Open Access Version Research Articles

Closing the Loop: Automating Links to Open Access Versions of Articles in Faculty Profiles at a Large Research Institution

Introduction: Universities implement faculty profile systems for a variety of reasons, including to increase visibility of research produced at the institution. These profiles often connect with other campus systems, particularly institutional repositories. This article describes a collaboration at the University of Colorado Boulder aimed at integrating the institutional repository with the faculty profile system, which then expanded to encompass the automated creation of profile links to open access versions of faculty articles from any journal or repository. Description of Program: To achieve the initial project goals, a cross-campus team from the University Libraries and the Faculty Information System developed a strategy of using Unpaywall as an intermediary data source to connect the institutional repository with the faculty profile system. This also allowed for the development of an automated process for generating links to open access content from any journal or repository, which resulted in the creation of over 35,000 links to openly available content in faculty profiles, including over 2,900 links to content in the institutional repository. These links provide public users of the faculty profile system with a simple way to access all openly available research produced at the university. This article describes the development and implementation of this project as well as lessons learned. Next Steps: The ongoing collaboration provides additional opportunities to unlock data for monitoring rates of open access publishing and self-archiving, informing library collection development decisions, and connecting to other data sources to reveal further insights.

The State of Open Science Practices in Psychometric Studies of Suicide: A Systematic Review.

The adoption of open science practices (OSPs) is crucial for promoting transparency and robustness in research. We conducted a systematic review to assess the frequency and trends of OSPs in psychometric studies focusing on measures of suicidal thoughts and behavior. We analyzed publications from two international databases, examining the use of OSPs such as open access publication, preregistration, provision of open materials, and data sharing. Our findings indicate a lack of adherence to OSPs in psychometric studies of suicide. The majority of manuscripts were published under restricted access, and preregistrations were not utilized. The provision of open materials and data was rare, with limited access to instruments and analysis scripts. Open access versions (preprints/postprints) were scarce. The low adoption of OSPs in psychometric studies of suicide calls for urgent action. Embracing a culture of open science will enhance transparency, reproducibility, and the impact of research in suicide prevention efforts.

Harnessing the open access version of ChatGPT for enhanced clinical opinions.

With the advent of Large Language Models (LLMs) like ChatGPT, the integration of Generative Artificial Intelligence (GAI) into clinical medicine is becoming increasingly feasible. This study aimed to evaluate the ability of the freely available ChatGPT-3.5 to generate complex differential diagnoses, comparing its output to case records of the Massachusetts General Hospital published in the New England Journal of Medicine (NEJM). Forty case records were presented to ChatGPT-3.5, prompting it to provide a differential diagnosis and then narrow it down to the most likely diagnosis. The results indicated that the final diagnosis was included in ChatGPT-3.5's original differential list in 42.5% of the cases. After narrowing, ChatGPT correctly determined the final diagnosis in 27.5% of the cases, demonstrating a decrease in accuracy compared to previous studies using common chief complaints. These findings emphasize the necessity for further investigation into the capabilities and limitations of LLMs in clinical scenarios while highlighting the potential role of GAI as an augmented clinical opinion. Anticipating the growth and enhancement of GAI tools like ChatGPT, physicians and other healthcare workers will likely find increasing support in generating differential diagnoses. However, continued exploration and regulation are essential to ensure the safe and effective integration of GAI into healthcare practice. Future studies may seek to compare newer versions of ChatGPT or investigate patient outcomes with physicians integrating this GAI technology. Understanding and expanding GAI's capabilities, particularly in differential diagnosis, may foster innovation and provide additional resources, especially in underserved areas in the medical field.

#52 - - Evaluation of an Open Access Version of the Trier Social Stress Test in Virtual Reality

#52 - - Evaluation of an Open Access Version of the Trier Social Stress Test in Virtual Reality

A Bayesian maximum entropy model for predicting tsetse ecological distributions

BackgroundAfrican trypanosomiasis is a tsetse-borne parasitic infection that affects humans, wildlife, and domesticated animals. Tsetse flies are endemic to much of Sub-Saharan Africa and a spatial and temporal understanding of tsetse habitat can aid surveillance and support disease risk management. Problematically, current fine spatial resolution remote sensing data are delivered with a temporal lag and are relatively coarse temporal resolution (e.g., 16 days), which results in disease control models often targeting incorrect places. The goal of this study was to devise a heuristic for identifying tsetse habitat (at a fine spatial resolution) into the future and in the temporal gaps where remote sensing and proximal data fail to supply information.MethodsThis paper introduces a generalizable and scalable open-access version of the tsetse ecological distribution (TED) model used to predict tsetse distributions across space and time, and contributes a geospatial Bayesian Maximum Entropy (BME) prediction model trained by TED output data to forecast where, herein the Morsitans group of tsetse, persist in Kenya, a method that mitigates the temporal lag problem. This model facilitates identification of tsetse habitat and provides critical information to control tsetse, mitigate the impact of trypanosomiasis on vulnerable human and animal populations, and guide disease minimization in places with ephemeral tsetse. Moreover, this BME analysis is one of the first to utilize cluster and parallel computing along with a Monte Carlo analysis to optimize BME computations. This allows for the analysis of an exceptionally large dataset (over 2 billion data points) at a finer resolution and larger spatiotemporal scale than what had previously been possible.ResultsUnder the most conservative assessment for Kenya, the BME kriging analysis showed an overall prediction accuracy of 74.8% (limited to the maximum suitability extent). In predicting tsetse distribution outcomes for the entire country the BME kriging analysis was 97% accurate in its forecasts.ConclusionsThis work offers a solution to the persistent temporal data gap in accurate and spatially precise rainfall predictions and the delayed processing of remotely sensed data collectively in the − 45 days past to + 180 days future temporal window. As is shown here, the BME model is a reliable alternative for forecasting future tsetse distributions to allow preplanning for tsetse control. Furthermore, this model provides guidance on disease control that would otherwise not be available. These ‘big data’ BME methods are particularly useful for large domain studies. Considering that past BME studies required reduction of the spatiotemporal grid to facilitate analysis. Both the GEE-TED and the BME libraries have been made open source to enable reproducibility and offer continual updates into the future as new remotely sensed data become available.

Celebrating BHL Australia through the Eye of the (Tasmanian) Tiger

BHL Australia, the Australian branch of the Biodiversity Heritage Library (BHL), was launched in 2010 and began operation with a single organisation, Museums Victoria in Melbourne. Since then, it has grown considerably. Funded by the Atlas of Living Australia, BHL Australia now digitises biodiversity literature on behalf of 42 organisations across the country. These organisations include museums, herbaria, state libraries, royal societies, government agencies, field naturalist clubs and natural history publishers, many of whom lack the resources to do this work themselves. BHL Australia’s national consortium model, which makes biodiversity literature accessible on behalf of so many organisations, is unique amongst the BHL global community. Most BHL operations digitise material on behalf of a single organisation. BHL Australia has now made over 530,000 pages of Australia’s biodiversity knowledge freely accessible online. The BHL Australia Collection includes both published works (books and journals) and unpublished material (collection registers, field diaries and correspondence). The pages of these works are filled with species descriptions, references to historically significant people and, most importantly, scientific data that is critical to ongoing research and conservation efforts. Providing access to materials published as far back as the 1600s and as recently as the current year, the collection chronicles the scientific discovery and understanding of Australia’s biodiversity. BHL Australia also leads the global initiative to bring the world's historic biodiversity and taxonomic literature into the modern linked network of scholarly research by incorporating article data into BHL and retrospectively assigning DOIs (Digital Object Identifiers) (Kearney et al. 2021). BHL has now assigned more than 162,000 DOIs to historic publications, making them persistently citable and trackable, both within BHL and beyond. This paper will celebrate the achievements of BHL Australia by journeying through the (now accessible, discoverable and DOI'd) Tasmanian Tiger literature. It will showcase: previously elusive descriptions (and beautiful illustrations) of Thylacines, including those by Gerhard Krefft (1871) https://doi.org/10.5962/p.314741, and John Gould (1863) https://doi.org/10.5962/p.312790; the invaluable creation of links to open access versions from paywalled publications that should be in the public domain, such as the first description of the Thylacine (Harris 1808): open access on BHL; paywalled by Oxford Academic; the many citations of historic taxonomic descriptions that are now appearing as clickable DOI links in modern scholarly articles, taxonomic databases, social media, and Wikipedia (Kearney and Page 2022); and the efforts being made to encourage more authors to cite the authoritative source of taxonomic names (Benichou 2022). previously elusive descriptions (and beautiful illustrations) of Thylacines, including those by Gerhard Krefft (1871) https://doi.org/10.5962/p.314741, and John Gould (1863) https://doi.org/10.5962/p.312790; the invaluable creation of links to open access versions from paywalled publications that should be in the public domain, such as the first description of the Thylacine (Harris 1808): open access on BHL; paywalled by Oxford Academic; the many citations of historic taxonomic descriptions that are now appearing as clickable DOI links in modern scholarly articles, taxonomic databases, social media, and Wikipedia (Kearney and Page 2022); and the efforts being made to encourage more authors to cite the authoritative source of taxonomic names (Benichou 2022). The extinction of the Thylacine is a stark reminder of the irreversible consequences that arise from a lack of understanding and appreciation of the natural world. Similarly, a lack of access and/or the inability to find biodiversity knowledge hinders our capacity to learn from the past, impeding scientific progress and conservation efforts. The Biodiversity Heritage Library was created “to address a major obstacle to scientific research: lack of access to natural history literature” (BHL 2019). BHL Australia has made a substantial contribution to this global mission and has played a significant role in BHL’s transition to a fully searchable, persistently linkable component of the biodiversity knowledge graph (Kearney 2020, Page 2016).

The NBER Orange Book Dataset: A user’s guide

This paper introduces a newly digitized, open-access version of the Food and Drug Administration’s “Orange Book”—a linkage between approved small-molecule drugs and the patents that protect them. The Orange Book also reports any applicable regulatory exclusivity that prevents competitive entry. We summarize the Orange Book’s coverage and discuss the opportunities and challenges associated with using these data for research. Empirical validations against various administrative datasets suggest that Orange Book records are, largely, complete and accurate. We conclude with a specific use case—calculating legal exclusivity periods for drugs—to highlight the types of choices that researchers must make when using this resource.

Light and temperature records of the seawater associated with southern elephant seal dives during foraging trips in South Atlantic and Pacific Oceans.

The dataset comprises geolocalised records of dive and surface interval durations, light level and temperature of the seawater during the post-resting and post-moulting tracks of 13 immature southern elephant seals, Miroungaleonina. It describes an unpublished open access version of the original data with records of light level and temperature of the water column using the Darwin Core standard (DwC) through ArOBIS, guaranteeing compliance with the FAIR principles, encompassing a wide time scale (2005, 2006 and 2007) and geographic range in the South Atlantic and Pacific Oceans (South West [-58.75, -81.29], North East [-37.60, -28.65]). Seals were simultaneously equipped with affordable light-temperature loggers (LTLs) and satellite tags. The LTLs recorded light level and temperature of the water column at 30-s intervals during dives and light-time records were applied to estimate dive parameters of diurnal records from 06:00 to 17:00 h, since movements up and down the water column are reflected by changes in light level. For that, the minimum light level reached at the surface of a dive was determined experimentally with diurnal dive simulations at sea using the LTLs devices before deployment. The dataset also includes variation of light and temperature of records between 17:00 to 06:00 h. Data can be used to identify temperature changes associated with seawater masses as drivers of the distribution of other taxa of interest and variation of light level in the seawater (light attenuation) could be linked to concentrations of phytoplankton assemblages as an index of primary productivity. This dataset provides unpublished data of the duration of dives and surface intervals and associated records of light level and temperature variations along the movements throughout the seawater of 13 immature southern elephant seals in the Southern Hemisphere. The location data were generated by satellite tags and the light and temperature data were recorded with light-temperature loggers (LTLs), both devices deployed on individuals simultaneously and uploaded following the Darwin Core standard and compliance with the FAIR principles.

Methodology to Prepare Patent Analysis and the Technological Maturity Cycle

The analysis of patents and the behavior of technology over time have aroused great interest at institutions and companies because they serve as a guide to make decisions on research and innovation projects. Based on this, a methodology that seeks to guide the reader in the preparation of this type of study; both the body of the document and its interpretation has been developed. Two software were used to describe the extraction of patent data; Orbit Intelligence (Licensed Software) and Lens (Open access version). The information obtained, using the same search equation, was presented. For the analysis of the technological maturity cycle, the logistic model was obtained, and it was executed in the Loglet Lab 4 software to obtain the growth curve S. Finally, the Yoon parameters were presented to give a predictive concept of the behavior of the technology over time. The case study that was taken as an example was the technology of “Antibacterial and self-cleaning surfaces based on TiO2/ZnO”, which applied this methodology, we found that the technology of interest is in the maturity phase. It has a high impact on the market, being an important indicator for decision-making focused on research and development. According to what has been proposed, the exposed methodology is a tool to have in consideration that allows to present a more accurate concept about the future projections of a technology, based on the analysis of patent data. Moreover, it is important to consider the trends of the market and the socio-political situation.

One Size Does Not Fit All: Self-Archiving Personas Based On Federally Funded Researchers at a Mid-Sized Private Institution

Introduction: This mixed-method study analyzes the self-archiving behaviors and underlying motivations of researchers at an institution very recently recategorized by the Carnegie Classification system from “Doctoral– High Research Activity (R2)” to “Doctoral–Very High Research Activity (R1).” Methods: A quantitative analysis of data provided by CHORUS, a multi-institutional open access (OA) infrastructure project designed to minimize the administrative costs of complying with federal public access mandates, was followed by semi-structured qualitative interviews with researchers to determine the underlying motivations for self-archiving research papers resulting from federal grant support. Results: Fifty-one authors with federal research funding published 71 journal articles; 139 OA versions of these 71 articles were intentionally made available by researchers across nine types of platforms, including and in addition to those provided by publishers. Interviews with 11 investigators revealed motivators such as a dedication to public access to knowledge, learned behaviors in specific disciplines, and enlightened self-interest. Challenges included concern regarding confidentiality, confusion about intellectual property and funder requirements, administrative overhead, and integrity of the scholarly record. Discussion: Despite concerns and a lack of an OA mandate and other drivers more commonly present at larger, more research-intensive universities, several researchers interviewed actively engaged in self-archiving article versions, not always with clear motivations. These findings have implications for both scholarly communications and collection development services. Conclusion: These quantitative and qualitative data informed the creation of three distinct personas intended to help librarians at similar universities design services in a manner that aligns with investigator motivations.

Jumping over the paywall: Strategies and motivations for scholarly piracy and other alternatives

Despite the advance of the Open Access (OA) movement, most scholarly production can only be accessed through a paywall. We conduct an international survey among researchers (N = 3304) to measure the willingness and motivations to use (or not use) scholarly piracy sites, and other alternatives to overcome a paywall such as paying with their own money, institutional loans, just reading the abstract, asking the corresponding author for a copy of the document, asking a colleague to get the document for them, or searching for an OA version of the paper. We also explore differences in terms of age, professional position, country income level, discipline, and commitment to OA. The results show that researchers most frequently look for OA versions of the documents. However, more than 50% of the participants have used a scholarly piracy site at least once. This is less common in high-income countries, and among older and better-established scholars. Regarding disciplines, such services were less used in Life & Health Sciences and Social Sciences. Those who have never used a pirate library highlighted ethical and legal objections or pointed out that they were not aware of the existence of such libraries.

Rebuilding our community networks post-COVID-19

Background. Communities of Practice (CoP) have long been discussed for their abilities to support individuals in decision making, knowledge sharing, and collegiate support[1]. Individuals who are actively involved in CoP can also act as agents for change within an institution[2]. The University of St Andrews Open Access team have developed strong links to School administrators and established ‘deposit hubs’ in Schools whereby researchers can get local support from the ‘hubbers' for creating new research output records in the University’s Current Research Information System (CRIS), as well as support for uploading open access versions and input based on specialist local knowledge such as linking research grants. Aims. To assess the impact of COVID-19 on the CRIS activity of our ‘hubbers’, to determine whether more could be done to improve resilience in the face of time-constraining factors. We also sought to determine what measures might be taken to improve communication channel within the University and how a network might develop and grow. Methods. A quantitative assessment of the impact of COVID on the CRIS activity of hubbers and administrators whom we have developed links with. Through qualitative assessment and dialogue with administrators we wanted to ascertain other issues that result in delays or non-deposit. Results. There was a correlation between the uptick in CRIS record creation and manuscript deposit activity by the Open Access team, and a decrease in activity by ‘hubbers'. Feedback received also suggested there was inertia due to common queries arising, and further inactivity due to inadequacies with communication channels. It was also clear that the uptick in administrative effort from the OA team needed to be addressed. Conclusion. Determining a correlative effect of a discrete set of administrative tasks based on quantitative indicators is prone to error. However, the Open Access team is confident that such Communities of Practice do add value to research culture, both in quantitative measurable results, and in terms of qualitative cultural effects. But more is needed to be done to enhance resilience, transparency, and confidence. It was decided therefore that a frictionless communication channel was required using Microsoft Teams, to bring together ‘hubbers’ and limit wasted effort by sharing best practice, a set of resources, and guides to ensure common standards and consistency, as well as an FAQ section.

Public Reporting of Adverse Events From Long-Term Care Facilities for Older Persons and People With Disability in Ireland 2013-2019: Development of an Openly Accessible Database and Descriptive Analyses.

To describe the development of an analyzable database of statutory notifications received from long-term care facilities (LTCFs) and to describe trends in receipt of notifications from 2013 to2019. Description of database development with descriptive and trend analyses. LTCFs for older persons and for people with disability in Ireland. Data on notifications received and on centers were extracted from a system internal to the health and social services regulator and combined into an analyzable database. Variables were screened for personal information, cleaned, transformed, or redacted and combined into a database suitable for open access publication. Descriptive analyses of the volume of notifications, trends over time and breakdown by service type, notification type, and risk-rating were conducted. The Database of Statutory Notifications from Social Care in Ireland was developed and an open access version published in February 2021. Protection of personal data was an important consideration in publishing the data publicly. Uses of the database include examination of national trends and identification of determinants of adverse events and areas for quality improvement. The number of notifications received increased over time. Quarterly notifications contributed to the largest proportion of notifications (older persons, 36.7%; disability, 39.1%). This was followed by serious injury notifications in LTCFs for older persons (33.3%) and abuse allegation notifications in LTCFs for people with disability (36.0%). Less than 1% of individual notifications were risk-rated red (highest severity level of impact on resident welfare). The types of notifications that were collectively risk-rated highest were staff misconduct, abuse allegations, and outbreaks of infectious disease. The methodology and findings can inform publications of notifications, planning and resourcing for receipt and submission of notifications, target areas for quality improvement initiatives, mandating of timelines for receipt of notifications, and the mandating of notifications in legislation.

‘A Community Legacy on Film’: using collaborative documentary filmmaking to go beyond representations of the Windrush Generation as ‘victims’

ABSTRACT Recent cultural representations of the Windrush Generation – economic migrants from African Caribbean nations who were invited to live and work in Britain between 1948 and 1972 – and their descendants have overwhelmingly represented British citizens of African Caribbean descent as ‘victims’. This is unsurprising; the so-called ‘Windrush Scandal’ in the late 2010s saw hundreds of members of the Windrush Generation wrongfully lose their British citizenship, many of whom faced detention and, in some cases, even deportation. ‘Windrush: The Years After – A Community Legacy on Film’, a lottery-funded heritage project in the North of England, represents the attempts of local filmmakers and community activists to instil a renewed sense of belonging for African Caribbean descendants who call Britain their home. The ethical innovation of this documentary filmmaking project lies in its ability to reframe descendants of the Windrush Generation as ‘more-than-victims’ – and, by extension, its redefinition of the role of the documentary ‘subject’ as an engaged participant and stakeholder. N.B. this article is an adapted version of a chapter from my PhD thesis, In Their Own Image: Voluntary Filmmaking at a Non-Profit Community Media Organisation (Bramley 2021b). The full open access version of this thesis can be found at: https://etheses.whiterose.ac.uk/29258/.

Making Healthcare Safe: The Story of the Patient Safety Movement

Making Healthcare Safe: The Story of the Patient Safety Movement

IsiXhosa Translation of the Patient Health Questionnaire (PHQ-9): A Pilot Study of Psychometric Properties [Stage 1

Depression is a debilitating illness, and stigma associated with it often prevents people from seeking support. Easy-to-administer and culturally-specific diagnostic tools can allow for early screening for depression in primary care clinics, especially in resource-limited settings. In this pilot study, we will produce the first open-access isiXhosa-language version of the nine-item Patient Health Questionnaire (PHQ-9), a well-validated measure of depression incidence and severity, using a transcultural translation framework. We will validate this isiXhosa PHQ-9 in a small sample of adolescents living with HIV in Cape Town, South Africa who speak isiXhosa at home. Participants have previously completed the ASEBA Youth Self Report (YSR) form, and responses from the YSR will be used as a gold standard to validate the isiXhosa PHQ-9. If validated through this Registered Report, this isiXhosa PHQ-9 may be an invaluable culturally-specific tool for clinicians serving Xhosa people in identifying clinical or sub-clinical depression.

How the Word Adjacency Network (WAN) works

Abstract The Word Adjacency Network (WAN) method is a newly invented method for attributing the authorship of texts based on internal evidence about the proximities of high-frequency words in those texts. The method has been the subject of mathematically rigorous explanations in scientific journals and here is offered instead a relatively non-technical account for humanist readers unfamiliar with advanced mathematical nomenclature. The description will refer to the operation of the algorithm as it is implemented in a newly completed open-source, open-access version that the authors have made available for free unlimited download on the WorldWide Web.

PROTOCOL: Evidence and gap map: studies of the effectiveness of transport sector interventions in low- and middle-income countries.

PROTOCOL: Evidence and gap map: studies of the effectiveness of transport sector interventions in low- and middle-income countries.

Tortura e Migrazioni/Torture and Migration, by Fabio Perocco (ed.).

Reviewing this volume edited by Fabio Perocco and published in open access version by University of Venice Ca' Foscari Editions is no easy task. What makes it hard to sum up this work is not its length (430 pages), but rather its interdisciplinary approach, the depth of observations, the richness in contents and points of view, its geographical width. Yet, these aspects make the book fundamental for anyone willing to understand migratory movements in today's world. Its main merit is having addressed, consistently and systematically, the close relation that has come to be, over the course of decades, between torture and migration. Such relation is no recent piece of news: for a long time, torture has been indicated as one of the most widespread reasons for leaving, one of the most frequent experiences lived along the migration path and, more and more often, a reality that migrants are forced to tackle in receiving countries. Nevertheless, the scientific narrative of such relation is often limited, fragmented and, sometimes, manipulated. Torture has thus far been studied systematically in relation to power (MacMaster 2004), wars and dictatorships (Hajjar 2013, Cohen 2005, Rejali 2009), it is considered as lying at the basis of modernity (Reemtsma 2012) or of the process of civilization (Linklater 2007), but never before it had been analyzed as a structured element of migration. Thus, the volume deserves to be recognized as paving the way for an innovative field of research.

Code of the Suburb: Inside the World of Young Middle-Class Drug Dealers

When we think about young people dealing drugs, we tend to picture it happening on urban streets, in disadvantaged, crime-ridden neighborhoods. But drugs are used and sold everywhere, even in upscale suburbs and top-tier high schools. Drawing on my fieldwork, Code of the Suburb examines the motives, methods, and problems of drug dealers living in a wealthy suburb of Atlanta. Why do otherwise "good kids" start selling? Who do they sell to and where? How do they prevent being victimized or getting in trouble with police and parents? What happens when such problems occur? And why do they eventually quit dealing? The book answers these questions and considers their implications for the war on drugs and more. (This is my only publication without an open access version. Truly sorry. I tried to change this, and will try again down the road.)