bluuebunny/crossref_metadata_2025_split huggingface dataset:
Botrytis cinereasmall RNAs are associated with tomato AGO1 and silence tomato defense-related target genes supporting cross-kingdom RNAi
Authors: He Baoye , Cai Qiang , Weiberg Arne , Li Wei , Cheng An-Po , Ouyang Shouqiang , Borkovich Katherine , Stajich Jason , Abreu-Goodger Cei , Jin Hailing 
Published: January 2023

AbstractCross-kingdom or cross-species RNA interference (RNAi) is broadly present in many interacting systems between microbes/parasites and their plant and animal hosts. A recent study by Qinet al. (2022) performed correlation analysis using global sRNA- and mRNA-deep sequencing data of culturedB. cinereaandB. cinerea-infected tomato leaves and claimed that cross-kingdom RNAi may not occur inB. cinerea–tomato interaction (Qinet al., 2022). Here, we use experimental evidence and additional bioinformatics analysis of the datasets produced by Qinet al. (2022) to identify the key reasons why a discrepancy between the conclusion of Qin et al. 2022 and previously published findings occurred. We also provided additional experimental evidence to support the presence of cross-kingdom RNAi between tomato andB. cinerea. We believe it is important to clarify the basic concept and mechanism of cross-kingdom/cross-species sRNA trafficking and illustrate proper bioinformatics analyses in this regard for all the scientists and researchers in this field.
Replacing continuous stimulation of one set of electrodes with successive stimulation of multiple sets of electrodes can improve the focality of transcranial temporal interference stimulation (tTIS), especially the focality of stimulation towards deep brain regions: A simulation study
Authors: Li Yixuan , Zhang Wei 
Published: January 2023

Withdrawal statementThe authors have withdrawn their manuscript because they suspect that there may have been an issue with the data collection process, despite the fact that their proposal is original and beneficial. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Regionalized protein localization domains in the zebrafish hair cell kinocilium
Authors: Erickson Timothy , Biggers William Paul , Williams Kevin , Butland Shyanne E. , Venuto Alexandra 
Published: January 2023

AbstractSensory hair cells are the receptors for auditory, vestibular, and lateral line sensory organs in vertebrates. These cells are distinguished by “hair”-like projections from their apical surface collectively known as the hair bundle. Along with the staircase arrangement of actin-filled stereocilia, the hair bundle features a single, non-motile, true cilium called the kinocilium. The kinocilium plays important roles in bundle development and the mechanics of sensory detection. To understand more about kinocilial development and structure, we performed a transcriptomic analysis of zebrafish hair cells looking for cilia-associated genes that have yet to be characterized in hair cells. Here, we focus on three such genes -ankef1a,odf3l2a, andsaxo2- because the human or mouse orthologs are either associated with sensorineural hearing loss or are located near uncharacterized deafness loci. We made transgenic fish that express fluorescently tagged versions of their proteins, demonstrating their localization to the kinocilia of zebrafish hair cells. Furthermore, we find that Ankef1a, Odf3l2a, and Saxo2 exhibit distinct localization patterns along the length of the kinocilium and within the cell body. Lastly, we report a novel overexpression phenotype for Saxo2. Overall, these results suggest that the hair cell kinocilium is regionalized along its proximal-distal axis and set the groundwork to understand more about the roles of these kinocilial proteins in hair cells.
RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data
Authors: Li Zhijian , Kuo Chao-Chung , Ticconi Fabio , Shaigan Mina , Gusmao Eduardo Gade , Allhoff Manuel , Manolov Martin , Zenke Martin , Costa Ivan G. 
Published: January 2023

AbstractBackgroundMassive amounts of data are produced by combining next-generation sequencing (NGS) with complex biochemistry techniques to characterize regulatory genomics profiles, such as protein-DNA interaction and chromatin accessibility. Interpretation of such high-throughput data typically requires different computation methods. However, existing tools are usually developed for a specific task, which makes it challenging to analyze the data in an integrative manner.ResultsWe here describe the Regulatory Genomics Toolbox (RGT), a computational library for the integrative analysis of regulatory genomics data. RGT provides different functionalities to handle genomic signals and regions. Based on that, we developed several tools to perform distinct downstream analyses, including the prediction of transcription factor binding sites using ATAC-seq data, identification of differential peaks from ChIP-seq data, and detection of triple helix mediated RNA and DNA interactions, visualization, and finding an association between distinct regulatory factors.ConclusionWe present here RGT; a framework to facilitate the customization of computational methods to analyze genomic data for specific regulatory genomics problems. RGT is a comprehensive and flexible Python package for analyzing high throughput regulatory genomics data and is available at:https://github.com/CostaLab/reg-gen. The documentation is available at:https://reg-gen.readthedocs.io
OptoCRISPRi-HD: engineering a green-light activated CRISPRi system with high dynamic range
Authors: Chen Ke-Ning , Ma Bin-Guang 
Published: January 2023

ABSTRACTThe ability to modulate gene expression is crucial for studying gene function and programming cell behaviors. Combining the reliability of CRISPRi and the precision of optogenetics, the opto-CRISPRi technique is emerging as an advanced tool for live-cell gene regulation. Since previous versions of opto-CRISPRi often exhibit a no more than 10 folds’ dynamic range due to the leakage activity, they are not suitable for targets that are sensitive to such leakage or critical for cell growth. Here, we describe a green-light activated CRISPRi system with high dynamic range (40-fold) and the flexibility of changing targets inEscherichia coli. Our optoCRISPRi-HD system can efficiently repress essential genes, non-essential genes or inhibit the initiation of DNA replication. Providing a regulative system with high resolution over space-time and extensive targets, our study would facilitate further researches involving complex gene networks, metabolic flux redirection or bioprinting.
Order of events in a developing genetic code
Authors: Yarus Michael 
Published: January 2023

AbstractPreexisting partial genetic codes can fuse to evolve toward the Standard Genetic Code (SGC). Code fusion provides a path of least selection, generating a code precursor that resembles the SGC, consequently evolving quickly. Optimal evolution requires wobble coding delayed until late in primordial codon assignment, because early wobble specifically retards evolution of complete and accurate codes. Given delayed wobble, the SGC can emerge after a modest selection for more proficient encoding.
The online metacognitive control of decisions
Authors: Bénon Juliette , Lee Douglas , Hopper William , Verdeil Morgan , Pessiglione Mathias , Vinckier Fabien , Bouret Sebastien , Rouault Marion , Lebouc Raphael , Pezzulo Giovanni , Schreiweis Christiane , Burguière Eric , Daunizeau Jean 
Published: January 2023

AbstractDifficult decisions typically involve mental effort, which scales with the deployment of cognitive (e.g., mnesic, attentional) resources engaged in processing decision-relevant information. But how does the brain regulate mental effort? A possibility is that the brain optimizes a resource allocation problem, whereby the amount of invested resources balances its expected cost (i.e. effort) and benefit. Our working assumption is that subjective decision confidence serves as the benefit term of the resource allocation problem, hence the “metacognitive” nature of decision control. Here, we present a computational model for theonline metacognitive control of decisionsor oMCD. Formally, oMCD is a Markov Decision Process that optimally solves the ensuing resource allocation problem under agnostic assumptions about the inner workings of the underlying decision system. We demonstrate how this makes oMCD a quasi-optimal control policy for a broad class of decision processes, including -but not limited to-progressive attribute integration. We disclose oMCD’s main properties (in terms of choice, confidence and response time), and show that they reproduce most established empirical results in the field of value-based decision making. Finally, we discuss the possible connections between oMCD and most prominent neurocognitive theories about decision control and mental effort regulation.
Innovation subsidies and entrepreneurial activity in an emerging market
Authors: Wang Chun-Hsien 
Published: January 2023

PurposeThis study aims to find that entrepreneurial activities can spur entrepreneurial firms' superior performance, but this effect is contingent on the different levels of government innovation subsidies. Extending the institutional perspective explanation and entrepreneurship perspective explanation, this study examines how a firm's entrepreneurial orientation (EO) affects its superior performance when it receives innovation subsidies.Design/methodology/approachEntrepreneurial firms in China, an emerging economy, are taken as the context for empirical evidence. A large-scale questionnaire survey is used for firm data collection. Ordinary least squares (OLS) regression is employed to test the hypothesized model using a sample of 287 entrepreneurial firms.FindingsThe results show a curvilinear, inverse U-shaped moderating effect in the relationship between EO and firm performance. This relationship is strongest at intermediate levels of innovation subsidies but is comparatively weaker when innovation subsidies are low or high.Originality/valueThe study contributes to entrepreneurship research by examining the nonlinear moderating effect of innovation subsidies on entrepreneurial firms' performance. The study also contributes to entrepreneurship theory by elaborating on the innovation subsidy scheme and how it facilitates the development of entrepreneurial activity.
Nurturing mental health and well-being using ordinary farms
Authors: Deegan Deirdre , Fingleton Emma , McEvoy Joseph James , Quigley Kate 
Published: January 2023

Purpose
This practice piece aims to review an occupational therapy led pilot programme – social farming as an intervention option in an adult community mental health setting in Ireland. It will also reflect on the practical implications of delivering the natural surroundings based programme through the COVID-19 pandemic and plans for the future development of such programmes in adult mental health services.

Design/methodology/approach
The Occupational Circumstances Assessment Interview Rating Scale (OCAIRS) was used to measure occupational participation (Forsyth, 2005). This was administered with participants’ pre and post their participation in the 10-week programme. An internal questionnaire was developed to further capture both the participant and farmer experiences of the social farming programme.

Findings
Whilst improvements were noted in a number of OCAIRS domains, it was difficult to identify small changes over a short period of time. The main domains of change were habits, roles, interests and personal causation. The success of the social farming placements was also reflected in the internal questionnaire. The pilot programme has resulted in the further development of the social farming programme and securing of funding for placements for five years.

Originality/value
It would be beneficial to consider other standardised assessments that assess quality of life and occupation for future placements. It is also beneficial to consider practical implications in delivering a social farming programme, particularly to those with barriers to transport. It is hoped this paper will contribute to the growing knowledge of social farming as a meaningful therapeutic intervention in mental health occupational therapy practice.
The role of teachers’ views and attitudes in the academic achievement of Roma students
Authors: Fehérvári Anikó 
Published: January 2023

Purpose
Inclusive education of Roma students is a priority goal of the European Union. However, synthesising analyses reveal precious little progress scored in this area. This study aims to explore the factors that have affect Roma students’ academic achievement, specifically, whether the views of their teachers have an impact on the performance besides individual and family background factors.

Design/methodology/approach
A large-sample questionnaire-based research study was conducted in the 2019/2020 academic year involving 4,674 seventh-grade students and 2,656 teachers from 194 Hungarian schools. On a self-admission basis, 374 of the students were Roma.

Findings
In the schools examined, the performance of Roma students is poorer, their commitment to learning is weaker, yet they have a higher opinion of their school and their teachers than their non-Roma peers. The involvement of majority students in extracurricular private tutoring, particularly foreign language learning, is greater. Roma students’ academic achievement is mainly affected by individual background factors, in particular by their school history.

Originality/value
The findings suggest that although the role of the school and pedagogical views is important, they are not predominant factors determining Roma students’ performance. The explanatory power of individual characteristics is stronger than that of school factors. The comparison between Roma and non-Roma students also shows that cooperation between different sectors (education, social and health) would be essential within and outside school in terms of home learning conditions, digital access and student well-being.
How does particulate air pollution affect barrier functions and inflammatory activity of lung vascular endothelium?
Authors: Olesiejuk Krzysztof , Chałubiński Maciej 
Published: January 2023

AbstractBoth particulate matter and gaseous components of air pollution have already been shown to increase cardiovascular mortality in numerous studies. It is, however, important to note that on their way to the bloodstream the polluting agents pass the lung barrier. Inside the alveoli, particles of approximately 0.4–1 μm are most efficiently deposited and commonly undergo phagocytosis by lung macrophages. Not only the soluble agents, but also particles fine enough to leave the alveoli enter the bloodstream in this finite part of the endothelium, reaching thus higher concentrations in close proximity of the alveoli and endothelium. Additionally, deposits of particulate matter linger in direct proximity of the endothelial cells and may induce inflammation, immune responses, and influence endothelial barrier dysfunction thus increasing PM bioavailability in positive feedback. The presented discussion provides an overview of possible components of indoor PM and how endothelium is thus influenced, with emphasis on lung vascular endothelium and clinical perspectives.
The Fontan immunophenotype and post‐transplant outcomes in children: A multi‐institutional study
Authors: Mantell Benjamin S. , Azeka Estela , Cantor Ryan S. , Carlo Waldemar F. , Chrisant Maryanne , Dykes John C. , Hoffman Timothy M. , Kirklin James K. , Koehl Devin , L'Ecuyer Thomas J. , McAllister Jennie M. , Prada‐Ruiz Adriana C. , Richmond Marc E. 
Published: January 2023

AbstractBackgroundPatients after Fontan palliation represent a growing pediatric population requiring heart transplant (HTx) and often have lymphopenia (L) and/or hypogammaglobinemia that may be exacerbated by protein‐losing enteropathy (PLE, P). The post‐HTx effects of this altered immune phenotype are not well studied.MethodsIn this study of the Pediatric Heart Transplant Society Registry, 106 Fontan patients who underwent HTx between 2005 and 2018 were analyzed. The impact of lymphopenia and PLE on graft survival, infection, rejection, and malignancy was analyzed at 1 and 5 years post‐HTx.ResultsThe following combinations of lymphopenia and PLE were noted: +L+P, n = 37; +L−P, n = 23; −L+P, n = 10; and −L−P, n = 36. Graft survival between the groups was similar within the first year after transplant (+L+P: 86%, +L−P: 86%, −L+P: 87%, −L−P: 89%, p = .9). Freedom from first infection post‐HTx was greatest among −L−P patients compared to patients with either PLE, lymphopenia, or both; with a 22.1% infection incidence in the −L−P group and 41.4% in all others. These patients had a significantly lower infection rate in the first year after HTx (+L+P: 1.03, +L−P: 1, −L+P: 1.3, −L−P: 0.3 infections/year, p < .001) and were similar to a non‐single ventricle CHD control group (0.4 infections/year). Neither freedom from rejection nor freedom from malignancy 1 and 5 years post‐HTx, differed among the groups.ConclusionsFontan patients with altered immunophenotype, with lymphopenia and/or PLE, are at increased risk of infection post‐HTx, although have similar early survival and freedom from rejection and malignancy. These data may encourage alternative immunosuppression strategies and enhanced monitoring for this growing subset of patients.
Long‐term mortality in pediatric solid organ recipients—A nationwide study
Authors: Salonen Rebekka , Jahnukainen Timo , Nikkilä Atte , Endén Kira 
Published: January 2023

AbstractBackgroundThe present study aimed at investigating long‐term mortality of patients who underwent solid organ transplantation during childhood and at identifying their causes of death.MethodsA cohort of 233 pediatric solid organ transplant recipients who had a kidney, liver, or heart transplantation between 1982 and 2015 in Finland were studied. Year of birth‐, sex‐, and hometown‐matched controls (n = 1157) were identified using the Population Register Center registry. The Causes of Death Registry was utilized to identify the causes of death.ResultsAmong the transplant recipients, there were 60 (25.8%) deaths (median follow‐up 18.0 years, interquartile range of 11.0–23.0 years). Transplant recipients' risk of death was nearly 130‐fold higher than that of the controls (95% CI 51.9–1784.6). The 20‐year survival rates for kidney, liver, and heart recipients were 86.1% (95% CI 79.9%–92.3%), 58.5% (95% CI 46.2%–74.1%), and 61.4% (95% CI 48.1%–78.4%), respectively. The most common causes of death were cardiovascular diseases (23%), infections (22%), and malignancies (17%). There were no significant differences in survival based on sex or transplantation era.ConclusionThe late mortality is still significantly higher among pediatric solid organ recipients in comparison with controls. Cardiovascular complications, infections, and cancers are the main causes of late mortality for all studied transplant groups. These findings emphasize the cruciality of careful monitoring of pediatric transplant recipients in order to reduce long‐term mortality.
Fibrinolytic therapy in patients with COVID-19 and ARDS: protocol for a systematic review and meta-analysis
Authors: Savioli Felicio , Ribeiro dos Santos Lucas , Duarte Marcio Luis , Feitosa do Carmo Andreia Cristina , Gois Aecio , Nakano Luis , Da Silva Ramos Fernando Jose , Pastore Laerte , Costa Eduardo Leite Vieira 
Published: January 2023

IntroductionIn COVID-19-related acute respiratory distress syndrome (ARDS), the clot play a role in gas exchange abnormalities. Fibrinolytic therapy can improve alveolar ventilation by restoring blood flow. In this systematic review and meta-analysis protocol, we aim to assess the safety and efficacy of fibrinolytic therapy in such a population.MethodsWe will perform a systematic search in MEDLINE, EMBASE, Cochrane CENTRAL and LILACS databases without language restrictions for relevant randomised controlled trials (RCTs) and quasi-RCTs. Two review authors will independently perform data extraction and quality assessments of data from included studies. In case of divergence, a third author will be contacted. The Cochrane handbook will be used for guidance. If the results are not appropriate for a meta-analysis, a descriptive analysis will be performed.DiscussionThis systematic review and meta-analysis protocol will provide current evidence about the safety and efficacy of fibrinolytic therapy in patients with COVID-19 and ARDS. These findings will provide if fibrinolytic therapy might be an option for a desperate clinical setting, where all medical efforts have been used.PROSPERO registration numberPROSPERO CRD42020187482.Ethics and disseminationEthics committee approval is not necessary. We intend to update the public registry, report any protocol amendments and publish the results in a widely accessible journal.
Evaluation of the England Community Pharmacy Quality Scheme (2018–2019 and 2019–2020) in reducing harm from NSAIDs in older patients
Authors: Parekh Sejal , Livingstone Carina , Jani Yogini H 
Published: January 2023

IntroductionNon-steroidal anti-inflammatory drugs (NSAIDs) are widely used for their analgesic and anti-inflammatory action, but the gastrointestinal (GI) adverse effects are a known cause of preventable harm. A medication safety audit was incentivised for community pharmacies in England in 2 successive years as part of the Pharmacy Quality Scheme (PQS) to address GI safety of NSAIDs.AimsTo evaluate community pharmacy’s contributions to NSAID safety and determine any change between audit 1 (2018–2019) and audit 2 (2019–2020).MethodPatients aged 65 years or over prescribed an NSAID were included in both audits. The audit tool assessed compliance with national standards relating to co-prescribed gastroprotection, referrals to the prescriber and patient advice on long-term NSAID use and effects, with responses submitted via an online portal. Descriptive analyses were performed to explore differences between the years and tested for significance using Χ2tests. Qualitative data were analysed using an inductive thematic approach.Key findingsData from 91 252 patients in audit 1 and 73 992 in audit 2 were analysed. More patients were prescribed gastroprotection in audit 2 (85.0%) than audit 1 (80.7%, p<0.001). More patients without gastroprotection in audit 2 had a current or recent referral (67.5%) than in audit 1 (58.8%, p<0.001). Verbal or other communications between pharmacists and patients about their NSAID medication were reported more frequently in audit 2 (76.0% vs 63.5%, p<0.001).ConclusionDuring two audits, community pharmacists in England reported referring more than 15 000 patients at risk of preventable harm from NSAIDs to prescribers for review. The audits demonstrated significant potential for year-on-year improvement in GI safety for a large cohort of older patients prescribed NSAIDs. This evaluation provides evidence of how the PQS can effectively address a specific aspect of medicines safety and the place of community pharmacy more broadly in improving medicines safety.