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In Silico Pipeline to Identify Tumor‑Specific Antigens for Cancer Immunotherapy Using Exome Sequencing Data

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Phenomics 2023年第2期3卷 130-137页

作者： Diego Morazán‑fernández Javier Mora Jose arturo Molina‑Mora Caja Costarricense de Seguro Social San José10104Costa Rica Centro de Investigación de Enfermedades Tropicales Centro de Investigación en Cirugía y Cáncerand Facultad de MicrobiologíaUniversidad de Costa RicaSan José2060Costa Rica

Tumor-specific antigens or neoantigens are peptides that are expressed only in cancer cells and not in healthy *** of these molecules can induce an immune response,and therefore,their use in immunotherapeutic strategies based on cancer vaccines has been extensively *** based on these approaches have been triggered by the current high-throughput DNA sequencing ***,there is no universal nor straightforward bioinformatic protocol to discover neoan-tigens using DNA sequencing ***,we propose a bioinformatic protocol to detect tumor-specific antigens associated with single nucleotide variants(SNVs)or“mutations”in tumoral *** this purpose,we used publicly available data to build our model,including exome sequencing data from colorectal cancer and healthy cells obtained from a single case,as well as frequent human leukocyte antigen(HLA)class I alleles in a specific *** data from Costa Rican Central Valley population was selected as an *** strategy included three main steps:(1)pre-processing of sequencing data;(2)variant calling analysis to detect tumor-specific SNVs in comparison with healthy tissue;and(3)prediction and characterization of peptides(protein fragments,the tumor-specific antigens)derived from the variants,in the context of their affinity with frequent alleles of the selected *** our model data,we found 28 non-silent SNVs,present in 17 genes in chromosome *** protocol yielded 23 strong binders peptides derived from the SNVs for frequent HLA class I alleles for the Costa Rican *** the analyses were performed as an example to implement the pipeline,to our knowledge,this is the first study of an in silico cancer vaccine using DNA sequencing data in the context of the HLA *** is concluded that the standardized protocol was not only able to identify neoantigens in a specific but also provides a complete pipeline for the eventual design of cancer vaccines using

关键词： Neopeptide Colorectal cancer Cancer vaccine Neoantigens Human leukocyte antigen Costa Rica

Atmospheric-pressure dielectric barrier discharge generation by a full-bridge flying capacitor multilevel inverter

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Plasma Science and Technology 2017年第7期19卷 40-49页

作者： Rosendo PE?A-EGUILUZ José A LóPEZ-fernández Antonio MERCADO-CABRERA Bethsabet JARAMILLO-SIERRA Régulo LóPEZ-CALLEJAS Benjamín RODRíGUEZ-Méndez Raúl VALENCIA-ALVARADO Allan A FLORES-FUENTES arturo E MU?OZ-CASTRO Plasma Physics Laboratory Instituto Nacional de Investigaciones Nucleares Tecnológico de Estudios Superiores de Tianguistenco Universidad Autónoma del Estado de México

A new configuration of a resonant full-bridge flying capacitor multicell inverter has been designed and constructed with the aim of achieving an extended output voltage frequency range with low harmonic distortion and reduced semiconductor commutation losses. This configuration was tested as a power supply for two different coaxial dielectric barrier discharge reactors, one of them employed for electric characterization and the other one for inorganic compound elimination in an aqueous solution. Two different gas mixtures, 90% Ar-10% 02 and 80% Ar-20% 02, were individually supplied during the experiments; the results showed a high- efficiency removal of meta-cresol （m-cresol） to the order of 98%, which was obtained by adding more oxygen to the plasma gas mixture.

关键词： plasma applications water pollution plasma sources power supply circuits electricdischarges

Guidelines for rational design of high-performance absorbents:A case study of zeolite adsorbents for emerging pollutants in water

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Green Energy & Environment 2017年第4期2卷 363-369页

作者： Xiaoxuan Wei Ya Wang arturo J.Hernndez-Maldonado Zhongfang Chen Department of Chemistry Institute for Functional Nanomaterials University of Puerto Rico Rio Piedras Campus Department of Chemical Engineering Institute for Functional Nanomaterials University of Puerto Rico Mayagüez Campus

Rational design is important to achieve high-performance sorbents used to remove the contaminants of emerging concern(CECs) from ***, it is hard to propose effective design guidelines due to the lack of a clear understanding of the interaction mechanisms. By means of systematic quantum chemical computations, as a case study, we investigated the interactions between zeolite X/M^(n+)-zeolite X(Si/Al=1,M^(n+)=Cu^(2+) and Ni^(2+)) and three commonly used CECs(namely salicylic acid, carbamazepine and ciprofloxacin) in water to clarify the adsorption mechanisms. Our computations found that anionic salicylic acid cannot be adsorbed by neither zeolite X nor M^(n+)-zeolite X in neutral water due to the high electrostatic repulsion. In comparison, carbamazepine and ciprofloxacin have favorable binding energies with both zeolite X and M^(n+)-zeolite X, and their interactions with M^(n+)-zeolite X are stronger due to the joint effects of H-bond, metal complexation and electrostatic interaction. The adsorption loading of ciprofloxacin, which has a large molecular size, on M^(n+)-zeolite X is limited due to the steric hindrance. In general, steric hindrance, electrostatic interaction, H-bond and metal complexation are dominant factors for the examined systems in this study. Thus, for the design of high-performance absorbing materials, we should fully consider the molecular properties of pollutants(molecular size, surface electrostatic potential and atomic type, etc.), and properly enhance the favorable effects and avoid the unfavorable factors as much as possible under the guidance of the interaction mechanisms.

关键词： Adsorption mechanism Adsorbent design guidelines Quantum chemical computations Contaminants of emerging concern Zeolite X

Morphological and genetic differentiation in isolated populations of Mexican beech Fagus grandifolia ***

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Journal of Forestry Research 2021年第5期32卷 2169-2179页

作者： Dulce María Galván-Hernández Pablo Octavio-Aguilar Luis Lazcano-Cruz arturo Sánchez-González Population Ecology Laboratory of the Biological Research Center Autonomous University of HidalgoKm 4.5 Pachuca-Tulancingo HighwayCP 42184 Mineral de La ReformaHidalgoMexico Genetic Laboratory of the Biological Research Center Autonomous University of HidalgoKm 4.5 Pachuca-Tulancingo HighwayCP 42184 Mineral de La ReformaHidalgoMexico

Mexican beech[Fagus grandifolia ***(Martinez)***]is a subspecies endemic to the Sierra Madre Oriental Mountains and considered endangered due to the low density of its populations and high degree of habitat fragmentation and environmental *** its morphological and genetic variation is associated with its ability to adapt to changes in environmental conditions,the objective of this study was to determine whether phenotypic and genotypic variation exist,and it relationships with population reduction *** four beech populations in the states of Hidalgo and Veracruz,we analyzed 11 morphological variables for leaves and 6 micros atellite *** morphological variables that to discriminate between populations were related to the size of the leaf,but a robust differentiation pattern was not found,given that independent groups of leaves were *** populations located closest to each other,had greater genetic variation and less genetic distance;populations in the extreme north and south had the lowest genetic *** differentiation among populations was associated with reduction in population *** the 3 localities in Hidalgo,recent bottlenecks were identified,and in Veracruz,an old bottleneck was *** in leaf morphology and genetic structure of Mexican beech populations could be the result of a combination of various geographical,climate and ecological factors.

关键词： Adaptation Bottleneck Genetic structure Leaf morphology Mexico Sierra madre oriental

Role of Reactive Oxygen Species in the Initiation of Plant Retrograde Signaling

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Phyton-International Journal of Experimental Botany 2022年第5期91卷 905-913页

作者： Eduardo-Antonio Trillo-Hernández arturo Duarte Sierra Martín Ernesto Tiznado-Hernández Centro de Investigación en Alimentación y Desarrollo A.C.Tecnología de Alimentos de Origen VegetalLaboratorio de Fisiología y Biología Molecular de PlantasHermosillo83304México Department of Food Science and Plant Research and Innovation Center Laval UniversityQuebecQCG1V 0A6Canada

The interaction between the nucleus and the different organelles is important in the physiology of the ***-tive oxygen species(ROS)are a by-product of the oxidation of organic molecules to obtain energy by the need to carry out the electron transfer between the different enzymatic ***,they also have a role in the generation of what is known as retrograde *** signal comes from the different organelles in which the oxidation of molecules or the electron transference is taking place such as mitochondria and ***,ROS can also induce the release of signals from the *** seems that these signals plays a role communicating to the nucleus the current status of the different parts of the plant cell to induce a changes in gene *** this review,the molecular mechanism of ROS retrograde signaling is described.

关键词： Reactive oxygen species retrograde signaling mitochondria chloroplast

Emerging melt quality control solution technologies for aluminium melt

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China Foundry 2009年第4期6卷 358-365页

作者： arturo Pascual Foseco Foundry(China)Co. Ltd.2002 Leishing International Plaza1319 Yan'an RoadShanghaiChinaJr

The newly developed ＂MTS 1500＂ Melt Treatment System is performing the specifically required melt treatment operations like degassing, cleaning, modification and/or grain refinement by an automated process in one step and at the same location. This linked process is saving time, energy and metal losses allowing - by automated dosage of the melt treatment agents - the production of a consistent melt quality batch after batch. By linking the MTS Metal Treatment System with sensors operating on-line in the melt, i.e., with a hydrogen sensor ＂Alspek H＂, a fully automated control of parts of the process chain like degassing is possible. This technology does guarantee a pre-specified and documented melt quality in each melt treatment batch. Furthermore, to ensure that castings are consistent and predictable there is a growing realization that cdtical parameters such as metal cleanliness must be measured prior to casting. There exists accepted methods for measuring the cleanliness of an aluminum melt but these can be both slow and costly. A simple, rapid and meaningful method of measuring and bench marking the cleanliness of an aluminum melt has been developed to offer the foundry a practical method of measuring melt cleanliness. This paper shows the structure and performance of the integrated MTS melt treatment process and documents achieved melt quality standards after degassing, cleaning, modification and grain refinement operations under real foundry conditions. It also provides an insight on a melt cleanliness measuring device ＂Alspek MQ＂ to provide foundry men better tools in meeting the increasing quality and tighter specification demand from the industry.

关键词： melt quality aluminum casting melt treatment cleanliness measuring

The Swirling Jet Generation Method and Its Effect on the Velocity Distribution

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Journal of Mechanics Engineering and Automation 2020年第1期10卷 16-26页

作者： fernández Roque Tiburcio Correa Arredondo Joséarturo Mejía Carmona Alejandro Sandoval Lezama Jorge Vázquez Flores JoséFélix Tiburcio fernández Roque Instituto Politécnico Nacional Escuela Superior de Ingeniería Mecánica y Eléctrica Unidad TicomanAv.Ticoman No.600Col.San JoséTicomanAlcaldía Gustavo A.MaderoC.P.07340 México DFMéxico 不详

The wing tip vortex has a great similarity with the swirling *** these are generated of a simpler and more economic form in a laboratory,it is relevant to determine which the best method is for the generation of the swirling *** this paper,the velocity distribution obtained experimentally with the method of generation here proposed,which consists of the employment of an axial fan without stators,is compared with the velocity distribution of swirling jets generated with three different *** is observed that the velocity distribution obtained with the proposed method is similar with one of the methods found in the references,which uses fixed blades guides at the entry of the *** proposed method is suitable for the generation of the swirling jet and it is considered that it is simpler and more economic to use blades fixed guides.

关键词： Swirling jet velocity distribution swirl intensity wingtip vortex tangential velocity

Introduction of Dr. Andrew V Schally

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Asian Journal of Andrology 2015年第6期17卷 923-924页

作者： arturo Mendoza-Valdes UROLOGO Hospital Medica Sur Puente dePiedra 150 T2-625 Col. Toriello Guerra Tlalpan14050Mexico DF.

Ifirst met Dr. Andrew V Schally （PhD, MDhc （Multi）, DSc, Distinguished Medical Research Scientist, U.S. Department of Veterans Affairs Professor of Pathology and Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA） many years ago, probably around the beginning of the 1990＇s in one of his visits to Mexico City （Figure 1）. He has many friends in my country since some of the investigations that led to the development of the LHRH agonists were made in a couple of Mexican hospitals in collaboration with some outstanding Mexican physicians that I will mention later. In that time, I was the head of the Department of Urology of the Mexican National Cancer Institute and our Director, Dr. Jaime de la Garza, invited him for a meeting. I was surprised by his humbleness, intelligence and easy going personality, in spite of being a Nobel Prize scientist.

关键词： Introduction Andrew Schally

Distributed Monitoring of Power System Oscillations Using Multiblock Principal Component Analysis and Higher-order Singular Value Decomposition

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Journal of Modern Power Systems and Clean Energy 2022年第4期10卷 818-828页

作者： arturo Román-Messina Alejandro Castillo-Tapia David A.Román-García Marcos A.Hernández-Ortega Carlos A.Morales-Rergis Claudia M.Castro-Arvizu Center for Research and Advanced Studies(CINVESTAV)of the National Polytechnic Institute of Mexico GuadalajaraJal.45017Mexico Instituto Tecnológico y de Estudios Superiores de Monterrey GuadalajaraJal.45070Mexico Autonomous University of Guadalajara GuadalajaraJal.45129Mexico Centro de Enseñanza Técnica Industrial and he is also with UAGGuadalajaraJal.44638Mexico

The primary goal in the analysis of hierarchical distributed monitoring and control architectures is to study the spatiotemporal patterns of the interactions between areas or *** this paper,a novel conceptual framework for distributed monitoring of power system oscillations using multiblock principal component analysis(MB-PCA)and higher-order singular value decomposition(HOSVD)is proposed to understand,characterize,and visualize the global behavior of the power *** proposed framework can be used to evaluate the influence of a given area or utility on the oscillatory behavior,uncover low-dimensional structures from high-dimensional data,and analyze the effects of heterogeneous data on the modal characteristics and interpretation of power *** metrics are then investigated to examine the relationships between the dynamic patterns and participation of individual data blocks in the global behavior of the *** application of these techniques is demonstrated by case studies of two systems:a 14-machine test system and a 5449-bus 635-generator equivalent model of a large power system.

关键词： Distributed monitoring multiblock principal component analysis(MB-PCA) higher-order singular value decomposition(HOSVD) Tucker decomposition