bluuebunny/crossref_metadata_2025_split huggingface dataset:
CAM/TMA-DPH as a promising alternative to SYTO9/PI for cell viability assessment in bacterial biofilms
Authors: Tchatchiashvili Tinatini , Jundzill Mateusz , Marquet Mike , Mirza Kamran A. , Pletz Mathias W. , Makarewicz Oliwia , Thieme Lara 
Published: January 2025

IntroductionAccurately assessing biofilm viability is essential for evaluating both biofilm formation and the efficacy of antibacterial treatments. Traditional SYTO9 and propidium iodide (PI) live/dead staining in biofilm viability assays often ace challenges due to non-specific staining, limiting precise differentiation between live and dead cells. To address this limitation, we investigated an alternative staining method employing calcein acetoxymethyl (CAM) to detect viable cells based on esterase activity, and 1-(4-trimethylammoniumphenyl)-6-phenyl-1,3,5-hexatriene p-toluenesulfonate (TMA-DPH) to assess the remaining biofilm population.MethodsBiofilms of Pseudomonas aeruginosa, Klebsiella pneumoniae, Staphylococcus aureus, and Enterococcus faecium were matured and exposed to varying concentrations of antibiotics or sterile medium. Biofilm viability was assessed using CAM/TMA-DPH or SYTO9/PIstaining, followed by analysis with confocal laser scanning microscopy (CLSM) and ImageJ-based biofilm surface coverage quantification. Viability findings were compared with colony-forming units (CFU/mL), a standard microbial viability measure.ResultsCAM/TMA-DPH staining demonstrated strong positive correlations with CFU counts across all bacterial species (r = 0.59 - 0.91), accurately reflecting biofilm vitality. In contrast, SYTO9/PI staining consistently underestimated the viability of untreated biofilms, particularly in Klebsiella pneumoniae, where a negative correlation with CFU/mL was observed (r = –0.04). Positive correlations for SYTO9/PI staining were noted in other species (r = 0.65 - 0.79). These findings underscore the limitations of membrane integrity-based staining methods and highlight the advantages of metabolic-based probes like CAM/TMA-DPH.DiscussionOur findings suggest that CAM/TMA-DPH staining provides a promising alternative to SYTO9/PI for cell viability assessment in bacterial biofilms, highlighting the advantages of metabolic-based probes over traditional membrane integrity assays. The consistency of CAM/TMA-DPH staining across different bacterial species underscores its potential to advance studies on biofilm and contribute to the development of more effective anti-biofilm treatments, which is essential for clinical management of biofilm-associated infections.
A systematic literature review to evaluate the cardiac and cerebrovascular outcomes of patients with Fabry disease treated with agalsidase Beta
Authors: Oudit Gavin Y. , DasMahapatra Pronabesh , Lyn Nicole , Wilson Florence R. , Adeyemi Adekemi , Lee Chae Sung , Crespo Ana , Namdar Mehdi 
Published: January 2025

BackgroundAgalsidase beta is used to treat Fabry disease (FD); however, data on cardiac and cerebrovascular outcomes with agalsidase beta treatment come from studies with limited numbers of patients.MethodsA systematic literature review of studies reporting on the efficacy and effectiveness of agalsidase beta in FD was conducted. Studies were identified in searches of MEDLINE, Embase, and the Cochrane Central Register of Controlled Trials from January 2000–June 2022. Outcomes of interest included cardiac structure and mass, cardiac events, and cerebrovascular events.ResultsFifty-two citations (41 studies) were included. Reductions in interventricular septal thickness (IVST) and/or left ventricular posterior wall thickness (LVPWT) were demonstrated in six studies (follow-up 1–6 years, n = 4 using echocardiography, n = 2 cardiac MRI). IVST ranged from 12.1–14.9 mm at baseline and 10.8–14.1 mm at follow-up (all p &lt; 0.05). LVPWT ranged from 11.7–16.0 mm at baseline and 10.7–13.0 mm at follow-up (all p &lt; 0.05). Significant reductions in cardiac mass were demonstrated after 1 year of treatment in a single-arm study using cardiac MRI [left ventricular mass (LVM) 193–178 g; LVM index 102–94 g/m2; both p &lt; 0.05]. Rates of composite cardiac events (3.8%–24.0%; four studies, follow-up 2–10 years) and cerebrovascular events (0.0%–18.9%; 12 studies, follow-up 1–10 years) were numerically lower than rates for placebo (follow-up 3 years).ConclusionLiterature over the last 20 years indicates that agalsidase beta treatment may lead to stabilization or regression of cardiac structural thickness and mass, and reduction in cardiac and cerebrovascular events relative to placebo.
Antibacterial activity of biodentine against Enterococcus faecalis: a systematic review
Authors: Subhi Hasan , Subhi Nashwah , Alhaidary Salah , Azeez Mahmood S. , Tabnjh Abedelmalek Kalefh 
Published: January 2025

IntroductionBiodentine is a well-known endodontic material that is applied in various endodontic therapies. Enterococcus faecalis (E. faecalis) is associated with endodontic failure and persistent periapical infection. The purpose of this systematic review was to summarize the available evidence regarding the antibacterial activity of Biodentine against E. faecalis and to compare it to other commercial endodontic materials.MethodsAn electronic search of literature was conducted in PubMed, Scopus, Web of Science, and Google Scholar in addition to a manual search in specialized journals up to May 2024. The eligibility criteria, data extraction, and evaluation of risk of bias were assessed by two independent authors. The risk of bias was evaluated in accordance with Modified CONSORT checklist items for pre-clinical in vitro studies on dental materials.ResultsOut of 343 studies, thirty-seven fulfilled the inclusion criteria and were included in this review. Thirty studies reported a good antibacterial efficacy of Biodentine against E. faecalis. Biodentine was superior to or, at least, as efficacious as MTA, MTA Angelus, GIC, RMGIC, DiaRoot BioAggregate, NeoPutty, iRoot FS, MTA Repair HP, MTA Biorep, Well-Root PT, Activa, NeoMTA 2, Calcimol LC, TotalFill, and IRM. The findings were supported by studies with medium to high risk of bias (low quality).ConclusionsConsidering the limitations of this systematic review, there is accumulating evidence on the antibacterial activity of Biodentine against E. faecalis in context of endodontics. However, randomized clinical trials with well-designed and robust methodologies are required in order to provide information about its clinical behaviour.
Development and validation of machine learning models for MASLD: based on multiple potential screening indicators
Authors: Chen Hao , Zhang Jingjing , Chen Xueqin , Luo Ling , Dong Wenjiao , Wang Yongjie , Zhou Jiyu , Chen Canjin , Wang Wenhao , Zhang Wenbin , Zhang Zhiyi , Cai Yongguang , Kong Danli , Ding Yuanlin 
Published: January 2025

BackgroundMultifaceted factors play a crucial role in the prevention and treatment of metabolic dysfunction-associated steatotic liver disease (MASLD). This study aimed to utilize multifaceted indicators to construct MASLD risk prediction machine learning models and explore the core factors within these models.MethodsMASLD risk prediction models were constructed based on seven machine learning algorithms using all variables, insulin-related variables, demographic characteristics variables, and other indicators, respectively. Subsequently, the partial dependence plot(PDP) method and SHapley Additive exPlanations (SHAP) were utilized to explain the roles of important variables in the model to filter out the optimal indicators for constructing the MASLD risk model.ResultsRanking the feature importance of the Random Forest (RF) model and eXtreme Gradient Boosting (XGBoost) model constructed using all variables found that both homeostasis model assessment of insulin resistance (HOMA-IR) and triglyceride glucose-waist circumference (TyG-WC) were the first and second most important variables. The MASLD risk prediction model constructed using the variables with top 10 importance was superior to the previous model. The PDP and SHAP methods were further utilized to screen the best indicators (including HOMA-IR, TyG-WC, age, aspartate aminotransferase (AST), and ethnicity) for constructing the model, and the mean area under the curve value of the models was 0.960.ConclusionsHOMA-IR and TyG-WC are core factors in predicting MASLD risk. Ultimately, our study constructed the optimal MASLD risk prediction model using HOMA-IR, TyG-WC, age, AST, and ethnicity.
Inflammatory burden index as a prognostic marker in patients with advanced gastric cancer treated with neoadjuvant chemotherapy and immunotherapy
Authors: Huang Jiao-Bao , Zhou Zhi-Yong , Lu Jun , Zhu Ji-Yun , Lai Bin , Mao Sheng-Xun , Cao Jia-Qing 
Published: January 2025

BackgroundBlood inflammation index has been shown to correlate with the prognosis of patients with gastric cancer. However, few studies have compared the efficacy of existing blood inflammatory markers in predicting the prognosis of patients with locally advanced gastric cancer in combination with neoadjuvant chemotherapy and immunotherapy.ObjectiveThe objective of this study was to compare the prognostic value of existing commonly used blood inflammatory index in patients with advanced gastric cancer treated with neoadjuvant chemotherapy combined with immunotherapy.MethodsThe clinicopathological data of patients with advanced gastric cancer from three centers in China were analyzed retrospectively. Univariate COX regression analysis was used to analyze the independent risk factors of poor tumor regression and overall survival (OS) in this part of patients, and the predictive value of different inflammatory indexes on prognosis was compared by C-index index. Finally, Inflammatory burden index(IBI) was grouped by X-tile software, and Kaplan-Meier method was used to compare the survival difference between groups.ResultsA total of 163 patients were enrolled in this study. The median age was 63 years(56-68). The median cycle of neoadjuvant therapy was 4(3-4). The median survival time was 85.1%(1 years), 65.6%(2 years), and 47.4%(3 years).Univariate analysis showed that IBI was an independent risk factor for non-TR(residual tumor cells&gt;50%) (HR=1.08,95%CI:1.00-1.45,p&lt;0.001)and OS(HR=1.04,95%CI:1.03-1.05,p&lt;0.001). IBI is the best predictor of OS (C-index: 0.82, 95% CI: 0.78-0.87) among all inflammatory indexes. The IBI cutoff value was 52.1. It was found that the high IBI group had a higher incidence of postoperative complications(32.1%vs14.3%, p=0.001), the proportion of non-TR patients was significantly higher than that of the low IBI group(64.3%vs35.7%, p =0.001), and the high IBI group had a significantly lower OS((47.6% vs 87.6%, p &lt; 0.001).ConclusionIBI is the best inflammatory index to predict the prognosis of advanced gastric cancer treated with neoadjuvant chemotherapy combined with immunotherapy, which will help guide patients’ treatment decisions. This result still needs to be verified by large prospective studies.
Humoral and cell-mediated immune responses to COVID-19 vaccines up to 6 months post three-dose primary series in adults with inborn errors of immunity and their breakthrough infections
Authors: Unninayar Dana , Falcone Emilia L. , Chapdelaine Hugo , Vinh Donald C. , Top Karina A. , Derfalvi Beata , Issekutz Thomas B. , Decaluwe Hélène , Pham-Huy Anne , Upton Julia , Betschel Stephen D. , Rubin Tamar , Suresh Sneha , Wright Nicola A. M. , Murguía-Favela Luis , Kalashnikova Tatiana , Barrett Lisa , Oldford Sharon , Langlois Marc-Andre , Arnold Corey , Sadarangani Manish , Zhang Tinghua , Ramsay Tim , Yazji Dina , Cowan Juthaporn 
Published: January 2025

PurposeMany individuals with inborn errors of immunity (IEIs) have poor humoral immune (HI) vaccine responses. Only a few studies have examined specific cell-mediated immune (CMI) responses to coronavirus disease 2019 (COVID-19) vaccines in this population. Therefore, the purpose of this study was to examine HI and CMI responses up to 6 months post-COVID-19 vaccine dose 3 in adults with IEIs.MethodsA multi-center prospective observational study was conducted across Canada to collect severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-specific HI and CMI data at 4- and 24-week intervals after vaccine doses 2 and 3 (D2 + 4wk/D2 + 24wk/D3 + 4wk/D3 + 24wk).ResultsA total of 149 adults with IEIs and 423 healthy controls were recruited from July 2021 to October 2023. Geometric mean anti-spike IgG (binding antibody units/mL) and spike-specific T-cell responses [IFN-γ+ T cells/106 peripheral blood mononuclear cells (PBMCs)] were significantly lower in IEIs compared to controls at D2 + 4wk, D3 + 4wk, and D3 + 24wk. However, at 6 months after completing the primary series (three doses for IEIs and two doses for healthy), both HI and CMI responses of both IEI participants and healthy controls persisted and were comparable. There was a strong correlation between neutralizing antibody titer (ID50) and anti-spike IgG but not between ID50 and CMI. There was only one reported case of hospitalized COVID-19 disease before and none after completing the primary series among IEI participants.ConclusionAdults with IEIs mounted both HI and CMI responses following COVID-19 vaccines, which were lower than those of healthy individuals but were present at least up to 6 months after dose 3. These data support the initial recommendation for a three-dose primary series among IEIs.
Development and validation of a nomogram for predicting lung cancer based on acoustic–clinical features
Authors: Lu Zhou , Sha Jiaojiao , Zhu Xunxia , Shen Xiaoyong , Chen Xiaoyu , Tan Xin , Pan Rouyan , Zhang Shuyi , Liu Shi , Jiang Tao , Xu Jiatuo 
Published: January 2025

ObjectiveLung cancer—with its global prevalence and critical need for early diagnosis and treatment—is the focus of our study. This study aimed to develop a nomogram based on acoustic–clinical features—a tool that could significantly enhance the clinical prediction of lung cancer.MethodsWe reviewed the voice data and clinical information of 350 individuals: 189 pathologically confirmed lung cancer patients and 161 non-lung cancer patients, which included 77 patients with benign pulmonary lesions and 84 healthy volunteers. First, acoustic features were extracted from all participants, and optimal features were selected by least absolute shrinkage and selection operator (LASSO) regression. Subsequently, by integrating acoustic features and clinical features, a nomogram for predicting lung cancer was developed using a multivariate logistic regression model. The performance of the nomogram was evaluated by the area under the receiver operating characteristic curve (AUC) and the calibration curve. The clinical utility was estimated by decision curve analysis (DCA) to confirm the predictive value of the nomogram. Furthermore, the nomogram model was compared with predictive models that were developed using six additional machine-learning (ML) methods.ResultsOur acoustic–clinical nomogram model demonstrated a strong discriminative ability, with AUCs of 0.774 (95% confidence interval [CI], 0.716–0.832) and 0.714 (95% CI: 0.616–0.811) in the training and test sets, respectively. The nomogram achieved an accuracy of 0.642, a sensitivity of 0.673, and a specificity of 0.611 in the test set. The calibration curve showed excellent agreement between the predicted and actual values, and the DCA curve underscored the clinical usefulness of our nomogram. Notably, our nomogram model outperformed other models in terms of AUC, accuracy, and specificity.ConclusionThe acoustic–clinical nomogram developed in this study demonstrates robust discrimination, calibration, and clinical application value. This nomogram, a unique contribution to the field, provides a reliable tool for predicting lung cancer.
How do various strategies for returning residues change microbiota modulation: potential implications for soil health
Authors: Jiang Nan , Chen Zhenhua , Ren Yi , Xie Shichang , Yao Zimeng , Jiang Dongqi , Zhang Yulan , Chen Lijun 
Published: January 2025

IntroductionResidue incorporation is a crucial aspect of anthropogenic land management practices in agricultural fields. However, the effects of various returning strategies on the soil microbiota, which play an essential vital role in maintaining soil health, remains largely unexplored.MethodsIn a study conducted, different residue management strategies were implemented, involving the application of chemical fertilizers and residues that had undergone chopping (SD), composting (SC), and pyrolysis (BC) processes, with conventional fertilization serving as the control (CK).Results and discussionUsing metagenomic sequencing, the analysis revealed that while all residue returning strategies had minimal effects on the diversity (both α and β) of microbiota, they did significantly alter microbial functional genes related to carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycling, as well as the presence of antibiotic resistance genes (ARGs) and pathogens. Specifically, chopped residues were found to enhance microbial genes associated with C, N, P, and S cycling, while composted residues primarily stimulated C and S cycling. Furthermore, all residue treatments resulted in a disruption of relationships among nutrient cycles, with varying degrees of impact observed across the different management strategies, with the sequence of impact being SD &lt; SC &lt; BC. Moreover, the residue additions resulted in the accumulation of ARGs, while only SC caused an increase in certain pathogens. Finally, through analyzing the correlation network among indices that exhibited active responses to residue additions, potential indicators for functional changes in response to residue additions were identified. This study further offered recommendations for future cropland management practices aimed at enhancing soil health through microbiomes.
The impact of abandoned iron ore on the endophytic bacterial communities and functions in the root systems of three major crops in the local area
Authors: Chen Shuyi , Tang Jie , Xu Junqiang , Peng Lianxin , Wu Peng , Li Qiang 
Published: January 2025

IntroductionGlobal mining activities have significant impacts on ecosystems, but most studies have focused only on the relationship between soil physicochemical properties and microbial diversity in soils. The present study provides an insight into the effects of mining activities on soil physico-chemical properties and endophytic bacterial community composition in the rhizosphere of three different crops.MethodsMusa basjoo Siebold L., Amygdalus persica L., and Triticum aestivum L. were collected from the inter-root soils and plant roots to determine the soil physicochemical properties and endophytic bacterial communities in the root system.ResultsThe results showed that mining resulted in soil acidification, altered trace element content and increased organic carbon. There was an increase in the Ascomycota and Actinobacteria phylum of crop root bacteria. Interestingly, the chao1 and shannon indices of the root endophytes of the mining crop were significantly elevated compared to the contro (p &lt; 0.05). Among them, Musa basjoo Siebold showed the highest level of community richness in the mining environment. The mining environment resulted in functional enrichment of histidine kinases and oxidoreductases in the bacterial community. The total potassium (TK) content in the soil, as well as the Fe and Pb content, were positively correlated with the α-diversity index and Streptomyces. Zn and Ti content were significantly negatively correlated with the α-diversity index.DiscussionThis study provides data support for exploring the mechanisms of plant response to the mining environment and developing ecological restoration strategies for mining areas.
Use of amantadine in traumatic brain injury: an updated meta-analysis of randomized controlled trials
Authors: Félix João , Araújo Luísa , Henriques Antônio , Pereira Ana , Carneiro Saul 
Published: January 2025

IntroductionAmantadine has been shown to accelerate cognitive and functional brain recovery after cerebrovascular accidents. However, the efficacy of this drug in TBI patients remains poorly defined.MethodsWe performed a systematic review and meta-analysis of randomized trials (RCTs) evaluating the effects of amantadine in TBI patients. The Cochrane, Embase, and PubMed databases were systematically searched for trials published up to March 24, 2024. Data from previous RCTs were extracted and quality assessed according to Cochrane recommendations. Means and standard deviations with 95% confidence intervals were aggregated across studies. The primary outcomes assessed were Glasgow Coma Scale (GCS), Mini Mental State Examination (MMSE) and the Disability Rating Scale (DRS).ResultsFrom 1,292 database results, 6 studies with 426 patients were included, of which 205 received amantadine (48.12%). The Glasgow Coma Scale score on day 7 (MD 1.50; 95% CI 0.08–2.92; p = 0.038; I2 = 68%) was significantly higher in patients treated with amantadine than those treated with placebo. The Mini Mental State Examination (MD 3.23; 95% CI 0.53–5.94; p = 0.019; I2 = 0%) was also better in patients treated with amantadine. No significant differences in Disability Rating Scale, day 3 GCS, Glasgow Outcome Scale (GOS), length of hospital stay, or duration of mechanical ventilation were observed between amantadine and placebo groups.ConclusionIn our analysis, TBI patients benefit from the use of amantadine in the day 7 GCS score and show better results in the MMSE test, but placebo patients benefit from not using amantadine in the DRS between weeks 3 and 4. No other statistically significant results were found related to the use of this medication.Systematic review registration: https://www.crd.york.ac.uk/prospero/display_ record.php?ID=CRD42024538110, CRD42024538110.