bluuebunny/crossref_metadata_2025_split huggingface dataset:
A
Burkholderia cenocepacia
-like environmental isolate strongly inhibits the plant fungal pathogen
Zymoseptoria tritici
Authors: Song Tingting , Gupta Suyash , Sorokin Yael , Frenkel Omer , Cytryn Eddie , Friedman Jonathan 
Published: April 2024

ABSTRACT

Fungal phytopathogens cause significant reductions in agricultural yields annually, and overusing chemical fungicides for their control leads to environmental pollution and the emergence of resistant pathogens. Exploring natural isolates with strong antagonistic effects against pathogens can improve our understanding of their ecology and develop new treatments for the future. We isolated and characterized a novel bacterial strain associated with the species
Burkholderia cenocepacia
, termed APO9, which strongly inhibits
Zymoseptoria tritici
, a commercially important pathogenic fungus causing
Septoria tritici
blotch in wheat. Additionally, this strain exhibits inhibitory activity against four other phytopathogens. We found that physical contact plays a crucial role for APO9’s antagonistic capacity. Genome sequencing of APO9 and biosynthetic gene cluster (BGC) analysis identified nine classes of BGCs and three types of secretion systems (types II, III, and IV), which may be involved in the inhibition of
Z. tritic
i and other pathogens. To identify genes driving APO9’s inhibitory activity, we screened a library containing 1,602 transposon mutants and identified five genes whose inactivation reduced inhibition efficiency. One such gene encodes for a diaminopimelate decarboxylase located in a terpenoid biosynthesis gene cluster. Phylogenetic analysis revealed that while some of these genes are also found across the
Burkholderia
genus, as well as in other
Betaproteobacteria
, the combination of these genes is unique to the
Burkholderia cepacia
complex. These findings suggest that the inhibitory capacity of APO9 is complex and not limited to a single mechanism, and may play a role in the interaction between various
Burkholderia
species and various phytopathogens within diverse plant ecosystems.

IMPORTANCE
The detrimental effects of fungal pathogens on crop yields are substantial. The overuse of chemical fungicides contributes not only to environmental pollution but also to the emergence of resistant pathogens. Investigating natural isolates with strong antagonistic effects against pathogens can improve our understanding of their ecology and develop new treatments for the future. We discovered and examined a unique bacterial strain that demonstrates significant inhibitory activity against several phytopathogens. Our research demonstrates that this strain has a wide spectrum of inhibitory actions against plant pathogens, functioning through a complex mechanism. This plays a vital role in the interactions between plant microbiota and phytopathogens.
Plasmodium yoelii
surface-related antigen (PySRA) modulates the host pro-inflammatory responses via binding to CD68 on macrophage membrane
Authors: Feng Xin , Yu Jia-Li , Sun Yi-Fan , Du Chen-Yan , Shen Yao , Zhang Lu , Kong Wei-Zhong , Han Su , Cheng Yang 
Published: April 2024

ABSTRACT

Malaria, one of the major infectious diseases in the world, is caused by the
Plasmodium
parasite.
Plasmodium
antigens could modulate the inflammatory response by binding to macrophage membrane receptors. As an export protein on the infected erythrocyte membrane,
Plasmodium
surface-related antigen (SRA) participates in the erythrocyte invasion and regulates the immune response of the host. This study found that the F2 segment of
P. yoelii
SRA activated downstream MAPK and NF-κB signaling pathways by binding to CD68 on the surface of the macrophage membrane and regulating the inflammatory response. The anti-PySRA-F2 antibody can protect mice against
P. yoelii
, and the pro-inflammatory responses such as IL-1β, TNF-α, and IL-6 after infection with
P. yoelii
are attenuated. These findings will be helpful for understanding the involvement of the pathogenic mechanism of malaria with the exported protein SRA.
Lipoic acid attachment to proteins: stimulating new developments
Authors: Cronan John E. 
Published: April 2024

SUMMARY

Lipoic acid-modified proteins are essential for central metabolism and pathogenesis. In recent years, the
Escherichia coli
and
Bacillus subtilis
lipoyl assembly pathways have been modified and extended to archaea and diverse eukaryotes including humans. These extensions include a new pathway to insert the key sulfur atoms of lipoate, several new pathways of lipoate salvage, and a novel use of lipoic acid in sulfur-oxidizing bacteria. Other advances are the modification of
E. coli
LplA for studies of protein localization and protein-protein interactions in cell biology and in enzymatic removal of lipoate from lipoyl proteins. Finally, scenarios have been put forth for the evolution of lipoate assembly in archaea.
Investigation of Plasma Flow Velocity in the Helical Magnetic Open Trap SMOLA
Authors: Inzhevatkina A. A. , Ivanov I. A. , Postupaev V. V. , Sudnikov A. V. , Tolkachev M. S. , Ustyuzhanin V. O. 
Published: April 2024

Abstract
The physics of confinement of plasma rotating in the magnetic field with linear helical symmetry is studied at the SMOLA open trap at Budker Institute of Nuclear Physics of the Siberian Branch of the Russian Academy of Sciences. The factor characterizing the quality of plasma confinement in the system is its flow velocity. The paper describes the diagnostics applied, which is based on the Mach probe used under the conditions of nonmagnetized plasma; this diagnostics made it possible to determine the longitudinal flow velocity in the experiments. In different operating regimes of the device, the measured longitudinal flow velocity was (0.5−5) × 106 cm/s. It is discussed how the velocity depends on the magnetic field corrugation. The reverse flow of trapped particles returning to the confinement zone was detected.
Shared genetic aetiology of Alzheimer’s disease and age-related macular degeneration by APOC1 and APOE genes
Authors: Zhang Xueli , Zhu Zhuoting , Huang Yu , Shang Xianwen , O'Brien Terence J , Kwan Patrick , Ha Jason , Wang Wei , Liu Shunming , Zhang Xiayin , Kiburg Katerina , Bao Yining , Wang Jing , Yu Honghua , He Mingguang , Zhang Lei 
Published: April 2024

BackgroundAlzheimer’s disease (AD) and age-related macular degeneration (AMD) share similar pathological features, suggesting common genetic aetiologies between the two. Investigating gene associations between AD and AMD may provide useful insights into the underlying pathogenesis and inform integrated prevention and treatment for both diseases.MethodsA stratified quantile–quantile (QQ) plot was constructed to detect the pleiotropy among AD and AMD based on genome-wide association studies data from 17 008 patients with AD and 30 178 patients with AMD. A Bayesian conditional false discovery rate-based (cFDR) method was used to identify pleiotropic genes. UK Biobank was used to verify the pleiotropy analysis. Biological network and enrichment analysis were conducted to explain the biological reason for pleiotropy phenomena. A diagnostic test based on gene expression data was used to predict biomarkers for AD and AMD based on pleiotropic genes and their regulators.ResultsSignificant pleiotropy was found between AD and AMD (significant leftward shift on QQ plots). APOC1 and APOE were identified as pleiotropic genes for AD–AMD (cFDR <0.01). Network analysis revealed that APOC1 and APOE occupied borderline positions on the gene co-expression networks. Both APOC1 and APOE genes were enriched on the herpes simplex virus 1 infection pathway. Further, machine learning-based diagnostic tests identified that APOC1, APOE (areas under the curve (AUCs) >0.65) and their upstream regulators, especially ZNF131, ADNP2 and HINFP, could be potential biomarkers for both AD and AMD (AUCs >0.8).ConclusionIn this study, we confirmed the genetic pleiotropy between AD and AMD and identified APOC1 and APOE as pleiotropic genes. Further, the integration of multiomics data identified ZNF131, ADNP2 and HINFP as novel diagnostic biomarkers for AD and AMD.
Predictive factors of clot propagation in patients with superficial venous thrombosis towards deep venous thrombosis and pulmonary embolism: a systematic review and meta-analysis
Authors: van Royen Florien Sophie-Anne , van Smeden Maarten , van Doorn Sander , Rutten Frans H , Geersing Geert-Jan 
Published: April 2024

ObjectiveA subset of patients with superficial venous thrombosis (SVT) experiences clot propagation towards deep venous thrombosis (DVT) and/or pulmonary embolism (PE). The aim of this systematic review is to identify all clinically relevant cross-sectional and prognostic factors for predicting thrombotic complications in patients with SVT.DesignSystematic review.Data sourcesPubMed/MEDLINE and Embase were systematically searched until 3 March 2023.Eligibility criteriaOriginal research studies with patients with SVT, DVT and/or PE as the outcome and presenting cross-sectional or prognostic predictive factors.Data extraction and synthesis of resultsThe CHecklist for critical Appraisal and data extraction for systematic Reviews of prediction Modelling (CHARMS) checklist for prognostic factor studies was used for systematic extraction of study characteristics. Per identified predictive factor, relevant estimates of univariable and multivariable predictor—outcome associations were extracted, such as ORs and HRs. Estimates of association for the most frequently reported predictors were summarised in forest plots, and meta-analyses with heterogeneity were presented. The Quality in Prognosis Studies (QUIPS) tool was used for risk of bias assessment and Grading of Recommendations, Assessment, Development and Evaluations (GRADE) for assessing the certainty of evidence.ResultsTwenty-two studies were included (n=10 111 patients). The most reported predictive factors were high age, male sex, history of venous thromboembolism (VTE), absence of varicose veins and cancer. Pooled effect estimates were heterogenous and ranged from OR 3.12 (95% CI 1.75 to 5.59) for the cross-sectional predictor cancer to OR 0.92 (95% CI 0.56 to 1.53) for the prognostic predictor high age. The level of evidence was rated very low to low. Most studies were scored high or moderate risk of bias.ConclusionsAlthough the pooled estimates of the predictors high age, male sex, history of VTE, cancer and absence of varicose veins showed predictive potential in isolation, variability in study designs, lack of multivariable adjustment and high risk of bias prevent firm conclusions. High-quality, multivariable studies are necessary to be able to identify individual SVT risk profiles.PROSPERO registration numberCRD42021262819.
Labour Care Guide implementation as a decision-making tool for monitoring labour among healthcare providers in Uganda: protocol for a mixed-methods study
Authors: Mugyenyi Godfrey R , Byamugisha Josaphat , Tumuhimbise Wilson , Atukunda Esther , Yarine Fajardo T 
Published: April 2024

IntroductionThe new WHO Labour Care Guide (LCG), also regarded as the ‘next-generation partograph’, is a core component of 2018 WHO consolidated guidelines on intrapartum care for positive childbirth experience. The Ugandan Ministry of Health is in the process of adopting the new WHO LCG with no local context-specific data to inform this transition. We will explore potential barriers and facilitators to healthcare providers’ (HCPs) sustained engagement in labour monitoring in Mbarara city, Southwestern Uganda, and use the data to refine the new WHO LCG and develop a suitable implementation strategy to effectively integrate LCG into routine maternity care in Uganda. We shall then assess effectiveness, validity and other preliminary implementation outcomes of using the new LCG in detecting prolonged labour.Methods and analysisThe study will use a mixed-methods approach to identify key LCG user perspectives to refine and customise the WHO LCG among 120 HCPs and stakeholders involved in maternity care and labour monitoring within facilities in Southwestern Uganda. The refined prototype will be deployed and used to monitor labour in all 14 basic and comprehensive emergency obstetric and newborn care facilities in the study area. We will review labour outcomes of 520 patients monitored using the new LCG and compare these outcomes with a historical cohort of 520 patients monitored using the partograph. The main effectiveness outcome will be the proportion of women diagnosed with prolonged labour and/or obstructed labour.Ethics and disseminationEthical approval was obtained from the Mbarara University of Science and Technology Research Ethics Committee (MUST-2023-808) and Uganda National Council for Science and Technology (HS2864ES). We shall obtain written informed consent from each participant. The results of this study will be published in international peer-reviewed journals and presented to the Ugandan Ministry of Health as policy briefs and at selected national/international conferences.Trial registration numberNCT05979194.
Functional therapy and adenotonsillectomy clinical trial for class II malocclusion (FACT-II): protocol for a randomised controlled trial
Authors: Guo Feiyang , Lv Chenxing , Tang Bojun , Lin Lizhuo , Zhang Chen , Zheng Jie , Zhao Tingting , He Hong 
Published: April 2024

IntroductionClass II malocclusion with mandibular retrognathia is a common complication of paediatric obstructive sleep apnoea (OSA), often accompanied by transverse maxillary deficiency. In early orthodontic treatment, a twin block (TB) is a regular functional appliance for correcting this malocclusion. For paediatric OSA, the most common risk factor is adenotonsillar hypertrophy (AHT). Untreated AHT may lead to the persistence and worsening of obstructive sleep-disordered breathing traits, including habitual mouth breathing. Additionally, the clockwise mandibular rotation associated with AHT-induced pharyngeal crowding can undermine the effectiveness and stability of TB treatment. Adenotonsillectomy (T&A) is currently the first-line treatment for paediatric OSA. This proposed trial will investigate the impact of T&A surgery timing on the efficacy and stability of TB functional treatment in children with class II mandibular retrognathia and ATH.Methods and analysisThis will be a single-centre, parallel-group, superiority randomised controlled trial with participants randomised to intervention (T&A followed by TB treatment) or control arms (TB treatment followed by T&A) in a 1:1 ratio. A total of 40 patients aged 8–14 years, diagnosed with class II mandibular retrognathia and co-existing ATH-induced OSA, and indicated for both T&A surgery and TB treatment, will be recruited at the School and Hospital of Stomatology, Wuhan University. The primary outcomes will be the changes in the apnoea-hypopnoea index and the point A-nasion-point B angle from baseline to postorthodontic treatment between the two groups. Secondary outcomes will include other dental, skeletal, upper airway and soft tissue changes, as well as subjective sleep-related and oral-related quality of life. Outcome changes within each group and between groups will be analysed.Ethics and disseminationThis study is approved by the Ethics Committee of the School and Hospital of Stomatology, Wuhan University (no. 2022-D07). The research findings will be faithfully disseminated through scientific conferences or published articles.Trial registration numberChiCTR2200061703 (https://www.chictr.org.cn).
Multicentre double-blind randomised placebo-controlled trial evaluating the efficacy of the meningococcal B vaccine, 4CMenB (Bexsero), againstNeisseria gonorrhoeaeinfection in men who have sex with men: the GoGoVax study protocol
Authors: Seib Kate L , Donovan Basil , Thng Caroline , Lewis David A , McNulty Anna , Fairley Christopher K , Yeung Barbara , Jin Fengyi , Fraser Doug , Bavinton Benjamin R , Law Matthew , Chen Marcus Y , Chow Eric P F , Whiley David M , Mackie Brent , Jennings Michael P , Jennison Amy V , Lahra Monica M , Grulich Andrew E 
Published: April 2024

IntroductionGonorrhoea, the sexually transmissible infection caused byNeisseria gonorrhoeae, has a substantial impact on sexual and reproductive health globally with an estimated 82 million new infections each year worldwide.N. gonorrhoeaeantimicrobial resistance continues to escalate, and disease control is largely reliant on effective therapy as there is no proven effective gonococcal vaccine available. However, there is increasing evidence from observational cohort studies that the serogroup B meningococcal vaccine four-component meningitis B vaccine (4CMenB) (Bexsero), licensed to prevent invasive disease caused byNeisseria meningitidis, may provide cross-protection against the closely related bacteriumN. gonorrhoeae. This study will evaluate the efficacy of 4CMenB againstN. gonorrhoeaeinfection in men (cis and trans), transwomen and non-binary people who have sex with men (hereafter referred to as GBM+).Methods and analysisThis is a double-blind, randomised placebo-controlled trial in GBM+, either HIV-negative on pre-exposure prophylaxis against HIV or living with HIV (CD4 count >350 cells/mm3), who have had a diagnosis of gonorrhoea or infectious syphilis in the last 18 months (a key characteristic associated with a high risk ofN. gonorrhoeaeinfection). Participants are randomised 1:1 to receive two doses of 4CMenB or placebo 3 months apart. Participants have 3-monthly visits over 24 months, which include testing forN. gonorrhoeaeand other sexually transmissible infections, collection of demographics, sexual behaviour risks and antibiotic use, and collection of research samples for analysis ofN. gonorrhoeae-specific systemic and mucosal immune responses. The primary outcome is the incidence of the first episode ofN. gonorrhoeaeinfection, as determined by nucleic acid amplification tests, post month 4. Additional outcomes consider the incidence of symptomatic or asymptomaticN. gonorrhoeaeinfection at different anatomical sites (ie, urogenital, anorectum or oropharynx), incidence byN. gonorrhoeaegenotype and antimicrobial resistance phenotype, and level and functional activity ofN. gonorrhoeae-specific antibodies.Ethics and disseminationEthical approval was obtained from the St Vincent’s Hospital Human Research Ethics Committee, St Vincent’s Hospital Sydney, NSW, Australia (ref: 2020/ETH01084). Results will be disseminated in peer-reviewed journals and via presentation at national and international conferences.Trial registration numberNCT04415424.
Predictors and long-term patterns of medication adherence to glaucoma treatment in Denmark—an observational registry study of 30 100 Danish patients with glaucoma
Authors: Kolko Miriam , Faergemann Hansen Rikke , G Dal Louise , Sabelström Emma , Brandel Magnus , Hoiberg Bentsen Andreas , Falch-Joergensen Anne Cathrine 
Published: April 2024

BackgroundSelf-treatment with glaucoma medication (eye drops) has been associated with adherence challenges. Poor adherence results in worse outcomes in terms of visual field loss.ObjectiveTo investigate patterns in medication adherence among Danish patients with glaucoma in relation to selected predictors of adherence, long-term adherence patterns, and long-term societal economic consequences of poor adherence.Methods and analysisThis register-based study included 30 100 glaucoma patients followed for 10 years between 2000 and 2018. Glaucoma was identified from the Danish national registers by diagnosis of Open Angle Glaucoma and/or by redeemed prescriptions of glaucoma medication. Logistic regression models were applied to estimate patient characteristics related to medical adherence. Diagnosis-related group fees were applied to estimate healthcare costs.ResultsHigh adherence in the first year(s) of treatment was less likely among men (ORfirst year: 0.78, 95% CI: 0.75 to 0.82), younger individuals and among those with a positive Charlson Comorbidity Index (CCI) score (ORfirst year/CCI≥3: 0.71, 95% CI: 0.63 to 0.80). Adherence in the first year and in the first two years was associated with adherence in the fifth (ORfirst year: 4.55, 95% CI: 4.30 to 4.82/ORfirst two years: 6.47, 95% CI: 6.10 to 6.86) as with adherence in the 10th year with slightly lower estimates. Being medical adherent was related to higher costs related to glaucoma medication after 5 and 10 years comparing with poor adherence, whereas poor adherence was associated with a marked increase in long-term costs for hospital contacts.ConclusionIncreasing age, female sex and low comorbidity score are correlated with better adherence to glaucoma treatment. Adherence in the first years of treatment may be a good predictor for future adherence. In the long term, patients with poor adherence are overall more expensive to society in terms of hospital contacts.
Implementation of a quality improvement initiative for standardising essential newborn care in a teaching public hospital in rural central India
Authors: Jain Manish , Meshram Payal , Bang Akash , Chauhan Varsha , Datta Vikram , Dhanireddy Ramasubbareddy 
Published: April 2024

ObjectiveOur aim was to refine the essential newborn care practices by employing the multidisciplinary peer team-led quality improvement (QI) projects.DesignIn 2017, concerning the same, the department focused on early initiation of breast feeding, prevention of hypothermia within an hour of life and rational usage of antibiotics among babies admitted to neonatal intensive care unit (NICU). Baseline data reported the rate of initiation of breast feeding, hypothermia and antibiotic exposure rate as 35%, 78% and 75%, respectively. Root causes were analysed and a series of Plan-Do-Study-Act cycles were conducted to test the changes. The process of change was studied through run charts (whereas control charts were used for study purpose).ResultAfter the implementation of the QI projects, the rate of initiation of breast feeding was found to be improved and sustained from 35% to 90%, the incidence of hypothermia got reduced from 78% to 10% and the antibiotic exposure rate declined from 75% to 40%. Along with the improvement in indicators related to essential newborn care, down the stream we found a decrease in the percentage of culture-positive sepsis rate in the NICU.ConclusionPeer team-led QI initiatives in a resource-limited setting proved beneficial in improving essential newborn care practices.
Achieving optimal cord management: a multidisciplinary quality improvement initiative
Authors: Burgess-Shannon Jessica , Clarke Rebecca , Rowell Victoria , Aladangady Narendra 
Published: April 2024

Optimal cord management (OCM), defined as waiting at least 60 seconds (s) before clamping the umbilical cord after birth, is an evidence-based intervention that improves outcomes for both term and preterm babies. All major resuscitation councils recommend OCM for well newborns.National Neonatal Audit Programme (NNAP) benchmarking data identified our tertiary neonatal unit as a negative outlier with regard to OCM practice with only 12.1% of infants receiving the recommended minimum of 60 s. This inspired a quality improvement project (QIP) to increase OCM rates of ≥ 60 s for infants <34 weeks. A multidisciplinary QIP team (Neonatal medical and nursing staff, Obstetricians, Midwives and Anaesthetic colleagues) was formed, and robust evidence-based quality improvement methodologies employed. Our aim was to increase OCM of ≥ 60 s for infants born at <34 weeks to at least 40%.The percentage of infants <34 weeks receiving OCM increased from 32.4% at baseline (June–September 2022) to 73.6% in the 9 months following QIP commencement (October 2022–June 2023). The intervention period spanned two cohorts of rotational doctors, demonstrating its sustainability. Rates of admission normothermia were maintained following the routine adoption of OCM (89.2% vs 88.5%), which is a complication described by other neonatal units.This project demonstrates the power of a multidisciplinary team approach to embedding an intervention that relies on collaboration between multiple departments. It also highlights the importance of national benchmarking data in allowing departments to focus QIP efforts to achieve long-lasting transformational service improvements.