bluuebunny/crossref_metadata_2025_split huggingface dataset:
Radioembolization Planning With Dual-Isotope Acquisition of 166Ho-Labeled Microparticles and 99mTc-Mebrofenin
Authors: Czibor Sándor , Bibok András , Horváthy Dénes , Fábián Krisztián , Györke Tamás 
Published: June 2023

Abstract
A 76-year-old man with hepatocellular carcinoma was referred for liver radioembolization. Given a prior left hemihepatectomy, it was clinically important to consider potentially irradiated healthy liver at planning. Thus, at the SPECT/CT imaging of the scout dose 166Ho-microparticles before injected superselectively in the right hepatic artery, 99mTc-mebrofenin was injected intravenously, and functional volumetry SPECT was performed simultaneously. Based on the 2 image sets, the nonirradiated healthy liver was calculated as 1589 mL (functional liver reserve of 85.5% on 99mTc-mebrofenin SPECT). Posttreatment dosimetry calculations showed optimal normal tissue and tumor absorbed doses, and the patient is clinically well after 3 months.
Proximal Instructions for Use Violations in Elective Endovascular Aneurysm Repair in the Vascular Quality Initiative: Retrospective Analysis
Authors: Ramirez Joel L , Govsyeyev Nicholas , Sorber Rebecca , Iannuzzi James C , Schanzer Andres S , Hicks Caitlin W , Malas Mahmoud B , Zarkowsky Devin S 
Published: June 2023

Background:
Endovascular aneurysm repair (EVAR) is often attempted in patients with marginal anatomy. These patients’ mid-term outcomes are available in the Vascular Quality Initiative (VQI) for analysis.

Study Design:
Retrospective analysis of prospectively collected data in the VQI from patients who underwent elective infrarenal EVAR between 2011 and 2018. Each EVAR was identified as on- or off-instructions for use (IFU) based on aortic neck criteria. Multivariable logistic regression models were used to assess associations between aneurysm sac enlargement, reintervention, and Type 1a endoleak with IFU status. Kaplan-Meier time-to-event models estimated reintervention, aneurysm sac enlargement, and overall survival.

Results:
We identified 5,488 patients with at least one follow-up recorded. Those treated off-IFU included 1,236 patients (23%) (mean follow-up, 401 days), in comparison to 4,252 (77%) treated on-IFU (mean follow-up, 406 days). There was no evidence of significant differences in crude 30-day survival (96% vs 97%; p=0.28) or estimated 2 year survival (97% vs 97%; log-rank p=0.28). Crude Type 1a endoleak frequency was greater in patients treated off-IFU (2% vs. 1%; p=0.03). Off-IFU EVAR was associated with Type 1a endoleak on multivariable regression model (odds ratio [OR] 1.84, 95% confidence interval [CI]: 1.23–2.76; p=0.003). Patients treated off-IFU vs on-IFU experienced increased risk of reintervention within 2 years (7% vs. 5%; log-rank p=0.02), a finding consistent with results from the Cox modeling (Hazard ratio [HR] 1.38, 95% CI: 1.06–1.81, p=0.02).

Conclusions:
Patients treated off-IFU were at greater risk for Type 1a endoleak and reintervention, although they had similar 2-year survival compared to those treated on-IFU. Patients with anatomy outside IFU should be considered for open surgery or complex endovascular repair to reduce the probability for revision.
Detection of multiple extensively-drug resistant hypervirulent Klebsiella pneumoniae clones from patients with ventilator-associated pneumonia in Egypt
Authors: Elzeny Hadeel , Mohamed Wegdan , Daef Enas , El-Badawy Omnia , Shaaban Lamiaa , Osman Naglaa S. , Hadiya Safy , Aly Sherine 
Published: June 2023

Graphical Abstract
Emergence of XDR-hvKP as the predominant

K. pneumoniae

pathotype responsible for ventilator associated pneumonia in Assiut, Egypt.
Predictive power of wastewater for nowcasting infectious disease transmission: a retrospective case study of five sewershed areas in Louisville, Kentucky
Authors: Klaassen Fayette , Holm Rochelle H. , Smith Ted , Cohen Ted , Bhatnagar Aruni , Menzies Nicolas A. 
Published: June 2023

AbstractBackgroundEpidemiological nowcasting traditionally relies on count surveillance data. The availability and quality of such data may vary over time, limiting their representation of true infections. Wastewater data correlates with traditional surveillance data and may provide additional value for nowcasting disease trends.MethodsWe obtained SARS-CoV-2 case, death, wastewater, and serosurvey data for Jefferson County, Kentucky, between August 2020 and March 2021, and parameterized an existing nowcasting model using combinations of these data. We assessed the predictive performance and variability at the sewershed level and compared the effects of adding or replacing wastewater data to case and death reports.FindingsAdding wastewater data minimally improved the predictive performance of nowcasts compared to a model fitted to case and death data (Weighted Interval Score (WIS) 0·208 versus 0·223), and reduced the predictive performance compared to a model fitted to deaths data (WIS 0·517 versus 0·500). Adding wastewater data to deaths data improved the nowcasts agreement to estimates from models using cases and deaths data. These findings were consistent across individual sewersheds as well as for models fit to the aggregated data of all 5 sewersheds. Retrospective reconstructions of epidemiological dynamics created using different combinations of data were in general agreement (coverage > 75%).InterpretationThese findings show that wastewater data may be valuable for infectious disease nowcasting when clinical surveillance data are absent, such as early in a pandemic or in low-resource settings where systematic collection of epidemiologic data is difficult.FundingCDC, Louisville-Jefferson County Metro Government, and other funders.
SparseRNAFolD: Sparse RNA pseudoknot-free Folding including Dangles
Authors: Gray Mateo , Will Sebastian , Jabbari Hosna 
Published: June 2023

AbstractMotivationComputational RNA secondary structure prediction by free energy minimization is indispensable for analyzing structural RNAs and their interactions. These methods find the structure with the minimum free energy (MFE) among exponentially many possible structures and have a restrictive time and space complexity (O(n3) time andO(n2) space for pseudoknot-free structures) for longer RNA sequences. Furthermore, accurate free energy calculations including dangles contributions can be difficult and costly to implement, particularly when optimizing for time and space requirements.ResultsHere we introduce a fast and efficient sparsified MFE pseudoknot-free structure prediction algorithm, SparseRNAFolD, that utilizes an accurate energy model that accounts for dangles contributions. While sparsification technique was previously employed to improve time and space complexity of a pseudoknot-free structure prediction method with a realistic energy model, SparseMFEFold, it was not extended to include dangles contributions due to complexity of computation. This may be at the cost of prediction accuracy. In this work, we compare three different sparsified implementations for dangles contributions and provide pros and cons of each method. As well, we compare our algorithm to LinearFold, a linear time and space algorithm, where we find in practice, SparseRNAFolD has lower memory consumption across all lengths of sequence and a faster time for lengths up to 1000 bases.ConclusionOur SparseRNAFolD algorithm is an MFE-based algorithm that guarantees optimality of result and employs the most general energy model including dangles contributions. We provide basis for applying dangles to sparsified recursion in a pseudoknot-free model which has the ability to be extended to pseudoknots.AvailabilitySparseRNAFolD’s algorithm and detailed results are available athttps://github.com/mateog4712/SparseRNAFolD.
Haplotype-resolved, chromosome-level assembly of white clover (Trifolium repensL., Fabaceae)
Authors: Santangelo James S. , Battlay Paul , Hendrickson Brandon T. , Kuo Wen-Hsi , Olsen Kenneth M. , Kooyers Nicholas J. , Johnson Marc T.J. , Hodgins Kathryn A. , Ness Rob. W. 
Published: June 2023

AbstractBackgroundWhite clover (Trifolium repensL.; Fabaceae) is an important forage and cover crop in agricultural pastures around the world, and is increasingly used in evolutionary ecology and genetics to understand the genetic basis of adaptation. Historically, improvements in white clover breeding practices and assessments of genetic variation in nature have been hampered by a lack of high-quality genomic resources for this species, owing in part to its high heterozygosity and allotetraploid hybrid origin.FindingsHere, we use PacBio HiFi and chromosome conformation capture (Omni-C) technologies to generate a chromosome-level, haplotype-resolved genome assembly for white clover totaling 998 Mbp (scaffold N50 = 59.3 Mbp) and 1 Gbp (scaffold N50 = 58.6 Mbp) for haplotypes 1 and 2, respectively, with each haplotype arranged into 16 chromosomes (8 per subgenome). We additionally provide a functionally annotated haploid mapping assembly (968 Mbp, scaffold N50 = 59.9 Mbp), which drastically improves on the existing reference assembly in both contiguity and assembly accuracy. We annotated 78,174 protein-coding genes, resulting in protein BUSCO completeness scores of 99.6% and 99.3% against the embryophyta_odb10 and fabales_odb10 lineage datasets, respectively.ConclusionsWe provide two white clover genome assemblies as part of this project: (1) a haplotype-resolved, chromosome-level assembly, and (2) a functionally annotated haploid mapping assembly. These assemblies place white clover among the best sequenced legumes to date, and one of the best assemblies for a plant of recent polyploid origins. This work promises to facilitate ongoing and future work in agricultural and evolutionary genetics in this agronomically and ecologically important species.
Modeling the Structure and DAP5 Binding Site of a Cap-Independent Translational Enhancer mRNA
Authors: Whittaker Amanda , Goss Dixie J. 
Published: June 2023

AbstractCap-independent translation initiation in eukaryotes involves initiation factor (eIF) binding to a transcript’s 5’ untranslated region (UTR). Internal-ribosome-entry-site (IRES)-like cap-independent translation initiation does not require a free 5’ end for eIF binding, as eIFs recruit the ribosome to or near the start codon. For viral mRNA, recruitment usually utilizes RNA structure, such as a pseudoknot. However, for cellular mRNA cap-independent translation, no consensus RNA structures or sequences have yet been identified for eIF binding. Fibroblast-growth factor 9 (FGF-9) is a member of a subset of mRNA that are cap-independently upregulated in breast and colorectal cancer cells using this IRES-like method. Death-associated factor 5 (DAP5), an eIF4GI homolog, binds directly to the FGF-9 5’ UTR to initiate translation. However, the DAP5 binding site within the FGF-9 5’ UTR is unknown. Moreover, DAP5 binds to other, dissimilar 5’ UTRs, some of which need a free 5’ end to stimulate cap-independent translation. We propose that a particular RNA structure involving tertiary folding, rather than a conserved sequence or secondary structure, acts as a DAP5 binding site. Using SHAPE-seq, we modeled the FGF-9 5’ UTR RNA’s complex secondary and tertiary structure in vitro. Further, DAP5 footprinting and toeprinting experiments show DAP5’s preference for one face of this structure. DAP5 binding appears to stabilize a higher-energy RNA fold that frees the 5’ end to solvent and brings the start codon close to the recruited ribosome. Our findings offer a fresh perspective in the hunt for cap-independent translational enhancers. Structural, rather than sequence-specific, eIF binding sites may act as attractive chemotherapeutic targets or as dosage tools for mRNA-based therapies.
Prokaryotic winged helix domains as dsDNA adenine methylation sensors
Authors: Helbrecht Igor , Heiter Daniel , Yang Weiwei , Lutz Thomas , Ettwiller Laurence , Bochtler Matthias , Xu Shuang-yong 
Published: June 2023

AbstractWinged helix (wH) domains, also termed winged helix-turn-helix (wHTH) domains, are widespread in all kingdoms of life, and have diverse roles. In the context of DNA binding and DNA modification sensing, some eukaryotic wH domains are known as sensors of non-methylated CpG. In contrast, the prokaryotic wH domains in DpnI and phi.HhiV4I act as sensors of adenine methylation in 6mApT (6mA = N6mA) context. DNA binding modes and interactions with the probed dinucleotide are vastly different in the two cases. Here, we show that the role of the wH domain as a sensor of adenine methylation is widespread in prokaryotes. We present previously uncharacterized examples of PD-(D/E)XK—wH (FcyTI, Psp4BI), PUA—wH—HNH (HtuIII, Hsa13891I), wH—GIY-YIG (Ahi29725I, Apa233I) and PLD—wH (Aba4572I, CbaI) fusion endonucleases that sense adenine methylation in the Dam G6mATC, and possibly other, slightly more relaxed contexts. Representatives of the wH domain endonuclease fusion families with the exception of the PLD—wH family could be purified, and anin vitropreference for adenine methylation in the Dam context could be demonstrated. Like most other MDREs, the new fusion endonucleases except those in the PD-(D/E)XK—wH family cleave close to, but outside the recognition sequence. Taken together, our data illustrate the widespread combinatorial use of prokaryotic wH domains as adenine methylation sensors.
METTL16 Controls Kaposi’s Sarcoma-Associated Herpesvirus Replication by RegulatingS-Adenosylmethionine Cycle
Authors: Zhang Xinquan , Meng Wen , Feng Jian , Gao Xinghong , Qin Chao , Feng Pinghui , Huang Yufei , Gao Shou-Jiang 
Published: June 2023

AbstractOncogenic Kaposi’s sarcoma-associated herpesvirus (KSHV) consists of latent and lytic replication phases, both of which are important for the development of KSHV- related cancers. As one of the most abundant RNA modifications,N6-methyladenosine (m6A) and its related complexes regulate KSHV life cycle. However, the role of METTL16, a new RNA methyltransferase, in KSHV life cycle remains unknown. In this study, we have identified a suppressive role of METTL16 in KSHV lytic replication. METTL16 knockdown increased while METTL16 overexpression reduced KSHV lytic replication. METTL16 binding to and writing of m6A on MAT2A transcript are essential for its splicing, maturation and expression. As a rate-limiting enzyme in the methionine-S-adenosylmethionine (SAM) cycle, MAT2A catalyzes the conversion of L-methionine to SAM required for the transmethylation of protein, DNA and RNA, transamination of polyamines, and transsulfuration of cystathionine. Consequently, knockdown or chemical inhibition of MAT2A reduced intracellular SAM level and enhanced KSHV lytic replication. In contrast, SAM treatment was sufficient to inhibit KSHV lytic replication and reverse the effect of the enhanced KSHV lytic program caused by METTL16 or MAT2A knockdown. Mechanistically, METTL16 or MAT2A knockdown increased while SAM treatment decreased the intracellular reactive oxygen species level by altering glutathione level, which is essential for efficient KSHV lytic replication. These findings demonstrate that METTL16 suppresses KSHV lytic replication by modulating the SAM cycle to maintain intracellular SAM level and redox homeostasis, thus illustrating the linkage of KSHV life cycle with specific m6A modifications, and cellular metabolic and oxidative conditions.
Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats
Authors: Tseng Yi-Ju , Malik Indranil , Deng Xiexiong , Krans Amy , Jansen-West Karen , Tank Elizabeth M.H. , Gomez Nicolas B. , Sher Roger , Petrucelli Leonard , Barmada Sami J. , Todd Peter K. 
Published: June 2023

ABSTRACTA GGGGCC (G4C2) hexanucleotide repeat expansion inC9ORF72causes amyotrophic lateral sclerosis and frontotemporal dementia (C9ALS/FTD), while a CGG trinucleotide repeat expansion inFMR1leads to the neurodegenerative disorder Fragile X-associated tremor/ataxia syndrome (FXTAS). These GC-rich repeats form RNA secondary structures that support repeat-associated non-AUG (RAN) translation of toxic proteins that contribute to disease pathogenesis. Here we assessed whether these same repeats might trigger stalling and interfere with translational elongation. We find that depletion of ribosome-associated quality control (RQC) factors NEMF, LTN1, and ANKZF1 markedly boost RAN translation product accumulation from both G4C2 and CGG repeats while overexpression of these factors reduces RAN production in both reporter cell lines and C9ALS/FTD patient iPSC-derived neurons. We also detected partially made products from both G4C2 and CGG repeats whose abundance increased with RQC factor depletion. Repeat RNA sequence, rather than amino acid content, is central to the impact of RQC factor depletion on RAN translation - suggesting a role for RNA secondary structure in these processes. Together, these findings suggest that ribosomal stalling and RQC pathway activation during RAN translation elongation inhibits the generation of toxic RAN products. We propose augmenting RQC activity as a therapeutic strategy in GC-rich repeat expansion disorders.Graphical Abstract
Trends shaping sustainable post-pandemic development of the V4 region in turbulent times until 2030
Authors: Gáspár Judit , Gubová Klaudia , Hideg Eva , Jagaciak Maciej Piotr , Mackova Lucie , Márton András , Rafał Weronika , Sacio-Szymańska Anna , Šerá Komlossyová Eva 
Published: June 2023

Purpose
The paper evaluates trends shaping the post-pandemic reality. The framework adopted is a case study of the V4 region (Poland, the Czech Republic, Slovakia and Hungary) that illustrates broader trends, their direction of change and their influence on the entire region. This paper aims to identify key trends and analyse how they can facilitate or hinder sustainable development.

Design/methodology/approach
The paper is based on a multidisciplinary literature review and an online real-time Delphi study carried out across four European countries.

Findings
The results indicate that the influence of negative trends on sustainability is much stronger than that of positive ones. Concerning the trends’ driving factors, the blockers of negative trends have a much higher influence on sustainability than the blockers of positive ones. The study shows that the most significant trends affecting sustainability are distributed throughout various fields of human activity, including geopolitics, social issues, education, the environment, technology and health.

Practical implications
The findings presented below can be used primarily by decision makers from the V4 region, who are responsible for crafting strategies regarding post-COVID recovery. The study illustrates trends that V4 countries and other European Union member states might be facing in the future and analyses how they relate to sustainability. The conclusions indicate that the most effective path to the desired level of sustainability is one that incorporates policies built around the blockers of negative trends.

Originality/value
The importance of this study lies in its focus on countries that had previously received little attention in scientific analyses. The paper shows their possible developmental pathways and sheds light on the framework of integrated foresight and its applications in sustainability-related areas.
Women in uniform breaking the glass ceiling? An exploratory study of female officers in leadership positions in Ghana’s Security Services
Authors: Markwei Ummu , Attiogbe Esther Julia , Asomaning Antwi Abena , Boafo Georgina Korkor 
Published: June 2023

Purpose
The purpose of the study is to examine how women become leaders in the Security Services in Ghana and the challenges they face in the discharge of their responsibilities.

Design/methodology/approach
A qualitative phenomenological approach was adopted to explore the intentions and opinions of the participants, interpret their worlds through their lived experiences and present a clearer understanding of their stories.

Findings
The study revealed that women deliberately positioned themselves to be considered for leadership placements in their male-dominated professions. The study’s findings also suggest that although both men and women are considered equal in the service, women were faced with challenges in their daily experiences as leaders due to their gender. The gender barriers created a strenuous situation for women to rise to top leadership placements in the Security Services.

Originality/value
This research is one of the first studies that explored the experiences of women in middle and top leadership positions in the national Security Services in Ghana. It contributes to the literature by presenting how female leaders in the Security Services successfully navigate into leadership placements, the challenges and their strategies in excelling in their duties. The study is important in bridging the gender gap in leadership positions in the Security Services.
Ride-sharing customers’ self-protection motivation in the post-COVID-19 world
Authors: Cheng Xusen , Bao Ying , de Vreede Triparna , de Vreede Gert-Jan , Gu Junhan 
Published: June 2023

PurposeThe COVID-19 pandemic has generated unprecedented public fear, impeding both individuals’ social life and the travel industry as a whole. China was one of the first major countries to experience the COVID-19 outbreaks and recovery from the pandemic. The demand for outings is increasing in the post-COVID-19 world, leading to the recovery of the ride-sharing industry. Integrating protection motivation theory and the theory of reasoned action, this study aims to investigate ride-sharing customers’ self-protection motivation to provide anti-pandemic measures and promote the resilience of ride-sharing industry.Design/methodology/approachThis study followed a two-phase mixed-methods design. In the first phase, the authors executed a qualitative study with 30 interviews. In the second phase, the authors used the results of the interviews to inform the design of a survey, with which 272 responses were collected. Both studies were conducted in China.FindingsThe present results indicate that customers’ perceived vulnerability of COVID-19 and perceived COVID protection efficacy (self-efficacy and response efficacy) are positively correlated with their attitude toward self-protection, thus leading to their self-protection motivation during the rides. Moreover, subjective norms and customers’ distrust appear to also impact their self-protection motivation during the ride-sharing service.Originality/valueThe present research provides one of the first in-depth studies, to the best of the authors’ knowledge, on customers’ protection motivation in ride-sharing services in the new normal. The empirical evidence provides important insights for ride-sharing service providers and managers in the post-pandemic world and promote the resilience of ride-sharing industry.