bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of BD BACTEC™ MGIT™ for the detection of non-tuberculous mycobacteria in sanitary water samples
Authors: Ferraro Vincenzo , Bisognin Francesco , Sorella Federica , Ruin Federica , Dal Monte Paola 
Published: October 2024

IntroductionThe most commonly used method for the detection of non-tuberculous mycobacteria (NTM) is culture in BD BACTEC™ MGIT™ Mycobacteria Growth Indicator Tubes incubated in an automated growth detection reader BD BACTEC™ MGIT™ 960 Instrument. The system is currently validated for the detection of mycobacteria from clinical specimens but not environmental matrices.MethodsFrom November 2018 to December 2023, 1,369 sanitary water samples from 92 heater–cooler units (HCUs) and 747 sanitary water samples from 489 haemodialysis instruments (dialysis) were concentrated, decontaminated, and cultured on MGIT and solid Lowenstein–Jensen media to evaluate the presence of NTM. NTM-positive cultures (n = 261 HCUs and n = 20 dialysis) were purified by Middlebrook 7H11 agar plate subcultures and identified by MALDI-TOF mass spectrometry technology.ResultsThe purpose of this study was to evaluate the accuracy and reproducibility of the MGIT system on sanitary water from HCU and dialysis, using the two strains most frequently isolated on these devices as sources of NTM during the Emilia- Romagna surveillance programme: M. chimaera (79%) and M. saskatchewanense (100%), respectively. To evaluate the accuracy, sanitary water was spiked with M. chimaera and M. saskatchewanense at the theoretical concentrations of 100 and 10 CFU/mL, and all resulted positive in MGIT tubes. No significant changes in time to positivity were observed when MGIT tubes were inoculated with NTM at the theoretical concentrations of 10 and 100 CFU/mL on 3 consecutive days, indicating that the detection method is reproducible.DiscussionThe MGIT system is suitable for detecting the presence of NTM in sanitary water samples as it was capable of detecting up to 4 CFU/mL for both M. chimaera and M. saskatchewanense. Our results indicate that the MGIT system can be used for NTM detection not only for clinical samples but also for environmental matrices.
Development of a prognostic model for early-stage gastric cancer-related DNA methylation-driven genes and analysis of immune landscape
Authors: Su Chen , Lin Zeyang , Ye Zhijian , Liang Jing , Yu Rong , Wan Zheng , Hou Jingjing 
Published: October 2024

Background and AimsThis study aimed to develop a prognostic model based on DNA methylation-driven genes for patients with early-stage gastric cancer and to examine immune infiltration and function across varying risk levels.MethodsWe analyzed data from stage I/II gastric cancer patients in The Cancer Genome Atlas which included clinical details, mRNA expression profiles, and level 3 DNA methylation array data. Using the empirical Bayes method of the limma package, we identified differentially expressed genes (DEGs), and the MethylMix package facilitated the identification of DNA methylation-driven genes (DMGs). Univariate Cox regression and LASSO (least absolute shrinkage and selector operation) analyses were utilized to pinpoint critical genes. A risk score prediction model was formulated using two genes that demonstrated the most significant hazard ratios (HRs). Model performance was evaluated within the initial cohort and verified in the GSE84437 cohort; a nomogram was also constructed based on these genes. We further examined 50 methylation sites associated with three CpG islands in C1orf35 and 14 methylation sites linked to one CpG island in FAAH. The CIBERSORT package was employed to identify immune cell clusters in the prediction model.ResultsA total of 176 DNA methylation-driven genes were refined down to a four-gene signature (ZC3H12A was hypermethylated; GATA3, C1orf35, and FAAH were hypomethylated), which exhibited a significant correlation with overall survival (OS), as evidenced by p-values below 0.05 following univariate Cox regression and LASSO analysis. Specifically, for the risk score prediction model, C1orf35, which had the highest hazard ratio (HR = 2.035, p = 0.028), and FAAH, with the lowest hazard ratio (HR = 0.656, p = 0.012), were selected. The Kaplan–Meier analysis demonstrated distinct survival outcomes between the high-risk and low-risk score groups. The model’s predictive accuracy was confirmed with an area under the curve (AUC) of 0.611 for 3-year survival and 0.564 for 5-year survival. Notably, the hypomethylation of the three CpG islands in C1orf35 and the single CpG island in FAAH was significantly different in stage I/II gastric cancer patients compared to normal tissues. Additionally, the high-risk score group showed a notable association with resting CD4 memory T cells.ConclusionPromoter hypomethylation of C1orf35 and FAAH in early-stage gastric cancer underscores their potential as biomarkers for accurate diagnosis and treatment. The developed predictive model employing genes affected by DNA methylation serves as a crucial independent prognostic factor in early-stage gastric cancer.
Biomarkers and Alzheimer’s disease: a bibliometric analysis
Authors: Yang Linyi , Zeng Jingyan , Li Linlin , Zhang Yunwei 
Published: October 2024

ObjectiveThe diagnosis and treatment of biomarkers in Alzheimer’s disease has emerged as a prominent topic within Alzheimer’s disease research. In this paper, we conducted a bibliometric analysis of data from a wide range of literature in this field to enhance the in-depth understanding of this area.MethodThe core collection of the Science Citation Index database (web of science) was used to search for relevant literature in the above fields from 1 January 2006 to 14 November 2022 and Citespace software was used to visualize and analyze the literature data.ResultsA total of 1,138 papers were included, of which the United States ranked first with 607 papers and China ranked 6th in the world with 84 papers. The value of mediational centrality is 0.49 in the United States and 0.05 in China. In terms of the number of articles published by the research authors, the Swedish scholar Blennow Kaj ranks first with 82 articles published, and the scholars who rank second and third are Zetterberg Henrik (78 articles) and Morris John C (64 articles), respectively; in terms of the mediational centrality, the American scholar Trojanowski John Q ranked first in the world with 0.1, and the second and third ranked scholars were Blennow Kaj (0.09) and Zetterberg Henrik (0.06) respectively. Scholar JACK CR ranked first with 377 citation frequency. The journal NEUROLOGY is ranked first with 943 citations.ConclusionIn recent years, global research in the field of biomarkers related to Alzheimer’s disease has shown signs of softening, and the momentum of research has slightly diminished. However, this trend does not imply a decline in the quality of research. It is essential to enhance collaboration among countries, major research institutions, and scholars, with a particular emphasis on fostering international partnerships in the future.
Poor nutrition doubles post-COVID-19 syndrome risk in cancer patients: insights from a Chinese multicentre study
Authors: Zhang Liangyuan , Yu Haihang , Yang Jianzhou , Su Rila , Zhang Jiaqi , Zeng Rongbiao , Liu Yajie , Zhang Lei , Xu Junjie 
Published: October 2024

BackgroundSince 2019, approximately 760 million SARS-CoV-2 cases have been reported globally, with post-COVID-19 syndrome posing significant challenges for cancer patients due to their immunosuppressed status and poor nutritional conditions. The role of nutritional status in influencing their infection risk and post-COVID-19 outcomes remains unclear, underscoring the need for targeted research and strategies.ObjectiveTo investigate the impact of baseline nutritional status on SARS-CoV-2 infection and the risk of post-COVID-19 syndrome in cancer patients.MethodsA multicenter cross-sectional study was conducted from December 2022 to June 2023 in four tertiary hospitals across China. Cancer inpatients aged 18 years and older were enrolled and classified into two groups based on their Nutritional Risk Screening (NRS) scores. The correlation between SARS-CoV-2 infection, post-COVID-19 syndrome and nutritional status were analyzed using multivariable logistic regression.ResultsAmong 834 eligible cancer patients, 10.8% were in the high nutritional risk group (NRS ≥ 3). The prevalence of SARS-CoV-2 infection was 58.8% (95% confidence interval, CI: 56.8–60.8%), and post-COVID-19 syndrome was 21.0% (95% CI: 10.4–14.4%). After adjusting for confounding factors, the high nutritional risk group had a significantly higher prevalence of post-COVID-19 syndrome compared to the low nutritional risk group (32.7% vs. 19.5%, AOR: 2.37, 95% CI: 1.23–4.54, p = 0.010). However, no significant difference in SARS-CoV-2 infection rates was found between the two groups (61.1% vs. 58.5%, AOR: 1.12, 95% CI: 0.70–1.80; p = 0.634).InterpretationPoor baseline nutritional status in cancer patients is associated with a higher prevalence of post-COVID-19 syndrome, providing preliminary information on post-COVID-19 syndrome in this population. These findings underscore the importance of adequate nutritional management in cancer patients, particularly during pandemic recurrences.
Application of preoperative NLR-based prognostic model in predicting prognosis of intrahepatic cholangiocarcinoma following radical surgery
Authors: Qi Shuo , Ma Zhongzhi , Shen Lian , Wang Jun , Zhou Lei , Tian Bingzhang , Liu Changjun , Chen Kang , Cheng Wei 
Published: October 2024

PurposeTo investigate the application value of the neutrophil to lymphocyte count ratio (NLR) in the prognostic analysis of intrahepatic cholangiocarcinoma (ICC) after radical resection, and to offer guidance for the individualized perioperative diagnosis and treatment of ICC.MethodsThe clinical data of 360 patients diagnosed with ICC following radical surgery were retrospectively analyzed. The cut-off value of NLR was calculated using the minimum p-value method, and then divided into High-NLR (H-NLR) group and Low-NLR (L-NLR) group according to the NLR cut-off value. The prognostic value of NLR in ICC was analyzed. Subsequently, the patients were divided into the hepatolithiasis-related intrahepatic cholangiocarcinoma (HICC) group and the non-hepatolithiasis-related intrahepatic cholangiocarcinoma (NHICC) group based on whether they combined with hepatolithiasis. Multiple regression models were constructed based on NLR and clinicopathological indicators to verify the application value of prognostic models in the survival and recurrence of ICC patients after radical surgery.ResultsThe cut-off value of NLR was 2.36, and the survival analysis disclosed that overall ICC patients with NLR ≥ 2.36 manifested a poor 5-year survival rate and a higher tumor recurrence rate (p &lt; 0.001). In the HICC group, patients with H-NLR presented a poor 5-year survival rate and a higher tumor recurrence rate compared with L-NLR (p &lt; 0.001). The NLR-based survival/recurrence prediction models in the HICC group demonstrated excellent predictive capacity (H-L test: 0.359/0.680, AUC: 0.764/0.791). In the NHICC group, patients with H-NLR exhibited a poor 5-year survival rate compared with L-NLR (p &lt; 0.001), yet there was no significant difference in tumor recurrence between the two groups (p = 0.071). The NLR-based survival prediction model in the NHICC group demonstrated acceptable predictive ability (H-L test: 0.268, AUC: 0.729), while the NLR-based recurrence prediction model did not show an effective predictive ability (H-L test: 0.01, AUC: 0.649).ConclusionNLR is an independent risk factor influencing postoperative survival and recurrence in ICC patients, particularly in HICC patients. Preoperative NLR ≥ 2.36 suggests that patients might have a poor prognosis. The survival and recurrence prediction model constructed based on NLR and other clinical indicators demonstrates good prediction accuracy and can effectively predict the risk of postoperative adverse prognosis in patients with HICC. This study offers a novel idea for the clinical treatment of HICC patients.
Comparing ischemic cardiovascular effectiveness and safety between individual SGLT-2 inhibitors and DPP-4 inhibitors in patients with type 2 diabetes: a nationwide population-based cohort study
Authors: Kim Hayeon , Seo Jun-Ho , Nam Jin Hyun , Lim Yejee , Choi Kyung Hee , Kim Kyungim 
Published: October 2024

ObjectivesThis study compared the ischemic cardiovascular events (iCVEs) effectiveness and safety of initiating empagliflozin or dapagliflozin with those of dipeptidyl peptidase-4 inhibitors (DPP-4is), as well as the comparative effects between empagliflozin and dapagliflozin.MethodsUsing data from the National Health Insurance Service in Korea, patients with type 2 diabetes mellitus (T2DM) who were newly prescribed empagliflozin, dapagliflozin, or DPP-4is from 2016 to 2019 and who did not have a recent CVE history were included. A Cox proportional hazards regression model was used to estimate the adjusted hazard ratio (aHR) with 95% confidence intervals (CIs) for iCVEs and safety events.ResultsEmpagliflozin and dapagliflozin significantly reduced the risks of ischemic stroke (aHR 0.568, 95% CI 0.408–0.791; aHR 0.612, 95% CI 0.476–0.786, respectively) and all-cause mortality (aHR 0.590, 95% CI 0.442–0.788; aHR 0.730, 95% CI 0.603–0.884, respectively) compared with DPP-4is. Initiating dapagliflozin or empagliflozin was associated with significantly lower incidence of severe hypoglycemia, bone fracture, urinary tract infection, and acute kidney injury than that of DPP-4is. No significant differences were observed between empagliflozin and dapagliflozin in iCVEs and most safety outcomes.ConclusionEmpagliflozin and dapagliflozin showed significant preventive effects on ischemic stroke and all-cause mortality compared with DPP-4is in patients with T2DM, and their protective effects were similar. Both empagliflozin and dapagliflozin were not related to the harmful effects on most safety events. These results suggest that it may be beneficial to initiate empagliflozin or dapagliflozin for ischemic stroke prevention in patients with T2DM. However, further validation studies, such as randomized controlled trials, are needed to generalize these results.
CardioMEA: comprehensive data analysis platform for studying cardiac diseases and drug responses
Authors: Lee Jihyun , Duperrex Eliane , El-Battrawy Ibrahim , Hohn Alyssa , Saguner Ardan M. , Duru Firat , Emmenegger Vishalini , Cyganek Lukas , Hierlemann Andreas , Ulusan Hasan 
Published: October 2024

IntroductionIn recent years, high-density microelectrode arrays (HD-MEAs) have emerged as a valuable tool in preclinical research for characterizing the electrophysiology of human induced pluripotent stem-cell-derived cardiomyocytes (iPSC-CMs). HD-MEAs enable the capturing of both extracellular and intracellular signals on a large scale, while minimizing potential damage to the cell. However, despite technological advancements of HD-MEAs, there is a lack of effective data-analysis platforms that are capable of processing and analyzing the data, particularly in the context of cardiac arrhythmias and drug testing.MethodsTo address this need, we introduce CardioMEA, a comprehensive data-analysis platform designed specifically for HD-MEA data that have been obtained from iPSCCMs. CardioMEA features scalable data processing pipelines and an interactive web-based dashboard for advanced visualization and analysis. In addition to its core functionalities, CardioMEA incorporates modules designed to discern crucial electrophysiological features between diseased and healthy iPSC-CMs. Notably, CardioMEA has the unique capability to analyze both extracellular and intracellular signals, thereby facilitating customized analyses for specific research tasks.Results and discussionWe demonstrate the practical application of CardioMEA by analyzing electrophysiological signals from iPSC-CM cultures exposed to seven antiarrhythmic drugs. CardioMEA holds great potential as an intuitive, userfriendly platform for studying cardiac diseases and assessing drug effects.
Comparative proteomic analysis provides insights into wood formation in immature xylem at different ages in Eucalyptus urophylla × Eucalyptus grandis
Authors: Liu Guo , Zhang Guowu , Wu Zhihua , Lu Wanhong , Lin Yan , Wang Chubiao , Shang Xiuhua , Huang Anying , Luo Jianzhong 
Published: October 2024

IntroductionWood formation is a crucial developmental stage in the life cycle of a woody plant; this process has substantial scientific research implications and practical applications. However, the mechanisms underlying woody plant development, especially the process of wood formation, remain poorly understood. As eucalyptus is one of the fastest growing tree species in the world, understanding the mechanism of wood formation in eucalyptus will greatly promote the development of molecular breeding technology for forest trees.ResultsIn this study, we investigated the proteomic profile of immature xylem at four different ages of Eucalyptus urophylla × Eucalyptus grandis (E. urograndis) using iTARQ technology. We identified 5236 proteins and 492 differentially abundant proteins (DAPs). The expression profiles of the DAPs corresponding to coding genes associated with wood formation were assessed using qRT-PCR. From the different expression profiles, it is inferred that the genes encoding kinesin, CDKD3, EXPA13, EXPA2, XTH27, EGases, UGT76E2, LAC, CCoAMT, CesA3, PAL, and CAD may undergo posttranscriptional regulation (PTR). Additionally, the genes encoding EIN2, ETR, MC4-like, and XCP may undergo posttranslational modifications (PTMs).ConclusionsWe investigated changes in wood formation-related proteins at the protein abundance level in the immature xylem of E. urograndis, thereby elucidating potential regulatory mechanisms of key proteins involved in eucalyptus wood formation. This study may provide theoretical guidance for further research on molecular breeding techniques and genetic improvement related to the cultivation of rapidly growing and high-quality trees.
The relationship between teacher–student relationships and academic grades among Chinese rural high school students: the moderating role of mental health symptoms and the conditional moderating effect of academic resilience
Authors: Chen Xiaohui , Bailey Richard Peter , Yin Xiaojiao , Samsudin Nadia 
Published: October 2024

ObjectiveThis study examines the relationship between Teacher–Student Relationships and academic grades among Chinese rural high school students, focusing on the moderating role of mental health symptoms and the conditional moderating effect of academic resilience.MethodA moderated moderation analysis was conducted via Mplus on data collected from a sample of rural Chinese high school students. SEM was used to test the direct and interactive effects of these variables on academic outcomes.ResultsTeacher–Student Relationships were found to have a significant positive association with students’ academic grades. Academic resilience plays a conditional moderating role, with students who have higher levels of resilience better able to maintain their academic performance, even when facing psychological distress. This suggests that resilience can buffer the impact of challenges, enhancing the positive influence of TSRs on academic outcomes.
The clock is ticking on schizophrenia: a study protocol for a translational study integrating phenotypic, genomic, microbiome and biomolecular data to overcome disability
Authors: Mercuriali Giacomo , Lodde Lorenzo , Paribello Pasquale , Sapienza Jacopo , Corona Alice , Ave Chiara , Pacini Delia , Nocera Daniela , Corrias Carolina , El Kacemi Sabrina , D'Incalci Michele , Frau Ilaria , Monzani Elena , Valtorta Flavia , Congiu Donatella , Meloni Anna , Scherma Maria , Fadda Paola , Dedoni Simona , Siddi Carlotta , Sut Stefania , Dall’Acqua Stefano , Nasini Sofia , Barzon Benedetta , Squassina Alessio , Cavallaro Roberto , Manchia Mirko , Pisanu Claudia , Bosia Marta , Comai Stefano 
Published: October 2024

BackgroundShared biological factors may play a role in both the cognitive deficits and the increased prevalence of metabolic syndrome observed in individuals with Schizophrenia (SCZ). These factors could entail disturbances in tryptophan (Trp) to both melatonin (MLT) and kynurenine (Kyn) metabolic pathways, as well as inflammation and alterations in the gut microbiome composition.MethodsThe present research project aims to investigate this hypothesis by recruiting 170 SCZ patients from two different recruitment sites, assessing their cognitive functions and screening for the presence of metabolic syndrome. Additionally, we plan to assess the impact of a 3-month cognitive remediation therapy on 30 of these patients. We will analyze clinical data alongside serum biomarkers and gene expression related to the Trp- to MLT and Kyn metabolic pathways, markers of inflammatory and composition of the gut microbiome. The association between Trp-MLT-Kyn levels, expression levels of selected genes, inflammatory markers and clinical phenotypes will be analyses in the context of general linear models.DiscussionThis project has the potential to identify some typical SCZ symptomatic clusters that will be more stringently associated with variations in the Trp-MLT-Kyn/inflammatory system and with a better response to cognitive remediation therapy. Moreover, in a future perspective, it may highlight a group of patients who may benefit from a pharmacological treatment aiming at reinstating the physiological Trp to MLT and Kyn system. Therefore, it has the potential to move research toward a personalized approach for SCZ management.
Effect of cognitive remediation therapy in anorexia nervosa: a systematic review and meta-analysis
Authors: Alserihi Anas R. , Hubayni Wejdan A. , Alotaibi Solaf Hilal , Bahkali Sadeem , Alqurashi Shatha , Abualola Muhannad Sadakah , Alsaleh Ahmad Mohammed 
Published: October 2024

BackgroundAnorexia nervosa (AN) can significantly affect cognitive well-being. Cognitive remediation therapy (CRT) is regarded as one of the effective treatments for cognitive impairment in some mental illnesses such as schizophrenia, bipolar disorder, and attention deficit. For this reason, this systematic review and meta-analysis aim to assess the effectiveness of CRT in patients with AN.MethodsWe conducted a search of Medline, ClinicalTrials.gov, and the Cochrane Database of Systematic Reviews from the inception of each database through April 8, 2023. Randomized clinical trials evaluating the effectiveness of CRT in comparison to placebo or other psychological treatments in patients with AN were included. The quality of the studies was assessed using the revised Cochrane risk-of-bias tool. For meta-analysis, effect sizes were measured using mean difference (MD) utilizing the random-effects model and inverse variance (IV) technique. To evaluate the certainty of the evidence, we applied the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) criteria. The study was registered in PROSPERO, ID: CRD42023411784.ResultsIn the systematic review, six studies were included, of which four underwent meta-analysis. Among these, three trials encompassing 413 participants showed that CRT was associated with improved cognitive flexibility compared to control at the end of treatment (MD = -0.21, 95% CI [-0.44, 0.02], P=0.81, I2 = 0%). In two trials with 143 patients, those who received CRT showed similar effects on the severity of AN symptoms compared to the control group in the self-reporting questionnaires: EDE-Q (MD = -0.25, 95% CI [-0.76, 0.27], P=0.77, I2 = 0%) and EDEQOL (MD = -0.19, 95% CI [-0.41, 0.03], P=0.84, I2 = 0%).ConclusionCRT did not show a statistically significant difference compared to the control group in improving abstract thinking skills and quality of life in individuals with AN. That indicates that CRT’s efficacy remains inconclusive. Further research with larger, more diverse samples is needed to determine its long-term effects and potential benefits.Systematic review registrationPROSPERO, identifier CRD42023411784.