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Glycoproteogenomics: Setting the Course for Next-generation Cancer Neoantigen Discovery for Cancer Vaccines

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Genomics, Proteomics & Bioinformatics 2021年第1期19卷 25-43页

作者： josé alexandre Ferreira Marta Relvas-Santos Andreia Peixoto AndréM.N.Silva Lúcio Lara Santos Experimental Pathology and Therapeutics Group Portuguese Institute of OncologyPorto 4200-072Portugal Institute of Biomedical Sciences Abel Salazar University of PortoPorto 4050-313Portugal Porto Comprehensive Cancer Center(P.ccc) Porto 4200-072Portugal REQUIMTE-LAQV Department of Chemistry and BiochemistryFaculty of Sciences of the University of PortoPorto 4169-007Portugal

Molecular-assisted precision oncology gained tremendous ground with high-throughput next-generation sequencing(NGS),supported by robust *** quest for genomicsbased cancer medicine set the foundations for improved patient stratification,while unveiling a wide array of neoantigens for *** pre-clinical and clinical studies have successfully used tumor-specific peptides in vaccines with minimal off-target ***,the low mutational burden presented by many lesions challenges the generalization of these solutions,requiring the diversification of neoantigen *** utilizing customized databases for protein annotation by mass spectrometry(MS)is a powerful tool toward this *** the concept toward exploring proteoforms originated from post-translational modifications(PTMs)will be decisive to improve molecular subtyping and provide potentially targetable functional nodes with increased cancer *** through the path of systems biology,we highlight that alterations in protein glycosylation at the cell surface not only have functional impact on cancer progression and dissemination but also originate unique molecular fingerprints for targeted ***,we discuss the outstanding challenges required to accommodate glycoproteomics in oncoproteogenomics *** envisage that such rationale may flag a rather neglected research field,generating novel paradigms for precision oncology and immunotherapy.

关键词： Glycoproteogenomics Oncoproteogenomics Cancer neoantigens Glycosylation Precision oncology

Instruments for the assessment of social anxiety disorder: Validation studies

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World Journal of Psychiatry 2012年第5期2卷 83-85页

作者： Flávia de Lima Osório josé alexandre de Souza Crippa Sonia Regina Loureiro Department of Neuroscience and Behavior Faculty of Medicine of Ribeirao Preto University of Sao Paulo INCT Translational Medicine Hospital das Clínicas FMRP-USP Avenida dos Bandeirantes 3900 Ribeirao Preto SP CEP 14049-900 Brazil

Great progress has been observed in the literature over the last decade regarding the validation of instruments for the assessment of Social Anxiety Disorder in the Brazilian context. Particularly outstanding in this respect is the production of a group of Brazilian investigators regarding the psychometric study of the following instruments: Liebowitz Social Anxiety Scale, Social Phobia Inventory, Brief Social Phobia Scale, Disability Profile, Liebowitz Self-Rated Disability Scale, Social Phobia Safety Behaviors Scale and Self-Statements During Public Speaking Scale, which have proved to be appropriate and valid for use in the adult Brazilian population, representing resources for the assessment of social anxiety in clinical and experimental situations.

关键词： Social anxiety Social phobia,Instruments Validation Scale

Stability of Brazilian Seasonally Dry Forests under Climate Change: Inferences for Long-Term Conservation

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American Journal of Plant Sciences 2013年第4期4卷 792-805页

作者： Rosane G. Collevatti Matheus Souza Lima-Ribeiro josé alexandre F. Diniz-Filho Guilherme Oliveira Ricardo Dobrovolski Levi Carina Terribile Departamento de Ecologia Instituto de Ciências Biológicas Universidade Federal de Goiás Goiania Brazil Laboratório de Genética & Biodiversidade Instituto de Ciências Biológicas Universidade Federal de Goiás Goiania Brazil Laboratório de Macroecologia Universidade Federal de Goiás Jataí Brazil

We identified climatically stable areas of seasonally dry forests (SDFs) from Central Brazil through time and assessed the effectiveness of the current reserves network in representing these climatically stable areas, as well as areas of high suitability in the present or in the future only. We used an ensemble approach based on several methods for ecological niche modelling (ENMs) to obtain potential distributions 16 SDF’ species for past (last glacial maximum), present, and future (end of XXI century) climate scenarios. We then computed how many current Brazilian reserves matched both stable areas (suitable areas for all time periods), present and future geographical ranges alone for each species, in a multi-level gap analysis. We found range shifts due to climate changes for SDF’ species. Although the future geographical range and stable areas for all analyzed species matched at least with one reserve, many protected areas will lose importance in protecting suitable areas for species in the future. Moreover, the current Brazilian reserves cover only a small amount of their climatically stable areas. However, some reserves will be suitable for many SDF’ species (90%) at the same time, but climatically stable for only half of them. Our findings show that vegetation community from SDFs may persist in Brazilian territories until the end of XXI century, and challenges about long-term conservation of the SDFs may be partially reached with already existing Brazilian reserve network, however the reserves should be connected to permit habitat tracking.

关键词： Cerrado Biome Ecological Niche Modelling Global Climate Change Quaternary Climate Change Gap Analysis

Influence of Chitosan Characteristics in the Microencapsulation of Essential Oils

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Journal of Biomedical Science and Engineering 2021年第3期14卷 119-129页

作者： Manuel josé Lis Arias Arianne López Mercè Vilaseca Betina Vallès Remedios Prieto Mercedes Simó josé alexandre Borges Valle Rita De Cássia Siqueira Curto Valle Fabriccio Maesta Bezerra Jordi Puiggalí Bellalta INTEXTER-UPC Terrassa Spain Universidade Federal de Santa Caterina Blumenau Brasil Federal Technological University og Paraná Apucarana Brasil Universidad Politecnica de Catalunya EEBE Barcelona Spain

The fight against nosocomial infections in hospitals, has promoted the use of microencapsulated essential oils on medical wearing uniforms. These types of microcapsules can be improved with the use of antimicrobial polymers in the shell structure. Chitosan is one of the most used biopolymers and the effectiveness of the treatment can be increased with the combination of different molecular weight chains of chitosan. This modification in the composition of shell structure allows controlling the rate of hydrolysis and, therefore the amount of its cationic form. The main objective of this work is to define a methodology to get microcapsules with different shell compositions, using surfactants as stabilizers in their first step. Once they have been obtained, these microcapsules will be fixed into textile substrates with the objective to use these tissues as surgical and medical clothes to spread the antibacterial effect, in sanitary staff, as well as in the own patient. In the process of microencapsulation the molecular weight distribution of polymers, influences strongly the delivery mechanisms of the active principle, as well as the chemical characteristics of the textile substrate used in every case. In this work, several chitosan biopolymers have been checked. Structural changes in the stabilization first step and the influence of the cross-linking extension have been related with the final antibacterial effect when fixed on cotton substrates.

关键词： Microcapsules Biopolymer Antimicrobial Biofunctional Textiles

Cluster Analysis for Political Scientists

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Applied Mathematics 2014年第15期5卷 2408-2415页

作者： Dalson Britto Figueiredo Filho Enivaldo Carvalho da Rocha josé alexandre da Silva Júnior Ranulfo Paranhos Mariana Batista da Silva Bárbara Sofia Félix Duarte Department of Political Science Federal University of Pernambuco Recife Brazil Institute of Social Science Federal University of Alagoas Maceió Brazil

This paper provides an intuitive introduction to cluster analysis. Our targeting audience are both scholars and students in Political Science. Methodologically, we use basic simulation to illustrate the underlying logic of cluster analysis and we replicate data from Coppedge, Alvarez and Maldonado (2008)?[1]?to classify political regimes according to Dahl’s (1971)?[2]?polyarchy dimensions: contestation and inclusiveness. With this paper, we hope to help novice scholars to understand and employ cluster analysis in Political Science empirical research.

关键词： Cluster Analysis Q Analysis Political Regimes

Mitochondria–cGAS–STING axis is a potential therapeutic target for senescence-dependent inflammaging-associated neurodegeneration

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Neural Regeneration Research 2025年第3期20卷 805-807页

作者： joséM.Izquierdo Centro de Biología Molecular Severo Ochoa(CBM) Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid(CSIC-UAM)MadridSpain

The word “senescence” comes from the Latin senescens, meaning “to begin to age”, and is characterized by a long-lasting but reversible block in proliferation, resulting from stress-induced cell cycle arrest of pre... 详细信息

关键词： Latin potential lasting

The emerging role of mesenchymal stem cell-derived extracellular vesicles to ameliorate hippocampal NLRP3 inflammation induced by binge-like ethanol treatment in adolescence

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Neural Regeneration Research 2025年第4期20卷 1153-1163页

作者： Susana Mellado María joséMorillo-Bargues Carla Perpiñá-Clérigues Francisco García-García Victoria Moreno-Manzano Consuelo Guerri María Pascual Department of Physiology School of Medicine and DentistryUniversity of ValenciaValenciaSpain Bioinformatics and Biostatistics Unit Príncipe Felipe Research CenterValenciaSpain Neuronal and Tissue Regeneration Laboratory Príncipe Felipe Research CenterValenciaSpain

Our previous studies have reported that activation of the NLRP3(NOD-,LRR-and pyrin domain-containing protein 3)-inflammasome complex in ethanol-treated astrocytes and chronic alcohol-fed mice could be associated with neuroinflammation and brain *** stem cell-derived extracellular vesicles(MSC-EVs)have been shown to restore the neuroinflammatory response,along with myelin and synaptic structural alterations in the prefrontal cortex,and alleviate cognitive and memory dysfunctions induced by binge-like ethanol treatment in adolescent *** the therapeutic role of the molecules contained in mesenchymal stem cell-derived extracellular vesicles,the present study analyzed whether the administration of mesenchymal stem cell-derived extracellular vesicles isolated from adipose tissue,which inhibited the activation of the NLRP3 inflammasome,was capable of reducing hippocampal neuroinflammation in adolescent mice treated with binge *** demonstrated that the administration of mesenchymal stem cell-derived extracellular vesicles ameliorated the activation of the hippocampal NLRP3 inflammasome complex and other NLRs inflammasomes(e.g.,pyrin domain-containing 1,caspase recruitment domain-containing 4,and absent in melanoma 2,as well as the alterations in inflammatory genes(interleukin-1β,interleukin-18,inducible nitric oxide synthase,nuclear factor-kappa B,monocyte chemoattractant protein-1,and C–X3–C motif chemokine ligand 1)and miRNAs(miR-21a-5p,miR-146a-5p,and miR-141-5p)induced by binge-like ethanol treatment in adolescent *** analysis further revealed the involvement of miR-21a-5p and miR-146a-5p with inflammatory target genes and NOD-like receptor signaling *** together,these findings provide novel evidence of the therapeutic potential of MSC-derived EVs to ameliorate the hippocampal neuroinflammatory response associated with NLRP3 inflammasome activation induced by binge drinking in adolescence.

关键词： adolescence binge-like ethanol treatment extracellular vesicles hippocampus mesenchymal stem cells neuroinflammation NOD-,LRR-and pyrin domain-containing protein 3(NLRP3)

Traits uncover quasi-neutral community assembly in a coastal heath vegetation

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Journal of Plant Ecology 2019年第4期12卷 703-712页

作者： joséLuiz Alves Silva alexandre Fadigas Souza Louis Stephen Santiago Programa de Pós-Graduação em Ecologia Departamento de EcologiaUniversidade Federal do Rio Grande do NorteNatal 59078-970Brazil Departamento de Ecologia Universidade Federal do Rio Grande do NorteNatal 59078-970Brazil Department of Botany and Plant Sciences University of California2150 Batchelor HallRiversideCA 92521USA Smithsonian Tropical Research Institute BalboaAncónPanamáRepublic of Panamá

Aims Trait-based approaches are increasingly being used in ecology due to their potential to explain and predict community structure and dynamic regardless of species ***,we asked whether coastal heath vegetation established in stressful habitats could be assembled by quasi-neutral mechanisms based on functional trait *** are organized through quasi-neutral dynamics if abiotic gradients and/or species interactions impose sorting on functional traits and species performances,but not on species phylogenetic relatedness and *** The study was conducted in a coastal area containing tall dunes near the sea,and relatively flat areas punctuated by short palaeodunes further inland,Northeastern South *** evaluated 10 traits of the 21 most abundant species,as well as eight abiotic variables in 70 plots(25 m^(2))established in dune tops,valleys,flat and steep *** effect of environmental filter was tested by linear mixed models(LMM)between each community-weighted mean(CWM)trait and the abiotic variables,and by two indices of environmental filtering based on intra-and interspecific-trait vari-ability relative to null *** evaluate the effect of species inter-actions,we used an index of niche overlap relative to null models,and LMMs between this index and the species richness of *** Findings The environmental filtering index did not deviate from null expect-ations for any *** that included individual variability per-formed similarly to models that used species mean ***,the explicit consideration of environmental gradients by CWM ana-lyses revealed functional patterns that would remain undetected if trait distribution was analyzed *** addition,intraspecific vari-ation in the stem length was an important driver of species diversity as suggested by the relationship between species richness and the niche overlap *** on the occurrence and phylogenetic re-latedness o

关键词： Restinga heath vegetation harsh environment stress-tolerant species response traits

Adjuvant therapy for gastric cancer:What have we learned since INT0116?

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World Journal of Gastroenterology 2015年第13期21卷 3850-3859页

作者： alexandre A Jácome Ajith K Sankarankutty josé Sebastiao dos Santos Department of Medical Oncology Hospital Mater DeiBelo Horizonte 30190-131Minas GeraisBrazil Department of Surgery and Anatomy University of Sao Paulo at Ribeirao PretoSchool of MedicineRibeirao Preto14049-900Sao PauloBrazil

Gastric cancer is one of the main cancer-related causes of death worldwide. The curative treatment of gastric cancer consists of tumor resection and lymphadenectomy. However, surgical treatment alone is associated with high recurrence rates. Adjuvant treatment strategies have been studied over the last decades, but there have been controversial results from the initial studies. The pivotal INT0116 study demonstrated that the use of adjuvant chemoradiotherapy with 5-fluorouracil increases relapse-free and overall survival, and it has been adopted across the Western world. The high toxicity of radiochemotherapy and suboptimal surgical treatment employed, with fewer than 10% of the patients submitted to D2 lymphadenectomy, were the main study limitations. Since its publication, other adjuvant treatment modalities have been studied, and radiochemotherapy is being refined to improve its efficacy and safety. A multimodal approach has been demonstrated to significantly increase relapsefree and overall survival, and it can be offered in the form of perioperative chemotherapy, adjuvant chemoradiotherapy or adjuvant chemotherapy, regardless of the extent of lymphadenectomy. The objective of the present review is to report the major advances obtained in the last decades in the adjuvant treatment of gastric cancer as well as the perspectives of treatment based on recent knowledge of the molecular biology of the disease.

关键词： Stomach neoplasms Adjuvant radiotherapy Adjuvant chemotherapy Histology Genes erbB-2