bluuebunny/crossref_metadata_2025_split huggingface dataset:
Common Analysis of Direct RNA SequencinG CUrrently Leads to Misidentification of 5-Methylcytosine Modifications at GCU Motifs
Authors: Watson Kaylee J. , Bromley Robin E. , Sparklin Benjamin C. , Gasser Mark T. , Bhattacharya Tamanash , Lebov Jarrett F. , Tyson Tyonna , Teigen Laura E. , Graf Karen T. , Michalski Michelle , Bruno Vincent M. , Lindsey Amelia R. I. , Hardy Richard W. , Newton Irene L. G. , Dunning Hotopp Julie C. 
Published: May 2023

ABSTRACTRNA modifications, such as methylation, can be detected with Oxford Nanopore Technologies direct RNA sequencing. One commonly used tool for detecting 5-methylcytosine (m5C) modifications is Tombo, which uses an “Alternative Model” to detect putative modifications from a single sample. We examined direct RNA sequencing data from diverse taxa including virus, bacteria, fungi, and animals. The algorithm consistently identified a 5-methylcytosine at the central position of a GCU motif. However, it also identified a 5-methylcytosine in the same motif in fully unmodifiedin vitrotranscribed RNA, suggesting that this a frequent false prediction. In the absence of further validation, several published predictions of 5-methylcytosine in human coronavirus and human cerebral organoid RNA in a GCU context should be reconsidered.IMPORTANCEThe detection of chemical modifications to RNA is a rapidly expanding field within epigenetics. Nanopore sequencing technology provides an attractive means of detecting these modifications directly on the RNA, but accurate modification predictions are dependent upon the software developed to interpret the sequencing results. One of these tools, Tombo, allows users to detect modifications using sequencing results from a single RNA sample. However, we find that this method falsely predicts modifications in a specific sequence context across a variety of RNA samples, including RNA that lacks modifications. Results from previous publications include predictions in human coronaviruses with this sequence context and should be reconsidered. Our results highlight the importance of using RNA modification detection tools with caution in the absence of a control RNA sample for comparison.
Soil viral communities differed by management and over time in organic and conventional tomato fields
Authors: Sorensen Jess W. , ter Horst Anneliek M. , Zinke Laura A. , Emerson Joanne B. 
Published: May 2023

AbstractViruses are known contributors to biogeochemical cycling in diverse habitats, but viral community studies in soil are relatively rare. Although prior work has suggested spatial structuring as a primary driver of local soil viral community ecological patterns, here we show that agricultural management can significantly impact soil viral community composition. We generated 18 soil viromes and 24 total metagenomes from six plots, three under organic and three under conventional management in Davis, CA, USA. Despite the significant impact of management on viral community structure and soil physicochemistry, approximately 44% of the detected viral ‘species’ (vOTUs) were present in soils from both management practices. These common vOTUs regularly comprised >65% of the viral community by relative abundance. Many (56%) of the vOTUs were detected both during the tomato growing season and post-harvest, indicating persistence through time. Together, these results indicate habitat-specific differences in viral community composition, yet relative stability and persistence of viral communities within agricultural soils, in contrast to their recently observed dynamics in natural soils.
Establishment of a CPER Reverse Genetics System for Powassan Virus Defines Attenuating NS1 Glycosylation Sites and an Infectious NS1-GFP11 Reporter Virus
Authors: Conde Jonas N. , Himmler Grace E. , Mladinich Megan C. , Setoh Yin Xiang , Amarilla Alberto A. , Schutt William R. , Saladino Nicolas , Gorbunova Elena E. , Salamango Daniel J. , Wimmer Eckard , Kim Hwan Keun , Mackow Erich R. 
Published: May 2023

AbstractPowassan virus (POWV) is an emerging tick-borne Flavivirus that causes lethal encephalitis and long term neurologic damage. Currently there are no POWV therapeutics, licensed vaccines or reverse genetics systems for producing infectious POWVs from recombinant DNA. Here we used a circular polymerase extension reaction (CPER) approach to generate recombinant LI9 (recLI9) POWVs with attenuating NS1 protein mutations and a recLI9-split-eGFP reporter virus. Flavivirus NS1 proteins are highly conserved glycoproteins that regulate replication, spread and neurovirulence. POWV NS1 proteins contain three putative N-linked glycosylation sites that we modified individually in infectious recLI9 mutants (N85Q, N208Q, N224Q). NS1 glycosylation site mutations reduced replication kinetics and were attenuated with a 1-2 log decrease in infectious titers. The severely attenuated recLI9-N224Q mutant exhibited a 2-3 day delay in focal cell-to-cell spread and reduced NS1 secretion. Like WT LI9, the recLI9-N224Q mutant was lethal when intracranially inoculated into suckling mice. However, footpad inoculation of recLI9-N224Q resulted in the survival of 80% of mice and demonstrated that NS1-N224Q mutations attenuate POWV neuroinvasionin vivo. To monitor NS1 trafficking, we CPER fused a split GFP11-tag to the NS1 C-terminus and generated an infectious reporter virus, recLI9-NS1-GFP11. Cells infected with recLI9-NS1-GFP11 revealed NS1 trafficking in live cells and the novel formation of large NS1 lined intracellular vesicles. An infectious recLI9-NS1-GFP11 reporter virus permits real-time analysis of NS1 functions in POWV replication, assembly and secretion, and provides a platform for evaluating antiviral compounds. Collectively, our robust POWV reverse genetics system permits analysis of viral spread and neurovirulence determinantsin vitroandin vivo, and enables the rational genetic design of live attenuated POWV vaccines.
The CCP4 suite: integrative software for macromolecular crystallography
Authors: Agirre Jon , Atanasova Mihaela , Bagdonas Haroldas , Ballard Charles B. , Baslé Arnaud , Beilsten-Edmands James , Borges Rafael J. , Brown David G. , Burgos-Mármol J. Javier , Berrisford John M. , Bond Paul S. , Caballero Iracema , Catapano Lucrezia , Chojnowski Grzegorz , Cook Atlanta G. , Cowtan Kevin D. , Croll Tristan I. , Debreczeni Judit É. , Devenish Nicholas E. , Dodson Eleanor J. , Drevon Tarik R. , Emsley Paul , Evans Gwyndaf , Evans Phil R. , Fando Maria , Foadi James , Fuentes-Montero Luis , Garman Elspeth F. , Gerstel Markus , Gildea Richard J. , Hatti Kaushik , Hekkelman Maarten L. , Heuser Philipp , Hoh Soon Wen , Hough Michael A. , Jenkins Huw T. , Jiménez Elisabet , Joosten Robbie P. , Keegan Ronan M. , Keep Nicholas , Krissinel Eugene B. , Kolenko Petr , Kovalevskiy Oleg , Lamzin Victor S. , Lawson David M. , Lebedev Andrey A. , Leslie Andrew G. W. , Lohkamp Bernhard , Long Fei , Malý Martin , McCoy Airlie J. , McNicholas Stuart J. , Medina Ana , Millán Claudia , Murray James W. , Murshudov Garib N. , Nicholls Robert A. , Noble Martin E. M. , Oeffner Robert , Pannu Navraj S. , Parkhurst James M. , Pearce Nicholas , Pereira Joana , Perrakis Anastassis , Powell Harold R. , Read Randy J. , Rigden Daniel J. , Rochira William , Sammito Massimo , Sánchez Rodríguez Filomeno , Sheldrick George M. , Shelley Kathryn L. , Simkovic Felix , Simpkin Adam J. , Skubak Pavol , Sobolev Egor , Steiner Roberto A. , Stevenson Kyle , Tews Ivo , Thomas Jens M. H. , Thorn Andrea , Valls Josep Triviño , Uski Ville , Usón Isabel , Vagin Alexei , Velankar Sameer , Vollmar Melanie , Walden Helen , Waterman David , Wilson Keith S. , Winn Martyn D. , Winter Graeme , Wojdyr Marcin , Yamashita Keitaro 
Published: May 2023

The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.
Finance – growth nexus: evidence from systemically important Islamic finance countries
Authors: Smolo Edib , Nagayev Ruslan 
Published: May 2023

Purpose
The purpose of this study is to examine the effects of financial development on the economic growth of jurisdictions with systemically important Islamic finance.

Design/methodology/approach
The authors use several estimation methods. The primary analysis is based on the LSDVC method using a sample of 23 countries covering the period of 2000–2019.

Findings
The findings suggest that the financial sector may not be a significant factor in determining economic growth, or that it may decrease it depending on the proxy used. These results are in line with recent studies and robust across different estimation specifications and methods used.

Practical implications
Finance practitioners may reconsider the way they conduct their daily activities as their impact on economic growth is fading away. Similarly, policymakers should consider the role that financial development plays in economic growth alongside other factors that may influence its impact. It may be necessary to examine the moderating effects of institutional development on the relationship between finance and growth and consider the channels through which financial development can contribute to economic growth. Additionally, it would be useful to study the impact of Islamic finance on economic growth using different data sources.

Originality/value
Although the topic has been explored using different data sets and focusing on different samples, it has not been explored considering the impact of Islamic finance development on economic growth. Given the global appeal of the Islamic finance industry, it is worth investigating its significance for economic growth.
Revolutionizing language processing in libraries with SheetGPT: an integration of Google Sheet and ChatGPT plugin
Authors: Panda Subhajit , Kaur Navkiran 
Published: May 2023

Purpose
The purpose of this research paper is to explore the significance of language processing in library systems and evaluate the effectiveness of integrating artificial intelligence and generative pre-trained transformer (GPT) technology in modern libraries. Specifically, the paper focuses on SheetGPT, a Google Sheet and GPT Plugin and its impact on language processing in library systems.

Design/methodology/approach
This paper adopts a comprehensive analysis approach to evaluate the integration of SheetGPT in library systems. The authors outlined a user-friendly approach for installation and use of SheetGPT using its “beginner plan”, appropriate for personal/student use or extended experimentation. The study includes a quantitative analysis to provide a thorough understanding of the benefits and limitations of SheetGPT in library systems.

Findings
The findings of this research paper suggest that SheetGPT is a highly effective language-processing tool for library systems. Additionally, ChatGPT’s integration with Google Sheets and easy accessibility over Google Marketplace makes it an efficient and user-friendly tool for library professionals. Overall, this study highlights the potential of SheetGPT to enhance language processing in library systems

Originality/value
This research paper contributes to the existing literature by providing a comprehensive analysis of the effectiveness of SheetGPT in library systems. The study’s approach is unique in that it evaluates SheetGPT’s impact on language processing and provides insights into its benefits and limitations. The study’s findings are original and provide a valuable resource for library professionals and researchers interested in exploring the potential of SheetGPT to enhance language processing in library systems.
Mothers' participation in family gatherings and social events with their children with autism spectrum disorder: A scoping review
Authors: Moorthy Shobana Devi , Carlstedt Anita Björklund , Fischl Caroline 
Published: May 2023

AbstractIntroductionParticipating in family gatherings can provide enjoyment and quality time together as a family. However, being the primary carers, mothers of children with autism spectrum disorder may experience this phenomenon differently. The purpose of this study is to explore how available literature describes mothers' experiences of participation in family gatherings and social events with their children with autism spectrum disorder.MethodsA scoping review was used to explore available literature and identify studies describing mothers' experiences of family gatherings and social events with their children. A thematic synthesis was performed to analyse and synthesise the findings.ResultsA total of 8 articles were included for review. The analysis of the included studies resulted in one central theme—Negative experiences despite strategies—and four analytical themes: Feeling fear, stress, and anxiety; Avoiding family gatherings; Enjoying less and becoming less confident; and Using strategies.ConclusionThese findings indicate that mothers of children with autism spectrum disorder experience difficulties during gatherings even when using strategies, hence limiting their participation.
Optimizing peritoneal dialysis initiation: A comparative cohort study of catheter placement methods for shortening break‐in periods
Authors: Chávez‐Chávez Hugo E. , Hernández‐Paredes Elisa Naomi , Cojuc‐Konigsberg Gabriel , Vargas‐Rodríguez Cecilia , Díaz‐Canchola Laura Margarita , Vergara‐Zavala Octavio , Fernández‐Venegas Alonso , Acevedo‐Juárez Nadia Stephani , Correa‐Rotter Ricardo , Ramirez‐Sandoval Juan C. 
Published: May 2023

AbstractIntroductionPeritoneal dialysis (PD) guidelines recommend a 14‐day break‐in period after catheter placement, yet this period could be shortened with new insertion techniques.MethodsWe conducted a prospective cohort study to compare percutaneous vs. surgical catheter insertion in a newly established PD program. The break‐in period was intentionally shortened to <24 h to start PD almost immediately.ResultsWe included 223 subjects who underwent percutaneous (34%) or surgical (66%) catheter placement. Compared to the surgical group, the percutaneous group had a higher proportion of early dialysis initiation within 24 h (97% vs. 8%,p < 0.001), similar successful initiation rates (87% vs. 92%,p = 0.34), and shorter lengths of stay (12 [9–18] vs. 18 [14–22] days,p < 0.001). Percutaneous insertion increased the likelihood of successful PD initiation within 24 h (OR 74, 95% CI 31–182), without increasing major complications.ConclusionPercutaneous placement could represent a cost‐effective and efficient technique to shorten break‐in periods.
Research culture in Australian and New Zealand radiation oncology: Fact or fantasy?
Authors: Roos Daniel 
Published: May 2023

AbstractIntroductionFostering a research culture is a key goal of the Royal Australian and New Zealand College of Radiologists, yet there has never been an organization‐wide enquiry into the extent to which this is being realized. The purpose of this work was to address that deficit for the Radiation Oncology (RO) Faculty to serve as a baseline for future comparison. The hypothesis was that such a culture is closer to fact than fantasy.MethodsWith College approval, three de‐identified Excel spreadsheets detailing 25 research‐related sub‐categories of the Faculty's Continuing Professional Development (CPD) database were interrogated for the 2019–21 triennium, accepting that research activity in 2020–21 would be COVID‐19 suppressed. The numbers obligated to self‐report CPD were 482, 496 and 511, respectively. Primary endpoints were the percentages of ROs claiming at least one research‐related activity overall, and in each of the sub‐categories individually, by year. Secondary endpoints were the “breadth” (number of sub‐categories claimed/individual) and “depth” (percentages solely claiming in one of four lower‐level sub‐categories), by year.ResultsROs claimed in 23/25 sub‐categories. The percentages of ROs claiming at least one research‐related activity were 71%, 44%, and 62% in 2019–21, respectively. The median number of sub‐categories claimed by these ROs was 2 (range 1–10) in each year. The commonest activity was journal article co‐author (25%, 16% and 27%, respectively). For 2019, the most representative year, other common activities were inhouse/local meeting presentation (17%), invited lecture at state level or above (15%), manuscript peer review and research project principal investigator (14% each). The percentages of ROs solely claiming in one lower‐level activity ranged between 4.4% and 5.9% per year.ConclusionA culture of research is arguably more fact than fantasy in ANZ. It is likely that Faculty curriculum requirements, research funding and other promotional initiatives have contributed substantively to this.
Immunosuppression for the treatment of pulmonary hypertension in patients with systemic lupus erythematosus: A systematic review
Authors: Bruera Sebastian , Sreedhar Arsha , Agarwal Sandeep K. , Muthukumar Varsha , Geng Yimin , Lopez‐Olivo Maria A. 
Published: May 2023

AbstractPurposeTo conduct a systematic review with meta‐analysis to determine the effects of immunosuppression on Group 1 Pulmonary Arterial Hypertension in patients with systemic lupus erythematosus (SLE).MethodsWe searched Medline, Embase, Web of Science, Clinicaltrials.gov, and Cochrane Central Register of Controlled Trials (CENTRAL) with a search strategy developed by a medical librarian. We included retrospective, cross‐sectional, case‐control, prospective studies, and randomized controlled trials (RCTs) in our analysis and only included studies that contained data for patients with SLE. We included any immunosuppressive agents (including but not limited to cyclophosphamide, glucocorticoids, mycophenolate mofetil, azathioprine, and rituximab) We assessed for risk of bias and certainty of evidence. Outcomes included hemodynamics (as measured by pulmonary arterial hypertension), functional status, 6 minute walk test (6MWT), quality of life, mortality, and serious adverse events.ResultsWe included three studies. One RCT and two single‐arm interventional observational studies. The RCT had a high risk of bias whereas the two single‐arm interventional studies were graded as fair quality. Meta‐analysis could not be conducted because of insufficient data. The RCT showed significant improvements in hemodynamics (as measured by pulmonary arterial pressures) and functional status. One observational study showed improvements in hemodynamics, functional status, and 6MWT. There were insufficient data for serious adverse events, mortality, and quality of life.ConclusionsDespite a high prevalence and with a poor prognosis, there is a paucity of data for the role of immunosuppression in the treatment of Group 1 Pulmonary Arterial Hypertension in SLE. More high‐quality studies are needed, especially to investigate serious adverse events and quality of life.
Predicting fluid responsiveness using esophagus Doppler monitoring and pulse oximetry derived pleth variability index; retrospective analysis of a hemodynamic study
Authors: Hahn Robert G. , Nilsson Lena , Bahlmann Hans 
Published: May 2023

AbstractBackgroundFluid therapy during major surgery can be managed by providing repeated bolus infusions until stroke volume no longer increases by ≥ 10%. However, the final bolus in an optimization round increases stroke volume by < 10% and is not necessary. We studied how different cut‐off values for the hemodynamic indications given by esophagus Doppler monitoring, as well as augmentation by pulse oximetry, are associated with a higher or smaller chance that stroke volume increases by ≥ 10% (fluid responsiveness) before fluid is infused.MethodsAn esophagus Doppler and a pulse oximeter that displayed the pleth variability index were used to monitor the effects of a bolus infusion in 108 patients undergoing goal‐directed fluid therapy during major open abdominal surgery.ResultsThe analyzed data set comprised 266 bolus infusions. The overall incidence of fluid responsiveness was 44%, but this varied greatly depending on pre‐infusion hemodynamics. The likelihood of being fluid‐responsive was 30%–38% in the presence of stroke volume > 80 mL, corrected flow time > 360 ms, or pleth variability index < 10%. The likelihood was 21% if stroke volume had decreased by <8% since the previous optimization, which decreased to 0% if combined with stroke volume > 100 mL. By contrast, the likelihood of fluid responsiveness increased to 50%–55% when stroke volume ≤ 50 mL, corrected flow time ≤ 360 ms, or pleth variability index ≥ 10. A decrease in stroke volume by > 8% since the previous optimization was followed by a 58% likelihood of fluid responsiveness that, in combination with any of the other hemodynamic variables, increased to 66%–76%.ConclusionsSingle or combined hemodynamic variables provided by esophagus Doppler monitoring and pulse oximetry derived pleth variability index could help clinicians avoid unnecessary fluid bolus infusions.
Systemic antibiotic treatment for meibomian gland dysfunction—A systematic review and meta‐analysis
Authors: Ben Ephraim Noyman Dror , Chan Clara C. , Mimouni Michael , Safir Margarita 
Published: May 2023

AbstractPurposeTo review the efficacy and safety of oral doxycycline antibiotics versus macrolides in the treatment of meibomian gland dysfunction (MGD).DesignSystematic review and meta‐analysis.MethodsWe performed a systematic search of electronic databases for all peer‐reviewed published studies which included clinical outcomes of oral antibiotic MGD treatment. Individual study data were extracted and evaluated in a weighted pooled analysis, including total sign and symptom scores, meibomian gland secretion score, tear break‐up time (TBUT), fluorescein staining score and rate of complications.ResultsTwo thousand nine hundred and thirty‐three studies were found, of which 54 were eligible for the systematic review, and six prospective studies were ultimately included for analysis, reporting on 563 cases from three countries. Age of affected patients ranged between 12 and 90 years. Overall, both treatment methods induced improvement in MGD signs and symptoms. In pooled analysis, macrolides were significantly superior in the total signs score (pooled standardized mean difference (SMD) −0.51, 95% confidence interval (CI): −0.99 to −0.03), meibomian gland secretion score (pooled SMD −0.25, 95%CI: [−0.48, −0.03]), TBUT (SMD −0.31, 95%CI: [−0.50, −0.13]) and fluorescein staining score (SMD −1.01, 95%CI: [−1.72, −0.29]). Moreover, while no severe complications were reported for both treatments, the macrolide group exhibited significantly less adverse events (pooled odds ratio 0.24 with a 95% CI of 0.16 to 0.34).ConclusionsBoth macrolides and tetracyclines are effective treatments for MGD. In this study, macrolides exhibited better efficacy and safety profile compared to tetracyclines.