A Data Ingestion Procedure towards a Medical Images Repository.

This article presents an ingestion procedure towards an interoperable repository called ALPACS (Anonymized Local Picture Archiving and Communication System). ALPACS provides services to clinical and hospital users, who can access the repository data through an Artificial Intelligence (AI) application called PROXIMITY. This article shows the automated procedure for data ingestion from the medical imaging provider to the ALPACS repository. The data ingestion procedure was successfully applied by the data provider (Hospital Clínico de la Universidad de Chile, HCUCH) using a pseudo-anonymization algorithm at the source, thereby ensuring that the privacy of patients' sensitive data is respected. Data transfer was carried out using international communication standards for health systems, which allows for replication of the procedure by other institutions that provide medical images. OBJECTIVES: This article aims to create a repository of 33,000 medical CT images and 33,000 diagnostic reports with international standards (HL7 HAPI FHIR, DICOM, SNOMED). This goal requires devising a data ingestion procedure that can be replicated by other provider institutions, guaranteeing data privacy by implementing a pseudo-anonymization algorithm at the source, and generating labels from annotations via NLP. METHODOLOGY: Our approach involves hybrid on-premise/cloud deployment of PACS and FHIR services, including transfer services for anonymized data to populate the repository through a structured ingestion procedure. We used NLP over the diagnostic reports to generate annotations, which were then used to train ML algorithms for content-based similar exam recovery. OUTCOMES: We successfully implemented ALPACS and PROXIMITY 2.0, ingesting almost 19,000 thorax CT exams to date along with their corresponding reports.

GenoVi, an open-source automated circular genome visualizer for bacteria and archaea.

The increase in microbial sequenced genomes from pure cultures and metagenomic samples reflects the current attainability of whole-genome and shotgun sequencing methods. However, software for genome visualization still lacks automation, integration of different analyses, and customizable options for non-experienced users. In this study, we introduce GenoVi, a Python command-line tool able to create custom circular genome representations for the analysis and visualization of microbial genomes and sequence elements. It is designed to work with complete or draft genomes, featuring customizable options including 25 different built-in color palettes (including 5 color-blind safe palettes), text formatting options, and automatic scaling for complete genomes or sequence elements with more than one replicon/sequence. Using a Genbank format file as the input file or multiple files within a directory, GenoVi (i) visualizes genomic features from the GenBank annotation file, (ii) integrates a Cluster of Orthologs Group (COG) categories analysis using DeepNOG, (iii) automatically scales the visualization of each replicon of complete genomes or multiple sequence elements, (iv) and generates COG histograms, COG frequency heatmaps and output tables including general stats of each replicon or contig processed. GenoVi's potential was assessed by analyzing single and multiple genomes of Bacteria and Archaea. Paraburkholderia genomes were analyzed to obtain a fast classification of replicons in large multipartite genomes. GenoVi works as an easy-to-use command-line tool and provides customizable options to automatically generate genomic maps for scientific publications, educational resources, and outreach activities. GenoVi is freely available and can be downloaded from https://github.com/robotoD/GenoVi.

PromoterLCNN: A Light CNN-Based Promoter Prediction and Classification Model.

Promoter identification is a fundamental step in understanding bacterial gene regulation mechanisms. However, accurate and fast classification of bacterial promoters continues to be challenging. New methods based on deep convolutional networks have been applied to identify and classify bacterial promoters recognized by sigma (σ) factors and RNA polymerase subunits which increase affinity to specific DNA sequences to modulate transcription and respond to nutritional or environmental changes. This work presents a new multiclass promoter prediction model by using convolutional neural networks (CNNs), denoted as PromoterLCNN, which classifies Escherichia coli promoters into subclasses σ70, σ24, σ32, σ38, σ28, and σ54. We present a light, fast, and simple two-stage multiclass CNN architecture for promoter identification and classification. Training and testing were performed on a benchmark dataset, part of RegulonDB. Comparative performance of PromoterLCNN against other CNN-based classifiers using four parameters (Acc, Sn, Sp, MCC) resulted in similar or better performance than those that commonly use cascade architecture, reducing time by approximately 30-90% for training, prediction, and hyperparameter optimization without compromising classification quality.

Content-Based Medical Image Retrieval and Intelligent Interactive Visual Browser for Medical Education, Research and Care.

Medical imaging is essential nowadays throughout medical education, research, and care. Accordingly, international efforts have been made to set large-scale image repositories for these purposes. Yet, to date, browsing of large-scale medical image repositories has been troublesome, time-consuming, and generally limited by text search engines. A paradigm shift, by means of a query-by-example search engine, would alleviate these constraints and beneficially impact several practical demands throughout the medical field. The current project aims to address this gap in medical imaging consumption by developing a content-based image retrieval (CBIR) system, which combines two image processing architectures based on deep learning. Furthermore, a first-of-its-kind intelligent visual browser was designed that interactively displays a set of imaging examinations with similar visual content on a similarity map, making it possible to search for and efficiently navigate through a large-scale medical imaging repository, even if it has been set with incomplete and curated metadata. Users may, likewise, provide text keywords, in which case the system performs a content- and metadata-based search. The system was fashioned with an anonymizer service and designed to be fully interoperable according to international standards, to stimulate its integration within electronic healthcare systems and its adoption for medical education, research and care. Professionals of the healthcare sector, by means of a self-administered questionnaire, underscored that this CBIR system and intelligent interactive visual browser would be highly useful for these purposes. Further studies are warranted to complete a comprehensive assessment of the performance of the system through case description and protocolized evaluations by medical imaging specialists.

Características del proceso enseñanza aprendizaje vinculado al pensamiento crítico desde la mirada de docentes y estudiantes de enfermería / Characteristics of the Teaching-Learning Process Associated to Critical Thinking from the Perspective of Nursing Teachers and Students

Introducción: Enfermería incorpora en su formación de pregrado la competencia genérica y específica de pensamiento crítico y reflexivo, esencial para brindar cuidados holísticos. Objetivo: Describir características del proceso enseñanza aprendizaje vinculado a pensamiento crítico desde la mirada de docentes y estudiantes de la carrera de enfermería. Métodos: Estudio cualitativo descriptivo; realizado en la carrera de enfermería de la Universidad Católica del Norte; Chile, 2017. Las unidades de análisis se conformaron por 8 académicos y 12 estudiantes, seleccionados mediante muestreo por conveniencia, de acuerdo a objetivos, necesidades y alcance metodológico. Se utilizó la técnica de grupo focal. Se realizó análisis de contenido que dieron origen a matrices categoriales que emergen de los discursos. Resultados: El pensamiento crítico para académicos representa un proceso reflexivo complejo, importante para desarrollar habilidades integrales. Desde lo metodológico utilizan estrategias como: aprendizaje basado en problema, estudio de casos, simulaciones de baja y alta fidelidad, trabajo colaborativo, seminarios, clases interactivas, se enfatiza en la indagación; el proceso de evaluación se enmarca en lo oral y escrito, usando pautas y rúbricas. Conclusiones: La enseñanza de pensamiento crítico es compleja, proceso vital en la formación, los docentes y estudiantes construyen una percepción positiva del pensamiento crítico en el desarrollo del proceso enseñanza aprendizaje; emergen categorías: enseñanza del pensamiento crítico, entendida como progreso para favorecer el desarrollo de pensamiento reflexivo, metodologías, para favorecer el aprendizaje consciente de los estudiantes y evaluación del pensamiento crítico-reflexivo, entendido como mecanismos para profundizar logros de aprendizaje(AU)

Introduction: The Nursing major incorporates, in its undergraduate training program, the generic and specific competences of critical and reflective thinking, essential to providing holistic care. Objective: To describe the characteristics of the teaching-learning process associated to critical thinking from the perspective of teachers and students of the Nursing major. Methods: Descriptive and qualitative study carried out, in 2017, in the Nursing major of Universidad Católica del Norte, Chile. The analysis units were made up of eight scholars and twelve students, selected through convenience sampling, according to objectives, needs and methodological scope. The focus group technique was used. Content analysis was carried out, which gave rise to categorical matrices that emerge from the discourses. Results: Critical thinking for scholars represents a complex reflective process, important to developing comprehensive skills. From the methodological point of view, they use strategies such as problem-based learning, case studies, low and high fidelity simulations, collaborative work, seminars and interactive classes, while emphasis is placed on inquiry. The evaluation process is framed within oral and written activities, using guidelines and headings. Conclusions: The teaching of critical thinking is complex, a vital process in training. Teachers and students build a positive perception of critical thinking in the development of the teaching-learning process. Several categories emerge, such as teaching critical thinking, understood as progress to promote the development of reflective thinking; methodologies, to promote the conscious learning of students; and assessment of critical-reflective thinking, understood as mechanisms to deepen learning achievements(AU)

Experiencia de profesionales de enfermería que se desempeñan en un recinto penitenciario del norte de chile

RESUMEN Durante las últimas décadas se han producido numerosos avances en Enfermería, sin embargo, las experiencias de enfermeros que desempeñan su labor en recintos penitenciarios continúan siendo una realidad desconocida. Objetivo: Describir las experiencias profesionales de enfermeros/as que trabajan en un recinto penitenciario en el norte de Chile. Material y Método: Estudio cualitativo, exploratorio y descriptivo centrado en relatos de la experiencia profesional; participaron 6 enfermeras(os). El estudio, aprobado por un comité de ética acreditado, se realizó entre agosto y octubre de 2018, utilizando la entrevista semiestructurada. Se consideraron criterios de calidad y rigor científico. Resultados: El centro de salud penitenciario cuenta con una gran infraestructura y equipo multidisciplinario para brindar atención de salud a la población, donde su organización se realiza en base a la demanda existente, basada en un conjunto de reglamentos y normas que regulan el funcionamiento de la Institución. Se describe que las áreas de enfermería más desarrolladas son el quehacer asistencial y de gestión, en donde el rol de enfermería es fundamental al interior de los equipos de salud. Así mismo, los/as enfermeros/as describen este campo laboral como una gran oportunidad de aprendizaje y manifiestan sentir un grato clima laboral, pese al estrés propio del contexto. Conclusión: El recinto penitenciario brinda a los profesionales de enfermería un lugar versátil de trabajo, que a su vez permite desarrollar capacidades de liderazgo y autonomía, difíciles de encontrar en otros puestos laborales; los mismos profesionales lo consideran un campo laboral muy recomendado para futuros colegas que busquen nuevos desafíos.

ABSTRACT During the last decades there have been several advances in nursing, however the experiences of nurses who work in prisons are still an unknown reality. Objective: To describe the professional experiences of nurses who work in a prison in the north of Chile. Material and Method: Qualitative, descriptive and exploratory study focused on the accounts of professional experience of 6 nurses. The research was approved by an accredited ethics committee and was carried out between August and October 2018, using a semi-structured interview. Quality criteria and scientific rigor were considered. Results: The prison health center has a large infrastructure and a multidisciplinary team to provide health care to the inmates, where organization is based on existing demand, based on a set of regulations and norms that regulate the operation of the correctional institution. It is noted that the most developed areas of nursing are care and management, where the role of nursing is considered essential within the health teams. Additionally, nurses describe this work field as a great learning opportunity and express a positive working environment despite the stressful context. Conclusion: Working in a prison offers nurses a versatile workplace that also allows them to develop leadership and autonomy skills, which are difficult to find in other jobs. Many nursing professionals recommend this work field for future colleagues seeking new challenges.

RESUMO Nas últimas décadas ocorreram inúmeros avanços na Enfermagem, porém, as vivências dos enfermeiros que realizam seu trabalho em instalações penitenciárias continuam sendo uma realidade desconhecida. Objetivo: Descrever as experiências profissionais de enfermeiras/os que atuam em uma penitenciária no norte do Chile. Material e Método: Estudo qualitativo, exploratório e descritivo com foco em relatos de experiência profissional; participaram 6 enfermeiras/os. O estudo, aprovado por um comitê de ética credenciado, foi realizado entre agosto e outubro de 2018, por meio de entrevista semiestruturada. Critérios de qualidade e rigor científico foram considerados. Resultados: O centro de saúde penitenciário possui ampla infraestrutura e equipe multiprofissional para atendimento à saúde da população, onde sua organização é realizada com base na demanda existente, a partir de um conjunto de regulamentos e normas que estabelecem o funcionamento da Instituição. Descreve-se que as áreas mais desenvolvidas da enfermagem são o trabalho assistencial e gerencial, onde a atuação da enfermagem é fundamental dentro das equipes de saúde. Da mesma forma, as/os enfermeiras/ os descrevem este campo de trabalho como uma grande oportunidade de aprendizagem e afirmam que sentem um ambiente de trabalho agradável, apesar do estresse inerente ao contexto. Conclusão: O estabelecimento penitenciário proporciona aos profissionais de enfermagem um ambiente de trabalho versátil, que por sua vez lhes permite desenvolver habilidades de liderança e autonomia, difíceis de encontrar em outros empregos; os mesmos profissionais consideram-no um campo de trabalho altamente recomendado para futuros colegas que procuram novos desafios.