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[Purpose/Significance] With the advancement of open science, the signing of transformative open access agreements will have a profound and long-term impact on the acquisition of library information resources. How libraries respond to this trend, how to evaluate open access conversion agreements, whether to sign reasonable open access conversion agreements, and actively adopt them suitable for China's domestic conditions, and scientific and effective collection acquisition and transformation strategies in an open publishing environment, how to ensure reasonable investment of institutional publishing funds, and how to play a role in promoting positive academic exchanges in an open scientific environment are all important issues that deserve industry attention and exploration. [Method/Process] We first reviewed the research progress on open access transformation at home and abroad. Second, based on the data statistics and analysis of DOAJ and related research reports and institutions, the relatiave concepts were elaborated, the impact on stakeholders was examined, and the trend of practical development was understood. Through the analysis and induction of practical cases in domestic and foreign university libraries, especially through the case analysis of the library of Shanghai Jiao Tong University, we elaborated on the issues that Chinese university libraries need to pay more attention to in the process of open access transformation, and proposes related strategies. [Results/Conclusions] To cope with the open access movement, on the one hand, we need to be vigilant against the emergence of new knowledge \"barriers\" and \"paywalls\" due to profit-driven, high APC, and transformative costs, as well as the lack of regulatory norms for author payments and the existence of financial risks and loopholes such as taxation. On the other hand, all parties adhere to the original intention of promoting the dissemination of academic knowledge, forming a transparent and reasonable APC price ecological market, establishing a hierarchical, reliable, and sustainable open publishing funding support, transformation, and regulation mechanism, and creating an economic and healthy academic information exchange environment. In this process, it is necessary for university libraries to comprehensively coordinate subscription fees and publishing fees, and fully guarantee and restructure knowledge exchange and information dissemination. This paper summarizes the three issues that need to be considered in the process of open access transformation, including the impact of open access on stakeholders, the phenomena that need to be monitored, and the key to ensuring sustainability. We proposed implementation strategies based on practical cases, including research and data preparation, analysis and evaluation, focusing on specific implementation points such as controlling elements of contract terms. The OA transformation is still in the transition period, and in order to avoid the loss of funds due to double payments, some overall management and guidance systems are needed during this period. For some publishers that prioritize commercial profit, it is necessary to send strong signals and strengthen supervision of APC pricing rationality through alliances and other levels. In addtion, we must strengthen China's leadership and discourse power in open science, and carry out the construction of related supporting systems.

Clarity and accuracy of reporting are fundamental to the scientific process. Readability formulas can estimate how difficult a text is to read. Here, in a corpus consisting of 709,577 abstracts published between 1881 and 2015 from 123 scientific journals, we show that the readability of science is steadily decreasing. Our analyses show that this trend is indicative of a growing use of general scientific jargon. These results are concerning for scientists and for the wider public, as they impact both the reproducibility and accessibility of research findings.

Findings from psychological research are usually difficult to interpret for non-experts. Yet, non-experts resort to psychological findings to inform their decisions (e.g., whether to seek a psychotherapeutic treatment or not). Thus, the communication of psychological research to non-expert audiences has received increasing attention over the last years. Plain language summaries (PLS) are abstracts of peer-reviewed journal articles that aim to explain the rationale, methods, findings, and interpretation of a scientific study to non-expert audiences using non-technical language. Unlike media articles or other forms of accessible research summaries, PLS are usually written by the authors of the respective journal article, ensuring that research content is accurately reproduced. In this study, we compared the readability of PLS and corresponding scientific abstracts in a sample of 103 journal articles from two psychological peer-reviewed journals. To assess readability, we calculated four readability indices that quantify text characteristics related to reading comprehension (e.g., word difficulty, sentence length). Analyses of variance revealed that PLS were easier to read than scientific abstracts. This effect emerged in both included journals and across all readability indices. There was only little evidence that this effect differed in magnitude between the included journals. In sum, this study shows that PLS may be an effective instrument for communicating psychological research to non-expert audiences. We discuss future research avenues to increase the quality of PLS and strengthen their role in science communication.

Patient portals that provide access to electronic health records offer a means for patients to better understand and self-manage their health. Yet, patient access to electronic health records raises many concerns among physicians, and little is known about the use practices and experiences of patients who access their electronic health records via a mature patient portal that has been available for citizens for over five years. We aimed to identify patients' experiences using a national patient portal to access their electronic health records. In particular, we focused on understanding usability-related perceptions and the benefits and challenges of reading clinical notes written by health care professionals. Data were collected from 3135 patient users of the Finnish My Kanta patient portal through a web-based survey in June 2021 (response rate: 0.7%). Patients received an invitation to complete the questionnaire when they logged out of the patient portal. Respondents were asked to rate the usability of the patient portal, and the ratings were used to calculate approximations of the System Usability Scale score. Patients were also asked about the usefulness of features, and whether they had discussed the notes with health professionals. Open-ended questions were used to ask patients about their experiences of the benefits and challenges related to reading health professionals' notes. Overall, patient evaluations of My Kanta were positive, and its usability was rated as good (System Usability Scale score approximation: mean 72.7, SD 15.9). Patients found the portal to be the most useful for managing prescriptions and viewing the results of examinations and medical notes. Viewing notes was the most frequent reason (978/3135, 31.2%) for visiting the portal. Benefits of reading the notes mentioned by patients included remembering and understanding what was said by health professionals and the instructions given during an appointment, the convenience of receiving information about health and care, the capability to check the accuracy of notes, and using the information to support self-management. However, there were challenges related to difficulty in understanding medical terminology, incorrect or inadequate notes, missing notes, and usability. Patients actively used medical notes to receive information to follow professionals' instructions to take care of their health, and patient access to electronic health records can support self-management. However, for the benefits to be realized, improvements in the quality and availability of medical professionals' notes are necessary. Providing a standard information structure could help patients find the information they need. Furthermore, linking notes to vocabularies and other information sources could also improve the understandability of medical terminology; patient agency could be supported by allowing them to add comments to their notes, and patient trust of the system could be improved by allowing them to control the visibility of the professionals' notes.

In this work there will be a critical discussion about transformative agreements and their development. Will they lead to a rapid change towards a fully equitable open scholarly publication system or are they just a new business model for the commercial publishers that won 't drive the necessary change in the system? The article will be based on a discussion on the policy development on Open Access in Sweden, from Council conclusions to National guidelines on Open Science, and how Sweden is striving to get from policy to practice. Finally, the article will describe how the Swedish Bibsam consortia are implementing the policy developments in their strategies and how they actually negotiate to get beyond the transformative agreements.

Background Whole exome capture sequencing allows researchers to cost-effectively sequence the coding regions of the genome. Although the exome capture sequencing methods have become routine and well established, there is currently a lack of tools specialized for variant calling in this type of data. Results Using statistical models trained on validated whole-exome capture sequencing data, the Atlas2 Suite is an integrative variant analysis pipeline optimized for variant discovery on all three of the widely used next generation sequencing platforms (SOLiD, Illumina, and Roche 454). The suite employs logistic regression models in conjunction with user-adjustable cutoffs to accurately separate true SNPs and INDELs from sequencing and mapping errors with high sensitivity (96.7%). Conclusion We have implemented the Atlas2 Suite and applied it to 92 whole exome samples from the 1000 Genomes Project. The Atlas2 Suite is available for download at http://sourceforge.net/projects/atlas2/ . In addition to a command line version, the suite has been integrated into the Genboree Workbench, allowing biomedical scientists with minimal informatics expertise to remotely call, view, and further analyze variants through a simple web interface. The existing genomic databases displayed via the Genboree browser also streamline the process from variant discovery to functional genomics analysis, resulting in an off-the-shelf toolkit for the broader community.

The idea of making science more accessible to nonscientists has prompted health researchers to involve patients and the public more actively in their research. This sometimes involves writing a plain language summary (PLS), a short summary intended to make research findings accessible to nonspecialists. However, whether PLSs satisfy the basic requirements of accessible language is unclear. We aimed to assess the readability and level of jargon in the PLSs of research funded by the largest national clinical research funder in Europe, the United Kingdom's National Institute for Health and Care Research (NIHR). We also aimed to assess whether readability and jargon were influenced by internal and external characteristics of research projects. We downloaded the PLSs of all NIHR National Journals Library reports from mid-2014 to mid-2022 (N=1241) and analyzed them using the Flesch Reading Ease (FRE) formula and a jargon calculator (the De-Jargonizer). In our analysis, we included the following study characteristics of each PLS: research topic, funding program, project size, length, publication year, and readability and jargon scores of the original funding proposal. Readability scores ranged from 1.1 to 70.8, with an average FRE score of 39.0 (95% CI 38.4-39.7). Moreover, 2.8% (35/1241) of the PLSs had an FRE score classified as \"plain English\" or better; none had readability scores in line with the average reading age of the UK population. Jargon scores ranged from 76.4 to 99.3, with an average score of 91.7 (95% CI 91.5-91.9) and 21.7% (269/1241) of the PLSs had a jargon score suitable for general comprehension. Variables such as research topic, funding program, and project size significantly influenced readability and jargon scores. The biggest differences related to the original proposals: proposals with a PLS in their application that were in the 20% most readable were almost 3 times more likely to have a more readable final PLS (incidence rate ratio 2.88, 95% CI 1.86-4.45). Those with the 20% least jargon in the original application were more than 10 times as likely to have low levels of jargon in the final PLS (incidence rate ratio 13.87, 95% CI 5.17-37.2). There was no observable trend over time. Most of the PLSs published in the NIHR's National Journals Library have poor readability due to their complexity and use of jargon. None were readable at a level in keeping with the average reading age of the UK population. There were significant variations in readability and jargon scores depending on the research topic, funding program, and other factors. Notably, the readability of the original funding proposal seemed to significantly impact the final report's readability. Ways of improving the accessibility of PLSs are needed, as is greater clarity over who and what they are for.

Concomitant with the increasing density of semiconductors, various attacks that threaten the integrity and security of dynamic random access memory (DRAM) have been devised. Among these, a side-channel attack called RAMBleed is a prolific one that utilizes a general user-level account without special rights to read secret information. Studies have reported that it can be used to obtain OpenSSH secret keys. However, a technique for deriving the Rivest–Shamir–Adleman (RSA) secret keys used in OpenSSL under realistic parameters and environments has not been reported. We propose a method that uses RAMBleed to obtain OpenSSL secret keys and demonstrate its efficacy using the example of an Apache server. The proposed method exploits the fact that, in the operation of an Apache server that uses OpenSSL, the RSA private keys are deployed on DRAM at a set time. Although the result of reading this secret information contains a few errors, error-free secret information is obtainable when it is used with RSA cryptanalysis techniques. We performed a series of attacks incorporating RAMBleed and eventually retrieved the OpenSSL RSA private key, indicating that secret information is obtainable with high probability. The proposed method can easily and externally be executed without administrator privileges on a server using DRAM that is vulnerable to RAMBleed, showing that RAMBleed is also a major threat to OpenSSL.

Here, we report the detection and complete genome sequence of a novel potexvirus, tentatively named “Adenium obesum virus X” (AobVX), isolated from Adenium obesum, that was sent for virus screening at Australian Government post-entry quarantine (PEQ) facilities after being imported into Australia from China. The AobVX genome is 6781 nucleotides in length excluding the poly(A) tail and is predicted to encode conserved potexvirus proteins and sequence motifs across five open reading frames. The RNA-dependent RNA polymerase of this virus shares the highest amino acid sequence similarity with that of nerine potexvirus 1 (58.7% identity) and nerine virus X (58.58% identity). This is the first report of a positive-sense single-stranded RNA virus in A. obesum related to members of the genus Potexvirus in the family Alphaflexiviridae.

There are many alternatives to direct journal access, such as podcasts, blogs, and news sites, that allow physicians and the general public to stay up to date with medical literature. However, there is a scarcity of literature that investigates the readership characteristics of open-access medical news sites and how these characteristics may have shifted during the COVID-19 pandemic. This study aimed to assess readership and survey data to characterize open-access medical news readership trends related to the COVID-19 pandemic and overall readership trends regarding pandemic-related information delivery. Anonymous, aggregate readership data were obtained from 2 Minute Medicine, an open-access, physician-run medical news organization that has published over 8000 original, physician-written texts and visual summaries of new medical research since 2013. In this retrospective observational study, the average number of article views, number of actions (defined as the sum of the number of views, shares, and outbound link clicks), read times, and bounce rates (probability of leaving a page in <30 s) were compared between COVID-19 articles published from January 1 to May 31, 2020 (n=40) and non-COVID-19 articles (n=145) published in the same time period. A voluntary survey was also sent to subscribed 2 Minute Medicine readers to further characterize readership demographics and preferences, which were scored on a Likert scale. COVID-19 articles had a significantly higher median number of views than non-COVID-19 articles (296 vs 110; U=748.5; P<.001). There were no significant differences in average read times (P=.12) or bounce rates (P=.12). Non-COVID-19 articles had a higher median number of actions than COVID-19 articles (2.9 vs 2.5; U=2070.5; P=.02). On a Likert scale of 1 (strongly disagree) to 5 (strongly agree), our survey data revealed that 65.5% (78/119) of readers agreed or strongly agreed that they preferred staying up to date with emerging literature about COVID-19 by using sources such as 2 Minute Medicine instead of journals. A greater proportion of survey respondents also indicated that open-access news sources were one of their primary sources for staying informed (86/120, 71.7%) compared to the proportion who preferred direct journal article access (61/120, 50.8%). The proportion of readers indicating they were reading one or less full-length medical studies a month were lower following introduction to 2 Minute Medicine compared to prior (21/120, 17.5% vs 38/120, 31.6%; P=.005). The readership significantly increased for one open-access medical literature platform during the pandemic. This reinforces the idea that open-access, physician-written sources of medical news represent an important alternative to direct journal access for readers who want to stay up to date with medical literature.