Research transparency in dental research : A programmatic analysis

Publisher Copyright: © 2022 The Authors. European Journal of Oral Sciences published by John Wiley & Sons Ltd on behalf of Scandinavian Division of the International Association for Dental Research.We assessed adherence to five transparency practices-data sharing, code sharing, conflict of interest disclosure, funding disclosure, and protocol registration-in articles in dental journals. We searched and exported the full text of all research articles from PubMed-indexed dental journals available in the Europe PubMed Central database until the end of 2021. We programmatically assessed their adherence to the five transparency practices using a validated and automated tool. Journal- and article-related information was retrieved from ScimagoJR and Journal Citation Reports. Of all 329,784 articles published in PubMed-indexed dental journals, 10,659 (3.2%) were available to download. Of those, 77% included a conflict of interest disclosure, and 62% included a funding disclosure. Seven percent of the articles had a registered protocol. Data sharing (2.0%) and code sharing (0.1%) were rarer. Sixteen percent of articles did not adhere to any of the five transparency practices, 29% adhered to one, 48% adhered to two, 7.0% adhered to three, 0.3% adhered to four, and no article adhered to all five practices. Adherence to transparency practices increased over time; however, data and code sharing especially remained rare. Coordinated efforts involving all stakeholders are needed to change current transparency practices in dental research.publishersversionPeer reviewe

Transparency of COVID-19-related research : A meta-research study

Funding Information: The computational analyses were performed on servers provided by UEF Bioinformatics Center, University of Eastern Finland, Finland. Uribe was supported by European Union’s Horizon 2020 grant 857287 for the Baltic Biomaterials Centre of Excellence, Headquarters at Riga Technical University, Riga, Latvia and the Uzn¸ēmuma MikroTik līgumam Nr. UL8, 2021 RSU (toward implementing the RSU data repository and the FAIR data management principles). Raittio was supported by the Finnish Dental Society Apollonia and the Aarhus University Research Foundation (#AUFF-E 2019-7-3). Publisher Copyright: © 2023 Sofi-Mahmudi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.BACKGROUND: We aimed to assess the adherence to five transparency practices (data availability, code availability, protocol registration and conflicts of interest (COI), and funding disclosures) from open access Coronavirus disease 2019 (COVID-19) related articles. METHODS: We searched and exported all open access COVID-19-related articles from PubMed-indexed journals in the Europe PubMed Central database published from January 2020 to June 9, 2022. With a validated and automated tool, we detected transparent practices of three paper types: research articles, randomized controlled trials (RCTs), and reviews. Basic journal- and article-related information were retrieved from the database. We used R for the descriptive analyses. RESULTS: The total number of articles was 258,678, of which we were able to retrieve full texts of 186,157 (72%) articles from the database Over half of the papers (55.7%, n = 103,732) were research articles, 10.9% (n = 20,229) were review articles, and less than one percent (n = 1,202) were RCTs. Approximately nine-tenths of articles (in all three paper types) had a statement to disclose COI. Funding disclosure (83.9%, confidence interval (CI): 81.7-85.8 95%) and protocol registration (53.5%, 95% CI: 50.7-56.3) were more frequent in RCTs than in reviews or research articles. Reviews shared data (2.5%, 95% CI: 2.3-2.8) and code (0.4%, 95% CI: 0.4-0.5) less frequently than RCTs or research articles. Articles published in 2022 had the highest adherence to all five transparency practices. Most of the reviews (62%) and research articles (58%) adhered to two transparency practices, whereas almost half of the RCTs (47%) adhered to three practices. There were journal- and publisher-related differences in all five practices, and articles that did not adhere to transparency practices were more likely published in lowest impact journals and were less likely cited. CONCLUSION: While most articles were freely available and had a COI disclosure, adherence to other transparent practices was far from acceptable. A much stronger commitment to open science practices, particularly to protocol registration, data and code sharing, is needed from all stakeholders.publishersversionPeer reviewe

Dental Research Data Availability and Quality According to the FAIR Principles

Funding Information: The authors disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This research was funded by MikroTik-RSU to S.E. Uribe (toward implementing the RSU data repository and the FAIR data management principles). S.E. Uribe also acknowledges financial support from the European Union’s Horizon 2020 Research and Innovation Programme (grant 857287). Publisher Copyright: © International Association for Dental Research and American Association for Dental, Oral, and Craniofacial Research 2022.According to the FAIR principles, data produced by scientific research should be findable, accessible, interoperable, and reusable—for instance, to be used in machine learning algorithms. However, to date, there is no estimate of the quantity or quality of dental research data evaluated via the FAIR principles. We aimed to determine the availability of open data in dental research and to assess compliance with the FAIR principles (or FAIRness) of shared dental research data. We downloaded all available articles published in PubMed-indexed dental journals from 2016 to 2021 as open access from Europe PubMed Central. In addition, we took a random sample of 500 dental articles that were not open access through Europe PubMed Central. We assessed data sharing in the articles and compliance of shared data to the FAIR principles programmatically. Results showed that of 7,509 investigated articles, 112 (1.5%) shared data. The average (SD) level of compliance with the FAIR metrics was 32.6% (31.9%). The average for each metric was as follows: findability, 3.4 (2.7) of 7; accessibility, 1.0 (1.0) of 3; interoperability, 1.1 (1.2) of 4; and reusability, 2.4 (2.6) of 10. No considerable changes in data sharing or quality of shared data occurred over the years. Our findings indicated that dental researchers rarely shared data, and when they did share, the FAIR quality was suboptimal. Machine learning algorithms could understand 1% of available dental research data. These undermine the reproducibility of dental research and hinder gaining the knowledge that can be gleaned from machine learning algorithms and applications.publishersversionPeer reviewe

Achievements of the Cochrane Iran Associate Centre: Lessons Learned

Healthcare decision-making is a process that mainly depends on evidence and involves increasing numbers of stakeholders, including the consumers. Cochrane evidence responds to this challenge by identifying, appraising, integrating and synthesizing high-quality evidence. Recently, a collaborative effort has been initiated in Iran with Cochrane to establish a representative local entity. A variety of multifaceted interventions were conducted according to Cochrane’s strategy to 2020, such as producing evidence, making Cochrane evidence accessible, advocating for evidence and building an effective and sustainable organization. In this report, the authors present the two and half year performance and achievements of Cochrane Iran based on a comprehensive and systematic approach. This case might be an example of health diplomacy, which is initiated by a successful international collaboration and proceed with recognizing the importance of adherence to the strategic action plans and goals

COVID-19 Vaccines Safety Tracking (CoVaST): Protocol of a Multi-Center Prospective Cohort Study for Active Surveillance of COVID-19 Vaccines' Side Effects.

Coronavirus disease (COVID-19) vaccine-related side effects have a determinant role in the public decision regarding vaccination. Therefore, this study has been designed to actively monitor the safety and effectiveness of COVID-19 vaccines globally. A multi-country, three-phase study including a cross-sectional survey to test for the short-term side effects of COVID-19 vaccines among target population groups. In the second phase, we will monitor the booster doses' side effects, while in the third phase, the long-term safety and effectiveness will be investigated. A validated, self-administered questionnaire will be used to collect data from the target population; Results: The study protocol has been registered at ClinicalTrials.gov, with the identifier NCT04834869. CoVaST is the first independent study aiming to monitor the side effects of COVID-19 vaccines following booster doses, and the long-term safety and effectiveness of said vaccines.This study protocol preparation was funded by Masaryk University, grant numbers MUNI/IGA/1543/2020 and MUNI/A/1608/2020.S

Diabetes mortality and trends before 25 years of age: an analysis of the Global Burden of Disease Study 2019

Background Diabetes, particularly type 1 diabetes, at younger ages can be a largely preventable cause of death with the correct health care and services. We aimed to evaluate diabetes mortality and trends at ages younger than 25 years globally using data from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019. Methods We used estimates of GBD 2019 to calculate international diabetes mortality at ages younger than 25 years in 1990 and 2019. Data sources for causes of death were obtained from vital registration systems, verbal autopsies, and other surveillance systems for 1990–2019. We estimated death rates for each location using the GBD Cause of Death Ensemble model. We analysed the association of age-standardised death rates per 100 000 population with the Socio-demographic Index (SDI) and a measure of universal health coverage (UHC) and described the variability within SDI quintiles. We present estimates with their 95% uncertainty intervals. Findings In 2019, 16 300 (95% uncertainty interval 14 200 to 18 900) global deaths due to diabetes (type 1 and 2 combined) occurred in people younger than 25 years and 73·7% (68·3 to 77·4) were classified as due to type 1 diabetes. The age-standardised death rate was 0·50 (0·44 to 0·58) per 100 000 population, and 15 900 (97·5%) of these deaths occurred in low to high-middle SDI countries. The rate was 0·13 (0·12 to 0·14) per 100 000 population in the high SDI quintile, 0·60 (0·51 to 0·70) per 100 000 population in the low-middle SDI quintile, and 0·71 (0·60 to 0·86) per 100 000 population in the low SDI quintile. Within SDI quintiles, we observed large variability in rates across countries, in part explained by the extent of UHC (r2=0·62). From 1990 to 2019, age-standardised death rates decreased globally by 17·0% (−28·4 to −2·9) for all diabetes, and by 21·0% (–33·0 to −5·9) when considering only type 1 diabetes. However, the low SDI quintile had the lowest decline for both all diabetes (−13·6% [–28·4 to 3·4]) and for type 1 diabetes (−13·6% [–29·3 to 8·9]). Interpretation Decreasing diabetes mortality at ages younger than 25 years remains an important challenge, especially in low and low-middle SDI countries. Inadequate diagnosis and treatment of diabetes is likely to be major contributor to these early deaths, highlighting the urgent need to provide better access to insulin and basic diabetes education and care. This mortality metric, derived from readily available and frequently updated GBD data, can help to monitor preventable diabetes-related deaths over time globally, aligned with the UN's Sustainable Development Targets, and serve as an indicator of the adequacy of basic diabetes care for type 1 and type 2 diabetes across nations.publishedVersio

The global burden of adolescent and young adult cancer in 2019 : a systematic analysis for the Global Burden of Disease Study 2019

Background In estimating the global burden of cancer, adolescents and young adults with cancer are often overlooked, despite being a distinct subgroup with unique epidemiology, clinical care needs, and societal impact. Comprehensive estimates of the global cancer burden in adolescents and young adults (aged 15-39 years) are lacking. To address this gap, we analysed results from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019, with a focus on the outcome of disability-adjusted life-years (DALYs), to inform global cancer control measures in adolescents and young adults. Methods Using the GBD 2019 methodology, international mortality data were collected from vital registration systems, verbal autopsies, and population-based cancer registry inputs modelled with mortality-to-incidence ratios (MIRs). Incidence was computed with mortality estimates and corresponding MIRs. Prevalence estimates were calculated using modelled survival and multiplied by disability weights to obtain years lived with disability (YLDs). Years of life lost (YLLs) were calculated as age-specific cancer deaths multiplied by the standard life expectancy at the age of death. The main outcome was DALYs (the sum of YLLs and YLDs). Estimates were presented globally and by Socio-demographic Index (SDI) quintiles (countries ranked and divided into five equal SDI groups), and all estimates were presented with corresponding 95% uncertainty intervals (UIs). For this analysis, we used the age range of 15-39 years to define adolescents and young adults. Findings There were 1.19 million (95% UI 1.11-1.28) incident cancer cases and 396 000 (370 000-425 000) deaths due to cancer among people aged 15-39 years worldwide in 2019. The highest age-standardised incidence rates occurred in high SDI (59.6 [54.5-65.7] per 100 000 person-years) and high-middle SDI countries (53.2 [48.8-57.9] per 100 000 person-years), while the highest age-standardised mortality rates were in low-middle SDI (14.2 [12.9-15.6] per 100 000 person-years) and middle SDI (13.6 [12.6-14.8] per 100 000 person-years) countries. In 2019, adolescent and young adult cancers contributed 23.5 million (21.9-25.2) DALYs to the global burden of disease, of which 2.7% (1.9-3.6) came from YLDs and 97.3% (96.4-98.1) from YLLs. Cancer was the fourth leading cause of death and tenth leading cause of DALYs in adolescents and young adults globally. Interpretation Adolescent and young adult cancers contributed substantially to the overall adolescent and young adult disease burden globally in 2019. These results provide new insights into the distribution and magnitude of the adolescent and young adult cancer burden around the world. With notable differences observed across SDI settings, these estimates can inform global and country-level cancer control efforts. Copyright (C) 2021 The Author(s). Published by Elsevier Ltd.Peer reviewe

The global burden of cancer attributable to risk factors, 2010-19 : a systematic analysis for the Global Burden of Disease Study 2019

Background Understanding the magnitude of cancer burden attributable to potentially modifiable risk factors is crucial for development of effective prevention and mitigation strategies. We analysed results from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019 to inform cancer control planning efforts globally. Methods The GBD 2019 comparative risk assessment framework was used to estimate cancer burden attributable to behavioural, environmental and occupational, and metabolic risk factors. A total of 82 risk-outcome pairs were included on the basis of the World Cancer Research Fund criteria. Estimated cancer deaths and disability-adjusted life-years (DALYs) in 2019 and change in these measures between 2010 and 2019 are presented. Findings Globally, in 2019, the risk factors included in this analysis accounted for 4.45 million (95% uncertainty interval 4.01-4.94) deaths and 105 million (95.0-116) DALYs for both sexes combined, representing 44.4% (41.3-48.4) of all cancer deaths and 42.0% (39.1-45.6) of all DALYs. There were 2.88 million (2.60-3.18) risk-attributable cancer deaths in males (50.6% [47.8-54.1] of all male cancer deaths) and 1.58 million (1.36-1.84) risk-attributable cancer deaths in females (36.3% [32.5-41.3] of all female cancer deaths). The leading risk factors at the most detailed level globally for risk-attributable cancer deaths and DALYs in 2019 for both sexes combined were smoking, followed by alcohol use and high BMI. Risk-attributable cancer burden varied by world region and Socio-demographic Index (SDI), with smoking, unsafe sex, and alcohol use being the three leading risk factors for risk-attributable cancer DALYs in low SDI locations in 2019, whereas DALYs in high SDI locations mirrored the top three global risk factor rankings. From 2010 to 2019, global risk-attributable cancer deaths increased by 20.4% (12.6-28.4) and DALYs by 16.8% (8.8-25.0), with the greatest percentage increase in metabolic risks (34.7% [27.9-42.8] and 33.3% [25.8-42.0]). Interpretation The leading risk factors contributing to global cancer burden in 2019 were behavioural, whereas metabolic risk factors saw the largest increases between 2010 and 2019. Reducing exposure to these modifiable risk factors would decrease cancer mortality and DALY rates worldwide, and policies should be tailored appropriately to local cancer risk factor burden. Copyright (C) 2022 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license.Peer reviewe

The global burden of adolescent and young adult cancer in 2019: a systematic analysis for the Global Burden of Disease Study 2019

Background: In estimating the global burden of cancer, adolescents and young adults with cancer are often overlooked, despite being a distinct subgroup with unique epidemiology, clinical care needs, and societal impact. Comprehensive estimates of the global cancer burden in adolescents and young adults (aged 15–39 years) are lacking. To address this gap, we analysed results from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019, with a focus on the outcome of disability-adjusted life-years (DALYs), to inform global cancer control measures in adolescents and young adults. Methods: Using the GBD 2019 methodology, international mortality data were collected from vital registration systems, verbal autopsies, and population-based cancer registry inputs modelled with mortality-to-incidence ratios (MIRs). Incidence was computed with mortality estimates and corresponding MIRs. Prevalence estimates were calculated using modelled survival and multiplied by disability weights to obtain years lived with disability (YLDs). Years of life lost (YLLs) were calculated as age-specific cancer deaths multiplied by the standard life expectancy at the age of death. The main outcome was DALYs (the sum of YLLs and YLDs). Estimates were presented globally and by Socio-demographic Index (SDI) quintiles (countries ranked and divided into five equal SDI groups), and all estimates were presented with corresponding 95% uncertainty intervals (UIs). For this analysis, we used the age range of 15–39 years to define adolescents and young adults. Findings: There were 1·19 million (95% UI 1·11–1·28) incident cancer cases and 396 000 (370 000–425 000) deaths due to cancer among people aged 15–39 years worldwide in 2019. The highest age-standardised incidence rates occurred in high SDI (59·6 [54·5–65·7] per 100 000 person-years) and high-middle SDI countries (53·2 [48·8–57·9] per 100 000 person-years), while the highest age-standardised mortality rates were in low-middle SDI (14·2 [12·9–15·6] per 100 000 person-years) and middle SDI (13·6 [12·6–14·8] per 100 000 person-years) countries. In 2019, adolescent and young adult cancers contributed 23·5 million (21·9–25·2) DALYs to the global burden of disease, of which 2·7% (1·9–3·6) came from YLDs and 97·3% (96·4–98·1) from YLLs. Cancer was the fourth leading cause of death and tenth leading cause of DALYs in adolescents and young adults globally. Interpretation: Adolescent and young adult cancers contributed substantially to the overall adolescent and young adult disease burden globally in 2019. These results provide new insights into the distribution and magnitude of the adolescent and young adult cancer burden around the world. With notable differences observed across SDI settings, these estimates can inform global and country-level cancer control efforts. Funding: Bill & Melinda Gates Foundation, American Lebanese Syrian Associated Charities, St Baldrick's Foundation, and the National Cancer Institute