Challenges of diagnosing homologous recombination deficiencies in metastatic prostate cancer: a six-year experience from a single institution.

PURPOSE: We evaluated the prevalence of homologous recombination deficiencies (HRD) to determine the efficacy of different techniques and clinical characteristics of patients. METHODS: This retrospective study included patients with metastatic prostate cancer who underwent molecular testing at our hospital between 2016 and 2022. We used tumor tissue, ctDNA, and lymphocytes for somatic or germline testing. We analyzed the clinical characteristics and survival outcomes. RESULTS: 144 patients were tested (113 somatic, 21 germline, and 10 both). Technical issues prevented the analysis of 23 prostatic samples (18.7%). 12 (8.3%) patients had HRD. BRCA2 was the most frequent mutation (66.7%). Patients with HRD were younger (57.5 years). Patients with BRCA mutations had poorer survival (31.9 vs 56.3 months, p = 0.048). CONCLUSION: In our institution, 8.3% of the patients had HRD. Tumor tissue analysis failed in 18.7% of tests. ctDNA analysis is an alternative detection method. BRCA mutations are correlated with poor prognosis.

Genome-Wide Identification, Characterization, and Comparative Analysis of NLR Resistance Genes in Coffea spp.

The largest family of disease resistance genes in plants are nucleotide-binding site leucine-rich repeat genes (NLRs). The products of these genes are responsible for recognizing avirulence proteins (Avr) of phytopathogens and triggering specific defense responses. Identifying NLRs in plant genomes with standard gene annotation software is challenging due to their multidomain nature, sequence diversity, and clustered genomic distribution. We present the results of a genome-wide scan and comparative analysis of NLR loci in three coffee species (Coffea canephora, Coffea eugenioides and their interspecific hybrid Coffea arabica). A total of 1311 non-redundant NLR loci were identified in C. arabica, 927 in C. canephora, and 1079 in C. eugenioides, of which 809, 562, and 695 are complete loci, respectively. The NLR-Annotator tool used in this study showed extremely high sensitivities and specificities (over 99%) and increased the detection of putative NLRs in the reference coffee genomes. The NLRs loci in coffee are distributed among all chromosomes and are organized mostly in clusters. The C. arabica genome presented a smaller number of NLR loci when compared to the sum of the parental genomes (C. canephora, and C. eugenioides). There are orthologous NLRs (orthogroups) shared between coffee, tomato, potato, and reference NLRs and those that are shared only among coffee species, which provides clues about the functionality and evolutionary history of these orthogroups. Phylogenetic analysis demonstrated orthologous NLRs shared between C. arabica and the parental genomes and those that were possibly lost. The NLR family members in coffee are subdivided into two main groups: TIR-NLR (TNL) and non-TNL. The non-TNLs seem to represent a repertoire of resistance genes that are important in coffee. These results will support functional studies and contribute to a more precise use of these genes for breeding disease-resistant coffee cultivars.

World Health Organization (WHO) antibiotic regimen against other regimens for the treatment of leprosy: a systematic review and meta-analysis.

BACKGROUND: To evaluate the effectiveness and safety of the World Health Organization antibiotic regimen for the treatment of paucibacillary (PB) and multibacillary (MB) leprosy compared to other available regimens. METHODS: We performed a search from 1982 to July 2018 without language restriction. We included randomized controlled trials, quasi-randomized trials, and comparative observational studies (cohorts and case-control studies) that enrolled patients of any age with PB or MB leprosy that were treated with any of the leprosy antibiotic regimens established by the WHO in 1982 and used any other antimicrobial regimen as a controller. Primary efficacy outcomes included: complete clinical cure, clinical improvement of the lesions, relapse rate, treatment failure. Data were pooled using a random effects model to estimate the treatment effects reported as relative risk (RR) with 95% confidence intervals (CI). RESULTS: We found 25 eligible studies, 11 evaluated patients with paucibacillary leprosy, while 13 evaluated patients with MB leprosy and 1 evaluated patients of both groups. Diverse regimen treatments and outcomes were studied. Complete cure at 6 months of multidrug therapy (MDT) in comparison to rifampin-ofloxacin-minocycline (ROM) found RR of 1.06 (95% CI 0.88-1.27) in five studies. Whereas six studies compare the same outcome at different follow up periods between 6 months and 5 years, according to the analysis ROM was not better than MDT (RR of 1.01 (95% CI 0.78-1.31)) in PB leprosy. CONCLUSION: Not better treatment than the implemented by the WHO was found. Diverse outcome and treatment regimens were studied, more statements to standardized the measurements of outcomes are needed.

Isolation and structural characterization of a non-diketopiperazine phytotoxin from a potato pathogenic Streptomyces strain.

Two Streptomyces spp. strains responsible for potato common scab infections in Uruguay which do not produce diketopiperazines were identified through whole-genome sequencing, and the virulence factor produced by one of them was isolated and characterized. Phylogenetic analysis showed that both pathogenic strains can be identified as S. niveiscabiei, and the structure of the phytotoxin was elucidated as that of the polyketide desmethylmensacarcin using MS and NMR methods. The metabolite is produced in yields of ∼200 mg/L of culture media, induces deep necrotic lesions on potato tubers, stuns root and shoot growth in radish seedlings, and is comparatively more aggressive than thaxtomin A. This is the first time that desmethylmensacarcin, a member of a class of compounds known for their antitumor and antibiotic activity, is associated with phytotoxicity. More importantly, it represents the discovery of a new virulence factor related to potato common scab, an economically-important disease affecting potato production worldwide.

The dream of health information for all.

In 2004, an influential report in The Lancet suggested that open health information for all could be achieved by 2015. Unfortunately, this goal has not yet been accomplished. Despite progress in obtaining quality scientific articles in Latin America, it remains difficult to reliably access new and cutting-edge research. As graduating Peruvian medical students, we have confronted many obstacles in obtaining access to quality and up-to-date information and a constant tension between accessing "what is available" rather than "what we need". As we have learned, these limitations affect not only our own education but also the choices we make in the management of our patients. In the following article, we state our point of view regarding limitations in access to scientific articles in Peru and Latin America.

Weaknesses in the reporting of cross-sectional studies according to the STROBE statement: the case of metabolic syndrome in adults from Peru / Las deficiencias en la presentación de los estudios transversales de acuerdo con la declaración STROBE: el caso del síndrome metabólico en adultos de Perú

Introduction: The inadequate reporting of cross-sectional studies, as in the case of the prevalence of metabolic syndrome, could cause problems in the synthesis of new evidence and lead to errors in the formulation of public policies. Objective: To evaluate the reporting quality of the articles regarding metabolic syndrome prevalence in Peruvian adults using the STROBE recommendations. Methods: We conducted a thorough literature search with the terms "Metabolic Syndrome", "Sindrome Metabolico" and "Peru" in MEDLINE/PubMed, LILACS, SciELO, LIPECS and BVS-Peru until December 2014. We selected those who were population-based observational studies with randomized sampling that reported prevalence of metabolic syndrome in adults aged 18 or more of both sexes. Information was analysed through the STROBE score per item and recommendation. Results: Seventeen articles were included in this study. All articles met the recommendations related to the report of the study's rationale, design, and provision of summary measures. The recommendations with the lowest scores were those related to the sensitivity analysis (8%, n= 1/17), participant flowchart (18%, n= 3/17), missing data analysis (24%, n= 4/17), and number of participants in each study phase (24%, n= 4/17). Conclusion: Cross-sectional studies regarding the prevalence of metabolic syndrome in peruvian adults have an inadequate reporting on the methods and results sections. We identified a clear need to improve the quality of such studies.

Introducción: El reporte inadecuado de estudios transversales, como en el caso de la prevalencia de síndrome metabólico, podría causar problemas en la síntesis de nueva evidencia y generar errores en la formulación de políticas públicas. Objetivo: Evaluar la calidad de reporte de estudios transversales sobre la prevalencia de síndrome metabólico en Perú utilizando las recomendaciones de STROBE. Métodos: Se realizó una búsqueda bibliográfica exhaustiva hasta Diciembre 2014 en MEDLINE/PubMed, LILACS, SciELO, LIPECS y BVS-Perú con los términos "Metabolic Syndrome", "Sindrome Metabolico" y "Peru". Se seleccionaron estudios observacionales con base poblacional, muestreo aleatorizado, que reportaran datos de prevalencia en adultos mayores de 18 años de ambos sexos. La información fue analizada a través de STROBE según puntuación por artículo y por recomendación. Resultados: Diecisiete artículos fueron incluidos en este estudio. Todos cumplieron con las recomendaciones relacionadas con el reporte de razones y fundamentos de la investigación, reporte del diseño de estudio y la proporción de medidas de resumen. Las recomendaciones con menor puntaje fueron las relacionadas a la descripción del análisis de sensibilidad (8%, n= 1/13), consideración del uso de diagrama de flujo para los participantes (18%, n= 3/17), explicación del análisis de datos ausentes (24%, n= 4/17) y del número de participantes en cada fase (24%, n= 4/17). Conclusión: Los estudios transversales sobre prevalencia de síndrome metabólico en adultos del Perú presentan un inadecuado reporte en las secciones de métodos y resultados. Se identifica una clara necesidad de mejorar la calidad de este tipo de estudios.

Weaknesses in the reporting of cross-sectional studies according to the STROBE statement: the case of metabolic syndrome in adults from Peru.

INTRODUCTION: The inadequate reporting of cross-sectional studies, as in the case of the prevalence of metabolic syndrome, could cause problems in the synthesis of new evidence and lead to errors in the formulation of public policies. OBJECTIVE: To evaluate the reporting quality of the articles regarding metabolic syndrome prevalence in Peruvian adults using the STROBE recommendations. METHODS: We conducted a thorough literature search with the terms "Metabolic Syndrome", "Sindrome Metabolico" and "Peru" in MEDLINE/PubMed, LILACS, SciELO, LIPECS and BVS-Peru until December 2014. We selected those who were population-based observational studies with randomized sampling that reported prevalence of metabolic syndrome in adults aged 18 or more of both sexes. Information was analysed through the STROBE score per item and recommendation. RESULTS: Seventeen articles were included in this study. All articles met the recommendations related to the report of the study's rationale, design, and provision of summary measures. The recommendations with the lowest scores were those related to the sensitivity analysis (8%, n= 1/17), participant flowchart (18%, n= 3/17), missing data analysis (24%, n= 4/17), and number of participants in each study phase (24%, n= 4/17). CONCLUSION: Cross-sectional studies regarding the prevalence of metabolic syndrome in peruvian adults have an inadequate reporting on the methods and results sections. We identified a clear need to improve the quality of such studies.

INTRODUCCIÓN: El reporte inadecuado de estudios transversales, como en el caso de la prevalencia de síndrome metabólico, podría causar problemas en la síntesis de nueva evidencia y generar errores en la formulación de políticas públicas. OBJETIVO: Evaluar la calidad de reporte de estudios transversales sobre la prevalencia de síndrome metabólico en Perú utilizando las recomendaciones de STROBE. MÉTODOS: Se realizó una búsqueda bibliográfica exhaustiva hasta Diciembre 2014 en MEDLINE/PubMed, LILACS, SciELO, LIPECS y BVS-Perú con los términos "Metabolic Syndrome", "Sindrome Metabolico" y "Peru". Se seleccionaron estudios observacionales con base poblacional, muestreo aleatorizado, que reportaran datos de prevalencia en adultos mayores de 18 años de ambos sexos. La información fue analizada a través de STROBE según puntuación por artículo y por recomendación. RESULTADOS: Diecisiete artículos fueron incluidos en este estudio. Todos cumplieron con las recomendaciones relacionadas con el reporte de razones y fundamentos de la investigación, reporte del diseño de estudio y la proporción de medidas de resumen. Las recomendaciones con menor puntaje fueron las relacionadas a la descripción del análisis de sensibilidad (8%, n= 1/13), consideración del uso de diagrama de flujo para los participantes (18%, n= 3/17), explicación del análisis de datos ausentes (24%, n= 4/17) y del número de participantes en cada fase (24%, n= 4/17). CONCLUSIÓN: Los estudios transversales sobre prevalencia de síndrome metabólico en adultos del Perú presentan un inadecuado reporte en las secciones de métodos y resultados. Se identifica una clara necesidad de mejorar la calidad de este tipo de estudios.

Determinación de factores de virulencia asociados a Escherichia Coli Enterohemorrágica en cepas peruanas aisladas entre 1999-2001 / Determination of virulence factors related to Escherichia Coli enterohemorragic Peruvian strain isolated between 1999-2001

En el presente estudio se intentó detectar la presencia del gen de toxina en cepas locales de Escherichia Coli serológicamente relacionados a la catergoria enterohemorrágica, caracterizando además un aislamiento reportado como serotipo 0157:H7 procedente de la ciudad de Tacna (cepa Tacna 410), mediante la reacción en cadena de la polimerasa (PCR) y secuenciamiento. Los resultados confirmaron la presencia del gen de la toxina shiga sólo en la cepa Tacna 410, obteniéndose una identidad del 100 por ciento entre la secuencia nucleótida del gen de la copa Tacna 410 y secuencias reportadas de la toxna shiga de tipo II en el Genebank. Asimismo, se detectó en la cepa Tacna 410 propiedades hemolíticas y el gen eae asociado al fenómeno de attaching and effacing, características de una típica cepa de ECEH.

We tried to detect the Shiga gene in local Escherichia Coli strains serologically related the enterohemorragic category. At the same time, using polymerase chain reaction (PCR) and sequencing, we characterized a strain confirmed as E. Coli 0157:H7 serotype, which was isolated in Tacna (a city in southern Peru) (Tacna 410 strain). Our results confirmed the presence of the Shiga toxin gene only in E. coli strain Tacna 410, and we found 100 percentage identify between the sequence from the amplified gene and reference sequence for type II Shiga toxin in the gene bank. We also detected in the Tacna 410 strain hemolytic properties and the eae gene, which is associated to attaching and effacing lesions, typical features of EHEC, strains.