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  1. AU="Isaza, Juan Pablo"
  2. AU=Matsuzaki Hiroshi
  3. AU="Dorfer, Sonja"
  4. AU="Ramirez, Jordan R"
  5. AU="Xiang, Andy Peng"
  6. AU="Hergott, Dianna E B"
  7. AU="Sava, Alexandru"
  8. AU="Strandwitz, Philip"
  9. AU="Modrau, Boris"
  10. AU="Sallese, Anthony"
  11. AU="T Kennedy, Patrick"
  12. AU="Cheng, XiaoQing"
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  1. Article ; Online: Bovine Leukemia Virus molecular detection and associated factors among dairy herd workers in Antioquia, Colombia.

    Mendoza, Willington / Isaza, Juan Pablo / López, Lucelly / López-Herrera, Albeiro / Gutiérrez, Lina A

    Acta tropica

    2024  Volume 256, Page(s) 107253

    Abstract: The Bovine Leukemia Virus (BLV) affects mainly cattle, is transmitted by exposure to contaminated biological fluids, and generates lymphomas in 5 % of infected animals. The zoonotic potential of BLV has been studied, and it is currently unknown if it ... ...

    Abstract The Bovine Leukemia Virus (BLV) affects mainly cattle, is transmitted by exposure to contaminated biological fluids, and generates lymphomas in 5 % of infected animals. The zoonotic potential of BLV has been studied, and it is currently unknown if it circulates in human workers on dairy herds in Antioquia. Objective: To determine the frequency of BLV detection, the genotypes of the virus, and the factors associated with its detection in workers for dairy herds in Antioquia, Colombia. Through a cross-sectional study in 51 dairy herds, 164 adults were recruited. A peripheral blood sample was collected from each participant for molecular detection of the BLV env and tax genes, and associated factors were explored through bivariate and multivariate mixed Poisson model analyses. The analysis showed that 82 % (134/164) of the participants were men, with an average age of 40. Using qPCR, the constitutive gene GAPDH was amplified to evaluate the presence of amplification inhibitors in the DNA samples. Using nested PCR, the amplification of the env viral gene was obtained in 13 % (22/164) of the total samples analyzed, while all the samples tested negative for tax. The amplicons of the env gene were sequenced, and the identity compatible with BLV was verified by BLAST analysis (NCBI). Using molecular phylogeny analysis, based on maximum likelihood and haplotype network analysis, it was identified that BLV genotype 1 is present in the evaluated population. 16 % (26/164) of the participants reported having ever had an accident with surgical material during work with cattle; this variable was associated with BLV positivity even after adjusting for other variables (PRa =2.70, 95 % CI= 1.01- 7.21). Considering that other studies have reported the circulation of BLV genotype 1 in cattle from this same region and the present report in humans from dairy herds, the results suggest a possible zoonotic transmission of BLV genotype 1 in Antioquia, reinforcing the need to continue investigating to determine the potential role of this virus as an etiological agent of disease in livestock farmers in the department.
    Language English
    Publishing date 2024-05-21
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 210415-5
    ISSN 1873-6254 ; 0001-706X
    ISSN (online) 1873-6254
    ISSN 0001-706X
    DOI 10.1016/j.actatropica.2024.107253
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  2. Article ; Online: Bovine leukemia virus detection in humans: A systematic review and meta-analysis.

    Mendoza, Willington / Isaza, Juan Pablo / López, Lucelly / López-Herrera, Albeiro / Gutiérrez, Lina A

    Virus research

    2023  Volume 335, Page(s) 199186

    Abstract: To review the available studies on the frequency of detection of the bovine leukemia virus in human samples, a systematic review with meta-analysis of the scientific literature was carried out, including papers published in English, Spanish, and ... ...

    Abstract To review the available studies on the frequency of detection of the bovine leukemia virus in human samples, a systematic review with meta-analysis of the scientific literature was carried out, including papers published in English, Spanish, and Portuguese in 5 multidisciplinary databases. We collected information from different populations following a detailed and reproducible search protocol in which two researchers verified the inclusion and exclusion criteria. We identified 759 articles, of which only 33 met the inclusion criteria. Analyzed studies reported that the presence of the virus was measured in human samples, such as paraffin-embedded breast tissue and peripheral blood from 10,398 individuals, through serological and molecular techniques. An overall virus frequency of 27% (Ranging between 17 and 37%) was observed, with a high-frequency data heterogeneity between studies. The presence of this virus in different human biological samples suggests the need to investigate further its transmission route to humans and its potential role in developing and progressing diseases.
    MeSH term(s) Humans ; Leukemia Virus, Bovine/isolation & purification
    Language English
    Publishing date 2023-08-10
    Publishing country Netherlands
    Document type Meta-Analysis ; Systematic Review ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 605780-9
    ISSN 1872-7492 ; 0168-1702
    ISSN (online) 1872-7492
    ISSN 0168-1702
    DOI 10.1016/j.virusres.2023.199186
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  3. Article: The "peel-away" technique for a ventriculoatrial shunt in a 6-month-old patient: A case report.

    Isaza, Juan Pablo Leal / Vallejo, Santiago / Aristizabal, Jorge Humberto / Rosales-Camargo, Santiago Andrés / Perilla-Estrada, Juan Pablo / Rueda, Diego Quintero

    Surgical neurology international

    2024  Volume 15, Page(s) 16

    Abstract: Background: A ventriculoatrial shunt (VAS) proves to be an excellent alternative in the treatment of hydrocephalus. Its usage is a viable option when ventriculoperitoneal shunt (VPS) is contraindicated in any age of patients.: Case description: This ... ...

    Abstract Background: A ventriculoatrial shunt (VAS) proves to be an excellent alternative in the treatment of hydrocephalus. Its usage is a viable option when ventriculoperitoneal shunt (VPS) is contraindicated in any age of patients.
    Case description: This report highlights a successful case involving a 6-month-old patient who underwent VAS catheter positioning. The child presented with hydrocephalus and biliary atresia, making him a candidate for a liver transplant. Notably, a VPS was considered a relative contraindication in this scenario.
    Conclusion: The VAS emerges as a viable option for patients in whom a VPS might be contraindicated. This case demonstrates the successful application of a VAS in a pediatric patient.
    Language English
    Publishing date 2024-01-19
    Publishing country United States
    Document type Case Reports
    ISSN 2229-5097
    ISSN 2229-5097
    DOI 10.25259/SNI_724_2023
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  4. Article ; Online: Genome microsatellite diversity within the Apicomplexa phylum.

    Isaza, Juan Pablo / Alzate, Juan Fernando

    Molecular genetics and genomics : MGG

    2016  Volume 291, Issue 6, Page(s) 2117–2129

    Abstract: The Apicomplexa phylum groups include unicellular and obligate intracellular protozoan parasites with an apical complex used for attachment and invasion to host cells. In this study, we analyze single sequence repeats (SSRs) in the whole genome of 20 ... ...

    Abstract The Apicomplexa phylum groups include unicellular and obligate intracellular protozoan parasites with an apical complex used for attachment and invasion to host cells. In this study, we analyze single sequence repeats (SSRs) in the whole genome of 20 apicomplexan organisms that represent four different lineages within the phylum. Only perfect SSRs with at least 12 nucleotides and composed of 2-6 mers were included. To better understand the association of SSR types with the genomic regions, the SSRs were classified accordingly with the genomic location into exon, intron and intergenic categories. Our results showed heterogeneous SSRs density within the studied genomes. However, the most frequent SSRs types were di- and tri-nucleotide repeats. The former was associated with intergenic regions, while the latter was associated with exon regions.
    MeSH term(s) Apicomplexa/genetics ; Exons ; Genetic Variation ; Genome Size ; Genome, Protozoan ; Introns ; Microsatellite Repeats
    Language English
    Publishing date 2016-12
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2044817-X
    ISSN 1617-4623 ; 1617-4615
    ISSN (online) 1617-4623
    ISSN 1617-4615
    DOI 10.1007/s00438-016-1244-6
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  5. Article: Metatranscriptomic characterization of the bacterial community of a contaminated mangrove from the Caribbean

    Isaza, Juan Pablo / Sandoval-Figueredo, Vanessa / Rodelo, Maria Camila / Muñoz-García, Andrea / Figueroa-Galvis, Ingrid / Vanegas, Javier

    Regional studies in marine science. 2021 May, v. 44

    2021  

    Abstract: Mangroves are considered biodiversity hotspots threatened by various anthropogenic tensors such as pollution, which affect the taxonomic and functional diversity of microorganisms and therefore the stability of the ecosystem. Despite metagenomic work, ... ...

    Abstract Mangroves are considered biodiversity hotspots threatened by various anthropogenic tensors such as pollution, which affect the taxonomic and functional diversity of microorganisms and therefore the stability of the ecosystem. Despite metagenomic work, knowledge of gene expression in contaminated mangroves is limited. Our general objective was to characterize the metatranscriptome at the taxonomic and functional level of bacteria associated with nutrient cycling and xenobiotic degradation of a mangrove contaminated by wastewater from the Colombian Caribbean. Total RNA was extracted from three soil samples from a mangrove affected by sewage for the construction of the cDNA library, and sequencing by the Illumina HiSeq 4000 platform. We found a domain of the phylum Firmicutes and Proteobacteria, represented mainly by Bacillus and Desulfuromonas respectively. Functional annotation showed high gene expression in metabolic pathways related to carbohydrate metabolism and processing of genetic information. Regarding biogeochemical cycles, the highest transcriptional activity was found in the assimilation of formaldehyde (methane metabolism), dissimilatory nitrate reduction (nitrogen metabolism), and reduction of sulfate (sulfur metabolism), which indicates a predominance of anaerobic processes and, decomposition of organic matter. Benzoate degradation was the pathway with the highest transcriptional activity in the degradation of xenobiotics. The predominance of few taxonomics could indicate selection of taxonomic groups by wastewater, advanced ecosystem degradation and loss of ecosystem resilience future.
    Keywords Desulfuromonas ; RNA ; bacterial communities ; cDNA libraries ; carbohydrate metabolism ; ecological resilience ; ecosystems ; formaldehyde ; functional diversity ; gene expression ; marine science ; metagenomics ; methane ; nitrate reduction ; nitrogen metabolism ; organic matter ; pollution ; sewage ; soil ; sulfates ; sulfur ; transcription (genetics) ; transcriptomics ; wastewater ; xenobiotics ; Caribbean
    Language English
    Dates of publication 2021-05
    Publishing place Elsevier B.V.
    Document type Article
    Note NAL-AP-2-clean
    ISSN 2352-4855
    DOI 10.1016/j.rsma.2021.101724
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  6. Article ; Online: Gene expression profiling identifies candidate biomarkers for new latent tuberculosis infections. A cohort study.

    Herrera, Mariana / Keynan, Yoav / McLaren, Paul J / Isaza, Juan Pablo / Abrenica, Bernard / López, Lucelly / Marin, Diana / Rueda, Zulma Vanessa

    PloS one

    2022  Volume 17, Issue 9, Page(s) e0274257

    Abstract: Objective: To determine the gene expression profile in individuals with new latent tuberculosis infection (LTBI), and to compare them with people with active tuberculosis (TB) and those exposed to TB but not infected.: Design: A prospective cohort ... ...

    Abstract Objective: To determine the gene expression profile in individuals with new latent tuberculosis infection (LTBI), and to compare them with people with active tuberculosis (TB) and those exposed to TB but not infected.
    Design: A prospective cohort study. Recruitment and follow-up were conducted between September 2016 to December 2018. Gene expression and data processing and analysis from April 2019 to April 2021.
    Setting: Two male Colombian prisons.
    Participants: 15 new tuberculin skin test (TST) converters (negative TST at baseline that became positive during follow-up), 11 people that continued with a negative TST after two years of follow-up, and 10 people with pulmonary ATB.
    Main outcome measures: Gene expression profile using RNA sequencing from PBMC samples. The differential expression was assessed using the DESeq2 package in Bioconductor. Genes with |logFC| >1.0 and an adjusted p-value < 0.1 were differentially expressed. We analyzed the differences in the enrichment of KEGG pathways in each group using InterMiner.
    Results: The gene expression was affected by the time of incarceration. We identified group-specific differentially expressed genes between the groups: 289 genes in people with a new LTBI and short incarceration (less than three months of incarceration), 117 in those with LTBI and long incarceration (one or more years of incarceration), 26 in ATB, and 276 in the exposed but non-infected individuals. Four pathways encompassed the largest number of down and up-regulated genes among individuals with LTBI and short incarceration: cytokine signaling, signal transduction, neutrophil degranulation, and innate immune system. In individuals with LTBI and long incarceration, the only enriched pathway within up-regulated genes was Emi1 phosphorylation.
    Conclusions: Recent infection with MTB is associated with an identifiable RNA pattern related to innate immune system pathways that can be used to prioritize LTBI treatment for those at greatest risk for developing active TB.
    MeSH term(s) Biomarkers/metabolism ; Cohort Studies ; Cytokines ; Gene Expression Profiling ; Humans ; Latent Tuberculosis/diagnosis ; Latent Tuberculosis/genetics ; Leukocytes, Mononuclear/metabolism ; Male ; Prospective Studies ; RNA ; Tuberculin Test ; Tuberculosis
    Chemical Substances Biomarkers ; Cytokines ; RNA (63231-63-0)
    Language English
    Publishing date 2022-09-28
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0274257
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  7. Article ; Online: Diagnostic concordance between BioFire® FilmArray® Pneumonia Panel and culture in patients with COVID-19 pneumonia admitted to intensive care units: the experience of the third wave in eight hospitals in Colombia.

    Molina, Francisco José / Botero, Luz Elena / Isaza, Juan Pablo / Cano, Luz Elena / López, Lucelly / Tamayo, Leidy / Torres, Antoni

    Critical care (London, England)

    2022  Volume 26, Issue 1, Page(s) 130

    Abstract: Background: The detection of coinfections is important to initiate appropriate antimicrobial therapy. Molecular diagnostic testing identifies pathogens at a greater rate than conventional microbiology. We assessed both bacterial coinfections identified ... ...

    Abstract Background: The detection of coinfections is important to initiate appropriate antimicrobial therapy. Molecular diagnostic testing identifies pathogens at a greater rate than conventional microbiology. We assessed both bacterial coinfections identified via culture or the BioFire® FilmArray® Pneumonia Panel (FA-PNEU) in patients infected with SARS-CoV-2 in the ICU and the concordance between these techniques.
    Methods: This was a prospective study of patients with SARS-CoV-2 who were hospitalized for no more than 48 h and on mechanical ventilation for no longer than 24 h in 8 ICUs in Medellín, Colombia. We studied mini-bronchoalveolar lavage or endotracheal aspirate samples processed via conventional culture and the FA-PNEU. Coinfection was defined as the identification of a respiratory pathogen using the FA-PNEU or cultures. Serum samples of leukocytes, C-reactive protein, and procalcitonin were taken on the first day of intubation. We analyzed the empirical antibiotics and the changes in antibiotic management according to the results of the FA-PNEUM and cultures.
    Results: Of 110 patients whose samples underwent both methods, FA-PNEU- and culture-positive samples comprised 24.54% versus 17.27%, respectively. Eighteen samples were positive in both techniques, 82 were negative, 1 was culture-positive with a negative FA-PNEU result, and 9 were FA-PNEU-positive with negative culture. The two bacteria most frequently detected by the FA-PNEU were Staphylococcus aureus (37.5%) and Streptococcus agalactiae (20%), and those detected by culture were Staphylococcus aureus (34.78%) and Klebsiella pneumoniae (26.08%). The overall concordance was 90.1%, and when stratified by microorganism, it was between 92.7 and 100%. The positive predictive value (PPV) was between 50 and 100% and were lower for Enterobacter cloacae and Staphylococcus aureus. The negative predictive value (NPV) was high (between 99.1 and 100%); MecA/C/MREJ had a specificity of 94.55% and an NPV of 100%. The inflammatory response tests showed no significant differences between patients whose samples were positive and negative for both techniques. Sixty-one patients (55.45%) received at least one dose of empirical antibiotics.
    Conclusions: The overall concordance was 90.1%, and it was between 92.7% and 100% when stratified by microorganisms. The positive predictive value was between 50 and 100%, with a very high NPV.
    MeSH term(s) Anti-Bacterial Agents/therapeutic use ; Bacteria ; COVID-19/diagnosis ; Coinfection ; Colombia ; Hospitals ; Humans ; Intensive Care Units ; Multiplex Polymerase Chain Reaction/methods ; Pneumonia/drug therapy ; Prospective Studies ; SARS-CoV-2
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2022-05-09
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041406-7
    ISSN 1466-609X ; 1364-8535
    ISSN (online) 1466-609X
    ISSN 1364-8535
    DOI 10.1186/s13054-022-04006-z
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  8. Article: Cytokine levels as predictors of mortality in critically ill patients with severe COVID-19 pneumonia: Case-control study nested within a cohort in Colombia.

    Molina, Francisco José / Botero, Luz Elena / Isaza, Juan Pablo / Cano, Luz Elena / López, Lucelly / Hoyos, Lina Marcela / Correa, Elizabeth / Torres, Antoni

    Frontiers in medicine

    2022  Volume 9, Page(s) 1005636

    Abstract: Background: High levels of different cytokines have been associated in COVID-19 as predictors of mortality; however, not all studies have found this association and its role to cause multi-organ failure and death has not been fully defined. This study ... ...

    Abstract Background: High levels of different cytokines have been associated in COVID-19 as predictors of mortality; however, not all studies have found this association and its role to cause multi-organ failure and death has not been fully defined. This study aimed to investigate the association of the levels of 10 cytokines with mortality in patients with COVID-19 admitted to the intensive care unit (ICU).
    Materials and methods: This is a case-control study nested within a cohort of patients with COVID-19 who were on mechanical ventilation and were not hospitalized for more than 48 h across nine ICUs in Medellín, Colombia. Serum samples were collected upon admission to the ICU and 7 days later and used to measure cytokine levels.
    Results: Upon admission, no differences in mortality between the cytokine levels were observed when comparisons were made quantitatively. However, in the multivariate analysis, patients with median IL-1β levels <1.365 pg/ml showed an increase in mortality (OR = 3.1; 1.24<7.71;
    Conclusion: At the time of admission, patients with median IL-1β levels lower than 1.365 pg/ml had increased mortality. An IL-1β/IL-10 ratio <2 at day 7 and IL-12p70 levels >1.666 pg/ml was associated with decreased survival.
    Language English
    Publishing date 2022-09-29
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2775999-4
    ISSN 2296-858X
    ISSN 2296-858X
    DOI 10.3389/fmed.2022.1005636
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  9. Article ; Online: Cerebral Myiasis, An Unexpected Intraoperative Finding - A Case Report and Systematic Review.

    Ramón-Cuellar, Juan Fernando / Mejía-Cordovez, Juan Armando / Quiñones-Ossa, Gabriel Alexander / Leal-Isaza, Juan Pablo / Vargas-Osorio, Maria Paula / Ramirez-Muñoz, Juan Daniel / Ordóñez-Rubiano, Edgar G / Ramirez, Alexandra Porras- / Amarillo, Diego Gómez- / Hakim-Daccach, Fernando

    World neurosurgery

    2024  Volume 186, Page(s) 138–144

    Abstract: Postoperative complications, exemplified by surgical site infections, are commonplace in the realm of daily surgical interventions. Conversely, certain infectious entities, such as cerebral myiasis (CM), are distinctly rare. This report elucidates the ... ...

    Abstract Postoperative complications, exemplified by surgical site infections, are commonplace in the realm of daily surgical interventions. Conversely, certain infectious entities, such as cerebral myiasis (CM), are distinctly rare. This report elucidates the clinical presentation of a 74-year-old female afflicted with a CSF fistula, within the context of a preceding surgical microvascular decompression employing a suboccipital craniotomy approach. Notably, the course of evaluation and treatment unveiled an intraoperative manifestation of severe CM. This case report underscores the critical significance of prompt identification, precise diagnostic elucidation, and comprehensive multidisciplinary management to optimize patient outcomes in instances of CM. Furthermore, a systematic literature review on CM supplements this report, contributing to the understanding of this infrequent complication.
    Language English
    Publishing date 2024-03-19
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2534351-8
    ISSN 1878-8769 ; 1878-8750
    ISSN (online) 1878-8769
    ISSN 1878-8750
    DOI 10.1016/j.wneu.2024.03.044
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  10. Article: Genome microsatellite diversity within the Apicomplexa phylum

    Isaza, Juan Pablo / Juan Fernando Alzate

    Molecular genetics and genomics. 2016 Dec., v. 291, no. 6

    2016  

    Abstract: The Apicomplexa phylum groups include unicellular and obligate intracellular protozoan parasites with an apical complex used for attachment and invasion to host cells. In this study, we analyze single sequence repeats (SSRs) in the whole genome of 20 ... ...

    Abstract The Apicomplexa phylum groups include unicellular and obligate intracellular protozoan parasites with an apical complex used for attachment and invasion to host cells. In this study, we analyze single sequence repeats (SSRs) in the whole genome of 20 apicomplexan organisms that represent four different lineages within the phylum. Only perfect SSRs with at least 12 nucleotides and composed of 2–6 mers were included. To better understand the association of SSR types with the genomic regions, the SSRs were classified accordingly with the genomic location into exon, intron and intergenic categories. Our results showed heterogeneous SSRs density within the studied genomes. However, the most frequent SSRs types were di- and tri-nucleotide repeats. The former was associated with intergenic regions, while the latter was associated with exon regions.
    Keywords exons ; genome ; intergenic DNA ; introns ; microsatellite repeats ; Miozoa ; nucleotides ; parasites ; Protozoa
    Language English
    Dates of publication 2016-12
    Size p. 2117-2129.
    Publishing place Springer Berlin Heidelberg
    Document type Article
    ISSN 1617-4615
    DOI 10.1007/s00438-016-1244-6
    Database NAL-Catalogue (AGRICOLA)

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