bluuebunny/crossref_metadata_2025_split huggingface dataset:
Open Science and COVID-19 Randomized Controlled Trials: Examining Open Access, Preprinting, and Data Sharing-Related Practices During the Pandemic
Authors: Borghi John A. , Payne Cheyenne , Ren Lily , Woodward Amanda L. , Wong Connie , Stave Christopher 
Published: August 2022

AbstractThe COVID-19 pandemic has brought substantial attention to the systems used to communicate biomedical research. In particular, the need to rapidly and credibly communicate research findings has led many stakeholders to encourage researchers to adopt open science practices such as posting preprints and sharing data. To examine the degree to which this has led to the adoption of such practices, we examined the “openness” of a sample of 539 published papers describing the results of randomized controlled trials testing interventions to prevent or treat COVID-19. The majority (56%) of the papers in this sample were free to read at the time of our investigation and 23.56% were preceded by preprints. However, there is no guarantee that the papers without an open license will be available without a subscription in the future, and only 49.61% of the preprints we identified were linked to the subsequent peer-reviewed version. Of the 331 papers in our sample with statements identifying if (and how) related datasets were available, only a paucity indicated that data was available in a repository that facilitates rapid verification and reuse. Our results demonstrate that, while progress has been made, there is still a significant mismatch between aspiration and the practice of open science in an important area of the COVID-19 literature.Open MaterialsWe are committed to making the details of our research process as open as possible. The data and code that underlie our analyses are archived and published through the Dryad Data Repository (https://doi.org/10.5061/dryad.mkkwh7137). Documentation and instructions for manuscript screening and data extraction are available on Protocols.io (https://dx.doi.org/10.17504/protocols.io.x54v9jx7zg3e/v1). Author contributions are outlined in Supplementary Table 1.
Tup1 is Critical for Transcriptional Repression in Quiescence inS. cerevisiae
Authors: Bailey Thomas B. , Whitty Phaedra A. , Selker Eric U. , McKnight Jeffrey. N. , McKnight Laura E. 
Published: August 2022

AbstractUpon glucose starvation,S. cerevisiaeshows a dramatic alteration in transcription, resulting in wide-scale repression of most genes and activation of some others. This coincides with an arrest of cellular proliferation. A subset of such cells enters quiescence, a reversible non-dividing state. Here, we demonstrate that the conserved transcriptional corepressor Tup1 is critical for transcriptional repression after glucose depletion. We show that Tup1-Ssn6 binds new targets upon glucose depletion, where it remains as the cells enter the G0 phase of the cell cycle. In addition, we show that Tup1 represses a variety of glucose metabolism and transport genes. We explored how Tup1 mediated repression is accomplished and demonstrated that Tup1 coordinates with the Rpd3L complex to deacetylate H3K23. We found that Tup1 coordinates with Isw2 to affect nucleosome positions at glucose transporter HXT family genes during G0. Finally, microscopy revealed that a quarter of cells with a Tup1 deletion contain multiple DAPI puncta. Taken together, these findings demonstrate the role of Tup1 in transcriptional reprogramming in response to environmental cues leading to the quiescent state.
Genetic dissection of crossover mutants defines discrete intermediates in mouse meiosis
Authors: Premkumar Tolkappiyan , Paniker Lakshmi , Kang Rhea , Biot Mathilde , Humphrey Ericka , Destain Honorine , Ferranti Isabella , Okulate Iyinyeoluwa , Nguyen Holly , Kilaru Vindhya , Frasca Melissa , Chakraborty Parijat , Cole Francesca 
Published: August 2022

AbstractCrossovers, the exchange of homolog arms, are required for accurate segregation during meiosis. Studies in yeast have established that the single end invasion intermediate is highly regulated to ensure crossover distribution. Single end invasions are thought to differentiate into double Holliday junctions that are resolved by MutLgamma (MLH1/3) into crossovers. Currently, we lack knowledge of early steps of mammalian crossover recombination or how intermediates are differentiated in any organism. Using comprehensive analysis of recombination and cytology, we infer that polymerized single-end invasion intermediates and nicked double Holliday junctions are crossover precursors in mouse spermatocytes. In marked contrast to yeast, MLH3 plays a structural role to differentiate single end invasions into double Holliday junctions with differentially polymerized 3’ ends. Therefore, we show independent genetic requirements for precursor formation and asymmetry with regard to 3’ end processing, providing mechanistic insight into crossover formation and patterning.
A single-administration therapeutic interfering particle reduces SARS-CoV-2 viral shedding and pathogenesis in hamsters
Authors: Chaturvedi Sonali , Beutler Nathan , Pablo Michael , Vasen Gustavo , Chen Xinyue , Calia Giuliana , Buie Lauren , Rodick Robert , Smith Davey , Rogers Thomas , Weinberger Leor S. 
Published: August 2022

AbstractThe high transmissibility of SARS-CoV-2 is a primary driver of the COVID-19 pandemic. While existing interventions prevent severe disease, they exhibit mixed efficacy in preventing transmission, presumably due to their limited antiviral effects in the respiratory mucosa, whereas interventions targeting the sites of viral replication might more effectively limit respiratory virus transmission. Recently, intranasally administered RNA-based therapeutic interfering particles (TIPs) were reported to suppress SARS-CoV-2 replication, exhibit a high barrier to resistance, and prevent serious disease in hamsters. Since TIPs intrinsically target the tissues with the highest viral replication burden (i.e., respiratory tissues for SARS-CoV-2), we tested the potential of TIP intervention to reduce SARS-CoV-2 shedding. Here, we report that a single, post-exposure TIP dose lowers SARS-CoV-2 nasal shedding and at 5 days post-infection infectious virus shed is below detection limits in 4 out of 5 infected animals. Furthermore, TIPs reduce shedding of Delta variant or WA-1 from infected to uninfected hamsters. Co-housed ‘contact’ animals exposed to infected, TIP-treated, animals exhibited significantly lower viral loads, reduced inflammatory cytokines, no severe lung pathology, and shortened shedding duration compared to animals co-housed with untreated infected animals. TIPs may represent an effective countermeasure to limit SARS-CoV-2 transmission.SignificanceCOVID-19 vaccines are exceptionally effective in preventing severe disease and death, but they have mixed efficacy in preventing virus transmission, consistent with established literature that parenteral vaccines for other viruses fail to prevent mucosal virus shedding or transmission. Likewise, small-molecule antivirals, while effective in reducing viral-disease pathogenesis, also appear to have inconsistent efficacy in preventing respiratory virus transmission including for SARS-CoV-2. Recently, we reported the discovery of a single-administration antiviral Therapeutic Interfering Particle (TIP) against SARS-CoV-2 that prevents severe disease in hamsters and exhibits a high genetic barrier to the evolution of resistance. Here, we report that TIP intervention also reduces SARS-CoV-2 transmission between hamsters.
Self-monitoring of blood glucose levels among pregnant individuals with gestational diabetes: a systematic review and meta-analysis
Authors: Yeh Ping Teresa , Kennedy Caitlin Elizabeth , Rhee Dong Keun , Zera Chloe , Tunçalp Özge , Lucido Briana , de Leon Rodolfo Gomez Ponce , Narasimhan Manjulaa 
Published: August 2022

1AbstractIntroductionThe World Health Organization (WHO) recommends treatment and management of gestational diabetes (GD) through lifestyle changes, including diet and exercise, and self-monitoring blood glucose (SMBG) to inform timely treatment decisions. To expand the evidence base of WHO’s guideline on self-care interventions, we conducted a systematic review of SMBG among pregnant individuals with GD.SettingWe searched for publications through November 2020 comparing SMBG with clinic-based monitoring during antenatal care (ANC) globally.Primary and secondary outcome measuresWe extracted data using standardized forms and summarized maternal and newborn findings using random effects meta-analysis in GRADE evidence tables. We also reviewed studies on values, preferences, and costs of SMBG.ResultsWe identified 6 studies examining SMBG compared to routine ANC care, 5 studies on values and preferences, and 1 study on costs. Nearly all were conducted in Europe and North America. Moderate-certainty evidence from 3 randomized controlled trials (RCTs) showed that SMBG as part of a package of interventions for GD treatment was associated with lower rates of preeclampsia, lower mean birthweight, fewer infants born large for gestational age, fewer infants with macrosomia, and lower rates of shoulder dystocia. There was no difference between groups in self-efficacy, preterm birth, C-section, mental health, stillbirth, or respiratory distress. No studies measured placenta previa, long-term complications, device-related issues, or social harms. Most end-users supported SMBG, motivated by health benefits, convenience, ease of use, and increased confidence. Health workers acknowledged SMBG’s convenience but were wary of technical problems. One study found SMBG by pregnant individuals with insulin-dependent diabetes was associated with decreased costs for hospital admission and length of stay.ConclusionSMBG during pregnancy is feasible and acceptable, and when combined in a package of GD interventions, is generally associated with improved maternal and neonatal health outcomes. However, research from resource-limited settings is needed.Systematic review registration numberPROSPERO CRD42021233862
Estimation of monkeypox spread in a non-endemic country considering contact tracing and self-reporting: a stochastic modeling study
Authors: Ko Youngsuk , Mendoza Renier , Mendoza Victoria May , Seo Yubin , Lee Jacob , Jung Eunok 
Published: August 2022

AbstractBackgroundIn May 2022, monkeypox started to spread in non-endemic countries. After the number of confirmed cases reached more than 16,000 in July, the World Health Organization declared the highest alert over the outbreak.MethodsTo investigate the effects of contact tracing and self-reporting of primary cases in the local community, a stochastic model is developed. A delay simulation algorithm based on Gillespie’s stochastic chemical kinetics is used to quantify the number of infections, contacts made by the infectors, and duration from the arrival of the primary case until the detection of the index case (and until there are no more local infections), under various scenarios.ResultsWe found that if the primary case does not self-report, taking into account a population of 10,000, the average number of infections could range from 30 to 67, while the number of contacts made by infectors could range from 221 to 498. On the other hand, if the primary case self-reports, the average number of infections and contacts could range from 5 to 7 and 40 to 52, respectively. The average duration from the primary case arrival until the first index case detection (or until there are no more local infections) ranged from 8 to 10 days (18 to 21 days) if the primary case does not self-report, and approximately 3 days (8 days) if the primary case self-reports. Moreover, if the number of close contacts per day is doubled in our simulation settings, then the number of infections could increase by 53%.ConclusionThe number and duration of the infections are strongly affected by the self-reporting behavior of the primary case and the delay in the detection of the index case. Our study emphasizes the importance of border control, which aims to immediately detect the primary case before secondary infections occur.
A common mechanism of Sec61 translocon inhibition by small molecules
Authors: Itskanov Samuel , Wang Laurie , Junne Tina , Sherriff Rumi , Xiao Li , Blanchard Nicolas , Shi Wei Q. , Forsyth Craig , Hoepfner Dominic , Spiess Martin , Park Eunyong 
Published: August 2022

AbstractThe Sec61 complex forms a protein-conducting channel in the endoplasmic reticulum (ER) membrane that is required for secretion of soluble proteins and production of many membrane proteins. Several natural and synthetic small molecules specifically inhibit the Sec61 channel, generating cellular effects that are potentially useful for therapeutic purposes, but their inhibitory mechanisms remain unclear. Here we present near-atomic-resolution structures of the human Sec61 channel inhibited by a comprehensive panel of structurally distinct small molecules— cotransin, decatransin, apratoxin F, ipomoeassin F, mycolactone, cyclotriazadisulfonamide (CADA) and eeyarestatin I (ESI). Remarkably, all inhibitors bind to a common lipid-exposed pocket formed by the partially open lateral gate and plug domain of the channel. Mutations conferring resistance to the inhibitors are clustered at this binding pocket. The structures indicate that Sec61 inhibitors stabilize the plug domain of Sec61 in a closed state, thereby preventing the protein-translocation pore from opening. Our study reveals molecular interactions between Sec61 and its inhibitors in atomic detail and offers the structural framework for further pharmacological studies and drug design.
Spatio-temporal regulation of endocytic protein assembly by SH3 domains in yeast
Authors: Hummel Daniel R. , Kaksonen Marko 
Published: August 2022

AbstractClathrin-mediated endocytosis is a conserved eukaryotic membrane trafficking pathway that is driven by a sequentially assembled molecular machinery that contains over 60 different proteins. SH3 domains are the most abundant protein-protein interaction domain in this process, but the function of most SH3 domains in protein dynamics remains elusive. Using mutagenesis and live-cell fluorescence microscopy in the budding yeast Saccharomyces cerevisiae, we dissected SH3-mediated regulation of the endocytic pathway. Our data suggest that multiple SH3 domains regulate the actin nucleation promoting Las17/Vrp1 complex, and that the network of SH3 interactions coordinate both Las17/Vrp1 assembly and dissociation. Furthermore, most endocytic SH3 domain proteins use the SH3 domain for their own recruitment, while a minority uses the SH3 domain to recruit other proteins, and not themselves. Our results provide a dynamic map of SH3 functions in yeast endocytosis and a framework for SH3 interaction network studies across biology.
What influences user participation in an online health community? The stimulus-organism-response model perspective
Authors: Zhou Peiyu , Zhao Shuping , Ma Yiming , Liang Changyong , Zhu Junhong 
Published: August 2022

PurposeThe purpose of this paper is to understand the effect of platform characteristics (i.e. media richness and interactivity) on individual perception (i.e. outcome expectations) and consequent behavioral response (i.e. user participation in online health communities (OHCs)) based on the stimulus-organism-response (S-O-R) model.Design/methodology/approachThis study developed a research model to test the proposed hypotheses, and the proposed model was tested using partial least squares structural equation modeling (PLS-SEM) for which data were collected from 321 users with OHC experience using an online survey.FindingsThe empirical results show the following: (1) the three dimensions of media richness significantly affect the three outcome expectations, except that richness of expression has no significant effect on the outcome expectation of health self-management competence. (2) Human-to-human interaction significantly affects the three outcome expectations. Moreover, compared with human-to-human interaction, human-to-system interaction has a stronger impact on the outcome expectation of health self-management competence. (3) The three outcome expectations have a significant influence on user participation in OHCs.Originality/valueThis study extends the understanding about how platform characteristics (i.e. media richness and interactivity) motivate user participation in the context of OHCs. Drawing on the S-O-R model, this study reveals the underlying mechanisms by which media richness and interactivity are associated with outcome expectations and by which outcome expectations is associated with user participation in OHCs. This study enriches the literature on media richness, interactivity, outcome expectations and user participation in OHCs, providing insights for developers and administrators of OHCs.
Ownership concentration and accounting information consistency—evidence from Chinese listed companies
Authors: Fan Shaojun , Chen Juan , Han Hong 
Published: August 2022

PurposeThe authors expand the connotation of the research on the accounting information quality characteristics, provide empirical evidence for the factors of consistency and also help to deepen further their understanding of the economic consequences of ownership concentration and other ownership structures.Design/methodology/approachUsing financial data of Chinese listed companies as samples, coupled with a method to calculate the consistency of the sample enterprises on the corporate level in the 2007–2019 period, the authors studied its impact of ownership concentration on consistency.FindingsThe study finds that after controlling other factors, ownership concentration could significantly reduce accounting information consistency. Further research finds that when the executives' shareholding is higher, the reduction effect of ownership concentration on consistency is weaker. After the robustness test, the conclusion remains basically unchanged.Research limitations/implicationsFirst, maybe there is a limitation of De Franco et al. (2011) method the authors use in China. As some scholars pointed out, the systematic component of returns variation is large in emerging markets (Morck et al., 2000), so it is hard to determine to what extent market stock returns will capture the net effect of earnings. As is mentioned above, there are multiple methods for measuring comparability and consistency, but it is not easy to judge which way is the best. Maybe the authors will have a perfect process in the future. Second, in addition to the factors mentioned in this study's hypotheses, there should be other factors (these include internal factors and external factors) that play moderating role in the impact of ownership concentration on accounting information consistency. The authors have not thoroughly studied the effect of those factors. These limitations all need to be further explored in the future.Originality/valueThe study finds that after controlling other factors, ownership concentration could significantly reduce accounting information consistency, but the reduction will be affected by some other factors related to corporate governance. The new insights from these advances are that the conclusions provide a technical path for management of companies to improve corporate governance efficiency and the quality of accounting information, and also provide more reference and empirical evidence for information users to identify the company's accounting information quality, which contributes to creating a prerequisite for the usefulness of accounting information.
Impact of XBRL adoption on financial reporting quality: a global evidence
Authors: Tawiah Vincent , Borgi Hela 
Published: August 2022

Purpose
This paper aims to examine the effect of eXtensible Business Reporting Language (XBRL) adoption on financial reporting quality at the country-level (developing and developed countries).

Design/methodology/approach
This study uses data from 98 developed and developing countries between 2005 and 2018. This study collected data from various sources such as the World Economic Forum, World Development Indicators, World Governance Indicators and XBRL website.

Findings
The results show that XBRL is associated with an increased financial reporting quality. However, the relationship is stronger in developing countries than in developed countries. This study also finds that the results remain the same after accounting for years of XBRL experience and the effect of accounting globalisation. The results are consistent with the assumption that XBRL-formatted financial statements improve information efficiency through increased searching efficiency, quality of display and comparability. The results are robust to alternative econometric modifications such as controlling for country, year effects and endogeneity.

Practical implications
The results can potentially assist the XBRL promoters and regulators in expeditiously assessing the benefits of XBRL and advocating its adoption by many countries. The findings offer more motivations for regulators around the world to mandate this new filing standard format.

Originality/value
This study contributes to the literature by providing empirical evidence on the consequences of XBRL at the country level. This study provides evidence on an important question of whether the XBRL, new information technology in the accounting field, can play a useful role in improving financial reporting.
Scientific production on corporate communication: a systematic study in Scopus with COVID-19 as a determining factor
Authors: Hidalgo-Marí Tatiana , Segarra-Saavedra Jesús , Herrero-Gutiérrez Javier 
Published: August 2022

PurposeSearching, identifying and analysing the scientific literature on “corporate communication” published in scientific journals during the twenty-first century (2000–2021) and indexed in the Scopus database, as well as its possible relationship with COVID-19.Design/methodology/approachA systematic bibliographic search was carried out in Scopus and a subsequent analysis of the literature, based on variables such as year of publication, authorship, original language of the text, most used terms and concepts, journal titles, keywords and possible allusions to COVID-19 or the pandemic.Findings2023 results were initially identified, but after applying the filters that limited the results in time (2000–2021) and discriminated—according to the type of document—the results only to scientific articles, the sample finally analysed was 1,280 articles relating to “corporate communication”. It was found that these were mainly published in journals such as Corporate Communications and Journal of Communication Management, in English, and with an accentuated thematic dispersion, but mostly related to public relations, advertising and communication in general.Originality/valueThere is an article published in 2012, before the COVID-19 pandemic, in the Italian journal Igiene e sanità publica, which already established the relevance of researching the challenges and solutions to communication risks in health crisis situations.