Dagoberto Armenta-Medina’s research while affiliated with Consejo Nacional de Ciencia y Tecnología and other places

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Publications (20)


Clinical, Immunological and Inflammatory Characteristics among Mexican Children with Different Subtypes of Juvenile Idiopathic Arthritis: Exploring the Correlation between Anti-Cyclic Citrullinated Peptide (anti-CCP) and Rheumatoid Factor (RF)
  • Article
  • Full-text available

February 2024

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31 Reads

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1 Citation

Pediatric Reports

Hayde Guadalupe Hernández-Huirache

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Dagoberto Armenta-Medina

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Introduction: Juvenile idiopathic arthritis (JIA) is the most common chronic rheumatic disease in childhood, affecting one to four of every 1000 children worldwide. It is characterized by joint inflammation lasting more than six weeks in children under 16 years. The aim of this study was to estimate the frequency of JIA subtypes in the Mexican patient population; compare clinical, immunological and inflammation markers by JIA subtype; and examine the correlation between these variables. Methods: We conducted a cross-sectional study of 50 patients with JIA (2–15 years). We estimated the frequency of each JIA subtype, assessed and compared the immunological characteristics (RF, ANA and anti-CCP) by JIA subtype at the time of diagnosis using Kruskal–Wallis or chi-square tests, and calculated Spearman correlation coefficients between the assessments. Results: Our analysis included 50 patients, 29 (58%) girls and 21 (42%) boys, aged at the time of diagnosis 10.56 ± 3.99 years. The frequencies of JIA subtypes were RF-seropositive polyarthritis (34%), RF-seronegative polyarthritis (28%), systemic arthritis (16%), oligoarthritis (14%) and arthritis-related enthesitis (8%). We found a significant association between sex and JIA subtype (p = 0.014). There was a significant difference in anti-CCP levels by JIA subtype (p < 0.001). We also detected positive correlations between RF and anti-CCP (r = 0.63, p < 0.001) and between age and anti-CCP (r = 0.29, p = 0.041). Conclusions: Our study suggests that the frequency of the polyarticular subtypes of JIA is higher in Mexican children compared to other populations. Our findings highlight the importance of considering the presence of anti-CCP and RF as important criteria when deciding on treatment for JIA patients as elevated levels of these antibodies may indicate early forms of adult rheumatoid arthritis.

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A Web Application for Biomedical Text Mining of Scientific Literature Associated with Coronavirus-Related Syndromes: Coronavirus Finder

April 2022

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53 Reads

Diagnostics

In this study, a web application was developed that comprises scientific literature associated with the Coronaviridae family, specifically for those viruses that are members of the Genus Betacoronavirus, responsible for emerging diseases with a great impact on human health: Middle East Respiratory Syndrome-Related Coronavirus (MERS-CoV) and Severe Acute Respiratory Syndrome-Related Coronavirus (SARS-CoV, SARS-CoV-2). The information compiled on this webserver aims to understand the basics of these viruses’ infection, and the nature of their pathogenesis, enabling the identification of molecular and cellular components that may function as potential targets on the design and development of successful treatments for the diseases associated with the Coronaviridae family. Some of the web application’s primary functions are searching for keywords within the scientific literature, natural language processing for the extraction of genes and words, the generation and visualization of gene networks associated with viral diseases derived from the analysis of latent semantic space, and cosine similarity measures. Interestingly, our gene association analysis reveals drug targets in understudies, and new targets suggested in the scientific literature to treat coronavirus.


Figure 4. Word co-occurrence network extracted from the titles of the articles associated with Mexican bioinformatics. Clusters in colors are derived from the walk trap algorithm. The word size is proportional to occurrences and the edges to the association strength index between words.
Figure 6. Thematic evolution map of Mexican bioinformatics over a 25-year window divided into three periods. The thickness of the arrows is proportional to the Inclusion index. The box area is proportional to the abundance of the theme in the literature.
Most relevant authors by publications (1994 to 2018).
A Bibliometric Analysis of Mexican Bioinformatics: A Portrait of Actors, Structure, and Dynamics

January 2022

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198 Reads

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4 Citations

Biology

Bioinformatics is a very important informatics tool for health and biological sciences, focusing on biological data management. The objective of this work was to perform a bibliometric analysis regarding the development of Mexican bioinformatics. An exhaustive revision of the literature associated with Mexican bioinformatics in a period of 25-years was performed. Bibliometric tools, such as performance analysis and science mapping were included in the analysis. We identified the main actors as well as the structure and dynamics of Mexican bioinformatics. Some of the main findings were as follows: the thematic structure in the field is defined by the research lines of outstanding authors; the outstanding collaborations of Mexican institutions with foreign countries and institutions are influenced by the geographic proximity and binational agreements, as well as philanthropic and academic programs that promote collaborations, and there is an inclination for health issues promoted by public health financing and philanthropic organizations. It is identified that publications had an explosion since 2012, we consider that this growth may be influenced by the democratization of data, derived from the mass sequencing of biological molecules stored in public databases.


Fig. 1. AtALMT1 expression and localization of STOP1-GFP in the nucleus during early responses to Al. The roots of hydroponically grown A. thaliana Col-0 (A, F), transgenic Col-0 expressing GUS under the control of the native AtALMT1 promoter (0 to −1100 bp from the ATG start codon; Native) or the AtALMT1 promoter mutated (mCIS-D) at the STOP1-binding site (B), and transgenic Col-0 carrying the STOP1 promoter::STOP1-GFP (C, D, E) were treated with 10 μM AlCl 3 (pH 5.5) or control solution (no AlCl 3 , pH 5.5). (A) Time course of Col-0 AtALMT1 expression in the presence (black bar) or absence (white bar) of 10 μM AlCl 3 . (B) Short-term (1.5 h) Al-responsive GUS expression in transgenic A. thaliana expressing GUS under the control of the mCIS-D or native promoter [see Tokizawa et al. (2015)]. (C) Fluorescence of GFP-tagged STOP1 in Arabidopsis roots following control and Al
Fig. 2. Identification of in vitro STOP1 interactions with cis-acting elements in the promoters of STOP1-regulated genes. (A) Schematic representation of the procedures used to identify cis-acting elements that interact with STOP1 in the promoters of STOP1-regulated genes. (B) Competitive AlphaScreen assay of putative STOP1-interacting cis-acting elements in the promoters of STOP1-regulated genes. The putative STOP1-binding sites were predicted by in-silico cis-element prediction assays (Supplementary Fig. S3; Table S3). The dsDNA probes, which were 30-34 bp long sequences including the putative STOP1-binding sites (Supplementary Table S4), were analysed in terms of their ability to compete with STOP1 for the STOP1-binding site in the AtALMT1 promoter (CIS-D). Positions of the putative STOP1-binding sites from the transcription start site are shown. The biotinylated AtALMT1 CIS-D probe was incubated with ten-fold higher concentrations of a series of unlabeled competitive probes in the AlphaScreen reactions, which generate AlphaScreen signals because of the binding of STOP1 to biotinylated AtALMT1 CIS-D. Competing probes decrease the AlphaScreen signals. Data are presented as the mean relative AlphaScreen signal (absence of competitor was set as 1) ±SD (n=3). Asterisks indicate a significant difference from the data in the absence of a competitor (*P<0.05, and **P<0.01; Student's t-test). (C) In vitro chemiluminescence assay for evaluating the binding capacity of promoter regions containing AtMATE-CIS1, GDH2-CIS1 and STOP2-CIS1 sequences with positive (AtALMT1 positive; containing CIS-D, which binds to STOP1 under the same experimental conditions; Tokizawa et al., 2015) and negative (AtALMT1 negative; containing the promoter region that does not interact with STOP1) controls. Relative AlphaScreen signals (chemiluminescence of a reactive biotinylated dsDNA probe relative to that of non-reactive unlabeled control dsDNA) were analysed for each promoter region. Data are presented as the mean ±SD (n=4). Different letters indicate a significant difference (P<0.05, Tukey's test).
Fig. 4. Gene expression profile of STOP1-regulated genes under Al treatment. (A) Time course of Al-inducible expression of AtALMT1, GDH2, STOP2, ALS3, and AtMATE. The transcript abundance of each gene was determined by quantitative real-time PCR (qRT-PCR) and normalized against UBQ1 expression. Relative values (values at time 0 were set as 1) are shown in panel (A). Data are presented as the mean ±SD (n=3). Asterisks indicate a significant difference compared with the data for time 0 (*P<0.05, Student's t-test). (B) Short-term (1.5 h) inducible expression of AtALMT1, GDH2, and STOP2 in Col-0 and STOP1-KO plants, which were incubated in 10 μM AlCl 3 . Data are presented as the mean ± standard deviation (n = 3). Asterisks indicate a significant difference between the control and treatments (*P < 0.05; Student's t-test). (C) Short-term (1.5 h) Al-responsive GUS expression in transgenic A. thaliana carrying GDH2 promoter::GUS (GDH2p::GUS) and STOP2 promoter::GUS, with or without a mutation in GDH2-CIS1, and STOP2-CIS1 (Fig. 2). Data are presented as the mean ±SD (n≥5). Asterisks indicate a significant difference from the GUS fold induction in native promoter (*P<0.05; Student's t-test). (D) Expression of AtMATE and ALS3 in the roots of Col-0 and STOP1-KO in the presence or absence of 10 μM AlCl 3 . ALS3 and AtMATE expression was determined by qRT-PCR using UBQ1 expression as the internal control. Data are presented as the mean ±SD (n=3). Asterisks indicate a significant difference from the expression in control (*P<0.05; Student's t-test).
Fig. 5. Characterization of promoter elements in the AtMATE and ALS3. (A) Chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) assay on AtMATE (left) and ALS3 loci (right) using transgenic plants carrying the STOP1 promoter::STOP1-GFP. Schematic diagrams of AtMATE and ALS3 loci are shown (upper panels). Gray shaded boxes indicate potential STOP1 binding promoter regions which were identified by in vitro ChIP-seq analysis (DAPseq, O'Malley et al., 2016). The amplified regions by ChIP-qPCR analysis are shown as D1 and D2 (Supplementary Table S1). Data are presented as the mean ±SD (n=3). The immunoprecipitated DNA by anti-GFP antibody was normalized against the input DNA. Asterisks indicate a significant difference
High affinity promoter binding of STOP1 is essential for the early aluminum-inducible expression of novel Al resistance genes GDH1 and GDH2 in Arabidopsis

January 2021

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192 Reads

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43 Citations

Journal of Experimental Botany

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Takuo Enomoto

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[...]

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Malate-efflux from roots, which is regulated by the transcription factor STOP1 (SENSITIVE-TO-PROTON-RHIZOTOXICITY1), which mediates aluminum-induced expression of ALUMINUM-ACTIVATED-MALATE-TRANSPORTER1 (AtALMT1), is critical for aluminum-resistance in Arabidopsis thaliana. Several studies showed that root AtALMT1 expression is rapidly observed in response to aluminum (within 1-hour), this early induction is an important mechanism to immediately protect roots from aluminum-toxicity. Additionally, identifying the molecular mechanisms that underlie rapid aluminum-resistance responses should lead to a better understanding of plant aluminum-sensing and -signal transduction mechanisms. In this study, histochemical analyses using GFP-tagged STOP1 proteins showed that STOP1 proteins were accumulated in the nucleus soon after aluminum-treatment. The rapid aluminum-induced STOP1-nuclear localization and AtALMT1-induction were observed in the presence of the protein synthesis inhibitor, suggesting that post-translational regulation is involved in these events. STOP1 also regulated rapid aluminum-induced expression for other genes that carry a functional/high-affinity STOP1-binding site in their promoter, including STOP2, GLUTAMATE-DEHYDROGENASE1 and 2 (GDH1 and 2), but not for Al resistance genes which have no functional STOP1-binding site such as ALUMINUM-SENSITIVE3, suggesting that the binding of STOP1 in the promoter is essential for the early induction. Finally, we report that GDH1 and 2 which are the target of STOP1 are novel aluminum-resistance genes in Arabidopsis.


Trends on Advanced Information and Communication Technologies for Improving Agricultural Productivities: A Bibliometric Analysis

December 2020

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126 Reads

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29 Citations

Agronomy

In this work, an exhaustive revision is given of the literature associated with advanced information and communication technologies in agriculture within a window of 25 years using bibliometric tools enabled to detect of the main actors, structure, and dynamics in the scientific papers. The main findings are a trend of growth in the dynamics of publications associated with advanced information and communication technologies in agriculture productivity. Another assertion is that countries, like the USA, China, and Brazil, stand out in many publications due to allocating more resources to research, development, and agricultural productivity. In addition, the collaboration networks between countries are frequently in regions with closer cultural and idiomatic ties; additionally, terms’ occurrence are obtained with Louvain algorithm predominating four clusters: precision agriculture, smart agriculture, remote sensing, and climate smart agriculture. Finally, the thematic-map characterization with Callon’s density and centrality is applied in three periods. The first period of thematic analysis shows a transition in detecting the variability of a nutrient, such as nitrogen, through the help of immature georeferenced techniques, towards greater remote sensing involvement. In the transition from the second to the third stage, the maturation of technologies, such as unmanned aerial vehicles, wireless sensor networks, and the machine learning area, is observed.


Bioinformatics in Mexico: A diagnostic from the academic perspective and recommendations for a public policy

December 2020

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150 Reads

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5 Citations

In this work, we present a diagnostic analysis of strengths, weaknesses, opportunities and threats (SWOT) of the current state of Bioinformatics in Mexico. We conducted semi-structured interviews among researchers and academics with key expertise in this field, identified by bibliometric analyses and qualitative sampling techniques. Additionally, an online survey was conducted reaching a higher number of respondents. Among the relevant findings of our study, the lack of specialized human resources and technological infrastructure stood out, along with deficiencies in the number and quality of academic programs, scarce public investment and a weak relationship between public and private institutions. However, there are great opportunities for developing a national Bioinformatics to support different economic sectors. In our opinion, this work could be useful to favor a comprehensive network among Mexican researchers, in order to lay the foundations of a national strategy towards a well designed public policy.


Monitoring of Ocimum basilicum seeds growth with image processing and fuzzy logic techniques based on Cloudino-IoT and FIWARE platforms

June 2020

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50 Reads

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18 Citations

Computers and Electronics in Agriculture

The monitoring systems on the climatic conditions in the agriculture industry are increasingly useful and applicable since they allow to improve the processes of growth in the plants. This paper develops a monitoring system for the germination of Ocimum basilicum seeds using image processing and fuzzy logic techniques. Besides, the system is based on the Cloudino-IoT and FIWARE platforms as a real-time monitoring alternative. Therefore, temperature and humidity parameters can be observed in real-time. On the one hand, the system controls the variables through fuzzy control techniques and image processing monitors the germination in the radicle seed, and on the other, context data is used by the Cloudino-IoT and FIWARE platforms. On the other hand, the use of these combined open-source platforms allows cloud computing to be enabled to maintain, specify, analyze the data and automate the environmental parameters that allow maintaining temperature and humidity levels at optimal levels to create a favorable germination environment. The performance of the set-point control is compared with experimental results and the function interconnection of the IoT devices.




Citations (13)


... 5 Other clinical features may include lowgrade fever, weight loss, anaemia, hepatosplenomegaly and growth retardation. 6,7 Chronic inflammation of the joints leads to limitation of patient's routine activities and productivity. RA factor and Anti-CCP antibody positivity and hip joint involvement are linked to high joint morbidity, deformity and disability. ...

Reference:

Seronegative Polyarticular Juvenile Idiopathic Arthritis: A Case Report
Clinical, Immunological and Inflammatory Characteristics among Mexican Children with Different Subtypes of Juvenile Idiopathic Arthritis: Exploring the Correlation between Anti-Cyclic Citrullinated Peptide (anti-CCP) and Rheumatoid Factor (RF)

Pediatric Reports

... The position of the bubbles was set according to the Callon centrality and the density of the cluster [19]. Both types of maps have been utilized in many recent studies regarding various research disciplines [37,38]. ...

A Bibliometric Analysis of Mexican Bioinformatics: A Portrait of Actors, Structure, and Dynamics

Biology

... In the complex process of detoxifying Al toxicity, there are many transcription factors involved in regulating the response of crops to Al stress [34][35][36][37]. The zinc finger protein STOP1 regulated plant response to Al toxicity by increasing the expression of MATE and ALMT, resulting in increasing the organic acid transported for detoxification [38,39]. OsWRKY22 enhances the expression level of OsFRDL4, thus improving Al-induced citrate secretion and Al tolerance in rice [40]. ...

High affinity promoter binding of STOP1 is essential for the early aluminum-inducible expression of novel Al resistance genes GDH1 and GDH2 in Arabidopsis

Journal of Experimental Botany

... Kushartadi et al. (2023) analysed research insights published from 1997 to 2021 to explore smart farming trends and suggested major themes in smart farming research, identifying future research trends. Similar studies were conducted in other fields of smart farming such as smart livestock (Zhou et al., 2022), deep learning (Unal, 2020), digital agricultural revolution (Bertoglio et al., 2021), agricultural digitalization (Latino et al., 2024), and ICT and agricultural productivities (Armenta-Medina et al., 2020). However, studies regarding the role of big data in smart farming are still limited. ...

Trends on Advanced Information and Communication Technologies for Improving Agricultural Productivities: A Bibliometric Analysis

Agronomy

... Data analysis software allowed the implementation of strategies for using bioinformatics tools within the framework of a given biological problem with a possibility of selecting molecule from a huge biological database [202], to choose the right software and parameters associated with it. Bioinformatics helped also the academic staff to be more awareness about collection, storage and management of biological data and their distribution through networks [14]. In many universities, bioinformatics is considered as a field of study and subdivided in several sub-domains and helping students to acquire a lot of experience and master algorithms, programming, database management systems and new web technologies as well as the design and development of new bioinformatics software [139]. ...

Bioinformatics in Mexico: A diagnostic from the academic perspective and recommendations for a public policy

... All these components will be connected to an internet of things (IoT) platform that serves as the monitoring and notification interface. As a result, users will receive notifications when the battery 119 approaches overcharge or overheating conditions, thus preventing damage and extending the battery's lifespan [6]- [8]. ...

Monitoring of Ocimum basilicum seeds growth with image processing and fuzzy logic techniques based on Cloudino-IoT and FIWARE platforms
  • Citing Article
  • June 2020

Computers and Electronics in Agriculture

... These regulators are frequently categorized into 15-20 families. Among them, LTTRs stand out as one of the largest and most diverse families [15,16]. Each LTTR typically exist as homo-tetramers and the subunit comprises an N-terminal DNA-binding domain followed by a lengthy helix connecting to an effectorbinding domain. ...

Abundance, diversity and domain architecture variability in prokaryotic DNA-binding transcription factors

... The initial adaptation to metabolise d-arabinose was sub-optimal, yielding less energy compared to native substrates. A mutation in the transcriptional regulator araC increased d-arabinose binding affinity resulting in upregulation of genes encoding arabinose metabolism (Schleif 2010;Utrilla et al. 2016). ...

Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution
  • Citing Article
  • April 2016

Cell Systems

... The identification of critical residues is of great interest for the field of protein engineering. Armenta-Medina et al. [10] introduced a hybrid approach called ANMA. SCA to determine the importance of a residue in proteins, based on coevolution and cross-correlation of simulated atomic fluctuations. ...

Hybrid approaches for the detection of networks of critical residues involved in functional motions in protein families

BMC Bioinformatics

... ATP and nucleic acids are crucial for the structure, metabolism, and energy transfer within cells [47,48]. They determine the extent of cellular damage by measuring ATP and nucleic acid levels. ...

Comparative genomics of nucleotide metabolism: A tour to the past of the three cellular domains of life

BMC Genomics