bluuebunny/crossref_metadata_2025_split huggingface dataset:
Broad-range amplification and sequencing of the
rpoB
gene: a novel assay for bacterial identification in clinical microbiology
Authors: Bivand Joanna Małgorzata , Dyrhovden Ruben , Sivertsen Audun , Tellevik Marit Gjerde , Patel Robin , Kommedal Øyvind 
Published: June 2024

ABSTRACT

The
rpoB
gene has been proposed as a promising phylogenetic marker for bacterial identification, providing theoretically improved species-level resolution compared to the 16S rRNA gene for a range of clinically important taxa. However, its utility in diagnostic microbiology has been limited by the lack of broad-range primers allowing for its amplification from most species with a single PCR assay. Here, we present an assay for broad-range partial amplification and Sanger sequencing of the
rpoB
gene. To reduce cross-reactivity and allow for
rpoB
amplification directly from patient samples, primers were based on the dual priming oligonucleotide principle. The resulting amplicon is ~550 base pairs in length and appropriate for species-level identification. Systematic
in silico
evaluation of a wide selection of taxa demonstrated improved resolution within multiple important genera, including
Enterococcus, Fusobacterium
,
Mycobacterium
,
Streptococcus
, and
Staphylococcus
species and several genera within the
Enterobacteriaceae
family. Broad-range
rpoB
amplification and Sanger sequencing of 115 bacterial isolates provided unambiguous species-level identification for 97 (84%) isolates, as compared to 57 (50%) using a clinical 16S rRNA gene assay. Several unresolved taxonomic matters disguised by the low resolution of the 16S rRNA gene were revealed using the
rpoB
gene. Using a collection of 33 clinical specimens harboring bacteria and assumed to contain high concentrations of human DNA, the
rpoB
assay identified the pathogen in 29 specimens (88%). Broad-range
rpoB
amplification and sequencing provides a promising tool for bacterial identification, improving discrimination between closely related species and making it amenable for use in culture-based and culture-independent diagnostic approaches.
Bile acid-sensitive human norovirus strains are susceptible to sphingosine-1-phosphate receptor 2 inhibition
Authors: Tenge Victoria , Ayyar B. Vijayalakshmi , Ettayebi Khalil , Crawford Sue E. , Hayes Nicole M. , Shen Yi-Ting , Neill Frederick H. , Atmar Robert L. , Estes Mary K. 
Published: June 2024

ABSTRACT

Human noroviruses (HuNoVs) are a diverse group of RNA viruses that cause endemic and pandemic acute viral gastroenteritis. Previously, we reported that many HuNoV strains require bile or bile acid (BA) to infect human jejunal intestinal enteroid cultures. BA was not essential for the replication of a pandemic-causing GII.4 HuNoV strain. We found the hydrophobic BA glycochenodeoxycholic acid (GCDCA) promotes the replication of the BA-dependent strain GII.3 in jejunal enteroids. Furthermore, we found that inhibition of the G-protein-coupled BA receptor, sphingosine-1-phosphate receptor 2 (S1PR2), by JTE-013, reduced GII.3 infection dose-dependently and inhibited GII.3 cellular uptake in enteroids. Herein, we sought to determine whether S1PR2 is required for other BA-dependent HuNoV strains, the BA-independent GII.4, and whether S1PR2 is required for BA-dependent HuNoV infection in HIEs from other small intestinal segments. We found a second S1PR2 inhibitor, GLPG2938, reduces GII.3 infection dose-dependently, and an S1PR2 agonist (CYM-5520) enhances GII.3 replication in the absence of GCDCA. GII.3 replication also is abrogated in the presence of JTE-013 and CYM-5520. JTE-013 inhibition of S1PR2 in jejunal HIEs reduces GI.1, GII.3, and GII.17 (BA-dependent) but not GII.4 Sydney (BA-independent) infection, providing additional evidence of strain-specific differences in HuNoV infection. Finally, GII.3 infection of duodenal, jejunal, and ileal lines derived from the same individual is reduced with S1PR2 inhibition, indicating a common mechanism of BA-dependent infection among multiple segments of the small intestine. Our results support a model where BA-dependent HuNoVs exploit BA effects on S1PR2 to infect the entire small intestine.

IMPORTANCE
Human noroviruses (HuNoVs) are important viral human pathogens that cause both outbreaks and sporadic gastroenteritis. These viruses are diverse, and many strains are capable of infecting humans. Our previous studies have identified strain-specific requirements for hydrophobic bile acids (BAs) to infect intestinal epithelial cells. Moreover, we identified a BA receptor, sphingosine-1-phosphate receptor 2 (S1PR2), required for infection by a BA-dependent strain. To better understand how various HuNoV strains enter and infect the small intestine and the role of S1PR2 in HuNoV infection, we evaluated infection by additional HuNoV strains using an expanded repertoire of intestinal enteroid cell lines. We found that multiple BA-dependent strains, but not a BA-independent strain, all require S1PR2 for infection. In addition, BA-dependent infection requires S1PR2 in multiple segments of the small intestine. Together, these results indicate that S1PR2 has value as a potential therapeutic target for BA-dependent HuNoV infection.
The distribution and generation of carbonatites
Authors: Gibson Sally , McKenzie Dan , Lebedev Sergei 
Published: June 2024

Abstract
The physio-chemical framework that generates carbonatites and, ultimately, the associated rare earth element deposits remains contentious. This primarily reflects the diverse tectonic settings in which carbonatites occur: large igneous provinces, continental rifts and major extensional terranes, syn- to post-collisional settings, or ocean islands. There is, however, a broad consensus that carbonatites (or their parental melts) originate in the mantle. These exotic melts have small volumes that make them ideal probes of conditions in their underlying source regions. We combine the carbonatite locations with global maps of lithospheric thickness, derived from seismic tomography, and show that post-Neoproterozoic carbonatites occur preferentially above the margins of thick cratonic lithosphere (e.g., adjacent to the South Atlantic and Indian Oceans or in North America, Greenland, and Asia) and where once thick lithosphere has undergone stretching (e.g., eastern Asia). Our thermal modeling reveals that lateral and vertical heat conduction on rifted craton margins, or rapid stretching of cratonic lithosphere, can mobilize carbonated peridotite at the temperatures (950–1250 °C) and pressures (2–3 GPa) required to form primary carbonatites or their parental alkali silicate melts. Importantly, our models show that heat conduction from upwelling mantle plumes or ambient mantle on rifted cratonic margins may sufficiently modify the temperature of the lithospheric mantle to cause melting of carbonated peridotite, settling the long-standing debate on the role of rifting and heating in the generation of carbonatites.
Shallow ocean deoxygenation drove trilobite turnover during the late Cambrian SPICE event
Authors: Yang Aihua , Chen Bo , Sun Zhixin , Tostevin Rosalie , He Tianchen , Chen Xi , Chen Jitao , Lu Miao , Hu Chunlin , Du Shengxian , Chen Jun , Jiao Wenjun , Zhu Maoyan 
Published: June 2024

Abstract
The spread of marine anoxia is believed to have played a key role in the development of the SPICE (Steptoean Positive Carbon Isotope Excursion) event and the end-Marjuman extinction in the late Cambrian (~497.5 m.y. ago), but their cause-and-effect relationship is poorly constrained. Here we present an integrated analysis of carbonate δ13C, cerium anomalies (Ce/Ce*), and genus-level diversity data of trilobites from the North China Platform. Our results show tightly coupled changes between the SPICE, an increase in Ce/Ce*, and a trilobite turnover event, which we interpret as indicating enhanced productivity and organic remineralization, leading to the development of low-oxygen conditions in shallow-water settings. This study therefore establishes a direct link between local ecological stress and trilobite turnover during the global SPICE event. Furthermore, the presence of low-oxygen rather than fully anoxic conditions during the peak of the SPICE event could explain the nature of the end-Marjuman crisis, which was characterized by the replacement of shallow-water fauna by deeper-water counterparts that were potentially more tolerant of hypoxia.
Lateral episiotomy or no episiotomy in vacuum assisted delivery in nulliparous women (EVA): multicentre, open label, randomised controlled trial
Authors: Bergendahl Sandra , Jonsson Maria , Hesselman Susanne , Ankarcrona Victoria , Leijonhufvud Åsa , Wihlbäck Anna-Carin , Wallström Tove , Rydström Emmie , Friberg Hanna , Kopp Kallner Helena , Brismar Wendel Sophia 
Published: June 2024

Abstract

Objective
To assess the effect of lateral episiotomy, compared with no episiotomy, on obstetric anal sphincter injury in nulliparous women requiring vacuum extraction.

Design
A multicentre, open label, randomised controlled trial.

Setting
Eight hospitals in Sweden, 2017-23.

Participants
717 nulliparous women with a single live fetus of 34 gestational weeks or more, requiring vacuum extraction were randomly assigned (1:1) to lateral episiotomy or no episiotomy using sealed opaque envelopes. Randomisation was stratified by study site.

Intervention
A standardised lateral episiotomy was performed during the vacuum extraction, at crowning of the fetal head, starting 1-3 cm from the posterior fourchette, at a 60° (45-80°) angle from the midline, and 4 cm (3-5 cm) long. The comparison was no episiotomy unless considered indispensable.

Main outcome measures
The primary outcome of the episiotomy in vacuum assisted delivery (EVA) trial was obstetric anal sphincter injury, clinically diagnosed by combined visual inspection and digital rectal and vaginal examination. The primary analysis used a modified intention-to-treat population that included all consenting women with attempted or successful vacuum extraction. As a result of an interim analysis at significance level P<0.01, the primary endpoint was tested at 4% significance level with accompanying 96% confidence interval (CI).

Results
From 1 July 2017 to 15 February 2023, 717 women were randomly assigned: 354 (49%) to lateral episiotomy and 363 (51%) to no episiotomy. Before vacuum extraction attempt, one woman withdrew consent and 14 had a spontaneous birth, leaving 702 for the primary analysis. In the intervention group, 21 (6%) of 344 women sustained obstetric anal sphincter injury, compared with 47 (13%) of 358 women in the comparison group (P=0.002). The risk difference was −7.0% (96% CI −11.7% to −2.5%). The risk ratio adjusted for site was 0.47 (96% CI 0.23 to 0.97) and unadjusted risk ratio was 0.46 (0.28 to 0.78). No significant differences were noted between groups in postpartum pain, blood loss, neonatal outcomes, or total adverse events, but the intervention group had more wound infections and dehiscence.

Conclusions
Lateral episiotomy can be recommended for nulliparous women requiring vacuum extraction to significantly reduce the risk of obstetric anal sphincter injury.

Trial registration

ClinicalTrials.gov
NCT02643108
.
How do patients perceive the retirement of their general practitioner? A qualitative interview study in France
Authors: Kerebel Yann , Duguet Théo , Kapassi Amar , Figoni Hugo , Colas-Charlap Anne-Laure , Pariente Laura , Perroteau Florent , Moussaoui Sohela , Bonello Kim , Chastang Julie 
Published: June 2024

ObjectivesThe perspective of general practitioners’ (GPs) on retirement and the factors influencing their attitude towards retirement have been previously investigated. However, while the number of GPs has been declining for many years in France, leading to the emergence of medical deserts, the impact on their patients remains to be explored. The aim of this study was to understand patients’ perceptions of their GP’s retirement.DesignA semistructured interview-based qualitative study was conducted, using Interpretative Phenomenological Analysis.SettingInterviews were conducted in two general practices located in Essonne, Ile-de-France, France, between January and April 2014.ParticipantsThirteen women and five men, aged 21–94 years, were included in this study. Exclusion criteria were the non-declaration of the physician as the declared doctor and being under 18 years of age.ResultsThe GP–patient relationship is a link that is built up over time, over the course of several consultations. Patients choose their GP based on qualities or skills they value. In this way, the physician chosen is unique for their patients; this choice reflects a certain loyalty to their physician. The interaction with the family sphere reinforces this relationship through the multiple links created during care. When a GP retires, this link is broken. Patients’ reactions can range from indifference to real grief.ConclusionThis study confirms the importance of the link between the GPs and their patients and highlights the need to prepare patients for their GP’s retirement.
Examining the role of resilience in the relationship between social support and fear of recurrence among patients with gastric cancer on chemotherapy: a cross-sectional study in Jiangsu, China
Authors: Yang Lihua , Li Yi , Wang Xiaoqing , Xia Chao , Yang Liping , Li Xun , Zou Yanling , Wang Qiong , Hou Qingmei , Duan Peibei , Zhang Ziyan 
Published: June 2024

ObjectivesThe objective of this study is to investigate the relationships between fear of cancer recurrence (FCR), social support and resilience, and further determine whether resilience mediates social support and FCR among Chinese patients with gastric cancer undergoing chemotherapy.DesignMulticentre cross-sectional survey.SettingFour hospitals in Jiangsu Province, China, with grade-A tertiary hospital settings.Participants755 patients with gastric cancer on chemotherapy across four hospitals in China were included from March 2021 to September 2022.Outcome measuresThe Fear of Progression Questionnaire-Short Form (FoP-Q-SF), Connor-Davidson Resilience Scale (CD-RISC) and Social Support Rating Scale (SSRS) were used to test the model’s constructs. Statistical analyses were conducted by using IBM SPSS V.26.0 software. PROCESS V.3.4 macro was used to analyse the mediating role of resilience in the relationship between social support and FCR.ResultsThe mean scores for SSRS, CD-RISC and FoP-Q-SF in patients with gastric cancer receiving chemotherapy were 41.55±7.79, 54.83±18.46 and 30.91±10.11, respectively. 43.3% (n=327) had psychological dysfunction, 56.8% (n=429) had low to medium resilience and 99.1% (n=748) had medium to robust social support. Significant differences exist among three variables, resilience positively correlated with social support, while FCR negatively correlated with resilience and social support (p<0.001). Resilience fully mediated the relationship between social support and FCR (a*b-path=−0.126, 95% CI −0.169 to –0.086).ConclusionsMediation analysis shows resilience mediates social support and FCR in patients with gastric cancer as the negative effect of social support on FCR was fully mediated by resilience. Interventions targeting these variables may reduce FCR in patients with gastric cancer undergoing chemotherapy.
Association between extremely high prognostic nutritional index and all-cause mortality in patients with coronary artery disease: secondary analysis of a prospective cohort study in China
Authors: Wu Ting-Ting , Pan Ying , Zhi Xiao-Yu , Deng Chang-Jiang , Wang Shun , Guo Xiao-Xia , Hou Xian-Geng , Yang Yi , Zheng Ying-Ying , Xie Xiang 
Published: June 2024

ObjectivesDecreased prognostic nutritional index (PNI) was associated with adverse outcomes in many clinical diseases. This study aimed to evaluate the relationship between baseline PNI value and adverse clinical outcomes in patients with coronary artery disease (CAD).DesignThe Personalized Antiplatelet Therapy According to CYP2C19 Genotype in Coronary Artery Disease (PRACTICE) study, a prospective cohort study of 15 250 patients with CAD, was performed from December 2016 to October 2021. The longest follow-up period was 5 years. This study was a secondary analysis of the PRACTICE study.SettingThe study setting was Xinjiang Medical University Affiliated First Hospital in China.ParticipantsUsing the 50th and 90th percentiles of the PNI in the total cohort as two cut-off limits, we divided all participants into three groups: Q1 (PNI <51.35, n = 7515), Q2 (51.35 ≤ PNI < 59.80, n = 5958) and Q3 (PNI ≥ 59.80, n = 1510). The PNI value was calculated as 10 × serum albumin (g/dL) + 0.005 × total lymphocyte count (per mm3).Primary outcomeThe primary outcome measure was mortality, including all-cause mortality (ACM) and cardiac mortality (CM).ResultsIn 14 983 participants followed for a median of 24 months, a total of 448 ACM, 333 CM, 1162 major adverse cardiovascular events (MACE) and 1276 major adverse cardiovascular and cerebrovascular events (MACCE) were recorded. The incidence of adverse outcomes was significantly different among the three groups (p <0.001). There were 338 (4.5%), 77 (1.3%) and 33 (2.2%) ACM events in the three groups, respectively. A restricted cubic spline displayed a J-shaped relationship between the PNI and worse 5-year outcomes, including ACM, CM, MACE and MACCE. After adjusting for traditional cardiovascular risk factors, we found that only patients with extremely high PNI values in the Q3 subgroup or low PNI values in the Q1 subgroup had a greater risk of ACM (Q3 vs Q2, HR: 1.617, 95% CI 1.012 to 2.585, p=0.045; Q1 vs Q2, HR=1.995, 95% CI 1.532 to 2.598, p <0.001).ConclusionThis study revealed a J-shaped relationship between the baseline PNI and ACM in patients with CAD, with a greater risk of ACM at extremely high PNI values.Trial registration numberNCT05174143.
Support for banning sale of smoked tobacco products among adults who smoke: findings from the International Tobacco Control Four Country Smoking and Vaping Surveys (2018–2022)
Authors: Le Grande Michael , Borland Ron , Gravely Shannon , Cummings Michael , McNeill Ann , Yong Hua H , Gartner Coral E 
Published: June 2024

BackgroundMany people continue to smoke despite strong policies to deter use, thus stronger regulatory measures may be required. In four high-income countries, we examined whether people who smoke would support a total ban on smoked tobacco products under two differing policy scenarios.MethodsData were from 14 363 adults (≥18) who smoked cigarettes (≥monthly) and participated in at least one of the 2018, 2020 or 2022 International Tobacco Control Four Country Smoking and Vaping Surveys in Australia, Canada, England and the USA. In 2018, respondents were asked whether they would support a law that totally bans smoked tobacco if the government provides smoking cessation assistance (Cessation Assistance scenario). In 2020 and 2022, respondents were asked a slightly different question as to whether they would support a law that totally bans smoked tobacco if the government encourages people who smoke to use alternative nicotine products like vaping products and nicotine replacement products instead (substitution scenario). Responses (support vs oppose/don’t know) were estimated on weighted data.ResultsSupport was greater for the cessation assistance scenario (2018, 36.6%) than the nicotine substitution scenario (2020, 26.9%; 2022, 26.3%, both p<0.0001). In the longitudinal analysis, there was a significant scenario by country interaction effect with lower support in Canada, the USA and Australia under the substitution scenario than in the cessation scenario, but equivalent levels in England under both scenarios. The strongest correlates of support under both scenarios were planning to quit smoking within 6 months, wanting to quit smoking ‘a lot’ and recent use of nicotine replacement therapy.ConclusionsOpposition to banning smoked tobacco predominates among people who smoke, but less with a cessation assistance scenario than one encouraging nicotine substitution. Wanting to quit a lot was the strongest indicator of support.
A note on the G-Itô Formula and a comment on “Averaging Principle for SDEs of Neutral Type Driven by G-Brownian Motion”
Authors: Liu Puchen , Zhu Yunlong , Liu Haitao 
Published: June 2024

This is a comment on the paper Stoch. Dyn. 19(1) (2019) 1950004, http://doi.org/10.1142/S0219493719500047 ) titled “Averaging Principle for SDEs of Neutral Type Driven by G-Brownian Motion”, preceded by a note on the G-Itô formula. In the commented paper, the authors provided a wrong result and incorrect computations in their Theorem 4.1 and Appendix B, which probably result from the misapplication of the G-Itô Formula in the sublinear expectation theory. Hence, we provide a differential form of the G-Itô formula with a calculation table and the correct computation on the solution related to Theorem 4.1 of the commented paper.
Laptev Rift System Composite Tectono-Sedimentary Element, East Siberian Arctic
Authors: Drachev Sergey S. , Ershova Victoria B. , Shkarubo Sergey I. 
Published: June 2024

Abstract
The Laptev Sea in the East Siberian Arctic is characterized by a system of extensional structures known as the Laptev Rift System (LRS), developed at the continental prolongation of an active divergent plate boundary - the Gakkel spreading ridge. The LRS hosts as much as 13–14 km of siliciclastic sedimentary strata of supposedly Late Cretaceous to Recent age. The strata accumulated atop of stretched and thinned continental crust that before the rifting onset was a complex tectonic juncture of Late Paleozoic/Early Mesozoic Taimyr and Late Mesozoic Verkhoyansk fold-and-thrust belts formed along the edges of the Siberian Palaeocontinent.
In the context of this volume, the LRS is described as a composite tectono-sedimentary element that includes sedimentary rocks accumulated during pre-rift and syn-rift phases. The latter includes at least two syn-rift sedimentary cycles separated by a sedimentary succession formed during a stalled rift phase.
In the absence of deep exploration wells, many aspects of the LRS geology and its petroleum prospects remain poorly constrained.