bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene expression signatures of mutualism and pathogenesis in flax roots
Authors: Quintans Isadora Louise Alves da Costa Ribeiro , Vukicevich Eric , Kokkoris Vasilis , Packard Erica , Adhikary Dinesh , Hart Miranda M. , Deyholos Michael K. 
Published: October 2024

IntroductionFusarium wilt, a devastating soil-borne fungal disease in flax (Linum usitatissimum), is caused by Fusarium oxysporum f. sp. lini, a hemibiotrophic plant pathogen that penetrates plant roots. There are several reports of the molecular response of L. usitatissimum to F. oxysporum f. sp. lini; however, comparisons of the effects of mutualistic and pathogenic fungi on plants are more limited.MethodsIn this study, we have integrated phenotyping and RNA-Seq approaches to examine the response of flax to F. oxysporum f.sp. lini and to a mutualistic arbuscular mycorrhizal fungus (AMF) Rhizoglomus irregulare. R. irregulare is a common soil fungus and also widely used as a commercial inoculant to improve plant growth. We measured flax growth parameters after plant inoculation with each or both fungi, in comparison with non-inoculated control. We performed transcriptome analysis of root tissues collected at 9 and 14 days post-inoculation.ResultsWe identified several differentially expressed genes (DEGs) in response to pathogenic and mutualistic fungi. These included genes related to ethylene and salicylic acid biosynthesis, carbohydrate binding, oxidoreductases, and sugar transmembrane transporters. Genes related to calcium signaling, nutrient transport, lipid metabolism, cell wall, and polysaccharide-modifying were up-regulated by R. irregulare; however, the same genes were down-regulated by F. oxysporum f. sp. lini when treated independently. In the combined treatment, genes related to cell wall modifications, hormone regulation and nutrient uptake were up-regulated. These results suggest that inoculation with R. irregulare reduced gene expression related to F. oxysporum f. sp. lini infection, leading to a reduced response to the pathogen. In response to AMF, flax prioritized mutualism-related gene expression over defense, reversing the growth inhibition caused by F. oxysporum f. sp.lini in the combined treatment.DiscussionThis research provides insights into the protective effects of AMF, revealing the pre-symbiotic gene expression profile of flax in response to mutualism in comparison with pathogenicity. Potential target genes for crop improvement were identified, especially defense related genes.
Triplex real-time qPCR for the simultaneous detection of Botryosphaeriaceae species in woody crops and environmental samples
Authors: Romero-Cuadrado Laura , Aguado Ana , Ruano-Rosa David , Capote Nieves 
Published: October 2024

IntroductionSpecies of Botryosphaeriaceae fungi are relevant pathogens of almond causing trunk cankers, extensive gumming, necrosis of internal tissues and plant dieback and dead, threatening almond productivity. A novel triplex quantitative real-time PCR (qPCR) assay was designed for the simultaneous detection and quantification of Neofusicoccum parvum, Botryosphaeria dothidea and the Botryosphaeriaceae family.Material and methodsThe method was validated in symptomatic and asymptomatic almond, avocado, blueberry and grapevine plants and in environmental samples, such as cropping soil and rainwater and in artificially inoculated trapped spores, demonstrating the same performance on several matrices.Results and discussionThe limit of detection of the triplex qPCR was 10 fg of genomic DNA for the three fungal targets, with high correlation coefficients (R2) and amplification efficiencies between 90 and 120%. Although the triplex qPCR demonstrated to be more sensitive and accurate than the traditional plate culturing and further sequencing method, a substantial agreement (kappa index = 0.8052 ± 0.0512) was found between the two detection methods. The highly sensitive qPCR assay allows for accurate diagnosis of symptomatic plants and early detection of Botryosphaeriaceae fungi in asymptomatic plants (rootstocks and grafting scions from almond nurseries). Furthermore, the triplex qPCR successfully detected Botryosphaeriaceae fungi in environmental samples, such as cropping soils and rainwater. It was also capable of detecting as few as 10 conidia in artificially inoculated tapes. Therefore, the triplex qPCR is a valuable tool for accurate diagnosis, aiding in the implementation of suitable control measures. It enables preventive detection in asymptomatic samples, helping to avoid the introduction and spread of these pathogens in production fields. Moreover, it assists in identifying inoculum sources and quantifying inoculum levels in crop environments, contributing to a precise phytosanitary application schedule, thereby reducing production costs and preserving the environment.
Integrated hormone and transcriptome profiles provide insight into the pericarp differential development mechanism between Mandarin ‘Shatangju’ and ‘Chunhongtangju’
Authors: Huang Yongjing , Zhu Congyi , Hu Yibo , Yan Sanjiao , Luo Zhimin , Zou Yanping , Wu Wen , Zeng Jiwu 
Published: October 2024

IntroductionCitrus reticulata cv. ‘Chunhongtangju’ was mutated from Mandarin ‘Shatangju’, which has been identified as a new citrus variety. Mandarin ‘Chunhongtangju’ fruits were late-ripening for about two months than Mandarin ‘Shatangju’.MethodsTo understand the pericarp differential development mechanism in Mandarin ‘Shatangju’ (CK) and ‘Chunhongtangju’ (LM), hormones and transcriptome profiles of pericarps were performed in different development stages: Young fruit stage (CK1/LM1), Expansion and Turning color stage (CK2), Expansion stage (LM2), Turning color stage (LM3), and Maturity stage (CK3/LM4).ResultsIn this study, the development of LM was significantly slower, and the maturity was significantly delayed. At the same stage, most hormones in Mandarin ‘Chunhongtangju’ pericarps were higher than that in ‘Shatangju’ such as gibberellin A24, cis(+)-12-oxophytodienoic acid, and L-phenylalanine. The deficiency of hormones in late-maturing pericarps was mainly manifested in ABA, 12-OHJA, MeSAG, and ABA-GE. Differences in transcriptome profiles between the two citrus varieties are primarily observed in energy metabolism, signal transduction such as MAPK signaling pathway and plant hormone signaling, and biosynthesis of secondary metabolites. After analyzing the hormones and transcriptome data, we found that the top genes and hormones, such as Cs_ont_5g020040 (transcription elongation factor, TFIIS), Cs_ont_7g021670 (BAG family molecular chaperone regulator 5, BAG5), Cs_ont_2g025760 (40S ribosomal protein S27, Rps27), 5-deoxystrigol, salicylic acid 2-O-β-glucosid, and gibberellin A24, contributed significantly to gene transcription and hormone synthesis.DiscussionThis study suggests that the variances of pericarp development between the two varieties are linked to variations in the transcription levels of genes associated with energy and secondary metabolism, signal transduction related genes. These findings expand our understanding of the complex transcriptional and hormonal regulatory hierarchy during pericarp development.
Mapping vulnerability for increased COVID-19 susceptibility and worse outcomes: a scoping review
Authors: Couto Rodrigo de Macedo , dos Santos Daniel Gonçalves , Sanine Patrícia Rodrigues , Pires dos Santos Andrea , Kmetiuk Louise Bach , Biondo Alexander Welker , Boing Alexandra Crispim 
Published: October 2024

IntroductionInfectious diseases can spread rapidly in the globalized world, and the complex intersection of individual, social, economic, and cultural factors make it difficult to identify vulnerabilities in the face of pandemics.MethodsTherefore, this study aimed to identify vulnerability factors to infection and worse outcomes associated with COVID-19. This is a scoping review study of six databases that selected publications between 2019 and 2023, focusing on individual, social, and programmatic dimensions of vulnerability. The results were recorded in a spreadsheet and analyzed, considering the interrelationships among these dimensions.ResultsA total of 45 articles were included in the review. Content analysis was conducted using the theoretical framework of health vulnerability, which divides vulnerability into individual, social, and programmatic dimensions. Race/ethnicity, homelessness, incarceration, socioeconomic level, food insecurity, and remote areas were classified as social dimensions. On the other hand, cancer, cardiovascular disease, HIV/AIDS, alcoholism, advanced age, obesity, mental disorders, diabetes, kidney disease, and pregnancy were classified as individual dimensions. None of the publications found explicitly mentioned programmatic vulnerabilities.DiscussionThe research found that social vulnerabilities reinforce individual vulnerabilities, creating a vicious cycle. In addition, programmatic vulnerabilities reinforce this relationship. This study emphasizes that public policies should address these different dimensions of vulnerability. It suggests that this information should be incorporated into health surveillance and future decision-making to face new pandemics.Systematic review registrationhttps://archive.org/details/osf-registrations-wgfmj-v1.
Recommendations for implementing digital alcohol interventions in primary care: lessons learned from a Norwegian feasibility study
Authors: Potthoff Sebastian , Brendryen Håvar , Bosnic Haris , Njå Anne Lill Mjølhus , Finch Tracy , Lid Torgeir Gilje 
Published: October 2024

IntroductionExcessive alcohol consumption is a leading global risk factor for ill-health and premature death. Digital alcohol interventions can be effective at reducing alcohol consumption, but their widespread adoption is lagging behind. This study aimed to identify factors promoting or inhibiting the implementation of a digital alcohol intervention in Norwegian primary care, by using Normalization Process Theory (NPT).MethodsA mixed methods feasibility study combining quantitative and qualitative methods. A digital alcohol intervention called “Endre” was implemented across four GP practices in Stavanger and Oslo. Usage of the intervention was logged on the digital platform. General practitioners (GPs) reported their perceived uptake of the intervention via a web-based survey. The Normalization MeAsure Development (NoMAD) survey was used to measure support staff's perceived normalization of the intervention. Qualitative data were analyzed using the NPT framework, with quantitative data analyzed descriptively and using χ2 and Wilcoxon signed-rank test for differences in current and future normalization.ResultsThirty-seven GPs worked in the clinics and could recruit patients for the digital intervention. Thirty-six patients registered for the intervention. Nine patients dropped out early and 25 completed the intervention as intended. Low normalization scores at follow-up (n = 27) indicated that Endre did not become fully embedded in and across practices. Nonetheless, staff felt somewhat confident about their use of Endre and thought it may become a more integral part of their work in the future. Findings from six semi-structured group interviews suggested that limited implementation success may have been due to a lack of tailored implementation support, staff's lack of involvement, their diminished trust in Endre, and a lack of feedback on intervention usage. The outbreak of the Covid-19 pandemic further limited opportunities for GPs to use Endre.ConclusionThis study investigated the real-world challenges of implementing a digital alcohol intervention in routine clinical practice. Future research should involve support staff in both the development and implementation of digital solutions to maximize compatibility with professional workflows and needs. Integration of digital solutions may further be improved by including features such as dashboards that enable clinicians to access and monitor patient progress and self-reported outcomes.
Do COVID-19 Infectious Disease Models Incorporate the Social Determinants of Health? A Systematic Review
Authors: John-Baptiste Ava A. , Moulin Marc , Li Zhe , Hamilton Darren , Crichlow Gabrielle , Klein Daniel Eisenkraft , Alemu Feben W. , Ghattas Lina , McDonald Kathryn , Asaria Miqdad , Sharpe Cameron , Pandya Ekta , Moqueet Nasheed , Champredon David , Moghadas Seyed M. , Cooper Lisa A. , Pinto Andrew , Stranges Saverio , Haworth-Brockman Margaret J. , Galvani Alison , Ali Shehzad 
Published: October 2024

ObjectivesTo identify COVID-19 infectious disease models that accounted for social determinants of health (SDH).MethodsWe searched MEDLINE, EMBASE, Cochrane Library, medRxiv, and the Web of Science from December 2019 to August 2020. We included mathematical modelling studies focused on humans investigating COVID-19 impact and including at least one SDH. We abstracted study characteristics (e.g., country, model type, social determinants of health) and appraised study quality using best practices guidelines.Results83 studies were included. Most pertained to multiple countries (n = 15), the United States (n = 12), or China (n = 7). Most models were compartmental (n = 45) and agent-based (n = 7). Age was the most incorporated SDH (n = 74), followed by gender (n = 15), race/ethnicity (n = 7) and remote/rural location (n = 6). Most models reflected the dynamic nature of infectious disease spread (n = 51, 61%) but few reported on internal (n = 10, 12%) or external (n = 31, 37%) model validation.ConclusionFew models published early in the pandemic accounted for SDH other than age. Neglect of SDH in mathematical models of disease spread may result in foregone opportunities to understand differential impacts of the pandemic and to assess targeted interventions.Systematic Review Registration:[https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42020207706], PROSPERO, CRD42020207706.
Production of Protein Hydrolysates Teff (Eragrostis tef) Flour with Antioxidant and Angiotensin-I-Converting Enzyme (ACE-I) Inhibitory Activity Using Pepsin and Cynara cardunculus L. Extract
Authors: Molina-Valero Gregorio , Buendía-Moreno Laura , Bande-De León Cindy , Bueno-Gavilá Estefanía , Tejada Luis 
Published: October 2024

In recent years, several studies have shown the antioxidant and antihypertensive potential of bioactive peptides. Thus, bioactive peptides are likely to be a valuable substance for the development of functional foods. There are a wide variety of sources of these peptides, including several cereals. Teff is an Ethiopian-rooted cereal with an interesting nutritional profile, mainly due to its high amount of protein. In this study, teff flour was subjected to a defatting process for optimizing the protein extraction. Such extraction was performed by precipitation from its isoelectric point, a crucial step that separates the protein from other components based on their charge. The protein obtained was subjected to enzymatic hydrolysis by pepsin and Cynara cardunculus L. The antihypertensive (angiotensin-I-converting enzyme ―ACE-I― inhibitory activity) and antioxidant activity (2,2-diphenyl-1-picrylhydrazyl ―DPPH― radical scavenging activity) of the peptides were determined. According to the IC50 values, the results obtained showed that the peptides from teff flour show promising bioactivity compared to other cereals. Furthermore, the peptides from teff flour obtained from C. cardunculus L. showed higher antioxidant activity (defatted teff flour ―DTF―: 0.59 ± 0.05; protein extract ―EP― : 1.04 ± 0.11) than those obtained with pepsin (DTF: 0.87 ± 0.09; EP: 1.73 ± 0.11). However, C. cardunculus L. hydrolyzate peptides showed lower inhibitory activity of ACE-I (DTF: 0.59 ± 0.07; EP: 0.61 ± 0.05) than the pepsin hydrolyzate (DTF: 0.15 ± 0.02; EP: 0.33 ± 0.05).
Cardiac Implantable Electronic Device Infections in Patients with Renal Insufficiency: A Systematic Review and Meta-Analysis
Authors: Chandramohan Deepak , Singh Prabhat , Garapati Hari Naga , Konda Raghunandan , Chandramohan Divya , Jena Nihar , Bali Atul , Simhadri Prathap Kumar 
Published: October 2024

(1) Background: Renal insufficiency is a risk factor for cardiac implantable electronic device (CIED) infection. (2) Methods: A comprehensive search was conducted from multiple electronic databases to identify studies. Using the random effects model, we calculated the pooled rates of CIED infection and their 95% confidence intervals. We also calculated the pooled odds ratios to determine the risk of CIED infections due to chronic kidney disease (CKD) and end-stage renal disease (ESRD). We utilized the Cochran Q and I2 statistics to detect and quantify heterogeneity. (3) Results: A total of 17 studies comprising 359,784 patients with renal insufficiency were added to the meta-analysis. Out of these, 263,819 were CKD patients and 89,617 were ESRD patients. The pooled rate of CIED infection in patients with CKD was 4.3% (95% CI: 2–8.8; I2: 95.7), and in patients with ESRD, it was 4.8% (95% CI: 2.6–8.7; I2: 99.4). The pooled risk of CIED infection in the CKD population was OR 2.5 (95% CI: 1.9–3.3; p < 0.001; I2: 21.1), and in the ESRD population, it was OR 2.4 (95% CI: 1.01–5.7; p = 0.046; I2: 88.8). ESRD was associated with higher mortality, OR 2.5 (95% CI: 1.4–4.4.8; p = 0.001; I2: 95). (4) Conclusions: The presence of renal insufficiency increases the number of CIED infections. In particular, patients with ESRD have an increased risk of mortality.
Elevated Cardiac Troponin Levels as a Predictor of Increased Mortality Risk in Non-Cardiac Critically Ill Patients Admitted to a Medical Intensive Care Unit
Authors: Akbas Turkay 
Published: October 2024

Background: Cardiac troponin I (TnI) is a specific marker of myocardial damage used in the diagnosis of acute coronary syndrome (ACS). TnI levels can also be elevated in patients without ACS, which is linked to a worse prognosis and mortality. We evaluated the clinical implications and prognostic significance of serum TnI levels in critically ill non-cardiac patients admitted to the intensive care unit (ICU) at a tertiary-level hospital. Materials and Methods: A three-year retrospective study including the years 2017–2020 was conducted to evaluate in-hospital mortality during ICU stay and mortality rates at 28 and 90 days, as well as one and two years after admission, in 557 patients admitted to the medical ICU for non-cardiac causes. Results: TnI levels were elevated in 206 (36.9%) patients. Patients with elevated TnI levels were significantly older and had higher rates of comorbidities, including chronic heart failure, coronary heart disease, and chronic kidney disease (p < 0.05 for all). Patients with elevated TnI levels required more invasive mechanical ventilation, vasopressor infusion, and dialysis in the ICU and experienced more shock within the first 72 h (p = 0.001 for all). High TnI levels were associated with higher Acute Physiological and Chronic Health Evaluation (APACHE) II (27.6 vs. 20.3, p = 0.001) and Sequential Organ Failure assessment (8.8 vs. 5.26, p = 0.001) scores. Elevated TnI levels were associated with higher mortality rates at 28 days (58.3% vs. 19.4%), 90 days (69.9% vs. 35.0%), one year (78.6% vs. 46.2%), and two years (82.5% vs. 55.6%) (p < 0.001 for all). Univariate logistic regression analysis revealed that high TnI levels were a strong independent predictor of mortality at all time points: 28 days (OR = 1.2, 95% CI: 1.108–1.3, p < 0.001), 90 days (OR = 1.207, 95% CI: 1.095–1.33, p = 0.001), one year (OR = 1.164, 95% CI: 1.059–1.28, p = 0.002), and two year (OR = 1.119, 95% CI: 1.026–1.22, p = 0.011). Multivariate analysis revealed that age, albumin level, APACHE II score, and requirements for dialysis and vasopressor use in the ICU were important predictors of mortality across all timeframes, but elevated TnI levels were not. Conclusions: Elevated TnI levels in critically ill non-cardiac patients are markers of disease severity. While elevated TnI levels were significant predictors of mortality in the univariate analysis, they lost significance in the multivariate model when adjusted for other factors. Patients with elevated TnI levels had higher mortality rates across all timeframes, from 28 days to two years.
Prevalence, Species Distribution and Resistance of Candidemia in Pediatric and Adult Patients in a Northeast Italy University Hospital
Authors: Meneghello Silvia , Bernabè Giulia , Di Pietra Giuseppe , Di Sopra Sarah , Del Vecchio Claudia , Cattelan Anna Maria , Castagliuolo Ignazio , Brun Paola 
Published: October 2024

Candidemia and invasive candidiasis (IC) are causes of morbidity and mortality in healthcare settings, with notable differences between children and adults. Understanding the species distribution and antimicrobial susceptibility profiles of clinical isolates can guide empiric therapy in patients at risk of IC. This study investigated the incidence and antifungal susceptibility patterns of yeasts involved in IC in pediatric and adult patients from 2019 to 2023. The average incidence of IC was 0.715 per 1000 patients, increasing over the study period; infants had the highest incidence rates. Over half of the IC episodes occurred in intensive care units (ICUs). Non-albicans Candida (NAC) species represented the most frequently isolated species in adults and children (55.96% and 50.0%, respectively), with the prevalence of C. parapsilosis (26.45% and 14.7%, respectively), N. glabratus (14.97% and 8.82%, respectively) and C. tropicalis (4.36% and 2.94%, respectively). C. lusitaniae was identified in 14.7% of pediatric IC cases. In NAC species, antifungal resistance has also increased over the five years of the study: 69.12% were resistant to azoles and 7.35% were resistant to micafungin. Resistance was higher in pediatric patients. Our study highlights differences in IC characteristics between pediatric and adult populations and emphasizes the importance of targeted antifungal stewardship in ICU patients with NAC invasive infections.
What Quality Suffices for Nanopore Metabarcoding? Reconsidering Methodology and Ectomycorrhizae in Decaying Fagus sylvatica Bark as Case Study
Authors: Dierickx Glen , Tondeleir Lowie , Asselman Pieter , Vandekerkhove Kris , Verbeken Annemieke 
Published: October 2024

Nanopore raw read accuracy has improved to over 99%, making it a potential tool for metabarcoding. For broad adoption, guidelines on quality filtering are needed to ensure reliable taxonomic unit recovery. This study aims to provide those guidelines for a fungal metabarcoding context and to apply them to a case study of ectomycorrhizae in the decaying bark of Fagus sylvatica. We introduce the eNano pipeline to test two standard metabarcoding approaches: (1) Reference-based mapping leveraging UNITE’s species hypothesis system (SH approach); (2) Constructing 98% OTUs (OTU approach). Our results demonstrate that both approaches are effective with Nanopore data. When using a reference database, we recommend strict mapping criteria rather than Phred-based filtering. Leveraging the SH-system further enhances reproducibility and facilitates cross-study communication. For the 98% OTUs, filtering reads at ≥Q25 is recommended. Our case study reveals that the decay gradient is a primary determinant of community composition and that specific mycorrhizal fungi colonize decaying bark. Complementing our metabarcoding results with root tip morphotypification, we identify Laccaria amethystina and Tomentella sublilacina as key ectomycorrhizae of saplings on decaying logs. These findings demonstrate that Nanopore sequencing can provide valuable ecological insights and support its broader use in fungal metabarcoding as read quality continues to improve.