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Urdu corpus linguistics is in its infancy, partly because the field lacks large, openly and freely accessible corpora. General purpose Urdu corpora created to date are unsuitable as shared reference data for the field due to barriers of cost or copyright. The novel Lancaster Urdu Web Corpus (luwc) is designed to fill this gap. It encompasses data from three news websites and an online chat forum. The corpus contains 24 million tokens, and is part-of-speech (pos) tagged. To overcome problems with distributing a corpus whose texts' intellectual property belongs to other parties, the luwc is available through a cqpweb server, disallowing access to full underlying data. However, the accessibility of source urls as text-level metadata gives users a means by which to see the full original context. In spite of issues of balance/representativeness the luwc can fulfil the role of a shared reference point for Urdu corpus analysis. [ABSTRACT FROM AUTHOR]

Objectives: Clinical microbiologists require easy-to-use open access tools with graphical interfaces to perform bacterial whole-genome sequencing (WGS) in routine practice. This study aimed to build a bioinformatics pipeline on the open-source Galaxy platform, facilitating comprehensive and reproducible analysis of bacterial WGS data in a few steps. We then used it to characterize our local epidemiology of ESBL-producing Enterobacterales isolated from patients with bacteremia. Methods: We built a bioinformatics pipeline consisting of the following sequential tools: Fastp (input data trimming); FastQC (read quality control); SPAdes (genome assembly); Quast (quality control of genome assembly); Prokka (gene annotation); Staramr (ResFinder database) and ABRicate (CARD database) for antimicrobial resistance (AMR) gene screening and molecular strain typing. Paired-end short read WGS data from all ESBL-producing Enterobacterales strains isolated from patients with bacteremia over one year were analysed. Results: The Galaxy platform does not require command line tools. The bioinformatics pipeline was constructed within one hour. It only required uploading fastq files and facilitated systematization of de novo assembly of genomes, MLST typing, and AMR gene screening in one step. Among the 66 ESBL-producing strains analysed, the two most frequent ESBL genes were blaCTX−M-15 (62.1%) and blaCTX−M-27 (13.6%). Conclusions: The open-access Galaxy platform provides a graphical interface and easy-to-use tools suitable for routine use in clinical microbiology laboratories without bioinformatics specialists. We believe that this platform will facilitate fast and low-cost analysis of bacterial WGS data, especially in resource-limited settings.

Background Hybrid and gold open-access (OA) are the most common publishing models. The latter requires fees to allow full-text visibility upon publishing, whereas hybrid journals offer the option to publish gold OA or for free (subscription-based) where only users with access can get the full-text. We aimed to evaluate the impact of the publishing model and other factors on medical journals’ impact. Methods A sample of hybrid and gold OA medical journals indexed in Web of Science (WOS) and Scopus were included. The effect of the publishing model and other factors on journals’ impact factor (IF), CiteScore, quartile, and number of citations was assessed. Results 402 journals were included, 201 in each group. Hybrid and gold OA journals had a median age of 32 and 21 years, respectively ( PP>0.05). However, gold OA model wasn’t significantly associated with Q1 ranking in Scopus (OR, 0.49; 95% CI, 0.25-0.94; P=0.032), which indicates that hybrid journals were more likely to have such ranking. Conclusion These findings indicate that gold OA publishing doesn’t necessarily result in higher impact, which contradicts the claim that such model enhances citations. Therefore, authors can continue to publish in hybrid journals without being concerned about getting cited. Gold OA journals are encouraged to reduce their fees to facilitate global research access.

Conservation literature addresses a broad spectrum of interdisciplinary questions and benefits. Conservation science benefits most when a diverse range of authors are represented, particularly those from countries where much conservation work is focused. In other disciplines, it is well known that barriers and biases exist in the academic publishing sphere, which can affect research dissemination and an author's career development. We used a discrete choice experiment to determine how 7 journal attributes affect authors’ choices of where to publish in conservation. We targeted authors directly by contacting authors published in 18 target journals and indirectly via communication channels for conservation organizations. We only included respondents who had previously published in a conservation‐related journal. We used a multinomial logit model and a latent class model to investigate preferences for all respondents and distinct subpopulations. We identified 3 demographic groups across 1038 respondents (older authors from predominantly middle‐income countries, younger authors from predominantly middle‐income countries, and younger authors from high‐income countries) who had published in conservation journals. Each group exhibited different publishing preferences. Only 2 attributes showed a consistent response across groups: cost to publish negatively affected journal choice, including authors in high‐income countries, and authors had a consistent preference for double‐blind review. Authors from middle‐income countries were willing to pay more for society‐owned journals, unlike authors from high‐income countries. Journals with a broad geographical scope that were open access and that had relatively high impact factors were preferred by 2 of the 3 demographic groups. However, journal scope and open access were more important in dictating journal choice than impact factor. Overall, different demographics had different preferences for journals and were limited in their selection based on attributes such as open access policy. However, the scarcity of respondents from low‐income countries (2% of respondents) highlights the pervasive barriers to representation in conservation research. We recommend journals offer double‐blind review, reduce or remove open access fees, investigate options for free editorial support, and better acknowledge the value of local‐scale single‐species studies. Academic societies in particular must reflect on how their journals support conservation and conservation professionals. [ABSTRACT FROM AUTHOR]

Electronic resources play a vital role in distributing scholarly material in the current digital age. This study investigates the information-seeking habits of research scholars at the University of Rajasthan, with a specific focus on their knowledge and utilization of open-access initiatives such as the Directory of Open Access Journals (DOAJ) and the Directory of Open Access Repositories (DOAR). Data was collected using an online survey and analysed using descriptive statistics. The results indicate that a large majority (91%) of participants are familiar with DOAJ and DOAR, yet a tiny percentage (8%) have never utilized these tools. Google Scholar is the platform that is used most frequently, with a usage rate of 24%. It is followed by JSTOR, which has a usage rate of 21%. Shodhganga has a usage rate of 20%, while ResearchGate has a usage rate of 10%. Nevertheless, scholars have obstacles while trying to access these materials, mostly because of intermittent internet connectivity, insufficient ICT infrastructure, language hurdles, and limited knowledge of information retrieval methods. Although eresource platforms are widely acknowledged, their practical utilization remains rather limited. In order to tackle this issue, the University of Rajasthan should adopt extensive educational initiatives, organize workshops, and offer training sessions to boost scholars' proficiency in efficiently navigating and utilizing various electronic information platforms. [ABSTRACT FROM AUTHOR]

Designing and developing inhibitors against the epigenetic target DNA methyltransferase (DNMT) is an attractive strategy in epigenetic drug discovery. DNMT1 is one of the epigenetic enzymes with significant clinical relevance. Structure-based de novo design is a drug discovery strategy that was used in combination with similarity searching to identify a novel DNMT inhibitor with a novel chemical scaffold and warrants further exploration. This study aimed to continue exploring the potential of de novo design to build epigenetic-focused libraries targeted toward DNMT1. Herein, we report the results of an in-depth and critical comparison of ligand- and structure-based de novo design of screening libraries focused on DNMT1. The newly designed chemical libraries focused on DNMT1 are freely available on GitHub. [ABSTRACT FROM AUTHOR]

Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, the lack of practices of sharing research outputs, such as data, source code and methods, affects transparency and reproducibility of studies, which are critical to the advancement of science. Many published studies are not reproducible due to insufficient documentation, code, and data being shared. We conducted a comprehensive analysis of 453 manuscripts published between 2016–2021 and found that 50.1% of them fail to share the analytical code. Even among those that did disclose their code, a vast majority failed to offer additional research outputs, such as data. Furthermore, only one in ten articles organized their code in a structured and reproducible manner. We discovered a significant association between the presence of code availability statements and increased code availability. Additionally, a greater proportion of studies conducting secondary analyses were inclined to share their code compared to those conducting primary analyses. In light of our findings, we propose raising awareness of code sharing practices and taking immediate steps to enhance code availability to improve reproducibility in biomedical research. By increasing transparency and reproducibility, we can promote scientific rigor, encourage collaboration, and accelerate scientific discoveries. We must prioritize open science practices, including sharing code, data, and other research products, to ensure that biomedical research can be replicated and built upon by others in the scientific community. [ABSTRACT FROM AUTHOR]

Intensive care units (ICUs) provide care for critical patients at high risk of morbidity and mortality, and require continuous monitoring of clinical, biological and, imaging parameters. Collaborative ventures have enabled the emergence of large open access databases for the secondary use of Electronic Health Records (EHRs). The objective of this work was to evaluate the availability of scripts and datasets in publications based on ICU open-access databases. We included 910 original articles based on four ICU open-access databases (Amsterdam University Medical Centers Database, eICU Collaborative Research Database, High time resolution ICU dataset, and Medical Information Mart for Intensive Care). The majority of the studies did not provide their data management scripts (n=839, 92.9%), neither the analysis script (n=843, 93.4%) in the article. Attempts to contact the 845 corresponding authors in question resulted in 89.11% (n=753) of our e-mail requests going unanswered over a two-month period. We received 51 automated messages (55.43%) indicating that emails have not been delivered, while 6 messages (6.52%) redirected to alternative email addresses. Only 20 corresponding authors (18.18%) answered, finally providing the requested materials. Despite scientific journals recommendations to share materials, our study unveils the absence of crucial components for the replication of studies by other research teams. [ABSTRACT FROM AUTHOR]

Objectives: Online educational platforms with open access have seen a growing adoption in the field of medical education. However, the extent of their global usage is still unclear. To fill this knowledge gap, our objective is to examine the usage patterns of two renowned open‐access resources in Otolaryngology. This includes identifying the most sought‐after topics and understanding the demographics of their users. Methods: Retrospective study of web analytics data between 2016 and 2021 extracted from the Headmirror.com and Mayo Clinic Otolaryngology YouTube channel platforms analyzing demographic and education topic trends via descriptive, geospatial, time‐series, t‐tests, and ANOVA analyses. Results: Viewership spanned 124 countries in 7 different geographic regions, with 72 countries comprising low‐ to middle‐income countries, mostly represented ages of 25–34 years old, came from high‐income countries rather than low‐income (p <.001), and used mobile phones followed by computers for device access. Video‐educational material comprised of subspecialty topics on Rhinology and Sinus Surgery (25%) at the highest end and Facial Trauma (1%) at the lowest. Controlling for the age of the video content, the most‐accessed videos comprised of subspecialty topics on Head and Neck Surgery at the highest end and Laryngology at the lowest with significant differentiation across topics of interest (p <.044). Conclusions: This assessment of web‐analytics platforms from two widely used otolaryngology free, online‐access materials showed increasing global usage trends with significant differentiating factors along viewership demographics, as well as sought‐after subspecialty topics of interest. In turn, our results not only lay the groundwork for characterizing the global otolaryngology audience but also for future development of targeted educational materials and accessibility initiatives aimed at ameliorating global educational disparities in the field. [ABSTRACT FROM AUTHOR]

Abstract Assessing sustainability of journals and publishers could guide the choice of a publication venue. However, sustainable scientific publishing is not sufficiently defined. We assessed motivations for sustainable scientific publishing and importance ratings of sustainability aspects of scientific publishing in an online survey. The questionnaire was answered by 129 participants, including publishing scientists, non-academic research institution employees, editors, administrative staff of scientific journals and publishing companies, and individuals working at sustainability organizations. Personal motivation was rated to be important for all stakeholders, especially for scientists (p

Successful bioinspired design depends on practitioners' access to biological data in a relevant form. Although multiple open-access biodiversity databases exist, their presentation is often adapted to life scientists, rather than bioinspired designers. In this paper, we present a new tool, "Bioinspire-Explore", for navigating biodiversity data in order to uncover biological systems of interest for a range of sectors. Bioinspire-Explore allows users to search for inspiring biological models via taxa (species, genera, etc.) as an entry point. It provides information on a taxon's position in the "tree of life", its distribution and climatic niche, as well as its appearance. Bioinspire-Explore also shows users connections in the bioinspiration literature between their taxon of interest and associated biological processes, habitats, and physical measurements by way of their semantic proximity. We believe Bioinspire-Explore has the potential to become an indispensable resource for both biologists and bioinspired designers in different fields. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic brought unprecedented challenges in radiology education. RadDiscord, a digital, open-access radiology educational platform now with over 4100 members internationally, emerged as a COVID-era innovation that has transformed radiology education, broken down institutional silos, and equalized access to high-quality education. This special report will discuss the origin of RadDiscord, overcoming early barriers, building an organization and community, innovation and impact, and the future of radiological education. This may offer helpful perspectives to trainees and educators who are interested in innovating in the realm of radiology education. [ABSTRACT FROM AUTHOR]

Artificial intelligence (AI) has the potential to bring transformative improvements to the field of radiology; yet, there are barriers to widespread clinical adoption. One of the most important barriers has been access to large, well‐annotated, widely representative medical image datasets, which can be used to accurately train AI programs. Creating such datasets requires time and expertise and runs into constraints around data security and interoperability, patient privacy, and appropriate data use. Recognizing these challenges, several institutions have started curating and providing publicly available, high‐quality datasets that can be accessed by researchers to advance AI models. The purpose of this work was to review the publicly available MRI datasets that can be used for AI research in radiology. Despite being an emerging field, a simple internet search for open MRI datasets presents an overwhelming number of results. Therefore, we decided to create a survey of the major publicly accessible MRI datasets in different subfields of radiology (brain, body, and musculoskeletal), and list the most important features of value to the AI researcher. To complete this review, we searched for publicly available MRI datasets and assessed them based on several parameters (number of subjects, demographics, area of interest, technical features, and annotations). We reviewed 110 datasets across sub‐fields with 1,686,245 subjects in 12 different areas of interest ranging from spine to cardiac. This review is meant to serve as a reference for researchers to help spur advancements in the field of AI for radiology. Level of Evidence: Level 4 Technical Efficacy: Stage 6 [ABSTRACT FROM AUTHOR]

Abstract Objectives Online educational platforms with open access have seen a growing adoption in the field of medical education. However, the extent of their global usage is still unclear. To fill this knowledge gap, our objective is to examine the usage patterns of two renowned open‐access resources in Otolaryngology. This includes identifying the most sought‐after topics and understanding the demographics of their users. Methods Retrospective study of web analytics data between 2016 and 2021 extracted from the Headmirror.com and Mayo Clinic Otolaryngology YouTube channel platforms analyzing demographic and education topic trends via descriptive, geospatial, time‐series, t‐tests, and ANOVA analyses. Results Viewership spanned 124 countries in 7 different geographic regions, with 72 countries comprising low‐ to middle‐income countries, mostly represented ages of 25–34 years old, came from high‐income countries rather than low‐income (p

This paper presents a geospatial approach for quantifying street-level on-road emissions of carbon dioxide (CO _2 ), nitrogen oxides (NO _x ), and carbon monoxide (CO). By leveraging an existing open-access database of real-time congestion information derived from floating car data, we tested three methods to map high-resolution dynamic traffic emissions. To demonstrate the robustness and accuracy of the methods, we showcased results for summer workdays and winter weekends in the Helsinki Metropolitan Area (HMA). The three methods employed include (1) a physics-based relation known as the macroscopic fundamental diagram, (2) a data-driven input-adaptive generalized linear model (GLM), and (3) their ensemble (ENS). These methods estimated traffic density with satisfactory accuracy ( R ^2 = 0.60–0.88, sMAPE = 31%–68%). Utilizing speed-dependent emission factors retrieved from a European database, the results compared favorably against the downscaled national emission inventory, particularly for CO _2 ( R ^2 = 0.70–0.77). Among the three methods, GLM exhibited the best overall performance in the HMA, while ENS provided a robust upscaling solution. The modeled emissions exhibited dynamic diurnal and spatial behavior, influenced by different functional road classes, fleet compositions and congestion patterns. Congestion-induced emissions were calculated to account for up to 10% of the total vehicular emissions. Furthermore, to anticipate the forthcoming transportation transformation, we calculated emission changes under scenarios with various penetration rates of connected and autonomous vehicles (CAVs) using this geospatial approach. The introduction of CAVs could result in emission reductions of 3%–14% owing to congestion improvements.

Successful bioinspired design depends on practitioners’ access to biological data in a relevant form. Although multiple open-access biodiversity databases exist, their presentation is often adapted to life scientists, rather than bioinspired designers. In this paper, we present a new tool, “Bioinspire-Explore”, for navigating biodiversity data in order to uncover biological systems of interest for a range of sectors. Bioinspire-Explore allows users to search for inspiring biological models via taxa (species, genera, etc.) as an entry point. It provides information on a taxon’s position in the “tree of life”, its distribution and climatic niche, as well as its appearance. Bioinspire-Explore also shows users connections in the bioinspiration literature between their taxon of interest and associated biological processes, habitats, and physical measurements by way of their semantic proximity. We believe Bioinspire-Explore has the potential to become an indispensable resource for both biologists and bioinspired designers in different fields.

Objectives: Clinical microbiologists require easy-to-use open access tools with graphical interfaces to perform bacterial whole-genome sequencing (WGS) in routine practice. This study aimed to build a bioinformatics pipeline on the open-source Galaxy platform, facilitating comprehensive and reproducible analysis of bacterial WGS data in a few steps. We then used it to characterize our local epidemiology of ESBL-producing Enterobacterales isolated from patients with bacteremia., Methods: We built a bioinformatics pipeline consisting of the following sequential tools: Fastp (input data trimming); FastQC (read quality control); SPAdes (genome assembly); Quast (quality control of genome assembly); Prokka (gene annotation); Staramr (ResFinder database) and ABRicate (CARD database) for antimicrobial resistance (AMR) gene screening and molecular strain typing. Paired-end short read WGS data from all ESBL-producing Enterobacterales strains isolated from patients with bacteremia over one year were analysed., Results: The Galaxy platform does not require command line tools. The bioinformatics pipeline was constructed within one hour. It only required uploading fastq files and facilitated systematization of de novo assembly of genomes, MLST typing, and AMR gene screening in one step. Among the 66 ESBL-producing strains analysed, the two most frequent ESBL genes were bla CTX-M-15 (62.1%) and bla CTX-M-27 (13.6%)., Conclusions: The open-access Galaxy platform provides a graphical interface and easy-to-use tools suitable for routine use in clinical microbiology laboratories without bioinformatics specialists. We believe that this platform will facilitate fast and low-cost analysis of bacterial WGS data, especially in resource-limited settings., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The aim of this article is to assess the market power of the state-owned incumbents within the open-access lines in Europe and compare it among themselves. This article investigates three open-access lines in Europe: Prague-Ostrava line (in the Czech Republic), Vienna-Salzburg line (in Austria) and Bratislava-Košice (in Slovakia). The market power assessment of each of the state-owned incumbents on these lines is based on their market shares, average revenues per passenger-kilometre, whether there is a vertical separation of the infrastructure owner and railway service provider and the role of state intervention. Our results show that the state-owned incumbent in the Czech Republic on the Prague-Ostrava line has the lowest market power in comparison to other investigated open-access lines. [ABSTRACT FROM AUTHOR]

Pāua (abalone) are a treasured natural resource that supports a recreational fishery worth $2 million annually to the local economy of the Kaikōura district in New Zealand. From 2016, the fishery was closed for 5 years in response to widespread mortality caused by co-seismic uplift in the 7.8 M w Kaikōura earthquake. The fishery re-opened in 2021 for three months with a recreational fishing allocation of 5 tonnes. We constructed scenario models informed by fishing pressure observations and show that this catch target was severely exceeded (by a factor of ∼9). We then evaluated alternative management settings involving daily bag limit (DBL) adjustments and temporal controls on the open season. Only the most drastic modelled scenarios could achieve the 5 t allocation with similar levels of daily fishing effort showing the need for a greater focus on fishing effort to achieve sustainable management. Severely reduced DBLs (1–2 pāua) were required in all scenarios suggesting a need for significant departure from this management focus since very low DBL settings force poor cost-return ratios on fishers. Instead, temporal controls that shift opening times away from high visitation periods provide a means of maintaining modest DBLs outside of longer-term protected areas. These seasonal timing strategies can also support a greater proportion of the harvest accruing to local fishers thereby influencing benefit-sharing aspects of the recreational fishery. We discuss insights for equitable solutions to potential influxes of fishing effort and highlight the opportune aspects of disaster recovery contexts for conceiving and implementing new policy directions. [ABSTRACT FROM AUTHOR]