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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

new insights into the relevance of mobile DnA to cancer resistance in blind mole rats:new lessons for cancer therapy

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Cellular & Molecular Immunology 2022年第4期19卷 458-459页

作者： Victor M.Arce Jose A.Costoya Molecular Oncology Laboratory MOL Departamento de FisioloxíaCentro Singular de Investigación en Medicina Molecular e Enfermidades Crónicas(CiMUS)Facultade de MedicinaUniversidade de Santiago de CompostelaInstituto de Investigación Sanitaria de Santiago de Compostela(IDIS)15782Santiago de CompostelaSpain

Although mammals differ substantially in their cancer incidence rates and in the importance of age as a cancer risk factor,there is a scaling of cancer incidence to the lifespan in most *** evolution has selected strategies that maximize reproductive success,which include the development of efficient mechanisms to defer the initiation of cancer until postreproductive age[1].Owing to this,cancers are very rare among wild animals(which do not typically live beyond their reproductive ages).

关键词： cancer insight resistance

Effects of Silicon nanoparticles on the Transient Liquid Phase Bonding of 304 Stainless Steel

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Journal of Materials Science & Technology 2014年第3期30卷 259-262页

作者： H.M.Hdz-García A.I.Martinez R.Mu?oz-Arroyo J.L.Acevedo-Dávila F.García-Vázquez F.A.Reyes-Valdes Corporación Mexicana de investigación en Materiales S.A.de C.V. Ciencia y Tecnología No.790 Fracc.Saltillo 400 Saltillo Coah.CP.25290 Mexico centro de investigación y de Estudios Avanzados del IPn Carr.Mty-Saltillo km.13 Ramos Arizpe Coah.CP.25900 Mexico

Transient liquid phase （TLP） bonding of 304 stainless steel with nickel based filler metal, Bni-9, was performed to study the influence of silicon nanoparticles （nPs） on the mechanical and structural properties of the bonding area. It was found that silicon nPs act as a melting point depressant in the brazing process; the formation of silicon TLP induces the dissolution of elements of the metal filler and promotes a uniform distribution in the bonding area. Silicon nPs induce the development of smaller eutectic structures in the melting zone; it has been related to microhardness measurements, which are lower when the silicon nPs are used in the brazing process.

关键词： Brazing nanoparticles Silicon Stainless steel

Cancer cells escape the immune system by increasing stemness through epigenetic reprogramming

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Cellular & Molecular Immunology 2023年第1期20卷 6-7页

作者： Jose A.Costoya Victor M.Arce Molecular Oncology Laboratory MOL Departamento de FisioloxíaCentro Singular de Investigación en Medicina Molecular e Enfermidades Crónicas(CiMUS)Facultade de MedicinaUniversidade de Santiago de CompostelaInstituto de Investigación Sanitaria de Santiago de Compostela(IDIS)15782Santiago de CompostelaSpain

Cancer stem cells(CSCs),also known as tumor initiating cells,are a minority subpopulation of undifferentiated cancerous cells within the entire tumor that hold self-renewal capacity and differentiation *** are critical for tumor progression,heterogeneity and metastasis and play a major role in chemo-and radiation-resistance and tumor recurrence[1].Although the molecular mechanisms underlying the ability of CSCs to give rise to new tumors and promote resistance to many cancer therapies are not completely understood,increasing knowledge suggests potential roles for these cells in the evasion of immune surveillance[2,3].

关键词： Cancer programming initiating

Effect of the sintering technique on the ferroelectric and d33 piezoelectric coefficients of Bi0.5(na0.84K0.16)0.5TiO3 ceramic

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Journal of Advanced Ceramics 2019年第2期8卷 278-288页

作者： G.HERnAndeZ-CUEVAS J.R.LEYVA MEnDOZA P.E.GARCíA-CASILLAS C.A.RODRíGUEZ GOnZáLEZ J.F.HERnAndeZ-PAZ G.HERRERA-PéREZ L.FUEnTES-COBAS S.DíAZ de LA TORRE O.RAYMOnD-HERRERA H.CAMACHO-MOnTES Instituto de Ingeniería y Tecnología Universidad Autónoma de Ciudad JuárezAv.Del Charro 450 Norte Cd.JuárezChihuahua32310México centro de investigación en Materiales Avanzados Miguel de Cervantes 120Chihuahua 31109ChihuahuaMéxico centro de investigación e Innovación Tecnológica Instituto Politécnico NacionalCerrada de Cecati s/nAzcapotzalcoSanta Catarina02250Ciudad de MéxicoMéxico centro de nanociencias y nanotecnología Universidad Nacional Autónoma de MéxicoKm.107 Carretera Tijuana-EnsenadaAP.14Ensenada 22860Baja CaliforniaMéxico

In the search of lead-free piezoelectric materials,ceramic processing techniques offer potential tools to increase the piezoelectric and ferroelectric properties in addition to new chemical *** of pure BnKT16(Bi0.5(na0.84K0.16)0.5TiO3)phase were synthesized by sol–gel method with a low crystallization temperature(750℃).Ceramic samples were sintered by pressureless sintering(PLS),sinter-forging(SF),and spark plasma sintering(SPS)***,morphological,and chemical characterizations were performed by XRD,Raman,EDS,and *** samples by PLS and SF exhibit rod-like grains associated to bismuth *** highest remanent polarization(11.05μC/cm2),coercive field(26.2 kV/mm),and piezoelectric coefficient(165 pC/n)were obtained for SF *** piezoresponse force microscopy(PFM)analysis shows that the crystallites at the nanoscale exhibit piezoelectric phenomenon and the highest piezoelectric response is reported for PLS *** presence of the rhombohedral phase,the increase in grain and crystallite size,and the oriented rod-like inclusions favoring the crystallographic texture are facts that enhance the piezoelectric coefficient for BnKT16 piezoceramics.

关键词： lead-free piezoelectrics sol–gel pressureless sintering (PLS) sinter-forging (SF) spark plasma sintering(SPS) piezoresponse

nano to micro size transition of hydroxyapatite in porcine bone during heat treatment with low heating rates

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Progress in natural Science:Materials International 2020年第4期30卷 494-501页

作者： Angélica M.Castillo-Paz Sandra M.Londo?o-Restrepo Liliana Tirado-Mejía M.A.Mondragón mario E.Rodríguez-García Grupo de Optoelectrónica Instituto Interdisciplinario de las Ciencias Universidad del Quindío centro de investigación y de Estudios Avanzados del IPn departamento de nanotecnología Centro de Física Aplicada y Tecnología Avanzada Universidad Nacional Autónoma de México Campus Juriquilla

This work focuses on the changes of raw hydroxyapatite obtained from porcine bones during heat treatment with heating rates of 2.5 and 5.0 °C/min between 600 °C and 1100 °C. High-Resolution transmission electron microscopy(HR-TEM) images showed that raw hydroxyapatite was formed by high-ordered nanometric platelet crystals with a length of around 18 nm and width around 7 nm. High-Resolution scanning electron microscopy(HR-SEM) images evidenced the coalescence phenomena during heating giving. It was found that the growth of the crystals and the transition from nano to a micro-size occurred at around 700 °C. And the changes in the full width at half maximum(FWHM) for the characteristic(002) plane of the X-ray diffraction patterns and the FWHM of the characteristic Raman band at 960 cm-1 for ν1 PO43-exhibited the transition from nano to a micro size, that was confirmed by HR-SEM images and the thermogravimetric(TG) analysis. The porosity of the BIOHAp changes from intra nanometric to intercrystalline.

关键词： Bone composition Hydroxyapatite nanoparticles Mineral composition Porosity formation Raman analysis

IKKβ overexpression together with a lack of tumour suppressor genes causes ameloblastic odontomas in mice

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International Journal of Oral Science 2020年第1期12卷 31-39页

作者： Angustias Page Ana Bravo Cristian Suarez-Cabrera Raquel Sanchez-Baltasar Marta Oteo Miguel Angel Morcillo MLlanos Casanova Jose CSegovia Manuel navarro Angel Ramirez Molecular Oncology Unit.centro de investigaciones Energéticas Medioambientales y Tecnológicas(CIEMAT)MadridSpain Instituto de investigación 12 de Octubre i+12 MadridSpain centro de investigación Biomédica en Red de Cáncer(CIBEROnC) MadridSpain department of Anatomy Animal Production and Veterinary Clinical SciencesLaboratory of Pathology Phenotyping of Genetically Engineered MiceFaculty of Veterinary MedicineUniversity of Santiago de CompostelaLugoSpain Biomedical Applications and Pharmacokinetics Unit Centro de Investigaciones EnergéticasMedioambientales y Tecnológicas(CIEMAT)MadridSpain Hematopoietic Innovative Therapies Division.centro de investigaciones Energéticas Medioambientales y Tecnológicas(CIEMAT).Centro de Investigación Biomédica en Red de Enfermedades Raras(CIBERER)MadridSpain Unidad Mixta de Terapias Avanzadas Fundación Instituto de Investigaciones Sanitarias Fundación Jiménez DíazMadridSpain

Odontogenic tumours are a heterogeneous group of lesions that develop in the oral cavity region and are characterized by the formation of tumoural structures that differentiate as teeth. Due to the diversity of their histopathological characteristics and clinical behaviour, the classification of these tumours is still under debate. Alterations in morphogenesis pathways such as the Hedgehog,MAPK and WnT/β-catenin pathways are implicated in the formation of odontogenic lesions, but the molecular bases of many of these lesions are still unknown. In this study, we used genetically modified mice to study the role of IKKβ(a fundamental regulator of nF-κB activity and many other proteins) in oral epithelial cells and odontogenic tissues. Transgenic mice overexpressing IKKβ in oral epithelial cells show a significant increase in immune cells in both the oral epithelia and oral submucosa. They also show changes in the expression of several proteins and mi RnAs that are important for cancer development. Interestingly, we found that overactivity of IKKβ in oral epithelia and odontogenic tissues, in conjunction with the loss of tumour suppressor proteins(p53, or p16 and p19), leads to the appearance of odontogenic tumours that can be classified as ameloblastic odontomas, sometimes accompanied by foci of secondary ameloblastic carcinomas. These tumours show nF-κB activation and increased β-catenin *** findings may help to elucidate the molecular determinants of odontogenic tumourigenesis and the role of IKKβ in the homoeostasis and tumoural transformation of oral and odontogenic epithelia.

关键词： IKKβ tumour suppressor

network-centric medicine for peripheral nerve injury:treating the whole to boost endogenous mechanisms of neuroprotection and regeneration

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neural Regeneration Research 2019年第7期14卷 1122-1128页

作者： David Romeo-Guitart Caty Casas Institut de neurociències(Inc) and department of Cell Biology Physiology and ImmunologyUniversitat Autònoma de Barcelona (UAB) & Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas(CIBERNED)

Peripheral nerve injuries caused by accidents may lead to paralysis,sensory disturbances,anaesthesia,and lack of autonomic *** recovery after disconnection of the motoneuronal soma from target tissue with proximal rupture of axons is determined by several factors:motoneuronal soma viability,proper axonal sprouting across inhibitory zones and elongation toward specific muscle,effective synapse contact rebuilding,and prevention of muscle ***,such as adjuvant drugs with pleiotropic effects,that promote functional recovery after peripheral nerve injury are *** this aim,we designed a drug discovery workflow based on a network-centric molecular vision using unbiased proteomic data and neural artificial computational *** focus is on boosting intrinsic capabilities of neurons for neuroprotection;this is in contrast to the common approach based on suppression of a pathobiological pathway known to be associated with disease *** our workflow,we discovered neuroheal,a combination of two repurposed drugs that promotes motoneuronal soma neuroprotection,is anti-inflammatory,enhances axonal regeneration after axotomy,and reduces muscle *** drug discovery workflow has thus yielded a therapy that is close to its clinical application.

关键词： motoneuron neurodegeneration axonal regeneration muscle atrophy systems biology neuroheal PI3K/AKT sirtuin 1 motor function recovery

A survey of static and dynamic potential games

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Science China Mathematics 2016年第11期59卷 2075-2102页

作者： GOnZALEZ-SAnCHEZ David HERnAndeZ-LERMA Onesimo Consejo nacional de Ciencia y Tecnología Universidad de Sonora Hermosillo 83000 Mexico Mathematics department Centro de Investigación y de Estudios Avanzados del Instituto Politecnico National Mexico City 07000 Mexico

Potential games are noncooperative games for which there exist auxiliary functions, called potentials,such that the maximizers of the potential are also nash equilibria of the corresponding game. Some properties of nash equilibria, such as existence or stability, can be derived from the potential, whenever it exists. We survey different classes of potential games in the static and dynamic cases, with a finite number of players, as well as in population games where a continuum of players is allowed. Likewise, theoretical concepts and applications are discussed by means of illustrative examples.

关键词： noncooperative games potential games nash equilibrium dynamic games Markov games differential games population games