Open Access Research Articles

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.

OA Journals in Subscription-Based Full-Text Databases in 2024: An Analysis of EBSCO’s Academic Search Complete

ABSTRACT This study examines the open access (OA) component in EBSCO’s Academic Search Complete (ASC) in 2024. Two sets of samples from all the 3,481 peer-reviewed non-embargoed full-text journals in ASC were examined. One set is 10% random samples, and the other set is journals from major publishers excluding gold OA publishers. Both sets have similar results that over 70% are OA journals. The findings may have impact on library’s collection development, reference and instruction services, or even the way to negotiate the price of aggregator databases.

Melatonin Pattern: A New Method for Machine Learning-Based Classification of Sleep Deprivation

Background: Pattern recognition and machine learning-based classification approaches are frequently used, especially in the health field. In this research, a new feature extraction model inspired by the melatonin hormone (sleep hormone) and named MelPat (melatonin pattern) has been developed. The developed model has been tested on an open access dataset. Materials and Methods: An open access sleep deprivation electroencephalography (EEG) dataset was tested to evaluate the MelPat method. There are two classes in the dataset. These are (a) sleep deprivation (SD) and (b) healthy control (HC) groups, respectively. In this study, EEG signals were divided into 15 s segments, thus obtaining 1377 SD and 1378 HC samples. In the next phase of the research, a new feature extraction model was proposed, and this model was named MelPat as it was inspired by the melatonin hormone. Additionally, the feature vector was expanded using the statistical moment approach. In the signal decomposition phase of the model, the Tunable Q-Wavelet Transform (TQWT) method was used. Thus, the signal was decomposed into sub-bands, and feature extraction was applied to each band. Neighborhood Component Analysis (NCA) and Chi2 methods were used together to reduce the dimension of the feature vector and select the most significant features. In this phase, the most significant features from both feature selection algorithms were combined, and the final feature vector was obtained. In the classification phase of the model, the Support Vector Machine (SVM) algorithm, which is a shallow classifier, was used. The dataset used in the research has 61 channels. Therefore, after obtaining channel-based results, the iterative majority voting (IMV) algorithm was applied to achieve higher classification performance and generalize the results, and the most accurate results were automatically selected. Results: With the proposed MelPat algorithm, a high classification success of 97.71% was achieved on the open access sleep deprivation dataset. Conclusions: The obtained results show that the MelPat-based new classification approach is highly effective on the dataset collected for SD detection. Moreover, the fact that the proposed method is inspired by the melatonin chemical, which is the sleep hormone, makes the method attractive and ironic.

Humanities scholars’ needs for open social scholarship platforms as online scholarly information sharing infrastructure

The contemporary scholarly communication environment is characterized by the growth in mandates and infrastructure for open access publication and open approaches to the research lifecycle, with a consequent explosion in the number of online platforms seeking to provide infrastructure for open scholarship. These include corporate academic social networks and scholar-governed infrastructure created as a reaction against those networks, as well as the recent major transformation of the social media landscape in the wake of changes at Twitter (now X), previously a major outlet for scholarly engagement with the public. Analysts of this environment have pointed out that most platform initiatives focus on narrow use cases rather than building up solutions through a holistic understanding of scholar workflows. This exploratory study uses focus group interviews to draw out responses to one academically governed platform, the Humanities and Social Sciences (HSS) Commons, in the context of humanities scholars’ existing work. It explores humanities scholars’ needs and behaviors related to sharing scholarly information with each other and broader audiences, particularly on the Internet. Feedback from participants sheds light on opportunities and challenges for academy-governed infrastructure for “open social scholarship.” Themes identified include technical fatigue and burnout in the current multi-platform environment, sustainability, and desires to reach and engage the right academic and non-academic audiences when appropriate.

Introducing Vegetation Ecology and Diversity (VED)

The current issue is the first one of the journal Vegetation Ecology and Diversity, formerly Plant Sociology, the international peer-reviewed journal of the Italian Society of Vegetation Science (SISV). Vegetation Ecology and Diversity (VED) publishes original research articles covering all aspects of vegetation, ranging from plant communities to landscapes, including dynamic processes and community ecology. It prioritizes papers that emphasize plant community ecology and vegetation surveys to advance ecological models, interpret and classify vegetation, map ecosystems, assess environmental quality, manage and conserve plant biodiversity, and interpret and monitor European habitats. All the articles are freely available in Open Access (OA). In the present Editorial, we introduce the new journal name, the new Editorial Board and Social Media Team, several Topical Collections, and initiatives to support young researchers.

Transformations in livestock systems: beyond ranching and pastoralism

Abstract Livestock systems across the world are transformed by capitalist forces. Understanding these social, economic, and cultural transformations is important because it has major implications for rural populations across the world. Traditionally, the study of livestock systems has been organized along the conceptual classification of ranching in North America and Australia and pastoralism in Africa and Asia, but this intellectual division has limited our understanding because of a priori assumptions about the extent to which these systems have been shaped by capitalism. The goal of our paper is to outline a conceptual framework to come to a better understanding of the different ways that livestock systems across the globe have become more and less capitalist. We use a comparative approach that considers a wide range of livestock systems in different parts of the world, ranging from pastoralism in open access and communally held grasslands to ranching in privately owned and fenced rangelands, and industrial agriculture, to examine the diversity, complexity, and dynamics of these systems at the intersection with capitalism. We describe how livestock keepers across the world adopt, adapt to, and challenge capitalist logics and offer new ways to raise livestock in the twenty-first century. One of the emergent themes of our review is the persistence of pastoral values and identities across livestock systems.

The Journal of Open Source Software (JOSS): Bringing Open-Source Software Practices to the Scholarly Publishing Communityfor Authors, Reviewers, Editors, and Publishers

Introduction: Open-source software (OSS) is a critical component of open science, but contributions to the OSS ecosystem are systematically undervalued in the current academic system. The Journal of Open Source Software (JOSS) contributes to addressing this by providing a venue (that is itself free, diamond open access, and all open-source, built in a layered structure using widely available elements/services of the scholarly publishing ecosystem) for publishing OSS, run in the style of OSS itself. A particularly distinctive element of JOSS is that it uses open peer review in a collaborative, iterative format, unlike most publishers. Additionally, all the components of the process—from the reviews to the papers to the software that is the subject of the papers to the software that the journal runs—are open. Background: We describe JOSS’s history and its peer review process using an editorial bot, and we present statistics gathered from JOSS’s public review history on GitHub showing an increasing number of peer reviewed papers each year. We discuss the new JOSSCast and use it as a data source to understand reasons why interviewed authors decided to publish in JOSS. Discussion and Outlook: JOSS’s process differs significantly from traditional journals, which has impeded JOSS’s inclusion in indexing services such as Web of Science. In turn, this discourages researchers within certain academic systems, such as Italy’s, which emphasize the importance of Web of Science and/or Scopus indexing for grant applications and promotions. JOSS is a fully diamond open-access journal with a cost of around US$5 per paper for the 401 papers published in 2023. The scalability of running JOSS with volunteers and financing JOSS with grants and donations is discussed.

Using Open Access Research Solutions to Improve the Academic Lifecycle for the Academic Community

Using Open Access Research Solutions to Improve the Academic Lifecycle for the Academic Community

A database of chief financial officer turnover and dismissal in S&P 1500 firms, 2000–2022

AbstractResearch SummaryUnderstanding the antecedents and consequences of executive turnover is an important topic in strategy research. Yet, due to limitations in data availability, we know little about the turnover and dismissal of executives beyond the CEO. To address this, we develop an open access database on CFO turnover and dismissal—given the unique interface CFOs form with CEOs as strategic partners—in S&P 1500 firms between 2000 and 2022. We search for media documentation of CFO turnover events and code for various types of departure with supporting evidence. We compare our CFO database with an open access CEO database and show distinct patterns of exit and interdependence between CFO and CEO departure. The results reveal important directions for strategy scholarship. The database is available on the OSF platform (osf.io/fh248/?view_only=2c62d6eb59bd433496ce101689df3adc).Managerial SummaryCFOs are key executives who shape the firm's strategy with CEOs. Consequently, understanding why CFOs leave their jobs and how this impacts the firm is important. Yet, the reasons why CFOs leave their jobs are rarely captured in existing databases. To address this, we develop an open access database documenting various types of CFO turnover and dismissal in S&P 1500 firms from 2000 to 2022. We establish a robust coding protocol and describe how we develop our database. We further explore how our CFO database contributes to the literature by comparing it with an open access CEO database; highlighting new lines of research and questions that it can stimulate. The database is available on the OSF platform (osf.io/fh248/?view_only=2c62d6eb59bd433496ce101689df3adc).

Judith Barnsby: On Her Career, Open Access, Artificial Intelligence, and Public Trust in Science

Judith Barnsby: On Her Career, Open Access, Artificial Intelligence, and Public Trust in Science

Publication Counts in Context: Normalization Using Query and Reference Terms in PubMed.

This article discusses the extensive use of publication counts as indicators of trends in the scientific activities of individual researchers, research groups, and entire disciplines. However, with the growing number of articles in general, these counts might produce false impressions among scientists. We propose a straightforward yet effective normalization method, which enables further context of publication counts by using a query and a reference term. Additionally, an open access implementation is readily available on the PubMed Normalization website.

Unlocking Disease-Modifying Treatments for TDP-43-Mediated Neurodegeneration.

Neurons degenerate in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), causing progressive and inevitably fatal neurological decline. The best therapeutic strategies target underlying disease mediators, but after decades of intensive research, the causes of these neurodegenerative diseases remain elusive. Recently, coordinated activities of large consortia, increasing open access to large datasets, new methods such as cryo-transmission electron microscopy, and advancements in high-resolution omics technologies have offered new insights into the biology of disease that bring us closer to understanding mechanisms of neurodegeneration. In particular, improved understanding of the roles of the key pathological protein TAR DNA binding protein 43 (TDP-43) in disease has revealed intriguing new opportunities that provide hope for better diagnostic tools and effective treatments for ALS and FTD.

Open Access Fees in Top Physiology Journals: How Indian Researchers May Miss the Opportunity of Publication in Top Journals

Open Access Fees in Top Physiology Journals: How Indian Researchers May Miss the Opportunity of Publication in Top Journals

Integration of data sets for modelling gender violence and perception of insecurity.

The dataset offers a comprehensive information to analyse cities and neighbourhood that are potentially unsafe for women, this information has been collected for four cities: Toluca (Mexico), Valencia (Spain), Dublin (Ireland) and San Francisco (USA). The collection includes quantitative and qualitative variables obtained and processed from open data, georeferenced publications from a social media platform, and points located through participatory mapping sessions. The data is structured in raw format, organized by country and city, and categorized according to the data source used while processing, which allows unrestricted access with most data analysis software and it does not depend on specific licenses. This format includes both geometric information and associated attributes allowing reusability and analysis in different environments. Additionally, the release of this data allows developing models tailored to specific local contexts and represents a significant advance in open data access as stated in the Sustainable Development Goal 5 (SDG 5), especially in relation to indicator 5.2.2. In general, this indicator faces a lack of sufficient data for accurate measurement, which limits the ability to accurately assess and address gender-based violence. By providing an open and flexible resource, the dataset not only facilitates comparative research and informed policymaking, it also supports the international commitment for transparency and contributes to filling existing gaps in information on violence and insecurity.

Patient Perspectives on an Open Access Model for Methadone Treatment

Patient Perspectives on an Open Access Model for Methadone Treatment

SO-TAD: A surveillance-oriented benchmark for traffic accident detection

Automatic traffic accident detection is a crucial component of Vehicle-to-Infrastructure (V2I) systems and is gaining increasing attention from researchers due to its significant impact on road safety. However, existing datasets often suffer from issues such as data contamination, small scale, and lack of open access, which hinder the advancement of research in this field. To overcome these challenges, we introduce the high-quality, large-scale Surveillance-Oriented Traffic Accident Detection (SO-TAD) dataset, designed with long-tail distribution characteristics. The SO-TAD dataset comprises 2,186 samples, including 282 traffic accident instances, each providing spatio-temporal localization information. Furthermore, within the proposed frame prediction-based traffic accident detection framework, we designed a three-channel scene feature fusion generative adversarial network (TCFF-GAN). This network integrates scene introduction features and scene difference features to generate predictive frame features. Subsequently, traffic accidents are detected based on the stability of the cosine similarity sequence between the predicted frames and the actual frames. We validated the effectiveness of the proposed TCFF-GAN not only through public datasets but also by conducting extensive experiments on the newly introduced SO-TAD dataset. This work also establishes a new benchmark for automatic traffic accident detection research. The code and dataset are available at https://github.com/cccxy-299/so-tad.

Interdisciplinarity and Stages in a Process of Engagement with Theatre Practice and Disability

Navigating recent shifts in diversity agenda in the theatre industry and ensuring continued moves towards the accurate representation, equal participation, and valued contribution of disabled people on and off stage requires interdisciplinary perspectives. Many involved in day-to-day theatre work lack knowledge commonplace to disability scholars. They also lack understanding of lived disability experience and perspectives crucial for understanding attitudes, structures, and environments experienced in theatre settings. This article considers the most necessary aspects of disability studies knowledge to share in building, and moving forward from, disability consciousness in the theatre sector and training. It introduces stages in a process of engagement with theatre practice and disability for actors and directors, and a reflective tool for personal positioning in a process of engagement with theatre practice and disability. The article examines how interdisciplinary perspectives support individuals’ processes of exploring new territory, building familiarity across disabled and nondisabled communities, and sharing responsibility for industry-wide change. This article was published open access under a CC BY-NC-ND licence: https://creativecommons.org/licenses/by-nc-nd/4.0/ .

Anorectal prolapse after anorectal reconstruction: Incidence and risk factors according to the ARM-Net Consortium.

There is a knowledge gap regarding which patients with anorectal malformations (ARMs) are at highest risk of anorectal prolapse (AP), and which risk factors predispose to AP in ARM. The aims of the study were to define the frequency of AP after ARM reconstruction, and explore risk factors. Data from the ARM-Net registry inserted between 2007 and 2023 were used. Inclusion criteria were the reconstruction performed, no stoma at 1-year follow-up and all data available at 1-year follow-up. The statistics used were univariable and multivariable logistic regression models. After exclusions the incidence of AP was 163 in 1117 patients (14.6%) in data inserted by 31 centres from 12 countries. The AP incidence was unevenly distributed between the centres (interquartile range 6.3%-21.7%). AP was more frequent in boys than girls (20.9% vs. 8.1%; P < 0.001). In both sexes the incidence of AP was higher in complex ARM subtypes (P < 0.001). AP was most frequent after laparotomy- and laparoscopic-assisted reconstructions (50.0% and 37.5%, respectively). Spinal and sacral anomalies constituted risk factors for AP in univariable analyses, while tethered cord did not. Adjusted risk factors for AP were severity of ARM subtype (40% in long-channel cloaca and bladder neck fistula, OR 3.1, 95% CI 1.0-10.2), laparotomy-assisted posterior sagittal anorectoplasty (50%, OR 3.7, 95% CI 1.6-8.4) and larger neo-anus at 1-year follow-up (Hegar 13.6 vs. 13.1; OR 1.2, 95% CI 1.1-1.4). Constipation was not a risk factor for AP. Anorectal prolapse is a frequent postoperative sequela. Adjusted analyses indicate that severity of ARM, abdominal open access during reconstruction and larger size of anus are risk factors.

Key challenges in epidemiology: Embracing open science

Open science is a movement that fosters research transparency, reproducibility, and equity. Open science has been put forward by numerous stakeholders in the research ecosystem as a key science policy goal, with the United Nations Educational, Scientific and Cultural Organization (UNESCO) creating recommendations on open science and aligning these with UN Sustainability Goals. Open science practices are not standard to epidemiology despite their potential value to the field and especially during disease outbreaks. This article highlights core open science practices, including study registration, open data, code, and material, use of reporting guideline, open access publishing and, preprints. It aims to provide readers with the fundamentals about open science, relevant international policy for open science, and the value of implementing open science for epidemiology and society as a whole. It is a practical piece that will provide readers with a starting point to expand their understanding of open science and to identify tools to learn more. The article also highlights the challenges of open science in its implementation and the importance of monitoring open science practices.

Protective effects and bioinformatic analysis of narciclasine on vascular aging via cross-talk between inflammation and metabolism through inhibiting skeletal muscle-specific ceramide synthase 1.

The senescence of smooth muscle is one of the independent risk factors in atherosclerosis progression in which the vascular inflammation plays an important role on vascular dysfunction. This study is designed to explore the novel vascular aging biomarkers and screen the potential molecular interventional targets through bioinformatic analysis. Transcriptional analysis was conducted based on the GSE16487 open access database, which included 15 human vascular tissue samples from two groups: young group (≤ 60 years old, n = 8) and aged group (≥ 75 years old, n = 7). There were 275 differential expression genes (119 upregulated and 156 downregulated genes) with minimum 1.5-fold change between two groups. 9 genes were mainly participated in inflammation-related signaling pathways, in which narciclasine was validated as the most effective candidate for modulation the ceramide synthesis. In vitro and animal study demonstrated that narciclasine reversed vascular aging by inhibiting skeletal muscle-specific ceramide synthase 1 (CerS1), reducing the ceramide level derived from CerS1, and improving fat deposition and circulating glycolipid metabolism. Narciclasine attenuates vascular aging and modulates the cross-talk between inflammation and metabolism via inhibiting skeletal muscle-specific ceramide synthase 1.