De Novo Design of Inhibitors of DNA Methyltransferase 1: A Critical Comparison of Ligand- and Structure-Based Approaches.

Designing and developing inhibitors against the epigenetic target DNA methyltransferase (DNMT) is an attractive strategy in epigenetic drug discovery. DNMT1 is one of the epigenetic enzymes with significant clinical relevance. Structure-based de novo design is a drug discovery strategy that was used in combination with similarity searching to identify a novel DNMT inhibitor with a novel chemical scaffold and warrants further exploration. This study aimed to continue exploring the potential of de novo design to build epigenetic-focused libraries targeted toward DNMT1. Herein, we report the results of an in-depth and critical comparison of ligand- and structure-based de novo design of screening libraries focused on DNMT1. The newly designed chemical libraries focused on DNMT1 are freely available on GitHub.

Pooled Cohort Profile: ReCoDID Consortium's Harmonized Acute Febrile Illness Arbovirus Meta-Cohort.

Infectious disease (ID) cohorts are key to advancing public health surveillance, public policies, and pandemic responses. Unfortunately, ID cohorts often lack funding to store and share clinical-epidemiological (CE) data and high-dimensional laboratory (HDL) data long term, which is evident when the link between these data elements is not kept up to date. This becomes particularly apparent when smaller cohorts fail to successfully address the initial scientific objectives due to limited case numbers, which also limits the potential to pool these studies to monitor long-term cross-disease interactions within and across populations. CE data from 9 arbovirus (arthropod-borne viruses) cohorts in Latin America were retrospectively harmonized using the Maelstrom Research methodology and standardized to Clinical Data Interchange Standards Consortium (CDISC). We created a harmonized and standardized meta-cohort that contains CE and HDL data from 9 arbovirus studies from Latin America. To facilitate advancements in cross-population inference and reuse of cohort data, the Reconciliation of Cohort Data for Infectious Diseases (ReCoDID) Consortium harmonized and standardized CE and HDL from 9 arbovirus cohorts into 1 meta-cohort. Interested parties will be able to access data dictionaries that include information on variables across the data sets via Bio Studies. After consultation with each cohort, linked harmonized and curated human cohort data (CE and HDL) will be made accessible through the European Genome-phenome Archive platform to data users after their requests are evaluated by the ReCoDID Data Access Committee. This meta-cohort can facilitate various joint research projects (eg, on immunological interactions between sequential flavivirus infections and for the evaluation of potential biomarkers for severe arboviral disease).

BIOMX-DB: A web application for the BIOFACQUIM natural product database.

Natural product databases are an integral part of chemoinformatics and computer-aided drug design. Despite their pivotal role, a distinct scarcity of projects in Latin America, particularly in Mexico, provides accessible tools of this nature. Herein, we introduce BIOMX-DB, an open and freely accessible web-based database designed to address this gap. BIOMX-DB enhances the features of the existing Mexican natural product database, BIOFACQUIM, by incorporating advanced search, filtering, and download capabilities. The user-friendly interface of BIOMX-DB aims to provide an intuitive experience for researchers. For seamless access, BIOMX-DB is freely available at www.biomx-db.com.

State of open science in cancer research.

PURPOSE: This study has been focused on assessing the Open Science scenario of cancer research during the period 2011-2021, in terms of the derived scientific publications and raw data dissemination. METHODS: A cancer search equation was executed in the Science Citation Index-Expanded, collecting the papers signed by at least one Spanish institution. The same search strategy was performed in the Data Citation Index to describe dataset diffusion. RESULTS: 50,822 papers were recovered, 71% of which belong to first and second quartile journals. 59% of the articles were published in Open Access (OA) journals. The Open Access model and international collaboration positively conditioned the number of citations received. Among the most productive journals stood out Plos One, Cancers, and Clinical and Translational Oncology. 2693 genomics, proteomics and metabolomics datasets were retrieved, being Gene Expression Omnibus the favoured repository. CONCLUSIONS: There has been an increase in oncology publications in Open Access. Most were published in first quartile journals and received higher citations than non-Open Access articles, as well as when oncological investigation was performed between international research teams, being relevant in the context of Open Science. Genetic repositories have been the preferred for sharing oncology datasets. Further investigation of research and data sharing in oncology is needed, supported by stronger Open Science policies, to achieve better data sharing practices among three scientific main pillars: researchers, publishers, and scientific organizations.

Evidence for the druggability of aldosterone targets in heart failure: A bioinformatics and data science-driven decision-making approach.

BACKGROUND: Aldosterone plays a key role in the neurohormonal drive of heart failure. Systematic prioritization of drug targets using bioinformatics and database-driven decision-making can provide a competitive advantage in therapeutic R&D. This study investigated the evidence on the druggability of these aldosterone targets in heart failure. METHODS: The target disease predictability of mineralocorticoid receptors (MR) and aldosterone synthase (AS) in cardiac failure was evaluated using Open Targets target-disease association scores. The Open Targets database collections were downloaded to MongoDB and queried according to the desired aggregation level, and the results were retrieved from the Europe PMC (data type: text mining), ChEMBL (data type: drugs), Open Targets Genetics Portal (data type: genetic associations), and IMPC (data type: genetic associations) databases. The target tractability of MR and AS in the cardiovascular system was investigated by computing activity scores in a curated ChEMBL database using supervised machine learning. RESULTS: The medians of the association scores of the MR and AS groups were similar, indicating a comparable predictability of the target disease. The median of the MR activity scores group was significantly lower than that of AS, indicating that AS has higher target tractability than MR [Hodges-Lehmann difference 0.62 (95%CI 0.53-0.70, p < 0.0001]. The cumulative distributions of the overall multiplatform association scores of cardiac diseases with MR were considerably higher than with AS, indicating more advanced investigations on a wider range of disorders evaluated for MR (Kolmogorov-Smirnov D = 0.36, p = 0.0009). In curated ChEMBL, MR had a higher cumulative distribution of activity scores in experimental cardiovascular assays than AS (Kolmogorov-Smirnov D = 0.23, p < 0.0001). Documented clinical trials for MR in heart failures surfaced in database searches, none for AS. CONCLUSIONS: Although its clinical development has lagged behind that of MR, our findings indicate that AS is a promising therapeutic target for the treatment of cardiac failure. The multiplatform-integrated identification used in this study allowed us to comprehensively explore the available scientific evidence on MR and AS for heart failure therapy.

The Gray Zone Between Legitimate and Predatory Open Access Scientific Publishing

ABSTRACT Certain open access publishers based on the article processing charges model have found it highly profitable to operate within a gray zone that encompasses both legitimate and predatory publishing practices. In this context, maximum profits can be obtained by adequate combinations of journal acceptance rates and elevated article processing charges. Considering that the gray zone can be particularly challenging to identify and that it poses risks for authors aiming to establish academic carreers, we believe it is important to provide a comprehensive description of it.

The gray zone between legitimate and predatory open access scientific publishing.

Certain open access publishers based on the article processing charges model have found it highly profitable to operate within a gray zone that encompasses both legitimate and predatory publishing practices. In this context, maximum profits can be obtained by adequate combinations of journal acceptance rates and elevated article processing charges. Considering that the gray zone can be particularly challenging to identify and that it poses risks for authors aiming to establish academic carreers, we believe it is important to provide a comprehensive description of it.

[Revista Médica del IMSS: Institutional heritage and Important reference]. / Revista Médica del IMSS: patrimonio institucional e importante referente formativo.

In a context that has tended towards globalization, in which obtaining economic resources is usually the driving force of societies, information resources have frequently been treated as private goods for which one must pay. A strategy for the above has been open and free access to information, a factor of great importance for the construction of more open media.

En un contexto que ha tendido a lo globalizado, en el que la obtención de recursos económicos suele ser el motor de las sociedades, los recursos de información han sido tratados con frecuencia como bienes privados por los que hay que pagar. Una estrategia a lo anterior ha sido el acceso abierto y gratuito a la información, un factor de gran importancia para la construcción de medios más abiertos.

[Who reads the Revista Médica del IMSS? Altmetrics answer it]. / ¿Quién lee la Revista Médica del IMSS? Las métricas alternativas responden.

The Revisa Médica del IMSS is considered a track of national and international scientific dissemination that presents the results of clinical research carried out within the Institute. Altmetrics, or alternative metrics, emerged as an alternative to citation-based metrics and allow authors to visualize the impact of their works that have not received citations to identify the characteristics of the readers who consult their published article. It is important that scientific journals have accurate information from their readers, as it will provide them with an overview of the use of the information produced in their area of expertise or in their institution. This editorial explores the characteristics of the readers of the Revista Médica del IMSS through the analysis of alternative metrics available in the Dimensions database.

La Revista Médica del IMSS es considerada como un medio de divulgación científica nacional e internacional que presenta los resultados de la investigación clínica realizada dentro del Instituto. Las Altmetrics, o métricas alternativas, surgieron como una alternativa a las métricas basadas en citación y permiten a los autores visibilizar el impacto de sus trabajos que no han recibido citas para identificar las características de los lectores que consultan su artículo publicado. Es importante que las revistas científicas cuenten con información precisa de sus lectores, pues les brindará un panorama sobre el uso de la información que se produce en su área de especialidad o en su institución. En este editorial se exploran las características de los lectores de la Revista Médica del IMSS a través del análisis de las métricas alternativas disponibles en la base de datos Dimensions.

Revistas depredadoras y secuestradas en cirugía. Qué se debe saber sobre ellas y cómo evitarlas

Las revistas depredadoras (RD), constituyen una gran amenaza para la publicación contemporánea, ya que ofrecen una publicación rápida de acceso abierto a cambio de tarifas sin procedimientos de revisión por pares para científicos jóvenes o inexpertos. Son compañías que priorizan el interés propio a expensas de la academia, caracterizándose por entregar información falsa o engañosa, distorsión de las mejores prácticas editoriales y de publicación, falta de transparencia y uso de tácticas de solicitud de manuscritos indiscriminadas y agresivas. El objetivo de este manuscrito fue generar un documento de estudio sobre las RD y secuestradas; así como de las conferencias depredadoras en cirugía.

Predatory journals (PD) are a major threat to contemporary publishing, as they offer rapid open access publication for fees without peer review procedures for young or inexperienced scientists. Are companies that prioritize self-interest at the expense of academia, characterized by providing false or misleading information, misrepresentation of publishing and editorial best practices, lack of transparency, and use of indiscriminate and aggressive manuscript solicitation tactics. The aim of this manuscript was to generate a study document regarding the PD, hijacked journals and predatory conferences in surgery.

Bibliometric indicators in Physical Education research: Brazil in comparison / Indicadores bibliométricos na pesquisa em Educação Física: o Brasil em comparação / Indicadores bibliométricos en la investigación en Educación Física: Brasil en comparación

ABSTRACT Scopus and Web of Science were used to evaluate papers on Physical Education worldwide and in Brazil. Most documents are published in the USA and England, Brazil being the 6th largest. Brazilians tend to publish in Brazil. Countries with a higher % of documents in Q1 journals have higher % of top 10% cited documents. Most countries increase their Top 10% score when publishing in open access, while Brazil decreases. Differentiation between country clusters is due to % documents in Q1 journals, international collaboration, Open Access, citations/paper and documents in Top 10%. Brazil researches similar topics to those worldwide. Publishing in Q1 journals, and more industry and international collaboration can increase the impact of publications by Brazilian authors.

RESUMO Scopus e Web of Science foram usados ​​para avaliar artigos sobre Educação Física no mundo e no Brasil. A maioria dos documentos é publicada nos EUA e na Inglaterra, sendo o Brasil o 6º maior. Brasileiros tendem a publicar no Brasil. Os países com maior % de documentos em periódicos do 1º quartil têm maior % dos citados. A maioria dos países aumenta seu impacto publicando em acesso aberto, enquanto o Brasil diminui. A diferença entre países deve-se à % de documentos em periódicos do 1º quartil, colaboração internacional, acesso aberto, citações/artigos e documentos no Top 10%. O Brasil pesquisa temas semelhantes aos do mundo. A publicação em periódicos do 1º quartil, mais colaboração industrial e internacional podem aumentar o impacto das publicações de autores brasileiros.

RESUMEN Scopus y Web of Science se utilizaron para evaluar artículos sobre Educación Física en el mundo y Brasil. La mayoría de los documentos se publican en EEUU e Inglaterra, siendo Brasil el sexto más grande. Los brasileños tienden a publicar en Brasil. Los países con un % más alto de documentos en revistas Q1 tienen un % más alto citados en el 10% superior, y publican en acceso abierto, mientras que Brasil disminuye. La diferenciación entre países se debe a % de documentos en revistas Q1, colaboración internacional, acceso abierto, citas/artículo y documentos en el 10% superior. Brasil investiga temas similares a los del mundo. La publicación en revistas Q1, una mayor colaboración internacional y de la industria pueden aumentar el impacto de las publicaciones de autores brasileños.

Publicações científicas ampliadas uma revisão integrativa / Extended scientific publications: an integrative review / Publicaciones científicas extendidas: una revisión integradora

Objetivo: investigar o estado da arte das publicações científicas ampliadas voltadas para a dinamização da ciência. Método: pesquisa qualitativa de cunho integrativo nas seguintes bases de dados Web of Science, Library, Information Science and Technology Abstracts e Scopus via Portal Periódicos Capes, Dimensions, PLOS ONE, Base de Dados Referencial de Artigos de Periódicos em Ciência da Informação e Scientific Eletronic Library Online no período de junho de 2022. Resultados: onze artigos divididos em duas categorias: caracterização das publicações ampliadas e infraestrutura de suporte para as publicações ampliadas. Conclusão: apesar de multivariadas, as publicações ampliadas possuem características peculiares que as tornam objetos digitais compostos e dinâmicos e com melhor experiência para o usuário. Os artigos apontam que não há infraestrutura de suporte nas plataformas de periódicos e quando encontrado, se apresenta simples e com poucos recursos.

Objectives: to investigate the state of the art of expanded scientific publications aimed at boosting science. Method: qualitative research of an integrative nature in the following databases: Web of Science, Library, Information Science and Technology Abstracts and Scopus via Portal Periodicals Capes, Dimensions, PLOS ONE, Reference Database of Journal Articles in Science of Information and Scientific Electronic Library Online in the period of June 2022. Results: eleven articles divided into two categories: characterization of expanded publications and support infrastructure for expanded publications. Conclusion: Despite being multivariate, expanded publications have peculiar characteristics that make them composite and dynamic digital objects with a better user experience. The articles point out that there is no support infrastructure on journal platforms and when found, it is simple and with few resources.

Objetivos:investigar el estado del arte de las publicaciones científicas ampliadas destinadas al impulso de la ciência. Método: investigación cualitativa de carácter integrador em las siguients bases de datos: Web of Science, Library, Information Science and Technology Abstracts y Scopus vía Portal Periodicals Capes, Dimensions, PLOS ONE, Reference Database of Journal Articles in Science of Information y Scientific Electronic Library Online en el período de junio de 2022. Resultados:once artículos divididos em dos ctegorías: caracterización de publicaciones expandidas e infraestructura de soporte para publicaciones expandidas. Conclusión: a pesar de ser multivariadas, las publicaciones expandidas tienen características peculiares que las convierten em objetos digitales compuestos y dinâmicos com uma mejor ecperiencia de usuário. Los artículos señalan que no existe uma infraestructura de apovo em las plataformas de revistas y cuando se encuentra es sencilla y com pocos recursos.

Homenaje a la Revista Médica de Chile en sus 150 años de vida (1872-2022) / A tribute to Revista Médica de Chile on its 150th Anniversary (1872-2022)

Revista Médica de Chile was founded in 1872 by Sociedad Médica de Santiago (currently Chilean Society of Internal Medicine) and it is one out of twenty five medical journals founded during the XIX Century that still remain active. In monthly issues it presents clinical and biomedical research articles, as well as research and position papers dealing with medical education, public health or medical ethics. Special attention receive the impact on health care given by the emergence of new private medical schools in Chile, the relevance of methodologies to assess clinical competences in graduates, the certification of specialty programs and specialists, the appropiate use of simulators in clinical training, telemedicine, organ transplants, and current issues in medical ethics, such as abortions and euthanasia. Institutional and international collaboration in medical research is clearly reflected in recent years. Articles are subjected to external peer review and ICMJE Recommendations are carefully considered throughout the review process. Most articles are published in Spanish but English abstracts are mandatory and a growing number of articles are currently published in English. An Open Access electronic version is published by SciELO. Revista Médica de Chile is indexed in the most important international data bases and it is a member of the ICMJE ruling committee. The long life and prestige of this journal can be considered a testimony of the cultural heritage and progress in Chilean medicine.

De la tecnocracia a la equidad y la sustentabilidad: por otra ciencia abierta / Da tecnocracia à equidade e à sustentabilidade: por uma outra ciência aberta / From technocracy to equity and sustainability: for another open science

Fue por medio de los estudios sobre softwares de periódicos científicos que Juan Pablo Alperin comenzó a desarrollar investigaciones sobre la comunicación científica, principalmente en relación a la temática de acceso abierto y su cuestión más amplia que envuelve la ciencia abierta. En entrevista con la Reciis, el profesor e investigador argumenta que es preciso pensar en cómo abrir el acceso al conocimiento y no apenas garantirlo. En ese sentido, la reflexión sobre cómo hacer ciencia abierta promueve discusiones para tornar el sistema de investigación científica con más equidad y más colaborativo. El profesor comenta sobre los efectos positivos y los desafíos que la pandemia de covid-19 promueve en relación a la comunicación científica. Alperin destaca iniciativas en la América Latina volcadas a una ciencia más democrática y reafirma la necesidad de defender una ciencia abierta que interrogue su modo de actuar, siendo con eso, menos tecnocrática. Juan Pablo Alperin es profesor asociado de la Simon Fraser University

Foi por meio dos estudos sobre softwares de periódicos científicos que Juan Pablo Alperin passou a desenvolver pesquisas sobre a comunicação científica, principalmente em relação à temática de acesso aberto e sua questão mais ampla que envolve a ciência aberta. Em entrevista à Reciis, o professor e pesquisador argumenta que é preciso pensar em como se abrir o acesso ao conhecimento e não apenas garanti-lo. Nesse sentido, a reflexão sobre como fazer ciência aberta promove discussões para tornar o sistema de pesquisa científica mais equânime e colaborativo. O professor comenta sobre os efeitos positivos e os desafios que a pandemia de covid-19 promoveu em relação à comunicação científica. Alperin destaca iniciativas na América Latina voltadas a uma ciência mais democrática e reafirma a necessidade de se defender uma ciência aberta que interrogue o seu modo de agir, sendo, com isso, menos tecnocrática. Juan Pablo Alperin é professor associado da Simon Fraser University.

Through studies on software for scientific journals, Juan Pablo Alperin began to develop research on scientific communication, mainly on the theme of open access and its broader issue that involves open science. in an interview with Reciis, the professor and researcher argues that it is necessary to think about how to open access to knowledge and not just guarantee it. In this sense, reflection on how to do open science promotes discussions to make the scientific research system more equitable and collaborative. The professor states the positive effects and challenges that the covid-19 pandemic has brought about for scientific communication. Alperin highlights initiatives in Latin America aimed at a more democratic science and reaffirms the need to defend an Open Science that questions its way of acting, being less technocratic. Juan Pablo Alperin is an associate professor at Simon Fraser University.

Individual integrity and public morality in scientific publishing.

Science and science reporting are under threat. Knowingly or not, researchers and clinicians are part of this debacle. This is not due so much to the notorious replication crisis, as to our acceptance of lowering common morality for personal gains, including the widespread, deprecable phenomenon of predatory publishing. Rather than fiercefully countering this loathsome practice, academics are accepting, often supporting a masquerade solution: paying several thousand dollars to publish for all their own papers. This new policy will create a disparity across richer and poorer disciplines; will result in concentrating even more in the hands of large, rich, Western institutions, also penalising younger researchers; will kill observational studies and exploratory research; and will make disseminating science depending more on finances than on quality. This article calls for the full awareness of the academic community on the risks of the current situation in scientific publishing.

A ciência e os relatórios científicos estão ameaçados. Conscientemente ou não, pesquisadores e médicos fazem parte desse desastre. Isso não se deve tanto à notória crise de replicação, mas à nossa aceitação de rebaixar a moralidade comum para ganhos pessoais, incluindo o fenômeno generalizado e depreciável da publicação predatória. Em vez de combater ferozmente essa prática repugnante, os acadêmicos estão aceitando, muitas vezes até apoiando uma solução de disfarce: pagar vários milhares de dólares para publicar seus próprios artigos. Essa nova política criará uma disparidade entre as disciplinas mais ricas e mais pobres, resultará na concentração ainda maior nas mãos de grandes e ricas instituições ocidentais, penalizando também os pesquisadores mais jovens; matará os estudos observacionais e a pesquisa exploratória e fará com que a divulgação científica dependa mais das finanças do que da qualidade. Este artigo apela à plena consciência da comunidade acadêmica sobre os riscos da situação atual da publicação científica.