PubMed and Beyond: Recent Advances and Best Practices in Biomedical Literature Search

Biomedical research yields a wealth of information, much of which is only accessible through the literature. Consequently, literature search is an essential tool for building on prior knowledge in clinical and biomedical research. Although recent improvements in artificial intelligence have expanded functionality beyond keyword-based search, these advances may be unfamiliar to clinicians and researchers. In response, we present a survey of literature search tools tailored to both general and specific information needs in biomedicine, with the objective of helping readers efficiently fulfill their information needs. We first examine the widely used PubMed search engine, discussing recent improvements and continued challenges. We then describe literature search tools catering to five specific information needs: 1. Identifying high-quality clinical research for evidence-based medicine. 2. Retrieving gene-related information for precision medicine and genomics. 3. Searching by meaning, including natural language questions. 4. Locating related articles with literature recommendation. 5. Mining literature to discover associations between concepts such as diseases and genetic variants. Additionally, we cover practical considerations and best practices for choosing and using these tools. Finally, we provide a perspective on the future of literature search engines, considering recent breakthroughs in large language models such as ChatGPT. In summary, our survey provides a comprehensive view of biomedical literature search functionalities with 36 publicly available tools.Comment: 27 pages, 6 figures, 36 tool

Doctoral Education in Ukraine: the Application of Digital Tools and Services by Doctoral Students under COVID-19 Pandemic

[EN] The paper aims to explore the peculiarities of doctoral education under COVID-19 in Ukraine. The application of digital instruments and services by doctoral students has become a priority during distance training. However, this approach is mainly a new experience and, accordingly, undergoes theoretical substantiation and piloting. The focus of the study is two-fold. It theoretically discusses the digital support of dissertation research at various stages. Secondly, based on the findings of the survey on the doctoral students application of digital tools and services the challenges have been identified. We conclude that the priority of digital education in the EU countries, especially under COVID-19 pandemic highlights the task of restructuring the doctoral education in Ukraine towards its dynamic digitalization. The digitization should be comprehensive and systematic. Systematization should include technical, organizational, motivational and developmental components aimed at synergy of institutions, doctoral students and supervisors. The complexity should include both the digitization of the training component and independent work of the doctoral students while writing a dissertation. The groups of DT&S for application by doctoral students are recommended for the inclusion into the doctoral students training curriculum both in the format of a separate course and by integration into the syllabi of other disciplines. Based on the research findings the targeted scientific/methodical events (seminars, master classes, doctoral schools, etc.) providing knowledge and skills on DT&S application are recommended.Khoruzha, L.; Lokshyna, O.; Mazur, N.; Proshkin, V. (2022). Doctoral Education in Ukraine: the Application of Digital Tools and Services by Doctoral Students under COVID-19 Pandemic. Multidisciplinary Journal for Education, Social and Technological Sciences. 9(1):87-112. https://doi.org/10.4995/muse.2022.16768OJS871129

Where was COVID-19 first discovered? Designing a question-answering system for pandemic situations

The COVID-19 pandemic is accompanied by a massive “infodemic” that makes it hard to identify concise and credible information for COVID-19-related questions, like incubation time, infection rates, or the effectiveness of vaccines. As a novel solution, our paper is concerned with designing a question-answering system based on modern technologies from natural language processing to overcome information overload and misinformation in pandemic situations. To carry out our research, we followed a design science research approach and applied Ingwersen’s cognitive model of information retrieval interaction to inform our design process from a socio-technical lens. On this basis, we derived prescriptive design knowledge in terms of design requirements and design principles, which we translated into the construction of a prototypical instantiation. Our implementation is based on the comprehensive CORD-19 dataset, and we demonstrate our artifact’s usefulness by evaluating its answer quality based on a sample of COVID-19 questions labeled by biomedical experts

The communication context of the measurement of health literacy levels : pilot study in a ruralized elderly population

Background: Health literacy (HL) has a crucial role in one’s global health state. The HL concept encompasses the ability in accessing, understanding and using the information to navigate the health system and for health-related decision making. Communication is a transversal concept in the HL operationalization, in the effective transmission, understanding and application of health information. The measurement of HL levels comprises an opportunity to study both dimensions. This study is particularly relevant for individuals over 65 years old, identified as a vulnerable group to low HL levels. Objectives: The primary objective is to assess the behaviour of two commonly used HL measurement tools when applied in a ruralized elderly cohort. The secondary objective is to assess if there are relations between social determinants of health and HL levels. Methods: This research is of quantitative and qualitative nature, being exploratory and descriptive. The sample comprises fifty participants. The used HL measurement tools were the European Health Literacy Survey (HLS-EU-PT) and the Newest Vital Sign (NVS). A questionnaire survey was produced to collect data regarding the social determinants of health. Results: A total of 50 valid HLS-EU-PT and 41 NVS surveys were collected, along with 50 valid questionnaire surveys. Low HL levels were verified in both tools, with aggravated Limited HL in the NVS. Possible relations between social determinants of health and HL levels were identified. Conclusion: Results do not suggest a concordance of results between tools. The NVS may not be a viable tool for samples with a significant proportion of illiterate participants, an obstacle that may be surpassed by using the HLS-EU-PT. Application protocols of HL measurement tools must encompass criteria and methods suited for limitations in this population segment. The identified low HL levels support the identified need for tailoring measures that strengthen HL in the elderly to maintain and improve their life and health qualityIntrodução: A Literacia em Saúde (LS) tem um papel crucial no estado global de saúde de cada pessoa. O conceito de LS abrange a capacidade de aceder, compreender e utilizar a informação para navegar no sistema de saúde e na tomada de decisões relacionadas com saúde. A Comunicação é um conceito transversal na operacionalização da LS, na transmissão eficaz, compreensão e aplicação da informação de saúde. A medição de níveis de LS representa uma oportunidade para o estudo de ambas as dimensões. Este estudo é particularmente relevante para pessoas com idade superior a 65 anos, identificados como grupo vulnerável a baixos níveis de LS. Objetivos: O objetivo principal é avaliar o comportamento de duas ferramentas de medição de LS comummente utilizadas, quando aplicadas a uma amostra de idosos ruralizados. O objetivo secundário é verificar se existem relações entre determinantes sociais de saúde e níveis de LS. Métodos: O presente estudo é de natureza quantitativa e qualitativa, seguindo uma abordagem descritivo-exploratória. A amostra foi composta por cinquenta participantes. As ferramentas utilizadas para a medição dos níveis de LS foram o HLS-EU-PT e o NVS. Foi também desenvolvido um inquérito por questionário para a recolha de dados sobre determinantes sociais de saúde. Resultados: Foram recolhidos 50 inquéritos válidos pelo HLS-EU-PT e 41 pelo NVS, bem como 50 inquéritos por questionário válidos. Verificaram-se baixos níveis de LS em ambas as ferramentas, com níveis agravados de LS Limitada no NVS. Foram identificadas possíveis relações entre determinantes sociais de saúde e níveis de LS. Conclusão: Os resultados não sugerem uma validade concorrente entre as duas ferramentas. O NVS pode não ser uma ferramenta viável para amostras com uma proporção significativa de participantes com iliteracia, um obstáculo que pode ser ultrapassado ao utilizar o HLSEU-PT. Os protocolos de aplicação das ferramentas de LS devem acomodar critérios e métodos adequados às limitações deste segmento da população. Os baixos níveis de LS identificados suportam a necessidade identificada de personalizar medidas que fortaleçam a LS nos idosos para a manutenção e melhoria da sua saúde e qualidade de vida

The QuaSARS method for conducting useful literature surveys in social media research: a step-by-step approach

The literature survey captures influential authors or works, developments, discourses, key concepts, controversies, or comparisons and trends on any social media research topic. This tutorial provides a step-by-step approach to conduct a literature survey on social media research and the critical quality issues needed. The section discusses: (a) why a literature survey is necessary for social media research, (b) recognizes various types of literature reviews and how they differ from the literature survey, (c) introduces the QuASARS conceptual framework (Question, Approach, Search, Administer, Report, Synthesis, and Share) as a method for literature surveys, (d) identifies literature sources on social media research and, (e) guides readers on techniques to synthesize the literature. A hypothetical study concerning the recent spate of fake news circulating on social media during the novel COVID-19 (coronavirus) is used to illustrate the concepts in the tutorial. This theoretical study shows how to focus the literature survey questions, techniques for managing the relevant literature. For example, how to build and apply literature matrix tables, concept maps, and the use of electronic reference managers. This work makes a detailed discussion on frameworks for gap-spotting and problematizing the literature to tease themes from the symbiotic relationship between the research questions and the argument. The tutorial applies some common social media research questions to illustrate the gap-spotting and problematization modes. Finally, a discussion is given on how to synthesize the literature review, i.e., the application of complex reasoning (different mapping and comparative thinking) to create a dialectic argument. The steps in this literature survey research design may not be followed rigidly as some steps may overlap with others or depend on another level or conducted before others

Is It Essential for Occupational Health and Safety Experts to Know the English Language? Results From Several Studies in Latvia

Funding Information: The focus group discussions and transcribing of the focus group discussions were funded by the National Research Programme of Latvia within the Project Life with COVID-19: Evaluation of Overcoming the Coronavirus Crisis in Latvia and Recommendations for Societal Resilience in the Future (Agreement No: VPP-COVID-2020/1-0013). The original datasets of the independent studies Work conditions and risks in Latvia were received from the data owners free of charge. Publisher Copyright: Copyright © 2022 Matisāne, Paegle, Akūlova, Eglı̄te and Vanadziṇš.Background: Poor knowledge of the language has been identified as a barrier to up-to-date occupational safety and health information, however, this question has not been addressed in the context of occupational safety and health expert competence in providing advice for employers in a small, non-English speaking country. Objectives: To analyze the available data on the use of languages for searching professional information by occupational safety and health (OSH) experts, and the sources of information on COVID-19 during the first wave of the pandemic in Latvia, and to assess if the knowledge of the English language among these experts is sufficient to react rapidly and effectively in case of emergency. Methods: Data were compiled from several different sources: three web-based surveys of occupational safety and health experts (data from 2006, 2010, and 2018) and ten focus group discussions with employers and occupational safety and health experts (data from 2020). Results: The results of the surveys show that between 2006 and 2018, the percentage of respondents using only one language (Latvian) for searching professional information in occupational safety and health has increased from 25 to 35.3%. In 2018, the English language was mentioned by only 42.8% of respondents and Russian by 46.8%. During the focus group discussions, the use of English was mentioned for obtaining trustful information from international organizations, for analysis of information received within international companies, for searching international experience, and for finding county-specific information. Discussion: Our study shows that knowledge of the English language for occupational safety and health experts working in Latvia is not sufficient. The companies providing external occupational safety and health services should establish a well-functioning internal training system to provide their non-English speaking experts with up-to-date information. Occupational safety and health-related non-governmental institutions should strengthen their capacity in sharing information related to different occupational safety and health aspects into the national language (Latvian in this particular case).publishersversionPeer reviewe