The case for formal methodology in scientific reform.
Ontology highlight
ABSTRACT:
SUBMITTER: Devezer B
PROVIDER: S-EPMC8101540 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill's critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative.
| S-EPMC3104413 | biostudies-literature
Project description:BackgroundIt is unclear how formal long-term care (LTC) availability affects formal /informal caregiving patterns and caregiver health. We tested the impact of reduced formal LTC availability on formal LTC service use, intensity of informal caregiving, and caregiver health.MethodsUsing a representative, repeated cross-sectional sample of Japanese caregivers providing care to co-resident family members from 2001 to 2016, we applied a difference-in-differences approach by observing caregivers before and after the major reform of the public Japanese LTC insurance (LTCI) in 2006. The reform reduced coverage benefits for non-institutionalized older persons with low care needs, but not for those with high care needs. We analyzed 12,764 caregivers aged ?30?years (mean age 64.3?±?11.8?years, 73.5% women) and measured indicators of formal LTC use, hours of informal caregiving, and caregiver self-reported health outcomes after propensity score matching to balance caregivers' background characteristics.ResultsWe found the 2006 LTCI reform relatively reduced the use of formal LTC services and relatively increased the percentage of experiencing long hours of informal caregiving (>?3?h per day) among the caregivers for seniors with low care needs compared to those for seniors with high care needs. The effects of the LTCI reform for the caregivers for seniors with low care needs were 2.2 percentage point higher on caregivers' experiencing poor self-rated health (95% confidence interval [CI]: 0.7-3.7; p?=?0.01), 2.7 percentage point higher on experiencing symptoms of a depressive state (95%CI: 0.5-4.8; p?=?0.03), and 4.7 percentage point higher on experiencing symptoms of musculoskeletal diseases (95%CI, 3.6-5.7; p?<?0.001), compared to those for seniors with high care needs.ConclusionsReduced formal care availability under the Japanese LTCI reform increased hours of informal caregiving corresponding to reduced use of formal LTC and deteriorated multiple dimensions of caregiver health. Our findings may highlight the importance of enhancing the availability of formal LTC services for caregiver health.
| S-EPMC7291452 | biostudies-literature
Project description:Background: Exponential increases in the development of medical knowledge, the expansion of areas where medicine develops its activities, the emergence of new pathologies ( e.g., COVID-19), novel diagnostic methods and therapeutic strategies, together with the appearance of multiple communication and information technologies, determined that the education of future physicians required targeted training in scientific methodology. Methods: The design and execution of a course in scientific methodology in the curriculum of Facultad de Medicina, Universidad de la República, Uruguay, is described. The course is carried out at an advanced stage of the medical studies for all the students, in which they develop a 10-month research project supervised by the medical school faculty. Students undergo all stages of a research endeavor: generation of hypothesis, elaboration of a research protocol, submission to the Research Ethics and Animal Welfare Committees, data recollection, analysis, interpretation and publication of the results. Results: The course is undertaken at the Facultad de Medicina, Universidad de la República, Uruguay, the main university of the country, with high numbers of students enrolled. The course involves the participation of 600 students and up to 300 professors per year, which implies a huge institutional effort Conclusions: The scientific methodology course resulted in one of the most important incorporations of the current 2008 curriculum. Local students, faculty and international evaluators have qualified this activity as an educational breakthrough, being a gratifying and productive experience. The course represented the first exposure of medical students to the research methodology, scientific literature and publication rules, and emphasized the dynamic nature of medical knowledge within modern medical education. Moreover, for some students it constituted the onset of academic research careers. An additional positive outcome was the reactivation of some faculty research projects, in a way that largely exceeded the boundaries of the course.
| S-EPMC9427080 | biostudies-literature
Project description:Covid-19 research made it painfully clear that the scandal of poor medical research, as denounced by Altman in 1994, persists today. The overall quality of medical research remains poor, despite longstanding criticisms. The problems are well known, but the research community fails to properly address them. We suggest that most problems stem from an underlying paradox: although methodology is undeniably the backbone of high-quality and responsible research, science consistently undervalues methodology. The focus remains more on the destination (research claims and metrics) than on the journey. Notwithstanding, research should serve society more than the reputation of those involved. While we notice that many initiatives are being established to improve components of the research cycle, these initiatives are too disjointed. The overall system is monolithic and slow to adapt. We assert that top-down action is needed from journals, universities, funders and governments to break the cycle and put methodology first. These actions should involve the widespread adoption of registered reports, balanced research funding between innovative, incremental and methodological research projects, full recognition and demystification of peer review, improved methodological review of reports, adherence to reporting guidelines, and investment in methodological education and research. Currently, the scientific enterprise is doing a major disservice to patients and society.
| S-EPMC8795888 | biostudies-literature
Project description:Psychological Assessment can be defined as a complex procedure of information collection, analysis and processing. Formal Psychological Assessment (FPA) tries to improve this procedure by providing a formal framework to build assessment tools. In this paper, FPA is applied to depression. Seven questionnaires widely used for the self-evaluation of depression were selected. Diagnostic criteria for major depressive disorder were derived from the DSM-5, literature and Seligman's and Beck's theories. A Boolean matrix was built, including 266 items from the questionnaires in the rows and 20 selected attributes, obtained through diagnostic criteria decomposition, in the columns. In the matrix, a 1 in a cell meant that the corresponding item investigated the specific attribute. It was thus possible to analyze the relationships between items and attributes and among items. While none of the considered questionnaires could alone cover all the criteria for the evaluation of depressive symptoms, we observed that a set of 30 items contained the same information that was obtained redundantly with 266 items. Another result highlighted by the matrix regards the relations among items. FPA allows in-depth analysis of currently used questionnaires based on the presence/absence of clinical elements. FPA allows for going beyond the mere score by differentiating the patients according to symptomatology. Furthermore, it allows for computerized-adaptive assessment.
| S-EPMC4398546 | biostudies-other
Project description:BackgroundThe electrocardiogram (ECG) is one of the most common diagnostic tools available to assess cardio-vascular health. The advent of advanced computational techniques such as deep learning has dramatically expanded the breadth of clinical problems that can be addressed using ECG data, leading to increasing popularity of ECG deep-learning models aimed at predicting clinical endpoints.ObjectivesThe purpose of this study was to define the current landscape of clinically relevant ECG deep-learning models and examine practices in the scientific reporting of these studies.MethodsWe performed a systematic review of PubMed and EMBASE databases to identify clinically relevant ECG deep-learning models published through July 1, 2022.ResultsWe identified 44 manuscripts including 53 unique, clinically relevant ECG deep-learning models. The rate of publication of ECG deep-learning models is increasing rapidly. The most common clinical applications of ECG deep learning were identification of cardiomyopathy (14/53 [26%]), followed by arrhythmia detection (9/53 [17%]). Methodologic reporting varied; while 33/44 (75%) publications included model architecture diagrams, complete information required to reproduce these models was provided in only 10/44 (23%). Saliency analysis was performed in 20/44 (46%) of publications. Only 18/53 (34%) models were tested within external validation cohorts. Model code or resources allowing for model implementation by external groups were available for only 5/44 (11%) publications.ConclusionsWhile ECG deep-learning models are increasingly clinically relevant, their reporting is highly variable, and few publications provide sufficient detail for methodologic reproduction or model validation by external groups. The field of ECG deep learning would benefit from adherence to a set of standardized scientific reporting guidelines.
| S-EPMC10824530 | biostudies-literature
Project description:Scientific thinking is a predicate for scientific inquiry, and thus important to develop early in psychology students as potential future researchers. The present research is aimed at fathoming the contributions of formal and informal learning experiences to psychology students' development of scientific thinking during their 1st-year of study. We hypothesize that informal experiences are relevant beyond formal experiences. First-year psychology student cohorts from various European countries will be assessed at the beginning and again at the end of the second semester. Assessments of scientific thinking will include scientific reasoning skills, the understanding of basic statistics concepts, and epistemic cognition. Formal learning experiences will include engagement in academic activities which are guided by university authorities. Informal learning experiences will include non-compulsory, self-guided learning experiences. Formal and informal experiences will be assessed with a newly developed survey. As dispositional predictors, students' need for cognition and self-efficacy in psychological science will be assessed. In a structural equation model, students' learning experiences and personal dispositions will be examined as predictors of their development of scientific thinking. Commonalities and differences in predictive weights across universities will be tested. The project is aimed at contributing information for designing university environments to optimize the development of students' scientific thinking.
| S-EPMC5301459 | biostudies-literature
Project description:Scientific mobility can stimulate entrepreneurship and intrapreneurship, acting as a catalyst for reducing imbalances between local and global science and the resulting socio-economic damage. This study evaluates both whether scientific mobility effectively promotes these concepts and the fundamental reasons to articulate effective policies for scientific mobility. Toward this end, a survey has been prepared following the methodology of Global Entrepreneurship Monitor (GEM) and current scientific literature. A total of 364 researchers involved in Spanish scientific mobility took part in the study: Spanish scientists abroad (135) and scientists returned to Spain (52), as mobile groups, and young researchers in Spain (177), as a group of scientists who could go abroad, but that have not yet begun to leave. The results demonstrate that scientific mobility does promote entrepreneurship and, especially intrapreneurship. Moreover, since permanent positions are scarce for these groups and their mobility decisions largely depend on job opportunities, the involved Spanish authorities and agents can improve scientific mobility by means suitable policies that make the most of this potential to the benefit of economic growth and job creation.
| S-EPMC6124723 | biostudies-literature
Project description:Environmentally enriched housing conditions affect pig welafre, immune system and gut microbiota in early life
| PRJEB44226 | ENA
Project description:BackgroundJapanese Kampo medicine is a traditional medicine with roots in ancient Chinese medicine. Because traditional physicians had been abolished in Japan, the present mainstream of Kampo treatment is that physicians who learned modern Western medicine prescribe Kampo extract products based on Western medical diagnosis. This situation is different from that in other east Asian countries, and the physicians require scientific clinical evidence.MethodsClinical studies were searched from literature databases, clinical trial registry sites, and "Evidence Reports of Kampo Treatment (EKAT)" published by the Japan Society for Oriental Medicine.ResultsAt the approval of Kampo products, scientific clinical evidence was not required because they have a long-period experience as a decoction. However, in the 1990s, Kampo products became a subject for national reevaluation; double-blind and placebo-controlled clinical trials. At the time, a methodological foundation for conducting clinical assessments of Kampo medicines was established. From 2000 onwards, with the evidence-based medicine era, the field of Kampo medicine also saw many randomized controlled trials, and their evidence was collected and published as EKAT. In the 2010s, post-marketing clinical trials of Kampo products also had to be conducted in this environment due to the need for ethical and scientific assurance. Currently, there are numerous clinical trials of Kampo products being conducted with high-grade trial designs.ConclusionThe situation of Kampo clinical studies reflects the unique history and position of Kampo medical system and Kampo products in Japan.
| S-EPMC8181179 | biostudies-literature