bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and validation of aging-related genes in neuropathic pain using bioinformatics
Authors: Gao Hui , Dong Guoqi , Yao Yong , Yang Huayuan 
Published: July 2024

BackgroundNeuropathic pain (NP) is a debilitating and refractory chronic pain with a higher prevalence especially in elderly patients. Cell senescence considered a key pathogenic factor in NP. The objective of this research is to discover genes associated with aging in peripheral blood of individuals with NP using bioinformatics techniques.MethodsTwo cohorts (GSE124272 and GSE150408) containing peripheral blood samples of NP were downloaded from the GEO database. By merging the two cohorts, differentially expressed aging-related genes (DE-ARGs) were obtained by intersection with aging-related genes. The potential biological mechanisms of DE-ARGs were further analyzed through GO and KEGG. Three machine learning methods, namely, LASSO, SVM-RFE, and Random Forest, were utilized to identify diagnostic biomarkers. A Nomogram model was developed to assess their diagnostic accuracy. The validation of biomarker expression and diagnostic effectiveness was conducted in three distinct pain cohorts. The CIBERSORT algorithm was employed to evaluate the immune cell composition in the peripheral blood of patients with NP and investigate its association with the expression of diagnostic biomarkers.ResultsThis study identified a total of 24 DE-ARGs, mainly enriched in “Chemokine signaling pathway,” “Inflammatory mediator regulation of TRP channels,” “HIF-1 signaling pathway” and “FOXO signaling pathway”. Three machine learning algorithms identified a total of four diagnostic biomarkers (CEBPA, CEACAM1, BTG3 and IL-1R1) with good diagnostic performance and the similar expression difference trend in different types of pain cohorts. The expression levels of CEACAM1 and IL-1R1 exhibit a positive correlation with the percentage of neutrophils.ConclusionUsing machine learning techniques, our research identified four diagnostic biomarkers related to aging in peripheral blood, providing innovative approaches for the diagnosis and treatment of NP.
Causal association of juvenile idiopathic arthritis or JIA-associated uveitis and gut microbiota: a bidirectional two-sample Mendelian randomisation study
Authors: Hong Jun-bin , Chen Yue-xuan , Su Zhi-ying , Chen Xin-ying , Lai Yan-ni , Yang Jing-hua 
Published: July 2024

BackgroundThe gut microbiota significantly influences the onset and progression of juvenile idiopathic arthritis (JIA) and associated uveitis (JIAU); however, the causality remains unclear. This study aims to establish a causal link between gut microbiota and JIA or JIAU.MethodsUsing publicly available genome-wide association studies (GAWS) summary data, we conducted a two-sample Mendelian randomisation (MR) analysis employing various methods, namely inverse variance weighted (IVW), simple mode, weighted mode, weighted median and MR-Egger regression methods, to assess the causal association between JIA or JIAU and gut microbiota. Sensitivity analyses, including Cochrane’s Q test, MR-Egger intercept test, leave-one-out analysis and MR-PRESSO, were performed to evaluate the robustness of the MR results. Subsequently, reverse MR analysis was conducted to determine causality between gene-predicted gut microbiota abundance and JIA or JIAU.ResultsThe MR analysis revealed a causal association between gut microbiota abundance variations and JIA or JIAU risk. Specifically, the increased abundance of genus Ruminococcaceae UCG013 (OR: 0.055, 95%CI: 0.006–0.103, p = 0.026) and genus Ruminococcaceae UCG003 (β: 0.06, 95%CI: 0.003–0.117, p = 0.041) correlated with an increased risk of JIA, while genus Lachnospiraceae UCG001 (OR: 0.833, 95%CI: 0.699~0.993, p = 0.042) was associated with a reduced risk of JIA, among others. Sensitivity analysis confirmed MR analysis robustness.ConclusionsThis study provides substantial evidence supporting a causal association between genetically predicted gut microbiota and JIA or JIAU. It highlights the significant role of intestinal flora in JIA or JIAU development, suggesting their potential as novel biomarkers for diagnosis and prevention. These findings offer valuable insights to mitigate the impact of JIA or JIAU.
Evidence of a causal relationship between blood pressure and pathological scars: a bidirectional Mendelian randomization study
Authors: Du Dan , Li Jiaqi , Jiang Xian 
Published: July 2024

BackgroundRecent advancements in basic medicine and epidemiology suggest a potential influence of blood pressure on scar formation, yet the specifics of this relationship are not fully understood. This study aims to clarify the causal link between blood pressure and the development of pathological scars using Mendelian randomization (MR).MethodsThis study employed genetic variants closely linked to blood pressure as instrumental variables to explore the relationship between blood pressure and pathological scars. The inverse variance weighted (IVW) method was used for analysis.ResultsOur analysis identified a notable association where higher blood pressure was correlated with a lower risk of pathological scars. Specifically, an increase in diastolic blood pressure (odds ratio [OR] per standard deviation increase: 0.67 [95% Confidence Interval [CI], 0.49–0.99]), systolic blood pressure (OR per standard deviation increase: 0.66 [95% CI, 0.46–0.93]), and hypertension (pooled OR: 0.39 [95% CI, 0.18–0.85]) were significantly associated with a reduced risk of keloids. Similarly, a genetic predisposition to hypertension (pooled OR: 0.31 [95% CI, 0.11–0.89]) was significantly associated with a reduced risk of hypertrophic scars. Neither reverse MR analysis nor Steiger’s test indicated a significant reverse causal relationship between hypertension and either keloids or hypertrophic scars.ConclusionThe findings suggest a protective role of higher blood pressure against the development of pathological scars, including keloids and hypertrophic scars. However, the inconsistency observed across different MR methods warrants cautious interpretation and underscores the need for further investigation to confirm these findings.
VdP5CDH is involved in melanin formation, stress resistance and play a regulatory role in virulence of Verticillium dahliae
Authors: Sun Wanqing , Zhao Lihong , Zhou Jinglong , Feng Hongjie , Zhang Yalin , Feng Zili , Zhu Heqin , Wei Feng 
Published: July 2024

IntroductionVerticillium dahliae, a soil-borne fungal pathogen, can cause cotton Verticillium wilt. In this study, VdP5CDH, the member of the ALDH_F4-17 family of carboxylate dehydrogenases, was identified in the genome of V. dahliae and investigated function in regulating virulence by generating gene deletion mutants and complementary mutants.MethodsHomologous recombination method was used to construct mutants, transcriptome sequencing revealed gene-related metabolic pathways, and disease degree of cotton was observed through pathogen infection experiments.ResultsThe conidial surface of VdP5CDH deletion strains was dented and shriveled, and the number of conidial spores increased. Compared with the wild-type (WT), the mycelial diameter of deletion mutants increased by 10.59%-11.16%, the mycelial growth showed irregular branching patterns, and misaligned arrangement. Although capable of penetrating cellophane, deletion mutants were unable to produce melanin. VdP5CDH was mainly associated with glucose metabolism, nitrogen metabolism, ABC transporter activity as well as various amino acid metabolic processes. After gene knockout, raffinose and pectin were used as the main carbon sources to promote the growth of strains and the growth rate of deletion strains in the medium containing raffinose was higher than that of WT. Consequently, the deletion mutant strains decreased utilization efficiency with which they utilized various nitrogen sources. The deletion mutants maintain responsiveness to osmotic stress and oxidative stress stimuli. Additionally, compared to WT strains, the deletion mutant strains exhibited differences in culture temperature tolerance, UV exposure response, and fungicide sensitivity. After cotton was infected with deletion strains conidial suspension, its disease index increased dramatically, while it gradually decreased after spraying with 2 mM glutamate in batches. With the increase of spraying times, the effect was more significant, and the disease index decreased by 18.95%-19.66% at 26 dpi.DiscussionThese results indicated that VdP5CDH regulates the pathogenicity of fungi and controls mycelia growth, melanin formation, conidia morphology, abiotic stress resistance, and the expression of infecting structure-related genes.
Plant species influences the composition of root system microbiome and its antibiotic resistance profile in a constructed wetland receiving primary treated wastewater
Authors: Riva Valentina , Vergani Lorenzo , Rashed Ahmed Ali , El Saadi Aiman , Sabatino Raffaella , Di Cesare Andrea , Crotti Elena , Mapelli Francesca , Borin Sara 
Published: July 2024

IntroductionConstructed wetlands (CWs) are nature-based solutions for wastewater treatment where the root system microbiome plays a key role in terms of nutrient and pollutant removal. Nonetheless, little is known on plant-microbe interactions and bacterial population selection in CWs, which are mostly characterized in terms of engineering aspects.MethodsHere, cultivation-independent and cultivation-based analyses were applied to study the bacterial communities associated to the root systems of Phragmites australis and Typha domingensis co-occurring in the same cell of a CW receiving primary treated wastewaters.Results and discussionTwo endophytic bacteria collections (n = 156) were established aiming to find novel strains for microbial-assisted phytodepuration, however basing on their taxonomy the possible use of these strains was limited by their low degrading potential and/or for risks related to the One-Health concept. A sharp differentiation arose between the P. australis and T. domingensis collections, mainly represented by lactic acid bacteria (98%) and Enterobacteriaceae (69%), respectively. Hence, 16S rRNA amplicon sequencing was used to disentangle the microbiome composition in the root system fractions collected at increasing distance from the root surface. Both the fraction type and the plant species were recognized as drivers of the bacterial community structure. Moreover, differential abundance analysis revealed that, in all fractions, several bacteria families were significantly and differentially enriched in P. australis or in T. domingensis. CWs have been also reported as interesting options for the removal of emerging contaminants (e.g, antibiotic resistance genes, ARGs). In this study, ARGs were mostly present in the rhizosphere of both plant species, compared to the other analyzed fractions. Notably, qPCR data showed that ARGs (i.e., ermB, blaTEM, tetA) and intl1 gene (integrase gene of the class 1 integrons) were significantly higher in Phragmites than Typha rhizospheres, suggesting that macrophyte species growing in CWs can display a different ability to remove ARGs from wastewater. Overall, the results suggest the importance to consider the plant-microbiome interactions, besides engineering aspects, to select the most suitable species when designing phytodepuration systems.
Effects of the rice-mushroom rotation pattern on soil properties and microbial community succession in paddy fields
Authors: Hao Haibo , Yue Yihong , Wang Qian , Xiao Tingting , Zhao Zelong , Zhang Jinjing , Chen Hui 
Published: July 2024

IntroductionCurrently, straw biodegradation and soil improvement in rice-mushroom rotation systems have attracted much attention. However, there is still a lack of studies on the effects of rice-mushroom rotation on yield, soil properties and microbial succession.MethodsIn this study, no treatment (CK), green manure return (GM) and rice straw return (RS) were used as controls to fully evaluate the effect of Stropharia rugosoannulata cultivation substrate return (SRS) on soil properties and microorganisms.ResultsThe results indicated that rice yield, soil nutrient (organic matter, organic carbon, total nitrogen, available nitrogen and available potassium) and soil enzyme (urease, saccharase, lignin peroxidase and laccase) activities had positive responses to the rice-mushroom rotation. At the interannual level, microbial diversity varied significantly among treatments, with the rice-mushroom rotation significantly increasing the relative alpha diversity index of soil bacteria and enriching beneficial microbial communities such as Rhizobium, Bacillus and Trichoderma for rice growth. Soil nutrients and enzymatic activities were significantly correlated with microbial communities during rice-mushroom rotation. The fungal-bacterial co-occurrence networks were modular, and Latescibacterota, Chloroflexi, Gemmatimonadota and Patescibacteria were closely related to the accumulation of nutrients in the soil. The structural equation model (SEM) showed that fungal diversity responded more to changes in soil nutrients than did bacterial diversity.DiscussionOverall, the rice-mushroom rotation model improved soil nutrients and rice yields, enriched beneficial microorganisms and maintained microbial diversity. This study provides new insights into the use of S. rugosoannulata cultivation substrates in the sustainable development of agroecosystems.
The effects of specific vegetable subtypes on constipation incidence in the general United States population
Authors: Jiang Chenyu , Shao Yaojian 
Published: July 2024

BackgroundWhile the intake of larger quantities of vegetables has been linked to a reduction in constipation risk, which vegetables in particular underlie this risk reduction remains incompletely understood. As such, the present study was developed to explore correlations between the intake of particular vegetable types and the risk of constipation.MethodsThis cross-sectional analysis was based on data from the National Health and Nutrition Examination Survey (NHANES) collected from 2005-2010. Classifications and intake assessments for different vegetables were assessed with the Food Patterns Equivalents Database (FPED), while stool frequency or stool consistency was used to define constipation. Relationships between the intake of particular vegetable components and constipation were assessed through a weighted logistic regression approach. Subgroup and restricted cubic spline (RCS) regression analyses were further employed to explore associations between specific vegetable subtypes and constipation.ResultsThis study included 13,860 eligible subjects, of whom 1,405 and 12,455 were respectively classified into the constipated and non-constipated groups. Following multivariate adjustment, the intake of non-starchy vegetables including orange, red, dark green, and other vegetables was found to be positively associated with a reduction in constipation risk. In contrast, constipation was unrelated to total starchy vegetable or potato intake. Tomatoes, in particular, were associated with a marked decrease in constipation risk (odds ratios: 0.80, 95% confidence interval: 0.71–0.91). These results were confirmed through RCS and subgroup analyses.ConclusionNon-starchy vegetables, particularly tomatoes, were found to be associated with a pronounced reduction in constipation risk, which was unaffected by the intake of potatoes or starchy vegetables.
Emergency response and preparedness among Polish human milk banks: a comparison of the COVID-19 pandemic and the 2022 Ukrainian refugee crisis
Authors: Gawrońska Małgorzata , Sinkiewicz-Darol Elena , Wesołowska Aleksandra 
Published: July 2024

IntroductionIn recent years, Poland has faced two major emergencies: the COVID-19 pandemic, a global-scale public health emergency in 2020, and the outbreak of a full-scale war in Ukraine, which forced over 9 million Ukrainians–mostly women and children–to flee from their country through the Polish–Ukrainian border in 2022.MethodsIn 2020 and 2022, we conducted two online questionnaires with human milk bank personnel to assess the impact of these emergencies on the human milk banking sector and its preparedness to face them. All 16 human milk bank entities operating in Poland were contacted and invited to participate in the study. For the first questionnaire, which was distributed in 2020, we obtained a 100% response rate. For the second questionnaire, the response rate was 88%, i.e., 14 out of 16 human milk banks completed the questionnaire. We compared these two emergencies in terms of the extent to which the potential of the Polish human milk bank network was exploited to support vulnerable infants who were not breastfed.Results and discussionOur findings indicate that recommendations to provide donor human milk to infants separated from their mothers during the COVID-19 pandemic were never fully implemented. Meanwhile, during the refugee crisis, national legislation allowing equal access to public healthcare for Ukrainian citizens were rapidly implemented, enabling a more effective response by human milk banks to support vulnerable infants. However, no specific measures were introduced to support refugees outside the standard criteria for donor human milk provision. Our results highlight the limited response from the sector during emergencies and the underutilization of the potential of a nationwide network of professional human milk banks. Drawing on Polish experiences, we emphasize the importance of having procedures and legal regulations regarding human milk banking in place even in non-crisis settings, which would facilitate a rapid emergency response. We also emphasize the need to include the implementation of emergency procedures in building a strong and resilient human milk banking system.
Pneumonectomy for broncho-pulmonary carcinoids: a single centre analysis of surgical approaches and patient outcomes
Authors: Diotti Cristina , Bertolaccini Luca , Girelli Lara , Uslenghi Clarissa , Donghi Stefano Maria , Guarize Juliana , Spada Francesca , Fazio Nicola , Spaggiari Lorenzo 
Published: July 2024

BackgroundPneumonectomy is a radical surgical procedure associated with significant morbidity and mortality. Its application in the context of pulmonary neuroendocrine tumours, including carcinoid tumours, requires meticulous preoperative planning and intraoperative precision. This study aims to assess the safety and efficacy of pneumonectomy in the management of these rare and challenging neoplasms.MethodsA retrospective analysis of patients who underwent pneumonectomy for pulmonary carcinoid tumours at our institution over a specified period was conducted. Data regarding patient demographics, tumour characteristics, surgical techniques, intraoperative complications, perioperative management, and long-term outcomes were collected and analysed.ResultsBetween March 2001 and October 2022, 21 patients (7 male, 14 female) with carcinoid tumours underwent pneumonectomy on a total of 459 surgical operations for carcinoid. Preoperative bronchoscopic procedures were conducted in 90.4% of cases, leading to histological diagnoses for most. The median hospital stay was eight days, with no reported perioperative deaths. Median follow-up after surgery was 73 months, with a five-year overall survival of 65.4 months. Recurrences occurred in 28.6% of cases, primarily in atypical carcinoids.ConclusionDespite the rarity of bronchial carcinoids, pneumonectomy is effective for low-grade malignancies, demonstrating positive short—and long-term outcomes. Radical lymph node dissection is fundamental in pathological staging and overall survival.
Adverse events related to neuromuscular blocking agents: a disproportionality analysis of the FDA adverse event reporting system
Authors: Li Liangxia , Xu Qianqian , Liu Yarui , Pang Liangfang , Cui Zhou , Lu Yuanyuan 
Published: July 2024

Background: Neuromuscular blocking agents (NMBAs) are primarily used during surgical procedures to facilitate endotracheal intubation and optimize surgical conditions. This study aimed to explore the adverse event signals of NMBAs, providing reference for clinical safety.Methods: This study collected reports of atracurium, cisatracurium, rocuronium, and vecuronium as primary suspect drugs in The US Food and Drug Administration Adverse Event Reporting System (FAERS) from the first quarter of 2004 to the third quarter of 2023. The adverse events (AEs) reported in the study were retrieved based on the Preferred Terms (PTs) of the Medical Dictionary for Regulatory Activities. In addition, we conducted disproportionality analysis on relevant reports using the reporting odds ratio (ROR) method and Bayesian confidence propagation neural network (BCPNN) method. A positive signal was generated when both algorithms show an association between the target drug and the AE.Results: A total of 11,518 NMBA-related AEs were reported in the FAERS database. The most AEs of rocuronium were collected. NMBA-related AEs involved 27 different system organs (SOCs), all of the four NMBAs had positive signals in “cardiac disorders,” “immune system disorders,” “respiratory, thoracic and mediastinal disorders” and “vascular disorders.” At the PTs level, a total of 523 effective AEs signals were obtained for the four NMBAs. AEs labled in the instructions such as anaphylaxis (include anaphylactic reaction and anaphylactic shock), bronchospasm, respiratory arrest and hypotension were detected positive signals among all NMBAs. In addition, we also found some new AEs, such as ventricular fibrillation for the four NMBAs, hyperglycaemia for atracurium, kounis syndrome and stress cardiomyopathy for rocuronium, hepatocellular injury for cisatracurium, hyperkalaemia for vecuronium. To further investigated the AEs associated with serious clinical outcomes, we found that cardiac arrest and anaphylaxis were the important risk factors for death due to NMBAs.Conclusion: NMBA-related AEs have a significant potential to cause clinically severe consequences. Our study provides valuable references for the safety profile of NMBAs, and considering the limitations of the FAERS database, further clinical data are needed to validate the findings of this study.