Identification of a Rice stripe necrosis virus resistance locus and yield component QTLs using Oryza sativa x O. glaberrima introgression lines.

BACKGROUND: Developing new population types based on interspecific introgressions has been suggested by several authors to facilitate the discovery of novel allelic sources for traits of agronomic importance. Chromosome segment substitution lines from interspecific crosses represent a powerful and useful genetic resource for QTL detection and breeding programs. RESULTS: We built a set of 64 chromosome segment substitution lines carrying contiguous chromosomal segments of African rice Oryza glaberrima MG12 (acc. IRGC103544) in the genetic background of Oryza sativa ssp. tropical japonica (cv. Caiapó). Well-distributed simple-sequence repeats markers were used to characterize the introgression events. Average size of the substituted chromosomal segments in the substitution lines was about 10 cM and covered the whole donor genome, except for small regions on chromosome 2 and 4. Proportions of recurrent and donor genome in the substitution lines were 87.59% and 7.64%, respectively. The remaining 4.78% corresponded to heterozygotes and missing data. Strong segregation distortion was found on chromosomes 3 and 6, indicating the presence of interspecific sterility genes. To illustrate the advantages and the power of quantitative trait loci (QTL) detection using substitution lines, a QTL detection was performed for scored traits. Transgressive segregation was observed for several traits measured in the population. Fourteen QTLs for plant height, tiller number per plant, panicle length, sterility percentage, 1000-grain weight and grain yield were located on chromosomes 1, 3, 4, 6 and 9. Furthermore, a highly significant QTL controlling resistance to the Rice stripe necrosis virus was located between SSR markers RM202-RM26406 (44.5-44.8 cM) on chromosome 11. CONCLUSIONS: Development and phenotyping of CSSL libraries with entire genome coverage represents a useful strategy for QTL discovery. Mapping of the RSNV locus represents the first identification of a genetic factor underlying resistance to this virus. This population is a powerful breeding tool. It also helps in overcoming hybrid sterility barriers between species of rice.

Biotea-2-Bioschemas, facilitating structured markup for semantically annotated scholarly publications.

The total number of scholarly publications grows day by day, making it necessary to explore and use simple yet effective ways to expose their metadata. Schema.org supports adding structured metadata to web pages via markup, making it easier for data providers but also for search engines to provide the right search results. Bioschemas is based on the standards of schema.org, providing new types, properties and guidelines for metadata, i.e., providing metadata profiles tailored to the Life Sciences domain. Here we present our proposed contribution to Bioschemas (from the project "Biotea"), which supports metadata contributions for scholarly publications via profiles and web components. Biotea comprises a semantic model to represent publications together with annotated elements recognized from the scientific text; our Biotea model has been mapped to schema.org following Bioschemas standards.

A guideline for reporting experimental protocols in life sciences.

Experimental protocols are key when planning, performing and publishing research in many disciplines, especially in relation to the reporting of materials and methods. However, they vary in their content, structure and associated data elements. This article presents a guideline for describing key content for reporting experimental protocols in the domain of life sciences, together with the methodology followed in order to develop such guideline. As part of our work, we propose a checklist that contains 17 data elements that we consider fundamental to facilitate the execution of the protocol. These data elements are formally described in the SMART Protocols ontology. By providing guidance for the key content to be reported, we aim (1) to make it easier for authors to report experimental protocols with necessary and sufficient information that allow others to reproduce an experiment, (2) to promote consistency across laboratories by delivering an adaptable set of data elements, and (3) to make it easier for reviewers and editors to measure the quality of submitted manuscripts against an established criteria. Our checklist focuses on the content, what should be included. Rather than advocating a specific format for protocols in life sciences, the checklist includes a full description of the key data elements that facilitate the execution of the protocol.

Biotea: semantics for Pubmed Central.

A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through a computational query. One approach to facilitate reuse of the scientific literature is to structure this information as linked data using standardized web technologies. In this paper we present the second version of Biotea, a semantic, linked data version of the open-access subset of PubMed Central that has been enhanced with specialized annotation pipelines that uses existing infrastructure from the National Center for Biomedical Ontology. We expose our models, services, software and datasets. Our infrastructure enables manual and semi-automatic annotation, resulting data are represented as RDF-based linked data and can be readily queried using the SPARQL query language. We illustrate the utility of our system with several use cases. Our datasets, methods and techniques are available at http://biotea.github.io.

Prognostic predictive model for PONV in cesarean delivery

Introduction: Apfel simplified risk score for postoperative nausea and vomiting (PONV) has shown to be useful in anesthesia; however, since it has not been calibrated in regional anesthesia or in pregnant patients, its use in cesarean section is limited. Objective: To develop a prognostic predictive model for postoperative nausea and vomiting in pregnant patients undergoing cesarean section under spinal anesthesia. Methods: In a cohort of 703 term pregnant patients scheduled of cesarean section, 15 variables were prospectively assessed, to design a prognostic predictive model for the development of postoperative nausea and vomiting. A logistic regression analysis was used to construct the model and its calibration and discrimination were based on the Hosmer-Lemeshow test, the calibration curves, and C statistic. Additionally, the internal calibration was performed with the Bootstrap resampling method. Results: Postoperative nausea and vomiting were experienced by 27% of the patients during the first six hours after surgery. The model included as prognostic variables the development of intraoperative nausea and vomiting, age under 28 years, a history of PONV, the mother's BMI and the weight of the newborn baby. The model showed an adequate calibration (x2: 4.65 p: 0.5888), though a low discrimination (Statistic C = 0.68). Conclusions: A prognostic predictive model was created for the development of PONV in cesarean section. This model was used to build a prognostic scale for the classification of patients into risk groups.

Introducción: La escala de riesgo simplificada de Apfel para náuseas y vómito posoperatorio (NVPO) ha mostrado utilidad en anestesia; sin embargo, al no haber sido calibrada en anestesia regional o en pacientes embarazadas, su utilidad en cesárea es limitado. Objetivo: Desarrollar un modelo de predicción pronóstica para náuseas y vómito posoperatorios en pacientes embarazadas, llevadas a cesárea bajo anestesia espinal. Métodos: En una cohorte de 703 pacientes con embarazo a término programadas para cesárea, se evaluaron 15 variables de forma prospectiva para construir un modelo de predicción pronóstica para el desarrollo de náuseas y vómito posoperatorio. Se utilizó el análisis de regresión logística para la construcción del modelo y se calculó su calibración y discriminación con la prueba de Hosmer-Lemeshow, las curvas de calibración y el estadístico C. Además, se realizó la calibración interna con el método de remuestreo Bootstrap. Resultados: Las náuseas y vómito posoperatorio se presentaron en el 27% de las pacientes durante las primeras seis horas después de la cirugía. El modelo incluyó como variables pro-nósticas el desarrollo de náuseas y vómito en el intraoperatorio, edad menor de 28 años, antecedentes de NVPO, índice de masa corporal (IMC) de la madre y el peso del recién nacido. El modelo mostró una adecuada calibración (x2: 4,65 p: 0,5888), aunque una baja discriminación (Estadístico C = 0,68). Conclusiones: Se construyó un modelo de predicción pronóstica para el desarrollo de NVPO en cirugía cesárea, y con este se construyó una escala pronóstica que permite clasificar a las pacientes por grupos de riesgo.

Using semantics for representing experimental protocols.

BACKGROUND: An experimental protocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas, e.g. biology, genetics, immunology, neurosciences, virology. Protocols often include references to equipment, reagents, descriptions of critical steps, troubleshooting and tips, as well as any other information that researchers deem important for facilitating the reusability of the protocol. Although experimental protocols are central to reproducibility, the descriptions are often cursory. There is the need for a unified framework with respect to the syntactic structure and the semantics for representing experimental protocols. RESULTS: In this paper we present "SMART Protocols ontology", an ontology for representing experimental protocols. Our ontology represents the protocol as a workflow with domain specific knowledge embedded within a document. We also present the S ample I nstrument R eagent O bjective (SIRO) model, which represents the minimal common information shared across experimental protocols. SIRO was conceived in the same realm as the Patient Intervention Comparison Outcome (PICO) model that supports search, retrieval and classification purposes in evidence based medicine. We evaluate our approach against a set of competency questions modeled as SPARQL queries and processed against a set of published and unpublished protocols modeled with the SP Ontology and the SIRO model. Our approach makes it possible to answer queries such as Which protocols use tumor tissue as a sample. CONCLUSION: Improving reporting structures for experimental protocols requires collective efforts from authors, peer reviewers, editors and funding bodies. The SP Ontology is a contribution towards this goal. We build upon previous experiences and bringing together the view of researchers managing protocols in their laboratory work. Website: https://smartprotocols.github.io/ .

Diagnóstico de la atención psicoterapéutica a pacientes adictos ingresados en el Hospital Pediátrico Provincial de Camagüey / Diagnosis of psychotherapeutic care for addicted patients admitted to the Provincial Pediatric Hospital of Camagüey

RESUMEN En la actualidad las drogas están consideradas como un problema social. Los adolescentes constituyen uno de los grupos más vulnerables ante su consumo. El trabajo tuvo como objetivo diagnosticar las principales debilidades en el tratamiento del paciente ingresado por consumo de drogas en el Hospital Pediátrico de Camagüey. Se utilizó la metodología cuanticualitativa mediante métodos teóricos y empíricos. Se trabajó con un total de 30 empleados, 16 pacientes ingresados durante el período evaluado, así como con 16 familiares. La muestra total estuvo integrada por 62 personas. Los resultados obtenidos en el diagnóstico demostraron que existen limitaciones en la atención integral de los adolescentes ingresados por consumo de drogas. Los señalamientos más importantes se centraron en el logro del compromiso del paciente y en la necesidad de crear un protocolo de actuación con temas previamente definidos.

ABSTRACT Drugs are currently considered a social problem. Adolescents are one of the most vulnerable groups to their use. The objective of the work was to diagnose the main weaknesses in the treatment of the patient admitted for drug use at the Pediatric Hospital of Camagüey. The quantitative methodology was used through theoretical and empirical methods. We worked with a total of 30 employees, 16 patients admitted during the evaluated period, as well as 16 family members. The total sample consisted of 62 people. The results obtained in the diagnosis made showed that there are limitations in the comprehensive care of adolescents admitted for drug use. The most important signs found focused on achieving patient commitment and the need to create an action protocol with previously defined topics.