Registros Hospitalares de Câncer: Proposta Metodológica para Correção do Estadiamento de Câncer de Pulmão / Hospital-Based Cancer Registry: Methodological Proposal for Correction of Lung Cancer Staging / Registros Hospitalarios de Cáncer: Propuesta Metodológica para la Corrección de la Estadificación del Cáncer de Pulmón

Introdução: Um grande desafio para a utilização de registros e bases de dados secundárias é a qualidade do registro e o percentual de perdas em variáveis estratégicas e necessárias à plena utilização do banco. Objetivo: Propor um método de correção para a variável de estadiamento no âmbito dos Registros Hospitalares de Câncer (RHC), a fim de aprimorar sua completude e qualidade. Método: Estudo descritivo, abrangendo as Unidades da Federação, utilizando-se como fonte de informação o RHC, de janeiro de 2013 a dezembro de 2019. O câncer de pulmão foi escolhido como caso para a correção do banco, em razão da sua alta taxa de mortalidade no Brasil e no mundo. As análises foram realizadas com o software de análises estatísticas SAS Studio e a base de dados organizada em Excel. Resultados: O total de casos registrados no RHC foi de 86.026, e a variável de interesse, o estadiamento, teve um total de 32,0% de perda. Ao final de todas as etapas de correção, a perda foi de 9,8%, correspondendo a 22,2% de recuperação. Conclusão: A metodologia proposta representa um avanço na correção do banco do RHC, possibilitando a utilização dos dados de base secundária, com melhor representatividade das diferentes Regiões do país, sobre o tratamento de câncer de pulmão, com possibilidade de expansão de seu uso para outras topografias

Introduction: A major challenge to utilize the registries and secondary databases is the quality of the data and the percentage of losses in strategic and necessary variables for better effectiveness of the database. Objective: To propose a correction method for the cancer staging variable of the HospitalBased Cancer Registry (HBCR), to improve its completeness and quality. Method: HBCR-based descriptive analysis covering Brazil's Federation Units from January 2013 to December 2019. Due to its high mortality in Brazil and worldwide, lung cancer was selected as case for database correction. The analyzes were performed with the software SAS Studio for statistical analyzes and the data were organized in Excel. Results: The total number of cases registered at the HBCR was 86,026, and 32% the variable of interest, staging, were missed. At the end of the correction process, the missed data reached 9.8%, corresponding to a recovery of 22.2%. Conclusion: The proposed methodology is an advance for the correction of the HBCR database on the treatment of lung cancer, allowing a more extensive use, with better representativeness of different country regions, and potential utilization in other topographies

Introducción: Un gran desafío para el uso de registros y bases de datos secundarias es la calidad del registro en sí, el porcentaje de pérdidas en variables estratégicas y necesarias para el pleno uso de la base de datos. Objetivo: Proponer un método de corrección de la variable estadificación en el ámbito de los Registros Hospitalarios de Cáncer (RHC), con el fin de mejorar su exhaustividad y calidad. Método: Análisis descriptivo, abarcando las Unidades de la Federación. Se utilizó el RHC como fuente de información, de enero de 2013 a diciembre de 2019. El cáncer de pulmón fue elegido como caso para la corrección de la base de datos, debido a su alta tasa de mortalidad en el Brasil y en el mundo. Los análisis se realizaron con el software de análisis estadístico SAS Studio y los datos se organizaron en Excel. Resultados: El total de casos registrados en el RHC fue de 86.026, y la variable de interés, la estadificación, tuvo una pérdida total del 32,0% Al final de todas las etapas esta fue de 9,8%, es decir el 22,2% de recuperación. Conclusión: La metodología propuesta representa un avance en la corrección del RHC, permitiendo una mejor utilización de la base de datos, con una mejor representatividad de las diferentes regiones del país, sobre el tratamiento del cáncer de pulmón, con la posibilidad de expandir su uso a otras topografías

Análise de modelos de triagem odontológica / Analysis of dental screening models / Análisis de modelos de cribado dental

Introdução: Diante da realidade virtual que se encontram os procedimentos burocráticos, observa-se a necessidade de se idealizar programas de triagem nas clínicas-escola com os objetivos de se encaminhar pacientes para a clínica mais compatível com as suas necessidades, e substituir os prontuários físicos pelos eletrônicos, numa alternativa ambientalmente correta.Objetivo: Avaliar a efetividade de um modelo de triagem informatizado, comparando-o ao modelo utilizado atualmente, no serviço de Serviço de Triagem e Documentação Odontológica do Departamento de Odontologia da Universidade Federal do Rio Grande do Norte. Metodologia: O estudo realizado foi do tipo descritivo, constituído de uma amostra de 50 pacientes, que foram submetidos ao modelo de triagem utilizado atualmente no Serviço de Triagem e Documentação Odontológica do Departamento de Odontologia da Universidade Federal do Rio Grande do Norte e a triagem com aplicação de um programa informatizado. Foi avaliada a efetividade do dispositivo e feita uma comparação entre os modelos. A análise estatística foi feita por meio do índice de correlação intra-classe, utilizando-se um banco de dados criado no software Statistical Package for Social Sciences, versão 20.0, adotando significância de 95% (p< 0,05).Resultados: Após análise estatística, com realização de correlação entre os resultados do software e o modelo atual de triagem, obteve-se coeficiente de correlação intra-classe de 0,578, com o nível de significância, para avaliação dos dados obtidos de (P<0,05), foi possível evidenciar que ocorreu correlação satisfatória positiva e significativa entre os resultados do software e o modelo atual de triagem.Conclusões:Os resultados denotam concordância entre os modelos de triagem estudados e demonstram que a utilização destes recursos apresenta resultados satisfatórios. Notadamente, evidenciando-se a vantagem da utilização do modelo de triagem informatizado (AU).

Introduction: In view of the virtual reality of bureaucratic procedures, it is necessary to devise screening programs in school clinics to refer patients to the clinic more compatible with their needs and replace physical with electronic records as an environmentally friendly alternative.Objective: To evaluate the effectiveness of a computerized screening model, comparing it to the model currently used in the Dental Documentation and Screening Service of the Dentistry Department of the Federal University of Rio Grande do Norte. Methodology: The descriptive study consisted of a sample of 50 patients who were submitted to the screening model currently used in the abovementioned service and the computerized screening model. The effectiveness of the device was evaluated and a comparison was made between the models. Statistical analysis was made using the intra-class correlation index and a database created in Statistical Package for Social Sciences version 20.0, adopting a significance of 95% (p < 0.05). Results: An intra-class correlation coefficient of 0.578 was obtained with the significance level of p < 0.05. There was a positive and significant satisfactory correlation between the software results and the current screening model.Conclusions: There was agreement between the studied models and the use of these resources yield satisfactory results. Therefore, the advantage of using the computerized screening model was confirmed (AU).

Introducción: Ante la realidad virtual de los trámites burocráticos, surge la necesidad de diseñar programas de cribado en las clínicas docentes con el objetivo de enviar a los pacientes a la clínica más compatible con sus necesidades, reemplazando los registros físicos y electrónicos en una alternativa ambientalmente correcta.Objetivo: Evaluar la efectividad de un modelo de cribado informatizado, comparándolo con el modelo utilizado actualmente en el Servicio de Cribado y Documentación Dental del Departamento de Odontología de la Universidad Federal de Rio Grande do Norte.Metodología: El estudio realizado fue de tipo descriptivo, constituido por una muestra de 50 pacientes que fueron sometidos al modelo de cribado actualmente utilizado en el dicho servicio y al cribado mediante programa informatizado. Se evaluó la efectividad del dispositivo y se realizó una comparación entre los modelos. El análisis estadístico se realizó mediante el índice de correlación intraclase, utilizando una base de datos creada en el software Statistical Package for Social Sciences, versión 20.0, adoptando un nivel de significación del 95% (p< 0,05).Resultados: Luego del análisis estadístico, con correlación entre los resultados del software y el modelo de cribadoactual, se obtuvo un coeficiente de correlación intraclase de 0.578, con nivel de significancia, para evaluación de los datos obtenidos de (P<0.05). Fue posible mostrar que hubo una correlación positiva y significativa satisfactoria entre los resultados del software y el modelo de cribado actual. Conclusiones: Los resultados muestran concordancia entre los modelos de cribado estudiados y demuestran que el uso de estos recursos presenta resultados satisfactorios. En particular, demostrando la ventaja de usar el modelo de cribado computarizado (AU).

Evaluación de los contenidos de los gestores de información y conocimiento en el Instituto Superior de Tecnologías y Ciencias Aplicadas-Universidad de la Habana / Contents assessment of information and knowledge managers at the Higher Institute of Applied Sciences and Technologies-University of Havana

Resumen Evaluar el funcionamiento de los gestores de información y conocimiento implementados en el Instituto Superior de Tecnologías y Ciencias Aplicadas (InSTEC) es el objetivo de la investigación. Ello, no solo posibilita el mejoramiento futuro del desempeño de estos, sino también sirve como estudio preliminar para la inserción de otros gestores en el futuro. Los métodos de análisis documental y evaluación heurística sustentan las bases teóricas, mientras que las herramientas automáticas Nibbler, GooglePageRank, SEOptimer, Website Grader, la entrevista y las encuestas a usuarios evidencian el desempeño de los gestores. Los resultados revelaron que la calidad del sitio externo y de la intranet obtuvo 69,4% de competencia global. Varios de los indicadores de estos sitios se deben perfeccionar en aras de brindar un mejor servicio a los usuarios del Instituto en la gestión de la información y el conocimiento, tan necesaria en las universidades.

Abstract The papers goal is to assess the already implemented information and knowledge managers at InSTEC. This allows improving the managers future work, and serves as a preliminary study for including others in the future. Documentary analysis and heuristics evaluation methods are the theoretical basis; meanwhile, automatic tools Nibbler, GooglePageRank, SEOptimer, Website Grader, interviews and polls to users evidenced the actual development of both sites. The studys outcomes revealed the quality of InSTECs external website and its intranet achieved 69,4 % of general competency. These sites indicators must be enhanced to provide a better service to users in the information and knowledge management so needed in universities.

A deep look into radiomics.

Radiomics is a process that allows the extraction and analysis of quantitative data from medical images. It is an evolving field of research with many potential applications in medical imaging. The purpose of this review is to offer a deep look into radiomics, from the basis, deeply discussed from a technical point of view, through the main applications, to the challenges that have to be addressed to translate this process in clinical practice. A detailed description of the main techniques used in the various steps of radiomics workflow, which includes image acquisition, reconstruction, pre-processing, segmentation, features extraction and analysis, is here proposed, as well as an overview of the main promising results achieved in various applications, focusing on the limitations and possible solutions for clinical implementation. Only an in-depth and comprehensive description of current methods and applications can suggest the potential power of radiomics in fostering precision medicine and thus the care of patients, especially in cancer detection, diagnosis, prognosis and treatment evaluation.

Propedia: a database for protein-peptide identification based on a hybrid clustering algorithm.

BACKGROUND: Protein-peptide interactions play a fundamental role in a wide variety of biological processes, such as cell signaling, regulatory networks, immune responses, and enzyme inhibition. Peptides are characterized by low toxicity and small interface areas; therefore, they are good targets for therapeutic strategies, rational drug planning and protein inhibition. Approximately 10% of the ethical pharmaceutical market is protein/peptide-based. Furthermore, it is estimated that 40% of protein interactions are mediated by peptides. Despite the fast increase in the volume of biological data, particularly on sequences and structures, there remains a lack of broad and comprehensive protein-peptide databases and tools that allow the retrieval, characterization and understanding of protein-peptide recognition and consequently support peptide design. RESULTS: We introduce Propedia, a comprehensive and up-to-date database with a web interface that permits clustering, searching and visualizing of protein-peptide complexes according to varied criteria. Propedia comprises over 19,000 high-resolution structures from the Protein Data Bank including structural and sequence information from protein-peptide complexes. The main advantage of Propedia over other peptide databases is that it allows a more comprehensive analysis of similarity and redundancy. It was constructed based on a hybrid clustering algorithm that compares and groups peptides by sequences, interface structures and binding sites. Propedia is available through a graphical, user-friendly and functional interface where users can retrieve, and analyze complexes and download each search data set. We performed case studies and verified that the utility of Propedia scores to rank promissing interacting peptides. In a study involving predicting peptides to inhibit SARS-CoV-2 main protease, we showed that Propedia scores related to similarity between different peptide complexes with SARS-CoV-2 main protease are in agreement with molecular dynamics free energy calculation. CONCLUSIONS: Propedia is a database and tool to support structure-based rational design of peptides for special purposes. Protein-peptide interactions can be useful to predict, classifying and scoring complexes or for designing new molecules as well. Propedia is up-to-date as a ready-to-use webserver with a friendly and resourceful interface and is available at: https://bioinfo.dcc.ufmg.br/propedia.

VirusCircBase: a database of virus circular RNAs.

Circular RNAs (circRNAs) are covalently closed long noncoding RNAs critical in diverse cellular activities and multiple human diseases. Several cancer-related viral circRNAs have been identified in double-stranded DNA viruses (dsDNA), yet no systematic study about the viral circRNAs has been reported. Herein, we have performed a systematic survey of 11 924 circRNAs from 23 viral species by computational prediction of viral circRNAs from viral-infection-related RNA sequencing data. Besides the dsDNA viruses, our study has also revealed lots of circRNAs in single-stranded RNA viruses and retro-transcribing viruses, such as the Zika virus, the Influenza A virus, the Zaire ebolavirus, and the Human immunodeficiency virus 1. Most viral circRNAs had reverse complementary sequences or repeated sequences at the flanking sequences of the back-splice sites. Most viral circRNAs only expressed in a specific cell line or tissue in a specific species. Functional enrichment analysis indicated that the viral circRNAs from dsDNA viruses were involved in KEGG pathways associated with cancer. All viral circRNAs presented in the current study were stored and organized in VirusCircBase, which is freely available at http://www.computationalbiology.cn/ViruscircBase/home.html and is the first virus circRNA database. VirusCircBase forms the fundamental atlas for the further exploration and investigation of viral circRNAs in the context of public health.

Applying graph database technology for analyzing perturbed co-expression networks in cancer.

Graph representations provide an elegant solution to capture and analyze complex molecular mechanisms in the cell. Co-expression networks are undirected graph representations of transcriptional co-behavior indicating (co-)regulations, functional modules or even physical interactions between the corresponding gene products. The growing avalanche of available RNA sequencing (RNAseq) data fuels the construction of such networks, which are usually stored in relational databases like most other biological data. Inferring linkage by recursive multiple-join statements, however, is computationally expensive and complex to design in relational databases. In contrast, graph databases store and represent complex interconnected data as nodes, edges and properties, making it fast and intuitive to query and analyze relationships. While graph-based database technologies are on their way from a fringe domain to going mainstream, there are only a few studies reporting their application to biological data. We used the graph database management system Neo4j to store and analyze co-expression networks derived from RNAseq data from The Cancer Genome Atlas. Comparing co-expression in tumors versus healthy tissues in six cancer types revealed significant perturbation tracing back to erroneous or rewired gene regulation. Applying centrality, community detection and pathfinding graph algorithms uncovered the destruction or creation of central nodes, modules and relationships in co-expression networks of tumors. Given the speed, accuracy and straightforwardness of managing these densely connected networks, we conclude that graph databases are ready for entering the arena of biological data.

Costos totales asociados a úlceras por presión y caídas en usuarios de los servicios clínicos de cirugía y medicina, en un establecimiento de alta complejidad, primer semestre del 2017 y primer semestre 2018, Chile / Total costs associated with pressure ulcers and falls in users of clinical surgery and medical services, in a highly complex establishment, first half of 2017 and first semester 2018, Chile

INTRODUCCIÓN: las actividades asistenciales relacionadas con la atención de pacientes en servicios clínicos tienen diferentes grados de riesgos para las personas que los reciben, el error en la atención sanitaria se denomina evento adverso y/o centinelas los que, según su gravedad, pueden llegar a causar la muerte de los usuarios. OBJETIVO: determinar los costos totales de úlceras por presión y caídas ocurridos en los usuarios de los servicios clínicos de cirugía y medicina en un establecimiento de alta complejidad durante el primer semestre del 2017 y primer semestre del 2018, en Chile. MÉTODO: estudio descriptivo retrospectivo. La ocurrencia de eventos relacionados a úlceras por presión y caídas son notificados a través del sistema informático Phoenix y son recepcionados por el Departamento de Calidad y Seguridad del Paciente del establecimiento, los datos económicos fueron proporcionados por el departamento de Finanzas. Los datos fueron procesados por programa computacional Excel. RESULTADOS: los costos totales asociado a úlceras por presión y caídas:Servicio de Cirugía, primer semestre del 2017:-Ulceras por presión $44.086.872 (U$ 57.557 dólares)-Caídas $39.630.517 (U$51.739 dólares)-Costo total $ 83.717.389 (U$109.297 dólares)Servicio de Medicina, primer semestre del 2017:-Úlceras por presión $22.654.894 (U$29.803 dólares)-Caídas $32.023.185 (U$41.807 dólares)-Costo total $ 54.678.079 (U$71.385 dólares)Servicio de Cirugía, primer semestre del 2018:-Ulceras por presión $76.979.440 (U$100.500 dólares)-Caídas $18.522.927 (U$24.182 dólares)-Costo total $ 95.502.367 (U$124.683 dólares)Servicio de Medicina, primer semestre del 2018:-Ulceras por presión $14.981.255 (U$19.558 dólares)-Caídas $55.258.625 (U$72.142 dólares)-Costo total $ 70.239.880 (U$91.701 dólares) CONCLUSIÓN: se logró levantar información actual sobre los recursos financieros y clínicos que determinan el impacto económico que generan los eventos adversos en los pacientes atendidos en un centro asistencial público. Es por esto, que el presente estudio, permitió cuantificar y evidenciar el impacto económico de dos eventos ocurridos en los servicios clínicos de un hospital de alta complejidad de Chile.

INTRODUCTION: healthcare activities related to the care of patients in clinical services, have different degrees of risks for the people who receive them, the error in health care is called an adverse event and / or sentinels which, depending on their severity, can arrive to cause the death of users. OBJECTIVE: to determine the total costs of pressure ulcers and falls that occurred in users of clinical services of surgery and medicine in a highly complex establishment during the first half of 2017 and the first half of 2018, in Chile. METHOD: retrospective descriptive study. The occurrence of events related to pressure ulcers and falls are notified through the Phoenix computer system and are received by the Department of Quality and Patient Safety of the establishment, the economic data were provided by the Department of Finance. The data were processed by Excel computer program. RESULTS: the total costs associated with pressure ulcers and falls:Surgery Service, first semester of 2017: -Pressure ulcers $ 44,086,872 (U$ 57,557)-Falls $ 39,630,517 (U$ 51,739) -Total cost$ 83,717,389 (U$ 109,297)Medicine Service, first semester of 2017: -Pressure ulcers $ 22,654,894 (U$29,803 dollars) -Falls $ 32,023,185 (U$41,807 dollars) -Total cost $ 54,678,079 (U$71,385 dollars)Surgery Service, first semester of 2018: -Pressure ulcers $ 76,979,440 (U$100,500 dollars) -Falls $ 18,522,927 (U$24,182 dollars) -Total cost $ 95,502,367 (U$124,683 dollars)Medicine Service, first semester of 2018: -Pressure ulcers $ 14,981,255 (U$19,558 dollars) -Falls $ 55,258,625 (U$72,142dollars) -Total cost $ 70,239,880 (U$91,701 dollars) CONCLUSIONS: it was possible to collect current information on financial and clinical resources that determine the economic impact generated by adverse events in patients treated in a public healthcare center. This is why the present study made it possible to quantify and demonstrate the economic impact of two events that occurred in the clinical services of a highly complex hospital in Chile.

Utility of digitising point of care HIV test results to accurately measure, and improve performance towards, the UNAIDS 90-90-90 targets.

INTRODUCTION: High rates of pre-treatment loss to care among persons diagnosed with HIV persist. Linkage to care can be improved through active digitally-based surveillance. Currently, record-keeping for HIV diagnoses in South Africa is paper-based. Aggregated testing data are reported routinely, and only discordant findings result in a specimen being tested at a laboratory and digitised. The Western Cape Province in South Africa has a Provincial Health Data Centre (PHDC) where person-level routine electronic data are consolidated in a single database, leveraging the existence of a unique patient identifier. To facilitate improved HIV surveillance, a pre-carbonated point-of-care test (PoCT) form was piloted, where one copy was routed to a central point and digitised for PHDC inclusion. METHODS: We evaluated the utility of the intervention using cross-sectional and retrospective cohort analyses, as well as comparisons with aggregate data. Data were linked to the Patient Master Index of the PHDC using unique identifiers. Prior evidences of HIV within the PHDC were used to differentiate newly diagnosed patients and those retesting, as well as linkage to care and treatment. RESULTS: From May 2017 to June 2018, 11337 digitised point-of-care HIV testing records were linked to the PHDC. Overall, 96% of records in the aggregate dataset were digitised, with 97% linked to the PHDC. Of those tested, 79% were female (median age 27 years). Linkage demonstrated that 51.3% (95% CI 48.4-54.1%) of patients testing HIV-positive were retesting. Of those newly diagnosed, 81% (95% CI 77.9-84.3%) were linked to HIV care and 25% (95% CI 21.6-28.7%) were initiated on antiretroviral therapy immediately. CONCLUSION: Digitisation of PoCT results provides individuated HIV testing data to assist in linkage to care and in differentiating newly diagnosed patients from positive patients retesting. Actionable and accurate data can improve the measurement of performance towards the UNAIDS 90-90-90 targets.

GREG-studying transcriptional regulation using integrative graph databases.

A gene regulatory process is the result of the concerted action of transcription factors, co-factors, regulatory non-coding RNAs (ncRNAs) and chromatin interactions. Therefore, the combination of protein-DNA, protein-protein, ncRNA-DNA, ncRNA-protein and DNA-DNA data in a single graph database offers new possibilities regarding generation of biological hypotheses. GREG (The Gene Regulation Graph Database) is an integrative database and web resource that allows the user to visualize and explore the network of all above-mentioned interactions for a query transcription factor, long non-coding RNA, genomic range or DNA annotation, as well as extracting node and interaction information, identifying connected nodes and performing advanced graphical queries directly on the regulatory network, in a simple and efficient way. In this article, we introduce GREG together with some application examples (including exploratory research of Nanog's regulatory landscape and the etiology of chronic obstructive pulmonary disease), which we use as a demonstration of the advantages of using graph databases in biomedical research. Database URL: https://mora-lab.github.io/projects/greg.html, www.moralab.science/GREG/.

Metabolic syndrome, metabolic components, and their relation to the risk of pancreatic cancer.

BACKGROUND: Components of the metabolic syndrome (MetS), such as elevated fasting glucose levels and abdominal obesity, have been suggested as potential risk factors for pancreatic cancer. However, data are still insufficient to assure the influence of MetS on incident pancreatic cancer. The objective of the current study was to investigate the association between MetS, metabolic components, and the risk of pancreatic cancer. METHODS: In the Korea National Health Information Database, 223,138 individuals who were without pancreatic cancer in 2009 were enrolled and followed until 2013. They were categorized into 4 groups according to the number of baseline metabolic components (0, 1, 2, 3, and 4-5). A multivariate Cox proportional hazard model was used to calculate the adjusted hazard ratios (HRs) and 95% CIs for incident pancreatic cancer according to the presence of MetS and the number of metabolic components. In addition, the risk of pancreatic cancer was evaluated in individuals who had a single metabolic component. RESULTS: The presence of MetS was significantly associated with incident pancreatic cancer (adjusted HR, 1.47; 95% CI, 1.19-1.81). The group with 4 or 5 baseline metabolic components had a higher risk of pancreatic cancer than the other groups (0 components: reference category; 1 component: adjusted HR, 0.94 [95% CI, 0.61-1.45]; 2 components: adjusted HR, 1.03 [95% CI, 0.68-1.56]; 3 components: adjusted HR, 1.35 [95% CI, 0.89-2.04]; 4-5 components: adjusted HR, 1.64 [95% CI, 1.06-2.51]). Regarding associations between the individual metabolic components and pancreatic cancer, no metabolic component alone had a statistically significant association with pancreatic cancer. CONCLUSIONS: MetS is a potential risk factor for pancreatic cancer. The presence of ≥4 metabolic components leads to a higher risk of pancreatic cancer even within categories of the MetS.

RBPTD: a database of cancer-related RNA-binding proteins in humans.

RNA-binding proteins (RBPs) play important roles in regulating the expression of genes involved in human physiological and pathological processes, especially in cancers. Many RBPs have been found to be dysregulated in cancers; however, there was no tool to incorporate high-throughput data from different dimensions to systematically identify cancer-related RBPs and to explore their causes of abnormality and their potential functions. Therefore, we developed a database named RBPTD to identify cancer-related RBPs in humans and systematically explore their functions and abnormalities by integrating different types of data, including gene expression profiles, prognosis data and DNA copy number variation (CNV), among 28 cancers. We found a total of 454 significantly differentially expressed RBPs, 1970 RBPs with significant prognostic value, and 53 dysregulated RBPs correlated with CNV abnormality. Functions of 26 cancer-related RBPs were explored by analysing high-throughput RNA sequencing data obtained by crosslinking immunoprecipitation, and the remaining RBP functions were predicted by calculating their correlation coefficient with other genes. Finally, we developed the RBPTD for users to explore functions and abnormalities of cancer-related RBPs to improve our understanding of their roles in tumorigenesis. Database URL: http: //www.rbptd.com.

A semantic database for integrated management of image and dosimetric data in low radiation dose research in medical imaging.

Medical ionizing radiation procedures and especially medical imaging are a non negligible source of exposure to patients. Whereas the biological effects of high absorbed doses are relatively well known, the effects of low absorbed doses are still debated. This work presents the development of a computer platform called Image and Radiation Dose BioBank (IRDBB) to manage research data produced in the context of the MEDIRAD project, a European project focusing on research on low doses in the context of medical procedures. More precisely, the paper describes a semantic database linking dosimetric data (such as absorbed doses to organs) to the images corresponding to X-rays exposure (such as CT images) or scintigraphic images (such as SPECT or PET images) that allow measuring the distribution of a radiopharmaceutical. The main contributions of this work are: 1) the implementation of the semantic database of the IRDBB system and 2) an ontology called OntoMEDIRAD covering the domain of discourse involved in MEDIRAD research data, especially many concepts from the DICOM standard modelled according to a realist approach.

GESgnExt: Gene Expression Signature Extraction and Meta-Analysis on Gene Expression Omnibus.

The gene expression omnibus (GEO) repository harbours an exponentially increasing number of gene expression studies. The expression data, as well as the related metadata, provides an abundant resource for knowledge discovery. Each study in GEO focuses on the gene expression perturbation of a specific subject (e.g., gene, drug, and disease). The identification of those subjects and the associations among them are beneficial for further in-depth studies. However, they cannot be directly inferred from the studies. A unified representation of those subjects (i.e., gene expression signatures) is desired. We developed GESgnExt for the automatic construction of gene expression signatures. The resultant 6542 signatures are built on 1934 series and 35 919 samples from GEO. To evaluate its significance, we calculated the similarities among those signatures and compared the discovered associations against the existing interaction databases. The signatures connect the genes, drugs, and diseases, covering most of the experimentally validated interactions. Besides, we have discovered 3307 novel signatures and their related associations, complementing the existing signature knowledge. The biomedical relevance of GESgnExt is demonstrated further in multiple case studies, providing mechanistic insights into its knowledge discovery process.

Application of Hereditary Renal Cell Carcinoma Risk Criteria to a Large Prospective Database.

AIMS: To evaluate the clinical impact of the Canadian criteria for identifying patients and families at risk for hereditary renal cell carcinoma (RCC). MATERIALS AND METHODS: The Canadian hereditary RCC risk criteria were applied to patients from 16 centres in the Canadian Kidney Cancer information system (CKCis) prospective database. The primary end point was the proportion of patients who met at least one criterion. RESULTS: Between January 2011 and May 2017, 8388 patients were entered in the database; 291 had inadequate risk data; 2827 (35%) met at least one criterion for genetic testing (at-risk population). Most (83%) met just one criterion. The criterion of non-clear cell histology contributed the largest proportion of at-risk patients (59%), followed by age ≤ 45 years (28%). Sixty-one patients had documentation of genetic testing, with 56 being classified at-risk (2% of at-risk). Twenty patients (35%) of the patients at risk and tested for hereditary RCC were found to harbour a germline mutation. CONCLUSIONS: Application of the Canadian hereditary RCC risk criteria to a large prospective database resulted in 35% of patients being identified at risk for hereditary RCC who could qualify for genetic testing. However, the true incidence of hereditary RCC in this population is unknown as most patients did not have documented genetic testing carried out and, thus, the sensitivity and specificity of the criteria cannot be determined. The low proportion of at-risk patients who underwent genetic testing is disappointing and highlights that there may be gaps in reporting, knowledge and/or barriers in access to genetic testing.

Bases de datos con ánimo de lucro y la mercantilización de las publicaciones científicas. Colombia, una vía de entrada / Data bases for profit and the commercialization of scientific publications. colombia, a reference case

RESUMEN En el marco del presente ensayo, esta discusión tiene como propósito poner en evidencia el embargo que ha venido sufriendo las producciones académica y la científica, en el ámbito de las publicaciones escritas, por parte de bases de datos propiedad de consorcios comerciales transnacionales, cuya misión corporativa ha estado orientada fundamentalmente al lucro. En este proceso de embargo, quienes investigan han perdido el dominio y la soberanía sobre su producción intelectual. La investigación se ha visto reducida a criterios de gestión, y la comunicación del conocimiento ha quedado restringida por las transacciones monetarias y la mercadotecnia empresarial.

ABSTRACT Within the framework of this essay, the purpose of this discussion is to highlight the embargo that academic and scientific productions have been suffering, in the field of written publications, by databases owned by transnational commercial consortia, whose corporate mission has been fundamentally oriented to profit. In this embargo process, researchers have lost control and sovereignty over their intellectual production. Research has been reduced to management criteria, and the communication of knowledge has been restricted by monetary transactions and corporate marketing.

Accuracy of an administrative database for pancreatic cancer by international classification of disease 10th codes: A retrospective large-cohort study.

BACKGROUND: Korean National Health Insurance (NHI) claims database provides large-cohort. However, studies regarding accuracy of administrative database for pancreatic cancer (PC) have not been reported. We aimed to identify accuracy of NHI database regarding PC classified by international classification of disease (ICD)-10 codes. AIM: To identify the accuracy and usefulness of administrative database in PC and the accurate ICD codes for PC with location. METHODS: Study and control groups were collected from 2003 to 2016 at Seoul National University Bundang Hospital. Cases of PC were identified in NHI database by international classification of diseases, 10th revision edition (ICD-10 codes) supported with V codes. V code is issued by medical doctors for covering 95% of medical cost by Korean government. According to pathologic reports, definite or possible diagnoses were defined using medical records, images, and pathology. RESULTS: A total of 1846 cases with PC and controls were collected. Among PC, only 410 (22.2%) cases were identified as specific cancer sites including head in 234 (12.7%) cases, tail in 104 (5.6%) cases and body in 72 (3.9%) cases. Among PC, 910 (49.3%) cases were diagnosed by definite criteria. Most of these were adenocarcinoma (98.0%). The rates of definite diagnosis of PC were highest in head (70.1%) followed by body (47.2%) and tail (43.3%). False-positive cases were pancreatic cystic neoplasm and metastasis to the pancreas. In terms of the overall diagnosis of PC, sensitivity, specificity, positive predictive value, and negative predictive value were 99.95%, 98.72%, 98.70%, and 99.95%, respectively. Diagnostic accuracy was similar both in terms of diagnostic criteria and tumor locations. CONCLUSION: Korean NHI claims database collected according to ICD-10 code with V code for PC showed good accuracy.