Unveiling potential virulence determinants in Vibrio isolates from Anadara tuberculosa through whole genome analyses.

The genus Vibrio includes pathogenic bacteria able to cause disease in humans and aquatic organisms, leading to disease outbreaks and significant economic losses in the fishery industry. Despite much work on Vibrio in several marine organisms, no specific studies have been conducted on Anadara tuberculosa. This is a commercially important bivalve species, known as "piangua hembra," along Colombia's Pacific coast. Therefore, this study aimed to identify and characterize the genomes of Vibrio isolates obtained from A. tuberculosa. Bacterial isolates were obtained from 14 A. tuberculosa specimens collected from two locations along the Colombian Pacific coast, of which 17 strains were identified as Vibrio: V. parahaemolyticus (n = 12), V. alginolyticus (n = 3), V. fluvialis (n = 1), and V. natriegens (n = 1). Whole genome sequence of these isolates was done using Oxford Nanopore Technologies (ONT). The analysis revealed the presence of genes conferring resistance to ß-lactams, tetracyclines, chloramphenicol, and macrolides, indicating potential resistance to these antimicrobial agents. Genes associated with virulence were also found, suggesting the potential pathogenicity of these Vibrio isolates, as well as genes for Type III Secretion Systems (T3SS) and Type VI Secretion Systems (T6SS), which play crucial roles in delivering virulence factors and in interbacterial competition. This study represents the first genomic analysis of bacteria within A. tuberculosa, shedding light on Vibrio genetic factors and contributing to a comprehensive understanding of the pathogenic potential of these Vibrio isolates.IMPORTANCEThis study presents the first comprehensive report on the whole genome analysis of Vibrio isolates obtained from Anadara tuberculosa, a bivalve species of great significance for social and economic matters on the Pacific coast of Colombia. Research findings have significant implications for the field, as they provide crucial information on the genetic factors and possible pathogenicity of Vibrio isolates associated with A. tuberculosa. The identification of antimicrobial resistance genes and virulence factors within these isolates emphasizes the potential risks they pose to both human and animal health. Furthermore, the presence of genes associated with Type III and Type VI Secretion Systems suggests their critical role in virulence and interbacterial competition. Understanding the genetic factors that contribute to Vibrio bacterial virulence and survival strategies within their ecological niche is of utmost importance for the effective prevention and management of diseases in aquaculture practices.

Selection signatures and population dynamics of transposable elements in lima bean.

The domestication process in lima bean (Phaseolus lunatus L.) involves two independent events, within the Mesoamerican and Andean gene pools. This makes lima bean an excellent model to understand convergent evolution. The mechanisms of adaptation followed by Mesoamerican and Andean landraces are largely unknown. Genes related to these adaptations can be selected by identification of selective sweeps within gene pools. Previous genetic analyses in lima bean have relied on Single Nucleotide Polymorphism (SNP) loci, and have ignored transposable elements (TEs). Here we show the analysis of whole-genome sequencing data from 61 lima bean accessions to characterize a genomic variation database including TEs and SNPs, to associate selective sweeps with variable TEs and to predict candidate domestication genes. A small percentage of genes under selection are shared among gene pools, suggesting that domestication followed different genetic avenues in both gene pools. About 75% of TEs are located close to genes, which shows their potential to affect gene functions. The genetic structure inferred from variable TEs is consistent with that obtained from SNP markers, suggesting that TE dynamics can be related to the demographic history of wild and domesticated lima bean and its adaptive processes, in particular selection processes during domestication.

Efficient homology-based annotation of transposable elements using minimizers.

Premise: Transposable elements (TEs) make up more than half of the genomes of complex plant species and can modulate the expression of neighboring genes, producing significant variability of agronomically relevant traits. The availability of long-read sequencing technologies allows the building of genome assemblies for plant species with large and complex genomes. Unfortunately, TE annotation currently represents a bottleneck in the annotation of genome assemblies. Methods and Results: We present a new functionality of the Next-Generation Sequencing Experience Platform (NGSEP) to perform efficient homology-based TE annotation. Sequences in a reference library are treated as long reads and mapped to an input genome assembly. A hierarchical annotation is then assigned by homology using the annotation of the reference library. We tested the performance of our algorithm on genome assemblies of different plant species, including Arabidopsis thaliana, Oryza sativa, Coffea humblotiana, and Triticum aestivum (bread wheat). Our algorithm outperforms traditional homology-based annotation tools in speed by a factor of three to >20, reducing the annotation time of the T. aestivum genome from months to hours, and recovering up to 80% of TEs annotated with RepeatMasker with a precision of up to 0.95. Conclusions: NGSEP allows rapid analysis of TEs, especially in very large and TE-rich plant genomes.

Communication transforms the impact of the COVID-19 pandemic on children with cancer and their families.

BACKGROUND: The COVID-19 pandemic altered healthcare systems globally, causing delays in care delivery and increased anxiety among patients and families. This study examined how hospital stakeholders and clinicians perceived the global impact of the COVID-19 pandemic on children with cancer and their families. METHODS: This secondary analysis examined data from a qualitative study consisting of 19 focus groups conducted in 8 languages throughout 16 countries. A codebook was developed with novel codes derived inductively from transcript review. In-depth analysis focused on the impact of the COVID-19 pandemic on children with cancer and their families. RESULTS: Eight themes describing the impact of the pandemic on patients and their families were identified and classified into three domains: contributing factors (COVID-19 Policies, Cancer Treatment Modifications, COVID-19 Symptoms, Beliefs), patient-related impacts (Quality of Care, Psychosocial impacts, Treatment Reluctance), and the central transformer (Communication). Participants described the ability of communication to transform the effect of contributing factors on patient-related impacts. The valence of impacts depended on the quality and quantity of communication among clinicians and between clinicians and patients and families. CONCLUSIONS: Communication served as the central factor impacting whether the COVID-19 pandemic positively or negatively affected children with cancer and families. These findings emphasize the key role communication plays in delivering patient-centered care and can guide future development of communication-centered interventions globally.

New algorithms for accurate and efficient de novo genome assembly from long DNA sequencing reads.

Building de novo genome assemblies for complex genomes is possible thanks to long-read DNA sequencing technologies. However, maximizing the quality of assemblies based on long reads is a challenging task that requires the development of specialized data analysis techniques. We present new algorithms for assembling long DNA sequencing reads from haploid and diploid organisms. The assembly algorithm builds an undirected graph with two vertices for each read based on minimizers selected by a hash function derived from the k-mer distribution. Statistics collected during the graph construction are used as features to build layout paths by selecting edges, ranked by a likelihood function. For diploid samples, we integrated a reimplementation of the ReFHap algorithm to perform molecular phasing. We ran the implemented algorithms on PacBio HiFi and Nanopore sequencing data taken from haploid and diploid samples of different species. Our algorithms showed competitive accuracy and computational efficiency, compared with other currently used software. We expect that this new development will be useful for researchers building genome assemblies for different species.

Utilizing Multilingual Methods and Rapid Analysis for Global Qualitative Research During a Pandemic.

Historically, qualitative research has complemented quantitative biologic and epidemiologic studies to provide a more complete understanding of pandemics. The COVID-19 pandemic has generated unique and novel challenges for qualitative researchers, who have embraced creative solutions including virtual focus groups and rapid analyses to continue their work. We present our experience conducting a multilingual global qualitative study of healthcare resilience among teams of pediatric oncology professionals during the COVID-19 pandemic. We provide an in-depth description of our methodology and an analysis of factors we believe contributed to our study's success including our use of technology, engagement of a large multilingual team, global partnerships, and framework-based rapid analysis. We hope these techniques may be useful to qualitative researchers conducting studies during the current pandemic, as well as for all pediatric oncology studies including multiple languages or geographically disparate subjects.

Robust and efficient software for reference-free genomic diversity analysis of genotyping-by-sequencing data on diploid and polyploid species.

Genotyping-by-sequencing (GBS) is a widely used and cost-effective technique for obtaining large numbers of genetic markers from populations by sequencing regions adjacent to restriction cut sites. Although a standard reference-based pipeline can be followed to analyse GBS reads, a reference genome is still not available for a large number of species. Hence, reference-free approaches are required to generate the genetic variability information that can be obtained from a GBS experiment. Unfortunately, available tools to perform de novo analysis of GBS reads face issues of usability, accuracy and performance. Furthermore, few available tools are suitable for analysing data sets from polyploid species. In this manuscript, we describe a novel algorithm to perform reference-free variant detection and genotyping from GBS reads. Nonexact searches on a dynamic hash table of consensus sequences allow for efficient read clustering and sorting. This algorithm was integrated in the Next Generation Sequencing Experience Platform (NGSEP) to integrate the state-of-the-art variant detector already implemented in this tool. We performed benchmark experiments with three different empirical data sets of plants and animals with different population structures and ploidies, and sequenced with different GBS protocols at different read depths. These experiments show that NGSEP has comparable and in some cases better accuracy and always better computational efficiency compared to existing solutions. We expect that this new development will be useful for many research groups conducting population genetic studies in a wide variety of species.

Resilient health care in global pediatric oncology during the COVID-19 pandemic.

BACKGROUND: In the face of unprecedented challenges because of coronavirus disease 2019, interdisciplinary pediatric oncology teams have developed strategies to continue providing high-quality cancer care. This study explored factors contributing to health care resilience as perceived by childhood cancer providers in all resource level settings. METHODS: This qualitative study consisted of 19 focus groups conducted in 16 countries in 8 languages. Seven factors have been previously defined as important for resilient health care including: 1) in situ practical experience, 2) system design, 3) exposure to diverse views on the patient's situation, 4) protocols and checklists, 5) teamwork, 6) workarounds, and 7) trade-offs. Rapid turn-around analysis focused on these factors. RESULTS: All factors of health care resilience were relevant to groups representing all resource settings. Focus group participants emphasized the importance of teamwork and a flexible and coordinated approach to care. Participants described collaboration within and among institutions, as well as partnerships with governmental, private, and nonprofit organizations. Hierarchies were advantageous to decision-making and information dissemination. Clinicians were inspired by their patients and explained creative trade-offs and workarounds used to maintain high-quality care. CONCLUSIONS: Factors previously described as contributing to resilient health care manifested differently in each institution but were described in all resource settings. These insights can guide pediatric oncology teams worldwide as they provide cancer care during the next phases of the pandemic. Understanding these elements of resilience will also help providers respond to inevitable future stressors on health care systems.

Errores en la preparación y administración de medicamentos: una revisión integradora de la Literatura Latinoamericana / Errors in the preparation and administration of medications: an integrative review of Latin American literature

Objetivo: Analizar, respecto su contenido, la producción científica de enfermeros latinoamericanos sobre error en la preparación y administración de medicamentos entre el año 2005 al 2011, en las bases de datos Centro Latinoamericano y del Caribe de Información en Ciencias de la Salud (LILACS) y Biblioteca Electrónica Científica (SciELO). Metodología: Consistió en una revisión integradora. La recolección fue realizada en el mes de Octubre de 2012 y de acuerdo a los criterios de inclusión, fueron seleccionados ocho artículos. Resultados: Los artículos fueron analizados en cuanto a los objetivos, trayectoria metodológica, principales resultados y propuestas de mejora. El análisis señala producción exclusiva de Brasil, estudios descriptivos, realizados en hospitales y con sugerencias generales como educación continua, notificación de los errores, implementación de una cultura de seguridad. Conclusiones: Considerando los aspectos enfatizados por la Organización Mundial de Salud (OMS) para alcanzar una atención más segura: buscar causas, proponer soluciones y evaluar impacto, se concluye que la producción necesita conocimiento que efectivamente mejore la práctica. Impulsar la investigación analítica con la mirada al sistema permitirá el desarrollo de propuestas efectivas y de acorde a la realidad (AU)

Objective: To analyze the contents the scientific production of Latin American nurses regarding on preparation and administration of medical drugs from 2005 to 2011 using Latin American and Caribbean Center Information the Health Sciences (LILACS) y Electronics Scientific Library (SciELO) databases. Methodology: The following research was an integrative review. Data collection was performed in the month of October 2012 and according to the inclusion criteria, were selected eight articles. Results: The articles were analyzed in terms of objectives, methodological path, main results and suggestions for improvement. The analysis indicates exclusive production of Brazil, descriptive studies, conducted in hospitals and general suggestions as continuing education, error reporting and implementation of a safety culture. Conclusions: Considering that aspects emphasized by the World Health Organization (OMS) to achieve safer care are: to find causes, to propose solutions and to evaluate the impact, it is concluded that production need of knowledge that effectively improve professional practice. Looking to the system, promoting researches with analytical studies will allow effective responses according to reality (AU)