Open Access Archives Research Articles

Platforms for Integration of Open Access Resources of Research and Educational Institutions

In order to study the involvement of Russian academic and educational institutions in joint projects to create open access (OA) archives, we have researched the websites of 106 Russian HEIs participating in the program “Priority 2030” and 453 research institutes (RIs) of the first three categories. As a result of the work carried out, it has been found out that 38% of educational institutions’ websites contain institutional repositories (IRs), but half of them are remotely inaccessible. 20% of repositories of educational organizations participate in joint projects to ensure OA. Only 6% of the research organizations’ websites contain IRs that are presented mainly as part of an electronic library (EL), but not as independent repositories. In addition, 10.5% of the total number of RIs do not maintain their own repositories or ELs, but provide information about research results of their employees, the most important academic achievements of researchers as well as give access to digitized texts of the most significant works published within the framework of joint projects. At the same time, information about participation in these projects is missing on the websites of academic institutions. The examination of the websites of Russian educational and research institutions has shown that their participation in projects to develop cooperative OA archives is not uniform: while some institutions are indifferent, others take an active part in several projects at once and provide information about themselves in foreign aggregators. As a result of the research, we have found 7 projects aimed at integrating OA information resources on a single platform. These resources are implemented mainly in ELs. They are different in number of participants, quantity and chronological depth of the content offered. The identified projects can be conditionally divided into multidisciplinary and thematic, national and regional. It has been found out that some ELs provide open access to all content only for project participants, i.e. remote users have the opportunity to familiarize themselves only with public pages or only a small part of the content is available to them.

Cognitive, behavioral, and affective mechanisms underlying the efficacy of Applied Relaxation in reducing psychopathological symptoms: A randomized controlled trial

BackgroundThis study examined the cognitive, behavioral, and affective mechanisms underlying the efficacy of Applied Relaxation (AR) in reducing psychopathological symptoms. AR is a cognitive-behavioral technique that allows for rapid relaxation at the first sign of stress or tension in daily life. MethodsA randomized controlled trial was conducted in 277 adults (18–55 years) with elevated symptoms of depression, anxiety, or stress but without a 12-month DSM-5 mental disorder at study entry. Participants were randomized to an intervention group receiving AR training (10 weeks, N = 139) and an assessment-only control group (N = 138). Mental health outcomes (depressive, anxiety, and stress symptoms) and potential cognitive (self-efficacy, perceived control), behavioral (coping behaviors) and affective (positive and negative affect) mediators of the intervention efficacy were assessed at baseline and post-assessment in both groups. ResultsStructural equation models indicated that baseline to post reductions in psychopathological symptoms due to AR partially passed through less avoidance-oriented and less other dysfunctional coping (proportion of total effect mediated; ratio of indirect to total effect: resignation: 55.0%, rumination: 27.9%, escape: 27.4%, aggression: 21.3%), less negative affect (46.3%), more positive affect (41.8%), lower external control beliefs (14.5%), and higher self-efficacy (13.3%). ConclusionsOur results suggest that improvements in cognitive, behavioral, and affective mediator variables partially explain the intervention efficacy of AR in improving mental health. Trial registration and data statementThe study protocol has been pre-registered on ClinicalTrials.gov (NCT03311529). The study protocol, minimum dataset, and analysis codes are available at OpARA - Open Access Repository and Archive. Supplementary materials (e.g., the course manual and additional training materials) are available on request from the last author (katja.beesdo-baum@tu-dresden.de).

The Global ALPL gene variant classification project: Dedicated to deciphering variants

BackgroundHypophosphatasia (HPP) is an inherited multisystem disorder predominantly affecting the mineralization of bones and teeth. HPP is caused by pathogenic variants in ALPL, which encodes tissue non-specific alkaline phosphatase (TNSALP). Variants of uncertain significance (VUS) cause diagnostic delay and uncertainty amongst patients and health care providers. ResultsThe ALPL gene variant database (https://alplmutationdatabase.jku.at/) is an open-access archive for interpretation of the clinical significance of variants reported in ALPL. The database contains coding and non-coding variants, including single nucleotide variants, insertions/deletions and structural variants affecting coding or non-coding sequences of ALPL. Each variant in the database is displayed with details explaining the corresponding pathogenicity, and all reported genotypes and phenotypes, including references. In 2021, the ALPL gene variant classification project was established to reclassify VUS and continuously assess and update genetic, phenotypic, and functional variant information in the database. For this purpose, the database provides a unique submission system for clinicians, geneticists, genetic counselors, and researchers to submit VUS within ALPL for classification. An international, multidisciplinary consortium of HPP experts has been established to reclassify the submitted VUS using a multi-step process adhering to the stringent ACMG/AMP variant classification guidelines. These steps include a clinical phenotype assessment, deep literature research including artificial intelligence technology, molecular genetic assessment, and in-vitro functional testing of variants in a co-transfection model to measure ALP residual activity. ConclusionThis classification project and the ALPL gene variant database will serve the global medical community, widen the genotypic and phenotypic HPP spectrum by reporting and characterizing new ALPL variants based on ACMG/AMP criteria and thus facilitate improved genetic counseling and medical decision-making for affected patients and families. The project may also serve as a gold standard framework for multidisciplinary collaboration for variant interpretation in other rare diseases.

Trends in the application of remote sensing in blue carbon science.

Blue carbon ecosystems (BCEs), such as mangroves, saltmarshes, and seagrasses, are increasingly recognized as natural climate solutions. Evaluating the current extent, losses, and gains of BCEs is crucial to estimating greenhouse gas emissions and supporting policymaking. Remote sensing approaches are uniquely suited to assess the factors driving BCEs dynamics and their impacts at various spatial and temporal scales. Here, we explored trends in the application of remote sensing in blue carbon science. We used bibliometric analysis to assess 2193 published papers for changes in research focus over time (1990 - June 2022). Over the past three decades, publications have steadily increased, with an annual growth rate of 16.9%. Most publications focused on mangrove ecosystems and used the optical spaceborne Landsat mission, presumably due to its long-term, open-access archives. Recent technologies such as LiDAR, UAVs, and acoustic sensors have enabled fine-scale mapping and monitoring of BCEs. Dominant research topics were related to mapping and monitoring natural and human impacts on BCEs, estimating vegetation and biophysical parameters, machine and deep learning algorithms, management (including conservation and restoration), and climate research. Based on corresponding author affiliations, 80 countries contributed to the field, with United States (27.2%), China (15.0%), Australia (7.5%), and India (6.0%) holding leading positions. Overall, our results reveal the need to increase research efforts for seagrasses, saltmarshes, and macroalgae, integrate technologies, increase the use of remote sensing to support carbon accounting methodologies and crediting schemes, and strengthen collaboration and resource sharing among countries. Rapid advances in remote sensing technology and decreased image acquisition and processing costs will likely enhance research and management efforts focused on BCEs.

Content Strategy or Strategic Content? Suggestions for Developing Sustainable Content Strategy in Advocacy Organizations

Using first-hand experience supplemented by an open-access archive, this article examines case examples of civically engaged, public-facing technical communication (e.g., training for community organizers) as well as the value of stories and storytelling for content strategy. By developing 10 best practices for content strategy in advocacy organizations, this article offers suggestions for how to design and sustain content strategy for community organizers and contributes to the field's knowledge of the content strategy of politically engaged nonprofits, particularly those with a strong digital presence.

Enhancing performance of multi-temporal tropical river landform classification through downscaling approaches

ABSTRACT Multi-temporal remote sensing imagery has the potential to classify river landforms to reconstruct the evolutionary trajectory of river morphologies. Whilst open-access archives of high spatial resolution imagery are increasingly available from satellite sensors, such as Sentinel-2, there remains a fundamental challenge of maximising the utility of information in each band whilst maintaining a sufficiently fine resolution to identify landforms. Although image fusion and downscaling methods on Sentinel-2 imagery have been investigated for many years, there is a need to assess their performance for multi-temporal object-based river landform classification. This investigation first compared three downscaling methods: area to point regression kriging (ATPRK), super-resolution based on Sen2Res, and nearest neighbour resampling. We assessed performance of the three downscaling methods by accuracy, precision, recall and F1-score. ATPRK was the optimal downscaling approach, achieving an overall accuracy of 0.861. We successively engaged a set of experiments to determine an optimal training model, exploring single and multi-date scenarios. We find that not only does remote sensing imagery with better quality improve river landform classification performance, but multi-date datasets for establishing machine learning models should be considered for contributing higher classification accuracy. This paper presents a workflow for automated river landform recognition that could be applied to other tropical rivers with similar hydro-geomorphological characteristics.

Personalised publication recommendation service for open-access digital archives

Increase in the number of open-access academic publications and open-access institutional academic archives led more researchers use these archives. No model offers personalised publication suggestions in academic archives. A central service architecture has been proposed towards personalised academic article recommendations for open-access digital archives. Thus, it has been possible to make personalised suggestions for open-access digital archives and enable researchers to discover new publications. A service based on the centralised micro-service architecture model was proposed in the study. Also, TF-IDF and article classification methods were used together for the personalised publication suggestion system. For the first time globally, the proposed method was used with 1464 real users in 49 open-access archives. F-measure success value was found to be higher than 0.8 for recommended publications.

THE OPEN DATABASE OF REGIONAL MODELS OF THE INTERNATIONAL SERVICE FOR THE GEOID

Abstract. This paper describes the development of a web application to facilitate the management and processing of geoid models in the ISG collection as well as of additional information available in the ISG website (mainly projects, services and publications). The ISG service pays significant attention to metadata and data interoperability from published geoid models. As a result, the possibility of creating a database with all necessary information for describing geoid models has been considered. PostgreSQL was chosen as the database for the implementation to take advantage of PostGIS geographic processing functions for developing a Database Management System for the resources available inside the ISG service catalogue (including geoid products, software, publications, etc.). The project's web development environment is Django, a web framework which is supported by the PostgreSQL database back-end and which makes it easier to integrate new applications or processing services into the website. A model solution for raster data integration using a PostGIS database back-end named Django-raster has also been investigated as part of the implementation, provided also that it is possible to take advantage of the vast Django community. The Django-raster model allows for the storage of datasets as tiles in the database, their exposure as a Tiled Map Services (TMS), and allows as well raster map algebra operations. TMS services will be utilized to share the geoid models and metadata included in the open access archive using a WebGIS, created with OpenLayers.

Manhua Modernity: Chinese Culture and the Pictorial Turn

Manhua Modernity: Chinese Culture and the Pictorial Turn

Collection Development of Digital Archives in India: A Case Study of Jadavpur University

The free flow of information is a fundamental principle for bridging the gaps between have and have not. ICT has a major impact of materials for research. Innovationin ICT has brought radical changes in the way information is generated, stored, processed and disseminated. Recent advances in converging technologies especially Internet and web technology has paved the way to create the open access archives on repositories. The objective of the open access movement is to make scholarly articles freely available in digital form to anyone anywhere in the world. The open access and open archives movement, the need for changes in the scholarly communication to remove barriers to access.

Global holiday datasets for understanding seasonal human mobility and population dynamics

Public and school holidays have important impacts on population mobility and dynamics across multiple spatial and temporal scales, subsequently affecting the transmission dynamics of infectious diseases and many socioeconomic activities. However, worldwide data on public and school holidays for understanding their changes across regions and years have not been assembled into a single, open-source and multitemporal dataset. To address this gap, an open access archive of data on public and school holidays in 2010–2019 across the globe at daily, weekly, and monthly timescales was constructed. Airline passenger volumes across 90 countries from 2010 to 2018 were also assembled to illustrate the usage of the holiday data for understanding the changing spatiotemporal patterns of population movements.

PARROT: A Pilot Study on the Open Access Provision of Particle-Discrete Tomographic Datasets.

In the present paper, as part of an interdisciplinary research project (Priority Programme SPP2045), we propose a possible way to design an open access archive for particle-discrete tomographic datasets: the PARROT database (https://parrot.tu-freiberg.de). This archive is the result of a pilot study in the field of particle technology and three use cases are presented for illustrative purposes. Instead of providing a detailed instruction manual, we focus on the methodologies of such an archive. The presented use cases stem from our working group and are intended to demonstrate the advantage of using such an archive with concise and consistent data for potential and ongoing studies. Data and metadata merely serve as examples and need to be adapted for disciplines not concerned here. Since all datasets within the PARROT database and its source code are freely accessible, this study represents a starting point for similar projects.

Archiving Feminist Truth in Trump’s Wake of Lies

This article is about an assignment I do in one of my Gender, Women, and Sexuality Studies social movement classes. I revised the assignment the first time teaching the class after Trump lost the 2020 election. For the assignment, students work in groups to research local feminist and gender justice organizations and deposit all of their original materials – recordings, photos, flyers, etc. – into a digital, open access archive I co-created several years ago with librarians and staff on my campus. In 2021 I had my students do the “post-Trump” edition where they researched local organizations about how their activism was shaped by Trump’s policies and rhetoric. This paper is about the archive and assignment writ-large, the importance of feminist knowledge production, and the place of feminists in the academy in challenging the wake of lies spread by the Trump administration.

Akademisyenlerin Açık Erişim ve Kurumsal Akademik Arşiv Konusunda Bilgi ve Farkındalık Düzeylerinin Belirlenmesi: Bartın Üniversitesi Uygulama Örneği

Institutional open repository systems are platforms where intellectual works which, produced by universities and research centers are archived electronically and freely accessible to everyone. Institutional repository systems are platforms where intellectual studies produced by universities and research centers are archived electronically and freely accessible to eve ryone. For the continuity of the institutional repository systems of universities, it is necessary to be updated by academicians. It is thought that high level of knowledge and awareness of academic staff about open access and institutional academic archiv e is important in ensuring this continuity. In this study, a training was carried out in order to increase the knowledge and awareness of Bartin University academicians on open access and institutional academic archives, and it was aimed to examine the cha nges in the opinions of the academicians before and after the training. In this context, quantitative research methods were used and a single sample pre - test post - test design was used. SPSS (Statistical Package for Social Sciences) 22.0 package program was used to analyze the data. As a result of the study, it was determined that academicians needed training on open access and effective and effective use of institutional repositories. In addition, it was concluded that a statistically significant positive c hange was observed in the knowledge and awareness of academicians about open access and institutional academic archives after the training provided.

The Workflow Trace Archive: Open-Access Data From Public and Private Computing Infrastructures

Realistic, relevant, and reproducible experiments often need input traces collected from real-world environments. In this work, we focus on traces of workflows-common in datacenters, clouds, and HPC infrastructures. We show that the state-of-the-art in using workflow-traces raises important issues: (1) the use of realistic traces is infrequent and (2) the use of realistic, open-access traces even more so. Alleviating these issues, we introduce the Workflow Trace Archive (WTA), an open-access archive of workflow traces from diverse computing infrastructures and tooling to parse, validate, and analyze traces. The WTA includes > 48 million workflows captured from > 10 computing infrastructures, representing a broad diversity of trace domains and characteristics. To emphasize the importance of trace diversity, we characterize the WTA contents and analyze in simulation the impact of trace diversity on experiment results. Our results indicate significant differences in characteristics, properties, and workflow structures between workload sources, domains, and fields.

Centromere-specific antibody-mediated karyotyping of Okinawan Oikopleura dioicasuggests the presence of three chromosomes.

Oikopleura dioica is a ubiquitous marine tunicate of biological interest due to features that include dioecious reproduction, short life cycle, and vertebrate-like dorsal notochord while possessing a relatively compact genome. The use of tunicates as model organisms, particularly with these characteristics, offers the advantage of facilitating studies in evolutionary development and furthering understanding of enduring attributes found in the more complex vertebrates. At present, we are undertaking an initiative to sequence the genomes of Oikopleura individuals in populations found among the seas surrounding the Ryukyu Islands in southern Japan. To facilitate and validate genome assemblies, karyotyping was employed to count individual animals' chromosomes in situ using centromere-specific antibodies directed against H3S28P, a prophase-metaphase cell cycle-specific marker of histone H3. New imaging data of embryos and oocytes stained with two different antibodies were obtained; interpretation of these data lead us to conclude that the Okinawan Oikopleura dioica has three pairs of chromosomes, akin to previous results from genomic assemblies in Atlantic populations. The imaging data have been deposited to the open-access EBI BioImage Archive for reuse while additionally providing representative images of two commercially available anti-H3S28P antibodies' staining properties for use in epifluorescent and confocal based fluorescent microscopy.

The PANGAEA mineralogical database.

Future human missions to the surface of the Moon and Mars will involve scientific exploration requiring new support tools to enable rapid and high quality science decision-making. Here, we describe the PANGAEA (Planetary ANalogue Geological and Astrobiological Exercise for Astronauts) Mineralogical Database developed by ESA (European Space Agency): a catalog of petrographic and spectroscopic information on all currently known minerals identified on the Moon, Mars, and associated with meteorites. The catalog also includes minerals found in the analog field sites used for ESA's geology and astrobiology training course PANGAEA, to broaden the database coverage. The Mineralogical Database is composed of the Summary Catalog of Planetary Analog Minerals and of the Spectral Archive and is freely available in the public repository of ESA PANGAEA. The Summary Catalog provides essential descriptive information for each mineral, including name (based on the International Mineralogical Association recommendation), chemical formula, mineral group, surface abundance on planetary bodies, geological significance in the context of planetary exploration, number of collected VNIR and Raman spectra, likelihood of detection using different spectral methods, and bibliographic references evidencing their detection in extraterrestrial or terrestrial analog environments. The Spectral Archive provides a standard library for planetary in-situ human and robotic exploration covering Visual-Near-Infrared reflective (VNIR) and Raman spectroscopy (Raman). To populate this library, we collected VNIR and Raman spectra for mineral entries in the Summary Catalog from open-access archives and analyzed them to select the ones with the best spectral features. We also supplemented this collection with our own bespoke measurements. Additionally, we compiled the chemical compositions for all the minerals based on their empirical formula, to allow identification using the measured abundances provided by LIBS and XRF analytical instruments. When integrated into an operational support system like ESA's Electronic Fieldbook (EFB) system, the Mineralogical Database can be used as a real-time and autonomous decision support tool for sampling operations on the Moon, Mars and during astronaut geological field training. It provides both robust spectral libraries to support mineral identification from instrument outputs, and relevant contextualized information on detected minerals.

Finding Traces in YouTube’s Living Archive: Exploring Informal Archival Practices

This article addresses the challenges that media historians face when they aim to reconstruct the early history of YouTube. Since the platform is constantly adapting its policies, there is a great level of uncertainty as to what is still there or what is no longer traceable. Therefore, addressing the question if and/or how YouTube can be understood as an archive is crucial and, in addition, the issue of how YouTube related content can be used as historical sources. Although many people, including media scholars, treat YouTube like an online open access archive, there are reasons to be cautious. The article will explore strategies dealing with formal but also with informal web archival practices. These informal archival practices concern users who curate early YouTube videos, user profiles and comments or even old layout versions of the website. Developing methods that critically acknowledges user-generated archival practices, and uses the insights of early generation of users’ reconstructions of the platform’s history, even if it might seem anecdotal evidence, can lead to deeper knowledge of that early community. By actively participating in reconstructing YouTube’s recent past these users shape nostalgic narratives while they also collect and share useful information that guide historians finding new traces.

Monitoring compliance with governmental and institutional open access policies across Spanish universities

Universities and research centers in Spain are subject to a national open access (OA) mandate and to their own OA institutional policies, if any, but compliance with these requirements has not been fully monitored yet. We studied the degree of OA archiving of publications of 28 universities within the period 2012-2014. Of these, 12 have an institutional OA mandate, 9 do not require but request or encourage OA of scholarly outputs, and 7 do not have a formal OA statement but are well known for their support of the OA movement. The potential OA rate was calculated according to the publisher open access policies indicated in Sherpa/Romeo directory. The universities showed an asymmetric distribution of 1% to 63% of articles archived in repositories that matched those indexed by the Web of Science in the same period, of which 1% to 35% were OA and the rest were closed access. For articles on work carried out with public funding and subject to the Spanish Science law, the percentage was similar or slightly higher. However, the analysis of potential OA showed that the figure could have reached 80% in some cases. This means that the real proportion of articles in OA is far below what it could potentially be.

Gridded birth and pregnancy datasets for Africa, Latin America and the Caribbean

Understanding the fine scale spatial distribution of births and pregnancies is crucial for informing planning decisions related to public health. This is especially important in lower income countries where infectious disease is a major concern for pregnant women and new-borns, as highlighted by the recent Zika virus epidemic. Despite this, the spatial detail of basic data on the numbers and distribution of births and pregnancies is often of a coarse resolution and difficult to obtain, with no co-ordination between countries and organisations to create one consistent set of subnational estimates. To begin to address this issue, under the framework of the WorldPop program, an open access archive of high resolution gridded birth and pregnancy distribution datasets for all African, Latin America and Caribbean countries has been created. Datasets were produced using the most recent and finest level census and official population estimate data available and are at a resolution of 30 arc seconds (approximately 1 km at the equator). All products are available through WorldPop.