico de Monterrey Mexico City Campus Mexico

Gait event detection is important for diagnosis and evaluation. This is a challenging endeavor due to subjectivity, high amount of data, among other problems. ANFIS (Artificial Neural Fuzzy Inference Systems), ARX (Autoregressive Models with Exogenous Variables), OE (Output Error models), NARX (Nonlinear Autoregressive Models with Exogenous Variables) and models based on NN (neural networks) were developed in order to detect gait events without the problems mentioned. The objective was to compare developed models" performance and determinate the most suitable model for gait events detection. Knee joint angle, heel foot switch and toe foot switch during normal walking in a treadmill were collected from a healthy volunteer. Gait events were classified by three experts in human motion. Experts" mean classification was obtained and all models were trained and tested with the collected data and experts" mean classification. Fit percentage was obtained to evaluate models performance. Fit percentages were: ANFIS: 79.49%, ARX: 68.8%, OE: 71.39%, NARX: 88.59%, NNARX: 67.66%, NNRARX: 68.25% and NNARMAX: 54.71%. NARX had the best performance for gait events classification. For ARX and OE, previous filtering is needed. NN"s models showed the best performance for high frequency components. ANFIS and NARX were able to integrate criteria from three experts for gait analysis. NARX and ANFIS are suitable for gait event identification. Test with additional subjects is needed.

关键词：控制论最优控制学习理论逻辑网络