Publications by authors named "Faviel F Gonzalez Galarza"

The allele frequency net database (AFND, http://www.allelefrequencies.net ) is an online web-based repository that contains information on the frequencies of immune-related genes and their corresponding alleles in worldwide human populations.

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Background: Osteoarthritis is a frequent rheumatic disease. Some single-nucleotide polymorphisms of the gene associated with fat mass and obesity are associated with increased body mass index and knee osteoarthritis.

Objective: The objective of this study was to analyze the association of single nucleotide polymorphism rs1477196 of the fat mass and obesity gene with primary knee osteoarthritis.

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Article Synopsis
  • Metabolic syndrome (MetS) is a combination of health issues like obesity, high blood sugar, high blood pressure, and unhealthy cholesterol levels, which can increase the risk of diabetes and heart disease.
  • * The development of MetS is influenced by both genetic and environmental factors, with recent studies emphasizing the importance of single nucleotide polymorphisms (SNPs) in its understanding.
  • * This review explores the genetics of MetS, focusing on diagnostic criteria, SNPs, and how personalized nutrition and multiomics approaches could enhance treatment strategies.
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To evaluate the influence of mitochondrial DNA haplogroups on the risk of knee OA in terms of their interaction with obesity, in a population from Mexico. Samples were obtained from (n = 353) knee OA patients (KL grade ≥ I) and (n = 364) healthy controls (KL grade = 0) from Mexico city and Torreon (Mexico). Both Caucasian and Amerindian mtDNA haplogroups were assigned by single base extension assay.

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Background: Antiretroviral therapy has significantly improved prognosis in treatment against HIV infection, however, prolonged exposure is associated to cardiovascular diseases, lipodystrophy, type 2 diabetes, insulin resistance, metabolic alteration, as obesity which includes the accumulation of oxidative stress in adipose tissue. FGF21 is a peptide hormone that is known to regulate glucose and lipid metabolism. FGF21 is expressed and secreted primarily in the liver and adipose tissue, promoting oxidation of glucose/fatty acids and insulin sensitivity.

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To examine potential risk factors associated with biochemical alterations in renal function in a population diagnosed with HIV/AIDS undergoing antiretroviral treatment.This is an observational, transversal, and relational design study that included 179 HIV-seropositive subjects. Glucose serum, cholesterol, triglycerides, total proteins, albumin, creatine, urea, blood urea nitrogen (BUN), and electrolytes levels were determined for each individual.

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The extensive allelic variability observed in several genes related to the immune response and its significance in different areas including transplantation, disease association studies, diversity in human populations, among many others, has led the scientific community to analyse these variants among individuals. Serving as an electronic data warehouse, the Allele Frequency Net Database (AFND, http://www.allelefrequencies.

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Article Synopsis
  • Emerging infectious diseases (EIDs), particularly those caused by viruses like SARS-CoV-2, are on the rise, highlighting the urgent need for better vaccine strategies that consider genetic diversity.
  • The genetic variations in human leukocyte antigen (HLA) molecules impact how different ethnic groups respond to vaccines, complicating vaccine candidate selection.
  • Predivac-3.0 is an innovative immunoinformatics tool designed to discover T-cell epitopes while factoring in these ethnic differences, demonstrating strong predictive accuracy compared to existing methods and showcasing its application in identifying potential immune responses against COVID-19 based on the HLA profiles of populations.
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Immunorelevant genes are among the most probable modulators of coronavirus disease 2019 (COVID-19) progression and prognosis. However, in the few months of the pandemic, data generated on host genetics has been scarce. The present study retrieved data sets of HLA-B alleles, KIR genes and functional single nucleotide polymorphisms (SNPs) in cytokines related to COVID-19 cytokine storm from two publicly available databases: Allele Frequency Net Database and Ensembl, and correlated these frequency data with Case Fatality Rate (CFR) and Daily Death Rates (DDR) across countries.

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To analyze the association of polymorphisms in the (rs3740199 and rs1871054) and (rs2073508) genes with knee osteoarthritis (KOA) in a population from northern Mexico. A total of 296 individuals were included in the study. Primary KOA was confirmed according to the criteria established by the American College of Rheumatology.

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To investigate the possible roles of the single nucleotide polymorphisms (SNPs) (rs77245812) and (rs12982744) with susceptibility to knee osteoarthritis (KOA) among mestizos from the northeast region of Mexico. In addition, we analyzed the relationship of their urinary levels of carboxy terminal telopeptide of collagen type II (CTX-II) and the radiological grade of disease. A total of 223 individuals from a Northeast Mexico Mestizo population were included in this study: 110 patients with primary KOA and 113 healthy controls.

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The Allele Frequency Net Database (AFND, www.allelefrequencies.net) provides the scientific community with a freely available repository for the storage of frequency data (alleles, genes, haplotypes and genotypes) related to human leukocyte antigens (HLA), killer-cell immunoglobulin-like receptors (KIR), major histocompatibility complex Class I chain related genes (MIC) and a number of cytokine gene polymorphisms in worldwide populations.

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Background & Aims: Bile duct tumors are rare and have poor prognoses. Natural killer (NK) cells are frequent in human liver and infiltrate these tumors but do not control their progression. Responses of NK cells are regulated by NK immunoglobulin-like receptors (KIRs), which interact with HLA class I ligands.

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Aims: (1) To evaluate the association between type 2 diabetes mellitus (T2D) and primary knee osteoarthritis (KOA); and (2) to compare synovial fluid (SF) cartilage oligomeric matrix protein (COMP) concentrations and glycemic control parameters in patients with T2D, with and without primary KOA.

Methods: A total of 231 individuals were included in this study. Primary KOA was confirmed according to the criteria established by the American College of Rheumatology.

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The allele frequency net database (AFND, http://www.allelefrequencies.net ) is an online web-based repository that contains information on the frequencies of immune-related genes and their corresponding alleles in worldwide human populations.

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Human leukocyte antigens (HLA) are an important family of genes involved in the immune system. Their primary function is to allow the host immune system to be able to distinguish between self and non-self peptides-e.g.

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The Allele Frequencies Net Database (AFND) is a freely accessible database which stores population frequencies for alleles or genes of the immune system in worldwide populations. Herein we introduce two new tools. We have defined new classifications of data (gold, silver and bronze) to assist users in identifying the most suitable populations for their tasks.

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Background: Peptide vaccination based on multiple T-cell epitopes can be used to target well-defined ethnic populations. Because the response to T-cell epitopes is restricted by HLA proteins, the HLA specificity of T-cell epitopes becomes a major consideration for epitope-based vaccine design. We have previously shown that CD4+ T-cell epitopes restricted by 95% of human MHC class II proteins can be predicted with high-specificity.

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This review describes a database for the collection, archiving, sorting, searching and display of gene and allele frequencies for immunogenetic genes.

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It has been 12 years since the Allele Frequency Net Database (AFND; http://www.allelefrequencies.net) was first launched, providing the scientific community with an online repository for the storage of immune gene frequencies in different populations across the world.

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The open XML format mzML, used for representation of MS data, is pivotal for the development of platform-independent MS analysis software. Although conversion from vendor formats to mzML must take place on a platform on which the vendor libraries are available (i.e.

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The range of heterogeneous approaches available for quantifying protein abundance via mass spectrometry (MS)(1) leads to considerable challenges in modeling, archiving, exchanging, or submitting experimental data sets as supplemental material to journals. To date, there has been no widely accepted format for capturing the evidence trail of how quantitative analysis has been performed by software, for transferring data between software packages, or for submitting to public databases. In the context of the Proteomics Standards Initiative, we have developed the mzQuantML data standard.

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The killer cell immunoglobulin-like receptors (KIR) play a fundamental role in the innate immune system, through their interactions with human leucocyte antigen (HLA) molecules, leading to the modulation of activity in natural killer (NK) cells, mainly related to killing pathogen-infected cells. KIR genes are hugely polymorphic both in the number of genes an individual carries and in the number of alleles identified. We have previously developed the Allele Frequency Net Database (AFND, http://www.

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The Human Proteome Organisation - Proteomics Standards Initiative (HUPO-PSI) has been working for ten years on the development of standardised formats that facilitate data sharing and public database deposition. In this article, we review three HUPO-PSI data standards - mzML, mzIdentML and mzQuantML, which can be used to design a complete quantitative analysis pipeline in mass spectrometry (MS)-based proteomics. In this tutorial, we briefly describe the content of each data model, sufficient for bioinformaticians to devise proteomics software.

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