Open Access Model Research Articles

The rise of predatory publishing and journals.

Predatory publishing is a practice where businesses offer illegitimate and unethical publishing where an open access model is generally used with very little or no peer review at all. These publishers also charge high fees for article processing without the standard editorial or publishing standards for scientific disciplines. Predatory journals are an increasing phenomenon in dentistry, as in any healthcare academic publishing. This can mean poor-quality or false research is given false legitimacy and becomes available for dissemination and public consumption. They can be seen as an easy route to publish any work, particularly by junior colleagues who are trying to advance their academic careers. This article discusses the features and issues with predatory publishing while also highlighting the importance of ensuring healthcare literature remains credible, reputable and trustworthy.

Special issues: The roles of special issues in scholarly communication in a changing publishing landscape

AbstractThis paper aims to enhance the understanding of the role of special issues in the evolving landscape of academic publishing, offering insights for publishers, editors, guest editors, and researchers, including how new technologies influence transparency in publishing processes, open access models, and metrics for success. Based upon original analysis, the paper also discusses the importance of special issues and opportunities to support diversity, equity, and inclusivity in special issue publishing programmes. The goal is to contribute to the discussion of maintaining research integrity through special issues, acknowledging their significance in scholarly communication, while offering suggestions for the future.

Open Access Bacillus cereus Cocktail Secondary Growth Model for the Food Industry.

A cost-effective algorithm is presented, using a virtual dataset of growth rates from a cocktail of Bacillus cereus strains, for developing an open access, extended-range secondary growth model. Extended-range growth models can span the range of processing conditions typically used in food manufacturing and are therefore more relevant for industry. The open access extended-range secondary growth model for a cocktail of B. cereus strains was created using publicly available data, and the methodology can be adapted for modelling growth of other pathogens. An extended-range model can help manage B. cereus hazards in novel food categories with non-traditional formulations as estimations of B. cereus risks in these foods become more precise. This open access model, however, needs to be validated using data from B. cereus strain cocktails isolated from production facilities. Once validated, these independent factor models are valuable tools, in a pathogen decision support platform, which are tuned to local production environments. Such a platform can address the needs of current and future food product portfolios, effectively mitigating risks associated with B. cereus and other relevant pathogens.

MUSE: an open-access platform for urban expansion simulation with multitype patch generation engine and multilevel morphology regulation

Urban expansion models (UEMs) help unfold the mechanism, future pathways, and relevant repercussions of urban landscape dynamics. Although a plethora of UEMs have been developed, the field of open-access modeling platform for urban expansion simulation still presents gaps in terms of representing urban development events, regulating multilevel urban morphologies, and reflecting underlying regularities of physical urban growth. This study develops an open-access Multiengine Urban Expansion Simulation (MUSE) platform together with software that addresses some of these limitations. MUSE employs patch-based concepts and different patch generation engines to represent urban development events of distinctive types, enabling control over spatial morphology at landscape, class and patch levels. Moreover, MUSE incorporates two general regularities on urban development waves and urban diffusion and coalescence to govern physical urban expansion processes. Experiments in two cities examine MUSE’s ability in simulating realistic urban dynamics, and a series of synthetic experiments verify the operational behavior of the patch generation engines. These experiments show that MUSE can simulate a range of urban expansion types, including infill, edge growth and leapfrog expansion, and various morphologies, such as aggregated, sprawl, fragmented and compact. MUSE can empower practitioners to better project, analyze and understand complex urbanization dynamics.

Open Access Publication at a Crossroads—Implications for Researchers and Beyond

This Viewpoint describes the wide range of open access (OA) models, examines controversies as OA publication attempts to achieve equitable access, and recommends ways to address gaps.

The costs of open access publication

This article explores the financial dynamics of open access (OA) publication in Catalan universities by combining four data sources: publication data coupled with article processing charge (APC) estimates; information on journal subscriptions, transformative agreements and APC payments made by universities; acknowledgements of APC funding sources in OA scholarly outputs; and a survey of authors. The findings reveal a consistent increase in OA publication across Catalan universities, with 60% of the articles indexed in the Web of Science being published in either gold or hybrid OA in 2022. In parallel, investment in the research publishing system shows an upward trend. Resources allocated to journal subscription licenses have been redirected towards transformative agreements, leading to a rise in hybrid OA publications. Additional budget allocations have been made to accommodate APCs for gold OA journals. Authors employ varied funding sources for gold and hybrid OA, with university funding programmes and research grants commonly facilitating gold OA, while transformative agreements often support hybrid OA. Authors associated with Catalan universities frequently benefit from funding schemes and transformative agreements that are accessible to their coauthors. However, survey responses underscore the multifaceted nature of researchers’ financial support, including personal assets and waivers. Authors express frustration with the evolving OA landscape, particularly concerning the exorbitant publication fees. Nevertheless, the allure of high-impact journals and expedited peer review processes continues to incentivize authors towards gold OA. Researchers voice concerns regarding the lack of equitable funding programmes and potential conflicts of interest within gold OA models, which signals the risk of compromising peer review integrity to prioritize profits. This study underscores the need for further research to deepen our understanding of scholarly publishing expenditure and inform strategies for fostering a sustainable, equitable OA ecosystem.

Assessing Retrieval-Augmented Large Language Model Performance in Emergency Department ICD-10-CM Coding Compared to Human Coders.

Accurate medical coding is essential for clinical and administrative purposes but complicated, time-consuming, and biased. This study compares Retrieval-Augmented Generation (RAG)-enhanced LLMs to provider-assigned codes in producing ICD-10-CM codes from emergency department (ED) clinical records. Retrospective cohort study using 500 ED visits randomly selected from the Mount Sinai Health System between January and April 2024. The RAG system integrated past 1,038,066 ED visits data (2021-2023) into the LLMs' predictions to improve coding accuracy. Nine commercial and open-source LLMs were evaluated. The primary outcome was a head-to-head comparison of the ICD-10-CM codes generated by the RAG-enhanced LLMs and those assigned by the original providers. A panel of four physicians and two LLMs blindly reviewed the codes, comparing the RAG-enhanced LLM and provider-assigned codes on accuracy and specificity. RAG-enhanced LLMs demonstrated superior performance to provider coders in both the accuracy and specificity of code assignments. In a targeted evaluation of 200 cases where discrepancies existed between GPT-4 and provider-assigned codes, human reviewers favored GPT-4 for accuracy in 447 instances, compared to 277 instances where providers' codes were preferred (p<0.001). Similarly, GPT-4 was selected for its superior specificity in 509 cases, whereas human coders were preferred in only 181 cases (p<0.001). Smaller open-access models, such as Llama-3.1-70B, also demonstrated substantial scalability when enhanced with RAG, with 218 instances of accuracy preference compared to 90 for providers' codes. Furthermore, across all models, the exact match rate between LLM-generated and provider-assigned codes significantly improved following RAG integration, with Qwen-2-7B increasing from 0.8% to 17.6% and Gemma-2-9b-it improving from 7.2% to 26.4%. RAG-enhanced LLMs improve medical coding accuracy in EDs, suggesting clinical workflow applications. These findings show that generative AI can improve clinical outcomes and reduce administrative burdens. This work was supported in part through the computational and data resources and staff expertise provided by Scientific Computing and Data at the Icahn School of Medicine at Mount Sinai and supported by the Clinical and Translational Science Awards (CTSA) grant UL1TR004419 from the National Center for Advancing Translational Sciences. Research reported in this publication was also supported by the Office of Research Infrastructure of the National Institutes of Health under award number S10OD026880 and S10OD030463. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The funders played no role in study design, data collection, analysis and interpretation of data, or the writing of this manuscript. A study showed AI models with retrieval-augmented generation outperformed human doctors in ED diagnostic coding accuracy and specificity. Even smaller AI models perform favorably when using RAG. This suggests potential for reducing administrative burden in healthcare, improving coding efficiency, and enhancing clinical documentation.

External Validation of SpineNetV2 on a Comprehensive Set of Radiological Features for Grading Lumbosacral Disc Pathologies

BackgroundIn recent years, the integration of Artificial Intelligence (AI) models has revolutionized the diagnosis of Low Back Pain (LBP) and associated disc pathologies. Among these, SpineNetV2 stands out as a state-of-the-art, open-access model for detecting and grading various intervertebral disc pathologies. However, ensuring the reliability and applicability of AI models like SpineNetV2 is paramount. Rigorous validation is essential to guarantee their robustness and generalizability across diverse patient cohorts and imaging protocols. MethodsWe conducted a retrospective analysis of MRI images of 1747 lumbosacral intervertebral discs (IVDs) from 353 patients (mean age, 54 ± 15.4 years, 44.5% female) with various spinal disorders, collected between September 2021 and February 2023 at X-Ray Service s.r.l. The SpineNetV2 system was used to grade 11 distinct lumbosacral disc pathologies, including Pfirrmann grading, disc narrowing, central canal stenosis, spondylolisthesis, (upper & lower) endplate defects, (upper & lower) marrow changes, (right & left) foraminal stenosis, and disc herniation, using T2-weighted sagittal MR images. Performance metrics included accuracy, balanced accuracy, precision, F1 score, Matthew's Correlation Coefficient, Brier Score Loss, Lin's concordance correlation coefficients, and Cohen's kappa coefficients. Two expert radiologists provide annotations for these discs. The evaluation of SpineNetV2′s grading is compared against expert radiologists' assessments. ResultsSpineNetV2 demonstrated strong performance across various metrics, with high agreement scores (Cohen's Kappa, Lin's Concordance, and Matthew's Correlation Coefficient exceeding 0.7) for most pathologies. However, lower agreement was found for foraminal stenosis and disc herniation, underscoring the limitations of sagittal MR images for evaluating these conditions. ConclusionsThis study highlights the importance of external validation, emphasizing the need for comprehensive assessments of deep learning models. SpineNetV2 exhibits promising results in predicting disc pathologies, with findings guiding further improvements. The open-source release of SpineNetV2 enables researchers to independently validate and extend the model's capabilities. This collaborative approach promotes innovation and accelerates the development of more reliable and comprehensive deep learning tools for the assessment of spine pathology.

"Like and Subscribe": A Compendium of Infectious Diseases Audio Podcasts.

In little more than 15 years, the podcast has gone from being virtually unknown to becoming a multibillion-dollar industry. There are an estimated half-billion podcast listeners worldwide. Podcasts are available for various interests, from entertainment to news, politics, sports, hobbies, and education. Podcasting in medicine has similar origins, beginning with journals and academic/educational institutions wishing to share information on new clinical trials or publications, as well as by those who wanted to promote the free and open access model of online education. The COVID-19 outbreak led to a renaissance in the availability of infectious diseases-oriented audio podcasts, due to the need for regular information about SARS-CoV-2 and the pandemic-related preference for virtual learning. However, many in the infectious diseases community have not yet been introduced to available infectious diseases podcast resources. In this article, we highlight 38 of the most popular infectious diseases-oriented audio podcasts.

An examination of the “top 100” articles published in 2023: an altmetric analysis

Purpose The purpose of this study is to examine the “Top 100” articles that received the highest online attention in 2023. Design/methodology/approach The author examined data obtained from the Dimensions database. They determined the top 100 articles with the highest Altmetric Attention Score published in 2023 using the Dimensions database. The search was done on December 31, 2023, and the publication type was limited to articles. Furthermore, articles were analyzed to identify online attention platforms, subject categories, publication sources, access types and authorship patterns. The data were organized in Microsoft Excel for eventual examination. Findings The most discoursed article in 2023 has an Article Attention Score of 26156. The “Top 100 List” is dominated by COVID-19-related studies. X (249,064), Mendeley (2,445) and News (1,977) are the most prominent sharing and discussion platforms. There is an unequal distribution of articles in 28 subject categories. The top 100 articles were published in 67 journals. The majority of articles are accessible under the open-access model. The top 100 articles are written by 1,323 authors, with an authorship range of 1 to 308. The majority of articles are the result of collaborative work, and the correlation analysis between citations and AAS indicates a weak positive correlation possibly because of different factors influencing each metric and their methods of measuring scholarly impact. Originality/value To the best of the authors’ knowledge, this study is the first to present online attention to academic articles published in 2023. This study examines the effect of online attention platforms on research, which may be used as a measure of research outcome.

Viscosity of deep eutectic solvents: Predictive modeling with experimental validation

Viscosity, the measure of a fluid's resistance to deformation, is a critical parameter in many industries. Being able to accurately predict viscosity is essential for the successful design and optimization of technological processes. In this research, regression models were created to predict the viscosity of deep eutectic solvents (DESs). Machine learning models were trained using a data set of 3440 data points for two component DESs. Different algorithms, such as Multiple Linear Regression, Random Forest, CatBoost, and Transformer CNF, were employed alongside a variety of structural representations like fingerprints, σ-profiles, and molecular descriptors. The effectiveness of the models was assessed for interpolation tasks within the training data and extrapolation outside of it. The results indicate that a rigorous splitting of the dataset into subsets is necessary to accurately evaluate the performance of the models. Two new choline chloride-based DESs were prepared and their viscosities were measured to evaluate the predictive capabilities of the models. The CatBoost algorithm with CDK molecular descriptors was chosen as the recommended model. The average absolute relative deviations (AARD) of this model exhibited fluctuations during 5-fold cross-validation, ranging from 10.8 % when interpolating within the dataset to 88 % when extrapolating to new mixture components. The open access model was presented in this study (http://chem-predictor.isc-ras.ru/ionic/des/).

From serials crisis to dollar crisis: The compelling evidence against APC‐based open access in sub‐Saharan Africa countries

Key points The article processing charges (APC)‐based model of open access has constituted a major obstacle to achieving open access in developing countries. High exchange rates of local currencies to the dollar make sustaining the APC open access model impractical. Other approaches should be used to achieve equitable and inclusive open access.

Open Access in language testing and assessment: The case of two flagship journals

This study is a systematic examination of the open access status of research in two flagship language testing and assessment journals: Language Testing and Language Assessment Quarterly. Coding and analysing 898 articles, we investigated (a) the prevalence of open access in four aspects—open manuscripts, open materials, open data, and open code, and (b) the relationship between open access and various characteristics of research, tests, and researchers. Our study revealed a positive trend in the adoption of open access over time, with open manuscripts and materials showing notable increases. Open code and data have remained scarce, though with a recent uptick from a low base. Notably, logistic regression results suggest inequitable participation in open access as authors from the Global South were less likely to have open manuscripts. Recognising the potential role of flagship journals as trend and standard setters, we call on the field to (a) shift towards more equitable open access models, (b) balance intellectual property concerns with validation needs, (c) recognise open code and open data with protected access via dedicated badges, and (d) adopt Research Transparency Statements, a new reporting structure inclusive of methodological and epistemological differences in open research practices.

S94 - Patient Perspectives on an Open Access Model for Methadone Treatment: A Research and Process Improvement Protocol

S94 - Patient Perspectives on an Open Access Model for Methadone Treatment: A Research and Process Improvement Protocol

Open Access: Opening or Closing Doors for Junior Faculty?

The Open Access movement has transformed the landscape of medical publishing. Federal regulations regarding Open Access have expanded in the USA, and journals have adapted by offering a variety of Open Access models that range widely in cost and accessibility. For junior faculty with little to no funding, navigating this ever-changing landscape while simultaneously balancing the pressures of publication and promotion may present a particular challenge. Open Access provides the opportunity to amplify the reach and impact of scientific research, yet it often comes at a cost that may not be universally affordable. In this perspective, we discuss the impact of Open Access through the lens of junior faculty in general internal medicine. We describe the potential benefits and pitfalls of Open Access on junior faculty with a focus on research dissemination and cost. Finally, we propose sustainable solutions at the individual and systems-level to help navigate the world of Open Access to promote career growth and development.

The Conceptual ‘APC Ring’: Is There a Risk of APC-Driven Guest Authorship, and Is a Change in the Culture of the APC Needed?

While guest or honourary authorship in academic papers is a broadly and widely discussed phenomenon in biomedical research, the issue of the use—or abuse—of article-processing charges (APCs) as a form of potential authorship exchange currency, that is, the ‘APC ring,’ is neither being considered nor discussed. The APC is central to the open-access (OA) movement, specifically the gold OA model. It is conceivable that, in a hyper-competitive academic publishing environment where the number of gold OA journals is growing, a segment of poorly funded researchers aiming to publish in ranked OA journals with out-of-reach APCs might turn to richer or well-funded researchers to cover the APC bill in exchange for authorship. Despite this, no published cases directly documenting APC-for-authorship schemes as a form of guest authorship appear to exist, which seems inconceivable. One possible explanation is that if such unethical behaviour were to be detected by APC-charging OA journals, it might not be reported as such. In this situation, APC-dependent OA journals would be conflicted between receiving a financial lifeline, the APC, and exposing authors that have abused the APC in their journals in exchange for authorship. How would publishers dependent on the APC-based OA model justify receiving APCs derived from an APC ring? Although this form of guest authorship is currently hypothetical, it seems highly likely, so this issue needs greater debate, and if actual case studies exist, these need to be openly and publicly debated to better appreciate how this phenomenon is taking place.

Celebrating a century of APMIS: a legacy of pathology, microbiology, and immunology

This manuscript commemorates the 100th anniversary of APMIS, highlighting its evolution from a regional journal, founded in 1924 as Acta Pathologica et Microbiologica Scandinavica, to an international platform fostering global collaboration in pathology, microbiology, and immunology. The journal's inception was driven by Ulrik Quensel's vision in 1919, leading to the establishment of the Northern Pathological Society and the launch of the journal in 1924. APMIS has consistently published landmark research, including significant contributions from prominent. These studies have advanced understanding in fields such as pathology, microbiology, and immunology. The journal expanded its scope in the 1970s to include immunology, rebranding as APMIS in the mid‐1980s. Recent decades have seen a continued commitment to cutting‐edge research and an increasing impact factor. As APMIS transitions to an Open Access model under Wiley, it will be renamed the PMI Journal (Pathology, Microbiology, and Immunology) to reflect its global reach and dedication to scientific excellence. This centennial celebration acknowledges the contributions of editors, authors, and readers, looking forward to future advancements in biomedical research.

Open Access Models of Russian Academic Journals

Open access (OA) to publications has been a global trend in publishing academic journals for a long time. The number of OA journals, including Russian ones, is growing steadily. The purpose of this study was to determine the main trends in the implementation of open access publishing models in Russian research journals. The article presents the results of a study of 396 journals included in the Russian Science Citation Index database: title of a journal; website address; international classification code (OECD group); quartile; Science Index indicator; open access model; license type; section of a journal’s website that contains information about the absence or presence and amount of an article processing charge (APC). It is concluded that the majority of journals implement Bronze OA which, firstly, does not comply with the key principles of open access, because it does not use open licenses, and, secondly, does not provide any guarantees that open access will continue to be open. The lack of accessible and transparent information about the conditions for further use of publications can create serious legal issues for the licensee. In turn, it will most likely be a problem for authors to calculate the amount of publication fee.

A Journey Through the First to Eighteenth Issue of JKAHS

The Journal of Karnali Academy of Health Sciences (JKAHS) is an official publication of Karnali Academy of Health Sciences (KAHS), a government organization founded on October 20, 2011, by an act of the Parliament of Nepal [1]. KAHS was established with the objective of enhancing the quality of healthcare services, medical education, and research in remote and underserved areas of Nepal. The establishment of JKAHS in 2018 is a reflection of commitment of KAHS to these goals, providing a dedicated platform for the dissemination of scientific knowledge and clinical experiences in the health sciences [2].JKAHS is a peer-reviewed, international medical journal that operates under a diamond open access model, that means all its contents are freely accessible to readers without any subscription or paywall barriers [2]. This model not only broadens the journal’s audience, including researchers, students, policymakers, and the general public, but also aligns with the mission of KAHS to disseminate knowledge widely and equitably [1]. Importantly, JKAHS does not charge any fees for the submission, processing, or publication of manuscripts, thus removing financial barriers for authors and promoting inclusivity in scientific publishing. Additionally, to ensure the long-term preservation and accessibility of its content in the internet, JKAHS archives all its articles in LOCKSS (Lots of Copies Keep Stuff Safe) and CLOCKSS (Controlled Lots of Copies Keep Stuff Safe) [2]. These archiving systems safeguard the integrity and usability of the published work, ensuring that it remains available to future generations.It is triannual journal publishing three issues per year, and is available both online and in print with pISSN 2616-0064 and eISSN 2676-1327 [2]. This regular publication schedule ensures a steady flow of new research and insights, contributing to the continuous advancement of medical knowledge.Achievements and milestonesOne of our significant achievements has been in indexing of JKAHS in two national databases namely Nepal JournalOnline (NepJol) in 2019 [3] and NepalMedLine (NepMed) in 2020 [4]. The NepJol is hosted by Central Library (TUCL) and it is hosted by Ubiquity Press [3] whereas NepMed is hosted my Nepal Health Research Council (NHRC) [4]. A part from these national databases, we have been indexed in DOAJ (Directory of Open Access Journal) [5] and Hinari [6] in 2023. In the earlier days after indexing in NepJol, individual articles were assigned an unique DOI (digital object identifier) from NepJol (10.3126/jkahs). Later on we have taken our own DOI (10.61814/jkahs) directly from CrossRef under the sponsroship under GEM (Global Equitable Membership (GEM) Program from CrossRef [7]. This recognition is a testament to the quality and impact of our published research. Being indexed has enhanced the visibility and accessibility of our articles, attracted a broader readership and fostered greater academic collaboration.

A narrative review of the phenomenon of predatory journals to create awareness among researchers in veterinary medicine.

In recent years, especially since the COVID-19 pandemic, the number of predatory journals has increased significantly. Predatory journals exploit the "open-access model" by engaging in deceptive practices such as charging high publication fees without providing the expected quality and performing insufficient or no peer review. Such behaviors undermine the integrity of scientific research and can result in researchers having trouble identifying reputable publication opportunities, particularly early-career researchers who struggle to understand and establish the correct criteria for publication in reputable journals. Publishing in journals that do not fully cover the criteria for scientific publication is also an ethical issue. This review aimed to describe the characteristics of predatory journals, differentiate between reliable and predatory journals, investigate the reasons that lead researchers to publish in predatory journals, evaluate the negative impact of predatory publications on the scientific community, and explore future perspectives. The authors also provide some considerations for researchers (particularly early-career researchers) when selecting journals for publication, explaining the role of metrics, databases, and artificial intelligence in manuscript preparation, with a specific focus on and relevance to publication in veterinary medicine.