Self-archiving Research Articles

Machine Learning Prediction of Pituitary Macroadenoma Consistency: Utilizing Demographic Data and Brain MRI Parameters.

Consistency of pituitary macroadenomas is a key determinant in surgical outcomes, with non-soft consistency linked to more complications and incomplete resections. This study aimed to develop a machine learning model to predict the consistency of pituitary macroadenomas to improve surgical planning and outcomes. A retrospective study of patients with pituitary macroadenomas was conducted. Data included brain magnetic resonance imaging findings (diameter and apparent diffusion coefficient), patient demographics (age and sex), and tumor consistency. Seventy patients were evaluated, 59 with soft consistency and 11 with non-soft consistency. The support vector machine (SVM) was the best model with ROC AUC score of 83.3% [95% CI 65.8, 97.6], AP AUC of 69.8% [95% CI 41.3, 91.1], sensitivity of 73.1% [95% CI 44.4, 100], specificity of 89.8% [95% CI 82, 96.7], F1 score of 0.63 [95% CI 0.36, 0.83], and Matthews correlation coefficient score of 0.57 [95% CI 0.29, 0.79]. These findings indicate a significant improvement over random classification, as confirmed by a permutation test (p < 0.05). Additionally, the model had a 67.4% probability of outperforming the second-best model in cross-validation, as determined through Bayesian analysis, and demonstrated statistical significance (p < 0.05) compared to non-ensemble models. Using explainability heuristics, both 2D and 3D probability maps highlighted areas with a higher probability of non-soft consistency. The attributes most influential in the correct classification by our best model were male sex and age ≤ 42.25years. Despite some limitations, the SVM model showed promise in predicting tumor consistency, which could aid in surgical planning. To address concerns about generalizability, we have created an open-access repository to promote future external validation studies and collaboration with other research centers, with the goal of enhancing model prediction through transfer learning.

From chaos to clarity: how controlled vocabularies shape Indian social science repositories

Purpose The Confederation of Open Access Repositories (COAR) prescribes three types of controlled vocabularies for open access repositories (OARs): access rights, resource type and version type. Interestingly, COAR does not suggest a subject-specific vocabulary for organising content, whereas the subject parameter is one of the most preferred search categories used by information seekers. The purpose of the study is to investigate the use of controlled vocabularies in subject arrangement in OARs. Design/methodology/approach The study comprises eight stages. The first is to identify the total number of repositories enlisted in OpenDOAR under the social science domain in India. Next, the samples are selected, followed by data harvesting using MarcEdit OAI-PMH harvester plug-ins. The next step is to process the data and then consolidated controlled vocabulary is constructed by merging six existing thesauri. Then, a similarity matching algorithm is used to determine the usage of controlled vocabularies for subject arrangement. The last step is to evaluate the efficacy of controlled vocabulary in information retrieval. Findings The results revealed that subject arrangement differs largely in each repository. The study also showed that the use of controlled vocabularies in OARs for subject arrangement still needs to be standardised to enhance interoperability. Originality/value This research reflected that those controlled terms address issues, such as ambiguity, inconsistency and synonym variation, typically found with uncontrolled keywords through standardising subject metadata. This standardisation gives users a more reliable and user-friendly search experience, ultimately improving the discoverability and usability of open access content.

AQuA-P: A machine learning-based tool for water quality assessment.

This study addresses the critical challenge of assessing the quality of groundwater and surface water, which are essential resources for various societal needs. The main contribution of this study is the application of machine learning models for evaluating water quality, using a national database from Mexico that includes groundwater, lotic (flowing), lentic (stagnant), and coastal water quality parameters. Notably, no comparable water quality classification system currently exists. Five advanced machine learning techniques were employed: extreme gradient boosting (XGB), support vector machines, K-nearest neighbors, decision trees, and multinomial logistic regression. The performance of the models was evaluated using the accuracy, precision, and F1 score metrics. The decision tree models emerged as the most effective across all water body types, closely followed by XGB. Therefore, the decision tree models were integrated into the AQuA-P software, which is currently the only software of its kind. It is recommended that these innovative water classification models be used through the AQuA-P software to facilitate informed decision-making in water quality management. This software provides a probability-based classification system that contributes to a deeper understanding of water quality dynamics. Lastly, an open-access repository containing all the datasets and Python notebooks used in our analysis is provided, allowing for easy adaptation and implementation of our methodology for other datasets worldwide.

Reliability of the Type System in TypeScript in Software Development

The article examines the TypeScript type system as a critical element influencing its use in software development. The primary objective of the study is to analyze the characteristics of the type system and identify methods for improving the accuracy of type checking. The article explores the principles underlying the type system, its vulnerabilities such as the use of the any type, type assertions, issues with object and array indexing, and proposes approaches to enhancing system reliability. The methodology includes an analysis of TypeScript's structure, the principles of its compiler, and the application of tools for static code analysis. The study references academic articles available in open-access online repositories, providing a broad perspective on the topic. Additionally, examples of code presented in the work illustrate key concepts and methods for working with type systems. Results demonstrate that configuring the compiler, avoiding the any type, and leveraging libraries for data validation improve the quality of type safety. The findings, based on the analysis of relevant sources, will be useful for programmers and corporate professionals. This review paper is a guide for software developers to understand the essence and the reliability of the Type System in TypeScript. This is a requirement to the scientific community as it guides software developers with the understanding and methods for efficiency in Type Checking. Principles, vulnerabilities and practice in code analysis are explicitly enumerated.

Understanding how and why users might use NHS repositories: A mixed methods study.

There is little evidence on the use or potential use of NHS repositories within the UK. A mixed methods (quantitative/qualitative) study of two repositories: amber-the home of ambulance service research, and East Midlands Evidence Repository (EMER). A structured online questionnaire was distributed via the repository home page, and promoted via social media, email networks, and lists. Next, three research leaders were interviewed in person online (see AppendixS1, supporting information). Transcripts of the recorded interviews were summarised using ChatGPT 3.5. From the 148 questionnaire responses, 38% of respondents had used an NHS repository. Librarian activities were key to encouraging repository use (that is, searching and depositing materials). ResearchGate was the most widely used alternative. Perceived benefits of using repositories included open access to materials, and knowledge sharing with colleagues. Users generally did not know the deposit process, and over 50% of respondents were unaware of Green Open Access. Building greater awareness, and institutional support is key to increasing repository usage. Marketing activities and educating researchers about the benefits of engaging with the repository are fundamental. NHS librarians need to market NHS repositories using principles of knowledge management and ensure that the grey literature of research and evaluation reports in repositories is better used.

Integrating literature and family insights: exploring the needs of families supporting adults with diabetes.

The considerable influence that family members can have on diabetes management is well recognized. Therefore, it is crucial for professionals to acknowledge the impact of the diagnosis on family members. This study aimed to comprehensively identify and understand the needs of family members with an adult diagnosed with diabetes using a two-phased research design. Phase 1 was a scoping literature review using databases such as MEDLINE®, CINAHL®, SciELO, and PsycINFO, and gray literature from the Scientific Open Access Repository of Portugal and OpenGrey, focusing on studies from 2017 to 2023, adhering to the Joanna Briggs Institute and PRISMA guidelines. Phase 2 involved a focus group to gather qualitative data on family experiences, which was analyzed using content analysis and following the Consolidated Criteria for Reporting Qualitative Research. Communication and emotional expression within families, the impact of diabetes on the family, diabetes-specific knowledge, socio-cultural and environmental influences on diabetes management, and communication with healthcare providers. Integrating these findings highlighted the specific needs of families, suggesting that tailored interventions should be developed to enhance diabetes management support and promote overall family well-being.

Understanding new dimensions of User Perceptions of Information Communication and Open Access Repositories in Academic Research in Developing Countries

Understanding new dimensions of User Perceptions of Information Communication and Open Access Repositories in Academic Research in Developing Countries

Researchers’ self-archiving behavior towards open-access institutional repositories

The success of open-access repositories depends heavily on researchers’ willingness to disseminate their research through self-archiving. Previous studies indicated that lack of self-archiving was a major obstacle to the success of institutional open-access repositories. This study aimed to identify factors influencing researchers' behavior in self-archiving. The analysis examined the influence of repository performance expectations, effort expectations, social influence, and facilitating conditions on researchers' self-archiving intentions and behavior. The study also explored the moderating role of demographic factors such as gender, age, and experience in the relationship between the analyzed factors and self-archiving intentions and behavior. Furthermore, this study also revealed the direct impact of regulatory awareness and research discipline on self-archiving intentions and behavior. The research findings showed that social influence significantly affected researchers' intentions to self-archive while facilitating conditions had a substantial impact on self-archiving behavior. Additionally, demographic variables, such as gender, age, and experience, were found to moderate the effects of social influence on behavioral intention, while awareness of regulations contributed directly to self-archiving behavior. These findings highlight the importance of strengthening social influence, providing adequate supporting conditions, and implementing supportive policies and regulations to enhance researchers' self-archiving behavior in open-access institutional repositories.

Editorial: Institutional Repository of the Kyiv Medical University: A New Open Access Database for Authors and Peer-Reviewed Journals

Open access repository is a database, or a virtual archive established to collect, disseminate and preserve scientific output like scientific articles and datasets and to make them freely available. An institutional repository is one of four types of repositories. The purposes of this article are (1) to highlight the most important points of the Regulation on the Institutional Repository of the Kyiv Medical University (IRKMU) and (2) to explain the advantages for authors and peer-reviewed journals of colonization of the repository of such type. Also, this paper highlights the experience of the Department of Oral and Maxillofacial Surgery and the Journal of Diagnostics and Treatment of Oral and Maxillofacial Pathology (JDTOMP) in depositing peer-reviewed articles in this repository. The Regulation on the IRKMU was put into effect by Order No. 29 of January 26, 2024. In the same year, all structural units of the university, including dental departments, joined the process of depositing their scientific and clinical works. The IRKMU was created using the open-source software DSpace, which supports the Open Access Initiative Protocol for Metadata Harvesting (OAI-PMH) data exchange protocol, allowing the repository to be integrated into the international registers of the Registry of Open Access Repositories (ROAR), Directory of Open Access Repositories (OpenDOAR), and other search engines. The article is reinforced with screenshots of the stages of depositing data of scientific works. Carlile Butterfield and colleagues (2022) emphasized, that despite all benefits, however, their research indicates that it can be difficult to encourage all faculties to upload the research reports onto the institutional repository. Moreover, the authors propose a potential route to maximize the number of publications that are uploaded to a university institutional repository. They utilize student workers and the resources of the institutional repository manager to get materials uploaded. The experience of our department consists in attracting a competent editor from the editorial staff of the JDTOMP with appropriate payment for services. In sum, colonizing this new institutional repository as a new database, authors and peer-reviewed journals can and will increase the visibility of their publications. Thus, it can bear fruit in terms of increasing the citation of articles and the journals as well.

Post-Communist Anti-Communism in Romania Secret Police Files, Transitional Justice and Production of Knowledge

This study examines the phenomenon of post-communist anti-communism in Romania and explores its multifaceted relationship with two key processes that unfolded after the bloody regime change of December 1989: the historical reconstruction of the communist past and the implementation of transitional justice. In Romania, the legal framework for transitional justice was adopted only in the late 1990s, and thus post-communist anti-communism also manifested as a battle for the opening of the archives of communism, including secret police archives. However, these archives remained closed throughout the 1990s, and as a result, memory emerged as the key term associated with justice, along with the complex processes of fact-finding and truth-seeking concerning the abuses committed under the communist regime. In this context, post-1989 research on communist and early post-communist Romania focused primarily on memory studies, as witness accounts abounded while archival sources were scarce, with emphasis on the recollections of those who suffered under communism. When transitional justice legislation was finally adopted, it did not enable lustration but allowed for the systematic public exposure of the wrongdoings committed under the communist regime. Paradoxically, the actual implementation of transitional justice, under the existing legislation, combined with the post-communist anti-communist ethos, led to the creation of a large, open-access online repository. This repository has allowed for a more sophisticated, and definitely more nuanced, approach to the complicated history of communist Romania.

Trends, gaps, and challenges in doctoral research on community engagement

The field of community engagement in higher education has expanded significantly in the last three decades. Its varied disciplinary perspectives, diverse stakeholders, and wide-ranging cultural contexts have positively contributed to student learning outcomes and community impact. With this expansion comes methodological challenges for doctoral scholars of community engagement, who often lack guidance around conducting community-engaged research that may question traditional epistemologies and ontologies. In this systematic literature review, we analyzed 36 dissertations published between 2018 and 2022 to identify the trends, gaps, and challenges in doctoral research on community engagement. Challenges identified included rethinking research designs, expanding subjects and participants, promoting cross-cultural and global studies, and revisiting epistemological and ontological stances. Recommendations include an open-access dissertation repository, formalized support for graduate students, recognition of “trendbreaking” scholars, and wider embrace of the global network of researchers of community engagement.

Librarians’ perceptions and use of open access resources for economic sustainability in selected university libraries in Kwara State, Nigeria

Purpose Open access (OA) resources are free to access and help in research and teaching/learning, allowing libraries to manage resources more sustainably and effectively. Hence, this study aims to examine use of OA resources for economic sustainability among librarians in selected university libraries in Kwara State, Nigeria. Design/methodology/approach This study adopts descriptive survey research design. Using total enumeration sampling technique, a sample of 46 professional librarians were drawn from the selected universities. Questionnaire was used for data collection, and descriptive statistics was used for data analysis. Findings The findings show that most of the librarians had high level of awareness about OA resources. Results demonstrate that majority of the librarians used PubMed Central bi-weekly. Findings show that the librarians used OA resources to support academic research, enhance library’s collection without additional cost and facilitate information access for users with limited financial resources. Results indicate that most of the librarians perceived that OA resources impact library’s operational cost and goal of economic sustainability. Practical implications This study highlights the need for targeted training and resource development to enhance the effective use of OA resources. Meanwhile, the consistent usage of OA resources suggests the importance of the resources to librarians, aligning with previous studies on frequent use of established OA repositories. Originality/value This study provides evidence on the relevance and impact of OA resources use on economic sustainability, demonstrating the importance of OA resources in knowledge dissemination and fostering innovation.

Good practices on open access publications of projects funded by Horizon 2020

This study aimed to analyse the results of open access publishing policies established for projects funded by the European Union's Horizon 2020 programme. It specifically sought to: Identify specific publication requirements, quantify the number of peer-reviewed articles published in open access and analyse the number of documents deposited in institutional repositories. The archive of Horizon 2020 project publications provided by the EU Publications Office was used as a database. It was possible to determine the reported peer-reviewed publications. From those with DOIs, the data were cross-checked with the OpenAIRE platform to analyse open access and repository information. From the original data, a total of 206,400 peer-reviewed articles are observed, of which 202,102 have a DOI, 4,269 include the ISSN of the publication and only 28 have no data to reach access. Cross-referencing the data from those with DOIs in OpenAIRE a total of 126,154 of these articles have no metadata. This analysis highlights the need to improve the tracking of the access address of publications and to encourage deposit in open access repositories with open licences.

Leveraging textured flickers: a leap toward practical, visually comfortable, and high-performance dry EEG code-VEP BCI

Reactive Brain-Computer Interfaces (rBCIs) typically rely on repetitive visual stimuli, which can strain the eyes and cause attentional distraction. To address these challenges, we propose a novel approach rooted in visual neuroscience to design visual Stimuli for Augmented Response (StAR). The StAR stimuli consist of small, randomly-oriented Gabor or Ricker patches that optimize foveal neural response while reducing peripheral distraction.&#xD;&#xD;Methods: In a factorial design study, 24 participants equipped with an 8-dry electrode EEG system focused on series of target flickers presented under three formats: traditional Plain flickers, Gabor-based, or Ricker-based flickers. These flickers were part of a five-class Code Visually Evoked Potentials (c-VEP) paradigm featuring low-frequency, short, and aperiodic visual flashes.&#xD;&#xD;Results: Subjective ratings revealed that Gabor and Ricker stimuli were visually comfortable and nearly invisible in peripheral vision compared to plain flickers. Moreover, Gabor and Ricker-based textures achieved higher accuracy (93.6% and 96.3%, respectively) with only 88 seconds of calibration data, compared to plain flickers (65.6%). A follow-up online implementation of this experiment was conducted to validate our findings in naturalistic operations. During this trial, remarkable accuracies of 97.5% in a cued task and 94.3% in an asynchronous digicode task were achieved, with a mean decoding time as low as 1.68 seconds.&#xD;&#xD;Conclusion: This work demonstrates the potential to expand BCI applications beyond the lab by integrating visually unobtrusive systems with gel-free, low-density EEG technology, thereby making BCIs more accessible and efficient. The datasets, algorithms, and BCI implementations are shared through open-access repositories.

Engaging stakeholders in Non-communicable diseases (NCDs) Implementation Research in low- and middle-income countries (LMICs): a scoping review protocol

IntroductionNon-communicable diseases (NCDs) present a significant health challenge globally, especially in low- and middle-income countries (LMICs). Effective Implementation Research (IR) is vital in addressing this challenge, with stakeholder engagement playing...

Editorial: The National Repository of Academic Texts and the Journal of Diagnostics and Treatment of Oral and Maxillofacial Pathology

Editorial teams with their publishers of all peer-reviewed journals in the world dream and strive to include journals in as many databases as they can. Journals that were "born" in Ukraine must go through their path of self-affirmation first on the Ukrainian scientific market, and then, or even in parallel, in the international academic world. One of the key factors in the recognition by the Ministry of Education and Science of Ukraine of a peer-reviewed publication as a scientific professional publication of category "B" is the inclusion of this publication (1) in the Vernadsky National Library of Ukraine and (2) in the National Repository of Academic Texts (NRAT). Peer-reviewed publications assigned category "A" or "B" are included in the list of scientific professional publications of Ukraine, in which the results of dissertations for the degrees of Doctor of Philosophy (PhD) and Doctor of Sciences (ScD) may be published. The purpose of this paper is to highlight the aspects of including the Journal of Diagnostics and Treatment of Oral and Maxillofacial Pathology (JDTOMP) in the NRAT and the process of depositing articles. "Proclamation (i.e., Regulations) on the National Repository of Academic Texts" was approved by Decree No. 541 of the Cabinet of Ministers of Ukraine dated July 19, 2017. According to the Order of the Ministry of Education and Science of Ukraine dated October 25, 2017, No. 1421 "On the Manager of the NRAT," the Manager of the NRAT is the State Scientific Institution "Ukrainian Institute of Scientific and Technical Expertise and Information." The article lists the areas of responsibility of the NRAT Manager. Also, a complete list of academic texts that can be accepted into the NRAT is provided. For clarity, both the article of our journal deposited in the NRAT and the step-by-step illustrated mechanism for depositing articles are presented. In the modern publishing world, increasing the prestige of a journal and getting into the top-rated databases is impossible without the journal's gradual colonization of both institutional and national repositories. Broadly speaking, open access repositories are key to the ability not only of institutions but also of journals to respond to future needs for more dynamic cross‐boundary communications services, articles dissemination and editorial collaboration.

Scientific, Educational and Geotourism Value of the Ballota Beach that Recorded the Old and Most Recent Geological Histories of the North-Northwest Part of the Iberian Peninsula

One of the enclaves that exhibits the best features to understand the old and most recent geological history of the north-northwest portion of the Iberian Peninsula is the Ballota Beach, located in Asturias, Spain. In the cliff above sea level that borders this beach to the south, a succession of Carboniferous “griotte” limestones crops out, deformed by spectacular ramp and detachment folds, as well as thrusts, backthrusts and duplexes. These structures are testimonies of the shortening produced in the cordillera originated during the Variscan orogeny of Devonian-Permian age, which extended throughout central Europe, northern Africa and eastern North America. Additionally, from a viewpoint located on the cliff, one can recognize a flat surface over the carbonate coastal cliffs and higher flat surfaces developed on quartzites. These flat surfaces, known as “rasas”, are marine abrasion surfaces elevated above current sea level resulting from Cenozoic-Quaternary land uplift and/or sea level fall. This region, already mentioned in the XIX century, has an extraordinary scientific and educational value, from the Structural Geology, Geomorphology, Historical Geology and Stratigraphy points of view, and is a great geotourism attraction due to its beauty. To make this region known, we propose to declare this area a geological interest site in the Global Geosites Spain project, make this article open access, upload a virtual outcrop model we have built in open-access online repositories, make information available to public entities that promote outreach and tourism, propose the realization of a “Geolodía” (Geology day), and make a video to celebrate the Geodiversity International Day.

The Genomic SSR Millets Database (GSMDB): enhancing genetic resources for sustainable agriculture.

The global population surge demands increased food production and nutrient-rich options to combat rising food insecurity. Climate-resilient crops are vital, with millets emerging as superfoods due to nutritional richness and stress tolerance. Given limited genomic information, a comprehensive genetic resource is crucial to advance millet research. Whole-genome sequencing provides an unprecedented opportunity, and molecular genetic methodologies, particularly simple sequence repeats (SSRs), play a pivotal role in DNA fingerprinting, constructing linkage maps, and conducting population genetic studies. SSRs are composed of repetitive DNA sequences where one to six nucleotides are repeated in tandem and distributed throughout the genome. Different millet species exhibit genomic variations attributed to the presence of SSRs. While SSRs have been identified in a few millet species, the existing information only covers some of the sequenced genomes. Moreover, there is an absence of complete gene annotation and visualization features for SSRs. Addressing this disparity and leveraging the de-novo millet genome assembly available from the NCBI, we have developed the Genomic SSR Millets Database (GSMDB; https://bioinfo.icgeb.res.in/gsmdb/). This open-access repository provides a web-based tool offering search functionalities and comprehensive details on 6.747645 million SSRs mined from the genomic sequences of seven millet species. The database, featuring unrestricted public access and JBrowse visualization, is a pioneering resource for the research community dedicated to advancing millet cultivars and related species. GSMDB holds immense potential to support myriad studies, including genetic diversity assessments, genetic mapping, marker-assisted selection, and comparative population investigations aiming to facilitate the millet breeding programs geared toward ensuring global food security. Database URL: https://bioinfo.icgeb.res.in/gsmdb/.

Repository (R)evolution: Metadata, Interoperability, and Sustainability

Introduction: Successfully managing an open-access repository requires constant attention to user community priorities in order to inform the development or selection of a platform that fulfills constantly evolving functional demands in an increasingly complex operational environment. This paper uses AgEcon Search (AES) as an example of the way that varying platforms address the metadata and other platform needs of a repository. AES is a successful subject repository with an international scope that has resided on several different platforms in its 25-year lifespan. Elements and Considerations: Critical among the technical requirements of a repository is interoperability with other information sources and the ability to accommodate and describe different types of objects, including data. Experienced in the use of easy and widely used Dublin Core (DC), as well as Machine-Readable Cataloging 21 (MARC 21)-based repository platforms, we discuss both metadata schemas from administrative and user perspectives. Reconsidering underlying metadata issues might positively impact both technical and administrative issues that are currently restricting the development of robust, interoperable systems. As managers of AES, we are uniquely placed to discuss both technical and sustainability issues. Conclusions: Although many institutional and subject repositories are on platforms that use DC for their metadata, other options are available. MARC, the well-established library standard, can provide the wide range of fields needed to fully and accurately describe the variety of document and data types that are included in repositories.

MDRepo-an open data warehouse for community-contributed molecular dynamics simulations of proteins.

Molecular Dynamics (MD) simulation of biomolecules provides important insights into conformational changes and dynamic behavior, revealing critical information about folding and interactions with other molecules. The collection of simulations stored in computers across the world holds immense potential to serve as training data for future Machine Learning models that will transform the prediction of structure, dynamics, drug interactions, and more. Ideally, there should exist an open access repository that enables scientists to submit and store their MD simulations of proteins and protein-drug interactions, and to find, retrieve, analyze, and visualize simulations produced by others. However, despite the ubiquity of MD simulation in structural biology, no such repository exists; as a result, simulations are instead stored in scattered locations without uniform metadata or access protocols. Here, we introduce MDRepo, a robust infrastructure that provides a relatively simple process for standardized community contribution of simulations, activates common downstream analyses on stored data, and enables search, retrieval, and visualization of contributed data. MDRepo is built on top of the open-source CyVerse research cyber-infrastructure, and is capable of storing petabytes of simulations, while providing high bandwidth upload and download capabilities and laying a foundation for cloud-based access to its stored data.