Intelligent Information System for Academic Institutions

Research and publication is considered an authenticated certificate of innovative work done by researchers in various fields. In research, new scientific results may be assessed, corrected, and further built up by the scientific neighborhood only if they are available in published form. Guidelines on accountable research and publication are currently set to encourage and promote high ethical standards in the conduct of research and in biomedical publications. They address various aspects of the research and publishing including duties of editors and authorship determination. The chapter presents research and publication system using big data analytics and research data management techniques with a background of information systems and need of information in research data management.

Feasibility of an Assessment Tool as a Data-Driven Approach to Reducing Racial Bias in Biomedical Publications

The editorial independence of biomedical journals allows flexibility to meet a wide range of research interests. However, it also is a barrier for coordination between journals to solve challenging issues such as racial bias in the scientific literature. A standardized tool to screen for racial bias could prevent the publication of racially biased papers. Biomedical journals would maintain editorial autonomy while still allowing comparable data to be collected and analyzed across journals. A racially diverse research team carried out a three-phase study to generate and test a racial bias assessment tool for biomedical research. Phase 1, an in-depth, structured literature search to identify recommendations, found near complete agreement in the literature on addressing race in biomedical research. Phase 2, construction of a framework from those recommendations, provides the major innovation of this paper. The framework includes three dimensions of race: 1) context, 2) tone and terminology, and 3) analysis, which are the basis for the Race Equity Vetting Instrument for Editorial Workflow (REVIEW) tool. Phase 3, pilot testing the assessment tool, showed that the REVIEW tool was effective at flagging multiple concerns in widely criticized articles. This study demonstrates the feasibility of the proposed REVIEW tool to reduce racial bias in research. Next steps include testing this tool on a broader sample of biomedical research to determine how the tool performs on more subtle examples of racial bias.

A Proposed Method for Residual Citation Allocation Based on Citation Contexts’ Similarity

This article proposes an approach for allocating residual citations to scientific publications and demonstrating this proposed approach with a sample of biomedical publications. Residue citations (i.e., citations that are lost due to citation practices termed “Obliteration by Incorporation” and the “Palimpsestic Syndrome”) in consequent citations in the second, third or nth generations are then reconstituted. The proposed approach takes into account citation contexts (i.e., the contribution of a cited publication) for allocating residual citation. The proposed method for allocating residual citation is based on the similarity between the citation contexts of a publication and those of its nth generation citations in their n+1th generation citations. The proposed method was demonstrated using a sample with ten base articles and their five generations of citations, from which 5,272 citation context pairs were obtained. The proposed indirect citation weighting was compared with the existing cascading citation weighting method using one T-test. Statistical tests were also performed to understand the differences in the residual citations from one generation to the other. Like the cascading citation system, residual citations from articles to their generations of citations decreased as the number of generations increased. However, residue citations accrued to publications at all the generations were statistically different between the proposed residual citation and the cascading citation system. This study proposes a method for assessing scientific communication based on the contribution of scientific publications beyond the conventional direct citation.

Research Progress of Gliomas in Machine Learning

In the field of gliomas research, the broad availability of genetic and image information originated by computer technologies and the booming of biomedical publications has led to the advent of the big-data era. Machine learning methods were applied as possible approaches to speed up the data mining processes. In this article, we reviewed the present situation and future orientations of machine learning application in gliomas within the context of workflows to integrate analysis for precision cancer care. Publicly available tools or algorithms for key machine learning technologies in the literature mining for glioma clinical research were reviewed and compared. Further, the existing solutions of machine learning methods and their limitations in glioma prediction and diagnostics, such as overfitting and class imbalanced, were critically analyzed.

An author’s guide to mastering academic writing skills: Discussion of a medical manuscript

Skilled scientific or academic writing is of great importance to research communication and journal publication ultimately. The four fundamental sections of a scholarly manuscript are introduction, methods, results and discussion. The discussion serves to interpret and analyze the study results in view of the existing body of evidence. Moreover, it serves to transform the usually rigid numerical statistical data of the results section into practical and clinically utilizable information. A well-formulated discussion can provide readers with informed decisions on the validity of the results and their exact generalizability to the broader community. It can also isolate shortcomings of the existing literature. Despite the extensive growth in biomedical publications lately, little attention has been paid to the importance of medical writing in general and to the discussion section of a medical manuscript in specific. This applies to curricular education and medical literature. The implications of well-executed studies with important findings can go unnoticed if authors are less skilled at writing a comprehensive discussion and conclusion among other manuscript sections. I intended to convey the experience I have accumulated in authoring and peer-reviewing for leading society journals and supervising in-house academic theses and dissertations. The objective of this article was to help authors present and communicate their research findings methodically, efficiently and impartially. Orthopedic research was taken as a practical example.

DISCLOSURE OF POTENTIAL CONFLICTS OF INTEREST IN BIOMEDICAL PUBLICATIONS IN VIEW OF THE INTERNATIONAL COMMITTEE OF MEDICAL JOURNAL EDITORS RECOMMENDATIONS

As potential conflicts of interest (COI) are common in biomedical research, handling related issues and managing disclosures is increasingly important. The International Committee of Medical Journal Editors (ICMJE) revised its guidance on COI in 2019 and introduced the latest version of the COI Disclosure Form in 2021. These documents provide guidance regarding COI policy for ICMJE member and non-member journals. The 2019 revision overviews the main changes in the ICMJE policy. The ICMJE prioritizes appropriate COI disclosures by authors and all others involved in scholarly publishing. Increasing the global awareness of the COI updated policies among all stakeholders is essential for strengthening ethical standing of journals.

Preparación de un manuscrito para su presentación a una revista científica

Publishing the product of scientific work is an art and a necessity. If the results of the research are not reported through publication in a scientific journal, researchers miss the opportunity for their work to be known. Preparation of the manuscript is a challenge, particularly for researchers who begin their experience in scientific publication. Each journal has its publication standards available to authors; however, most biomedical publications follow the recommendations of the International Committee of Medical Journal Editors. This document describes the importance of the research process, each of its parts and the different types of scientific documents, but focuses on the description of original articles, highlighting practical recommendations for their proper realization, and presents the most frequent errors observed with the intention of guiding novice researchers throughout the process. Keywords: Scientific paper, Medical publication, Research, recommendations to publish, Original articles.

Effective image visualization for publications – a workflow using open access tools and concepts

Today, 25% of figures in biomedical publications contain images of various types, e.g. photos, light or electron microscopy images, x-rays, or even sketches or drawings. Despite being widely used, published images may be ineffective or illegible since details are not visible, information is missing or they have been inappropriately processed. The vast majority of such imperfect images can be attributed to the lack of experience of the authors as undergraduate and graduate curricula lack courses on image acquisition, ethical processing, and visualization. Here we present a step-by-step image processing workflow for effective and ethical image presentation. The workflow is aimed to allow novice users with little or no prior experience in image processing to implement the essential steps towards publishing images. The workflow is based on the open source software Fiji, but its principles can be applied with other software packages. All image processing steps discussed here, and complementary suggestions for image presentation, are shown in an accessible “cheat sheet”-style format, enabling wide distribution, use, and adoption to more specific needs.

Multiple Voices on Authorship and Authority in Biomedical Publications

The intersection of industry sponsorship, government regulation, academic interests, and medical journals is a core interest in biomedical research, and one that overlaps with concerns in the rhetoric of health and medicine (RHM). At stake in conversations about this intersection are authority and participation: who is and is not invited to offer opinions and, even when invited, whose opinions are taken seriously. Following, colleagues with ties to the International Society of Medical Publication Professionals (ISMPP) present their ideas in response to questions about authorship and authority posed by another, who is also an RHM scholar. The answers of medical journal editors and publications professionals employed by corporate entities largely align with the view that both authorship and authority should be determined by scientific practice and knowledge rather than power relations or politics. A philosopher who gave an invited plenary talk at the national ISMPP meeting and participated in the organization’s first white paper offers a different perspective, considering the ways that fields self-constitute in part by bounding authority and authorship.

Effective image visualization for publications – a workflow using open access tools and concepts

Today, 25% of figures in biomedical publications contain images of various types, e.g. photos, light or electron microscopy images, x-rays, or even sketches or drawings. Despite being widely used, published images may be ineffective or illegible since details are not visible, information is missing or they have been inappropriately processed. The vast majority of such imperfect images can be attributed to the lack of experience of the authors as undergraduate and graduate curricula lack courses on image acquisition, ethical processing, and visualization. Here we present a step-by-step image processing workflow for effective and ethical image presentation. The workflow is aimed to allow novice users with little or no prior experience in image processing to implement the essential steps towards publishing images. The workflow is based on the open source software Fiji, but its principles can be applied with other software packages. All image processing steps discussed here, and complementary suggestions for image presentation, are shown in an accessible “cheat sheet”-style format, enabling wide distribution, use, and adoption to more specific needs.