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

Transcultural adaptation and reliability of the spanish version of a questionnaire of oral hygiene advice given by dentists in Chile

Aim: To adapt and evaluate validity-reliability the spanish version of the questionnaire for oral hygiene advice given by dentist in Chile. Materials and methods: Validation study conducted according COSMIN recommendations. The original questionnaire in english was adapted to spanish by translation, back translation, expert review and pilot test sample of 56 dentists. The instrument consisted of 3 sections: recommendations for oral hygiene, relevance given to the delivery of oral hygiene instruction and training and experience in delivering oral hygiene recommendations. It was reapplied in 5 of them a week later. Reliability was measured by internal consistency (Cronbach's alpha), test-retest (Cohen's kappa and weighted kappa) and measurement error (limits of agreement, LdA). Content validity was evaluated by experts and construct validity through convergent validity (Pearson correlation). Results: A good level of internal consistency that applies to 5 items (Cronbach's alpha = 0.73) was obtained. For items of nominal scale the Cohen kappa coefficient was 0.80 (95% CI = 0.64 to 0.95) and for ordinal items weighted kappa coefficient (linear weighting) was 0.76 (95% CI = 0.65 to 0.88). The difference between the scores calculated for the measurements was 1 standard deviation 2.35. 95% of the differences were between -5.7 to 3.7 (+/- 4.7 LdA = 1) and the variance of the total score was 29 to 41. A good level of convergent validity (Pearson correlation = 0.63) was obtained. Conclusion: The final questionnaire obtained is valid and reliable for use in chilean dentists with a profile like those included in this study to identify and quantify the oral hygiene instruction they provide to patients. Future studies should assess the validity and reliability of this adaptation other spanish-speaking countries.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

COVID-19 as an opportunity for minimally-invasive dentistry : a national cross-sectional survey

Funding Information: IM acknowledges financial support from Post-doctoral-Research-Aid-Programme (European Regional Development Fund; 1.1.1.2/VIAA/3/19/543, Contract No 9.-14.5/27). All authors were part-time financed by the project of National Research Program “Impact of COVID-19 on health care system and public health in Latvia; ways in preparing health sector for future epidemics” (Project Nr. VPP-COVID-2020/1-0011). SEU acknowledges financial support from the European Union’s Horizon 2020 Research and Innovation Programme under Grant Agreement No. 857287. Publisher Copyright: © 2022, The Author(s).BACKGROUND: During the COVID19 pandemic, the Latvian government issued first absolute restrictions (elective treatments prohibited, only emergency care) and later relative restrictions (preference for non-aerosol-generating procedures (AGP) and emergency care) on dental care. This study aims to assess the impact of these restrictions on the decision made by Latvian dentists about caries treatment. METHODS: A Survey-based cross-sectional study was used. A minimum sample size of 174 dentists was estimated for national representativeness (N = 1524). The questionnaire was developed by experts and sent three times via email to Latvian dentists from July to September 2020 and was also delivered in printed form at two national conferences in September and October 2020. Descriptive statistics were calculated. RESULTS: We received 373 completed questionnaires, with a total response rate of 24.5%. Under the recommendation to reduce AGP for the treatment of uncomplicated caries, 10% of the dentists stated that they would stop attending, 54% would only attend emergencies, and 36% would attend as usual. Under prohibition, the percentages are 15%, 74%, and 11%, respectively. Regarding the type of treatment, more than 75% would opt to proceed with selective caries removal for both primary and permanent teeth and 10% for extraction. CONCLUSION: Latvian dentists are willing to treat patients with caries during the pandemic and state that they prefer to use non- or minimally invasive and less aerosol-generating methods for caries treatment.publishersversionPeer reviewe

WarpPINN: Cine-MR image registration with physics-informed neural networks

Heart failure is typically diagnosed with a global function assessment, such as ejection fraction. However, these metrics have low discriminate power, failing to distinguish different types of this disease. Quantifying local deformations in the form of cardiac strain can provide helpful information, but it remains a challenge. In this work, we introduce WarpPINN, a physics-informed neural network to perform image registration to obtain local metrics of the heart deformation. We apply this method to cine magnetic resonance images to estimate the motion during the cardiac cycle. We inform our neural network of near-incompressibility of cardiac tissue by penalizing the jacobian of the deformation field. The loss function has two components: an intensity-based similarity term between the reference and the warped template images, and a regularizer that represents the hyperelastic behavior of the tissue. The architecture of the neural network allows us to easily compute the strain via automatic differentiation to assess cardiac activity. We use Fourier feature mappings to overcome the spectral bias of neural networks, allowing us to capture discontinuities in the strain field. We test our algorithm on a synthetic example and on a cine-MRI benchmark of 15 healthy volunteers. We outperform current methodologies both landmark tracking and strain estimation. We expect that WarpPINN will enable more precise diagnostics of heart failure based on local deformation information. Source code is available at https://github.com/fsahli/WarpPINN.Comment: 18 pages, 10 figure

The global prevalence of early childhood caries: a systematic review with meta-analysis using the WHO diagnostic criteria

Aim To estimate the global prevalence of early childhood caries using the WHO criteria. Design Systematic review of studies published from 1960 to 2019. Data sources: PubMed, Google Scholar, SciELO, and LILACS. Eligibility criteria were articles using: dmft-WHO diagnostic criteria with calibrated examiners, probability sampling, and sample sizes. Study selection: Two reviewers searched, screened, and extracted information from the selected articles. All pooled analyses were based on random-effects models. The protocol is available on PROSPERO 2014 registration code CRD42014009578. Results From 472 reports, 214 used WHO criteria and 125 fit the inclusion criteria. Sixty-four reports of 67 countries (published 1992-2019) had adequate data to be summarised in the meta-analysis. They covered 29 countries/59018 children. Global random-effects pooled prevalence was (percentage[95% CI]) 48[43, 53]. The prevalence by continent was Africa: 30[19, 45]; Americas: 48 [42, 54]; Asia: 52[43, 61]; Europe: 43[24, 66]; and Oceania: 82[73, 89]. Differences across countries explain 21.2% of the observed variance. Conclusions Early childhood caries is a global health problem, affecting almost half of preschool children. Results are reported from 29 of 195 countries. ECC prevalence varied widely, and there was more variance attributable to between-country differences rather than continent or change over time

Energy loss of protons and deuterons at low energies in Pd polycrystalline thin films

We have investigated experimentally and by computer simulations the energy loss  distributions of low energy (E <10 keV) protons and deuterons transmitted through  polycrystalline palladium thin flms. In contrast with previous experiments on various transition metals we find that the stopping power of Pd is proportional to the ion velocity. Data of protons and deuterons are coincident within the experimental uncertainties, showing the absence of an isotopic effect on the stopping power of Pd in this energy range. The experimental results were analyzed and compared with Monte Carlo computer simulations and previous theoretical models. The dference in the velocity dependence of the energy loss of hydrogen ions in Pd with respect to other transition metals (Cu, Ag and Au) is explained by a theoretical analysis based on the properties of the d-electron bands of those elements.Fil: Celedón, C.. Comisión Nacional de Energía Atómica. Gerencia del Area de Energía Nuclear. Instituto Balseiro; Argentina. Comisión Nacional de Energía Atómica. Gerencia del Area de Investigación y Aplicaciones No Nucleares. Gerencia de Física (Centro Atómico Bariloche); ArgentinaFil: Sanchez, Esteban Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Comisión Nacional de Energía Atómica. Gerencia del Area de Investigación y Aplicaciones No Nucleares. Gerencia de Física (Centro Atómico Bariloche); Argentina. Comisión Nacional de Energía Atómica. Gerencia del Area de Energía Nuclear. Instituto Balseiro; ArgentinaFil: Moreno, Mario Sergio Jesus. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Comisión Nacional de Energía Atómica. Gerencia del Area de Investigación y Aplicaciones No Nucleares. Gerencia de Física (Centro Atómico Bariloche); Argentina. Comisión Nacional de Energía Atómica. Gerencia del Area de Energía Nuclear. Instituto Balseiro; ArgentinaFil: Arista, Nestor Ricardo. Comisión Nacional de Energía Atómica. Gerencia del Area de Investigación y Aplicaciones No Nucleares. Gerencia de Física (Centro Atómico Bariloche); Argentina. Comisión Nacional de Energía Atómica. Gerencia del Area de Energía Nuclear. Instituto Balseiro; ArgentinaFil: Uribe, J. D.. Universidad Técnica Federico Santa María. Departamento de Física. Laboratorio de Colisiones Atómicas; ChileFil: Mery, M.. Universidad Técnica Federico Santa María. Departamento de Física. Laboratorio de Colisiones Atómicas; ChileFil: Valdés, J. E.. Universidad Técnica Federico Santa María. Departamento de Física. Laboratorio de Colisiones Atómicas; ChileFil: Vargas, P.. Universidad Técnica Federico Santa María. Departamento de Física. Laboratorio de Colisiones Atómicas; Chil

Comparison between Radiographic and Visual-Tactile Exams for the Detection and Assessment of Proximal Caries

Background: The optimal management of a caries lesion involves a precise and reliablediagnosis along with an appropriate treatment decision. The traditional diagnostic methodcontinues being the visual-tactile and it is focused in the detection of cavitated lesions.Currently, caries classification systems that include the early caries lesions and allow fornon-operative or operative treatment decisions are known. The radiography is known as acomplement for the current diagnosis of dental caries. The agreement between the visualtactileand the radiographic caries tests varies depending upon the caries prevalence. Purpose:To compare the number of proximal caries lesions detected radiographically and thevisual-tactile method. Methods: Visual-tactile (DMF-S criteria) and radiographic (bite-wingx-rays) examinations were conducted in 40 16-to-35 year olds. Results: The mean DMF-T was4.9±3.4 (D: 0.2±0.4; M: 0; F: 4.9±3.4). The visual-tactile exam in the posterior teeth showed amean DF-S of 5.0±4.0 (D: 0.2±0.5), and the radiographic of 16.0±3.4 (Radiolucency in dentine:2.9±1.7; in enamel: 13.1±3.3). The level of agreement (Kappa coefficient) between thevisual-tactile and the radiographic methods was insignificant (0.0012-0.08). Conclusion: Theradiographic exam detects 220 % more proximal caries lesions than the visual-tactile examin posterior teeth, which allows emphasizing the importance of the radiographic examinationfor the detection of dental caries.publishersversionPeer reviewe

Clinical effectiveness/child-patient and parent satisfaction of two topical fluoride treatments for caries: a randomised clinical trial

Knowledge gaps exist regarding optimal silver diammine fluoride (SDF) regimens and the efficacy of new products for arresting dental caries in young children. We evaluated the effectiveness of 38%-SDF (SDI-RivaStar), Tiefenfluorid (TF) comparing with Placebo (P), all in conjunction with behavioural modification (BM), in preventing major complications (endodontic/extractions/pain)—a patient-centred outcome—due to early childhood caries over 12 months in children under 71-months. A six-arm, patient/parent-blinded, superiority, placebo-controlled randomised control trial at the university clinic in Riga, Latvia, from 1/9/20-31/8/22 (Protocol registration ISRCTN17005348). The trial tested six protocols, using three compounds (P/SDF/TF) under two regimes: annual and biannual (P1/P2/TF1/TF2/SDF1/SDF2) for major complications. Secondary outcomes included minor complications and parental satisfaction. All groups received BM. 373/427 randomised children (87.3%) completed the study. SDF2 had a significantly lower rate and risk of major (21.5%, OR = 0.28, 95%CI [0.11, 0.72], p 0.05). SDF biannual application with BM effectively prevented major complications of early childhood caries and was well accepted by children and their parents. Trial registration number: ISRCTN17005348, principal investigator: Ilze Maldupa, registration date: 30/06/2021. Clinical trial registration number: ISRCTN registry: ISRCTN17005348, https://doi.org/10.1186/ISRCTN17005348, registration date: 30/06/2021