bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spectroscopic characterization of bacterial colonies through UV hyperspectral imaging techniques
Authors: Ezenarro Josune J. , Al Ktash Mohammad , Vigues Nuria , Gordi Jordi Mas , Muñoz-Berbel Xavi , Brecht Marc 
Published: February 2025

IntroductionPlate culturing and visual inspection are the gold standard methods for bacterial identification. Despite the growing attention on molecular biology techniques, colony identification using agar plates remains manual, interpretative, and heavily reliant on human experience, making it prone to errors. Advanced imaging techniques, like hyperspectral imaging, offer potential alternatives. However, the use of hyperspectral imaging in the VIS-NIR region has been hindered by sensitivity to various components and culture medium changes, leading to inaccurate results. The application of hyperspectral imaging in the ultraviolet (UV) region has not been explored, despite the presence of specific absorption and emission peaks in bacterial components.MethodsTo address this gap, we developed a predictive model for bacterial colony detection and identification using UV hyperspectral imaging. The model utilizes hyperspectral images acquired in the UV wavelength range of 225–400 nm, processed with principal component analysis (PCA) and discriminant analysis (DA). The measurement setup includes a hyperspectral imager, a PC for automated data analysis, and a conveyor belt system to transport agar plates for automated analysis. Four bacterial species (Escherichia coli, Staphylococcus, Pseudomonas, and Shewanella) were cultured on two different media, Luria Bertani and Tryptic Soy, to train and validate the model.ResultsThe PCA-DA-based model demonstrated high accuracy (90%) in differentiating bacterial species based on the first three principal components, highlighting the potential of UV hyperspectral imaging for bacterial identification.DiscussionThis study shows that UV hyperspectral imaging, coupled with advanced data analysis techniques, offers a robust and automated alternative to traditional methods for bacterial identification. The model's high accuracy emphasizes the untapped potential of UV hyperspectral imaging in microbiological analysis, reducing human error and improving reliability in bacterial species differentiation.
Clinical application of targeted next-generation sequencing in pneumonia diagnosis among cancer patients
Authors: Yang Ke , Zhao Jiuzhou , Wang Tingjie , Wang Zhizhong , Sun Rui , Gu Dejian , Liu Hao , Wang Weizhen , Zhang Cuiyun , Zhao Chengzhi , Guo Yongjun , Ma Jie , Wei Bing 
Published: February 2025

BackgroundCancer patients are highly susceptible to infections due to their immunocompromised state from both the malignancy and intensive treatments. Accurate and timely identification of causative pathogens is crucial for effective management and treatment. Targeted next-generation sequencing (tNGS) has become an important tool in clinical infectious disease diagnosis because of its broad microbial detection range and acceptable cost. However, there is currently a lack of systematic research to evaluate the diagnostic value of this method in cancer patients.MethodsTo evaluate the diagnostic value of tNGS for cancer patients with pneumonia, a retrospective analysis was conducted on 148 patients with suspected pneumonia who were treated at the Henan Cancer Hospital. The tNGS results were compared with conventional microbiological tests (CMT) and clinical diagnoses based on symptoms and imaging studies to assess the diagnostic performance of tNGS in cancer patients with pneumonia.ResultsAmong these 148 patients, 130 were ultimately diagnosed with pneumonia. tNGS demonstrated significantly higher sensitivity (84.62% vs. 56.92%) and diagnostic accuracy (85.81% vs. 62.16%) compared to the CMT method. The tNGS method identified more pathogens than CMT method (87.50% vs 57.14%), regardless of whether they were bacteria, fungi, or viruses, primarily due to its broader pathogen detection range and higher sensitivity compared to the CMT method. tNGS had significantly higher diagnostic accuracy for Pneumocystis jirovecii and Legionella pneumophila than the CMT method, but for most pathogens, tNGS showed higher sensitivity but with a correspondingly lower specificity compared to CMT.ConclusiontNGS demonstrates higher sensitivity and a broader pathogen detection spectrum compared to CMT, making it a valuable diagnostic tool for managing pneumonia in cancer patients.
Multiomics insights into BMI-related intratumoral microbiota in gastric cancer
Authors: Liu Kang , Jiang Zhengchen , Ma Yubo , Xia Ruihong , Zheng Yingsong , Yin Kailai , Pang Chuhong , Yuan Li , Cheng Xiangdong , Liu Zhuo , Zhang Bo , Wang Shi 
Published: February 2025

IntroductionBody mass index (BMI) is considered an important factor in tumor prognosis, but its role in gastric cancer (GC) remains controversial. There is a lack of studies exploring the effect of BMI on gastric cancer from the perspective of intratumoral microbiota. This study aimed to compare and analyze the differences in and functions of intratumoral microbiota among GC patients with varying BMIs, aiming to ascertain whether specific microbial features are associated with prognosis in low-BMI (LBMI) gastric cancer patients.MethodsA retrospective analysis of the clinicopathological features and prognosis of 5567 patients with different BMIs was performed between January 2010 and December 2019. Tumor tissues from 189 GC patients were collected for 16S rRNA sequencing, 64 samples were selected for transcriptome sequencing, and 57 samples were selected for untargeted metabolomic analysis.ResultsClinical cohort analysis revealed that GC patients with a low BMI presented poorer clinical and pathological characteristics than those with a non-low-BMI (NLBMI). LBMI was identified as a significant independent risk factor for adverse prognosis, potentially exerting immunosuppressive effects on postoperative adjuvant chemotherapy. 16S rRNA sequencing revealed no significant differences in the alpha and beta diversity of the intratumoral microbiota between the two groups of GC patients. However, LEfSe analysis revealed 32 differential intratumoral microbiota between the LBMI and NLBMI groups. Notably, the genus Abiotrophia was significantly enriched in the LBMI group. Further in-depth analysis indicated that the genus Abiotrophia was inversely associated with eosinophils, P2RY12, and SCN4B genes, and positively linked with LGR6 in LBMI gastric cancer patients. Metabolomic assessments revealed that LBMI was positively associated with purine metabolites, specifically guanine and inosine diphosphate (IDP).DiscussionIn conclusion, LBMI is an independent risk factor for poor prognosis in gastric cancer patients and may have an inhibitory effect on postoperative adjuvant chemotherapy. Intratumor flora of gastric cancer patients with different BMI levels differed, with different immune cell infiltration and metabolic characteristics. The genus Abiotrophia may promote gastric cancer development and progression by regulating eosinophils and the purine metabolism pathway, which provides a new idea for the precise treatment of gastric cancer.
MicroRNAs as regulators of cardiac dysfunction in sepsis: pathogenesis and diagnostic potential
Authors: Liu Zhen , Li Feiyang , Li Ningcen , Chen Yong , Chen Zelin 
Published: February 2025

IntroductionSepsis, a life-threatening condition arising from an uncontrolled immune response to infection, can lead to organ dysfunction, with severe inflammation potentially causing multiple organ failures. Sepsis-induced cardiac dysfunction (SIMD) is a common and severe complication of sepsis, significantly increasing patient mortality. Understanding the pathogenesis of SIMD is crucial for improving treatment, and microRNAs (miRNAs) have emerged as important regulators in this process.MethodsA comprehensive literature search was conducted in PubMed, Science Direct, and Embase databases up to September 2024. The search terms included [“miRNA” or “microRNA”] and [“Cardiac” or “Heart”] and [“Sepsis” or “Septic”], with the language limited to English. After initial filtering by the database search engine, Excel software was used to further screen references. Duplicate articles, those without abstracts or full texts, and review/meta-analyses or non-English articles were excluded. Finally, 106 relevant research articles were included for data extraction and analysis.ResultsThe pathogenesis of SIMD is complex and involves mitochondrial dysfunction, oxidative stress, cardiomyocyte apoptosis and pyroptosis, dysregulation of myocardial calcium homeostasis, myocardial inhibitory factors, autonomic nervous regulation disorders, hemodynamic changes, and myocardial structural alterations. miRNAs play diverse roles in SIMD. They are involved in regulating the above-mentioned pathological processes.DiscussionAlthough significant progress has been made in understanding the role of miRNAs in SIMD, there are still challenges. Some studies on the pathogenesis of SIMD have limitations such as small sample sizes and failure to account for confounding factors. Research on miRNAs also faces issues like inconsistent measurement techniques and unclear miRNA-target gene relationships. Moreover, the translation of miRNA-based research into clinical applications is hindered by problems related to miRNA stability, delivery mechanisms, off-target effects, and long-term safety. In conclusion, miRNAs play a significant role in the pathogenesis of SIMD and have potential as diagnostic biomarkers. Further research is needed to overcome existing challenges and fully exploit the potential of miRNAs in the diagnosis and treatment of SIMD.
Effect of sex, pubertal stage, body mass index, oral contraceptive use, and C-reactive protein on vitamin D binding protein reference values
Authors: von Heimburg Philipp , Baber Ronny , Willenberg Anja , Wölfle Philip , Kratzsch Jürgen , Kiess Wieland , Vogel Mandy 
Published: February 2025

ObjectiveVitamin D binding protein (DBP) regulates the transport and availability of vitamin D. We aimed to establish age- and sex-specific reference ranges for serum concentrations of DBP in healthy infants, children, and adolescents. In addition, we investigated DBP’s associations with age, sex, puberty, body mass index (BMI), and oral contraceptive use.Design and methods2,503 serum samples from children and adolescents aged 3 months to 17 years from the LIFE Child cohort were analyzed to study DBP levels in this population (49.3% female subjects, 50.7% male subjects). Age- and sex-dependent reference percentiles were established using generalized additive models. We used linear mixed effects models to assess DBP’s associations with age, sex, pubertal status, the BMI standard deviation score (SDS), and oral contraceptives. To investigate associations between DBP and vitamin D metabolites, we applied univariate regression analysis. We used hierarchical regression models and linear mixed effects models to assess DBP’s associations with bone parameters, hormones, and inflammatory markers.ResultsMean DBP values differed between males (347 mg/l) and females (366 mg/l) (p &lt; 0.001). Age had no significant association with DBP levels. In both males and females, DBP levels remained relatively stable from infancy through late adolescence. Children and adolescents with obesity had lower mean DBP levels compared with normal-weight subjects (ß = -14.28, p &lt; 0.001). The BMI-SDS was inversely associated with DBP levels in males (ß = -5.7, p &lt; 0.001). Female subjects using oral contraceptives had higher levels of DBP (ß = 141.38, p &lt; 0.001). DBP was positively associated with the vitamin D metabolites: 25(OH)D3 (females: ß = 0.8, p &lt; 0.001; males: ß = 1.2, p &lt; 0.001) and 1,25(OH)2-D3 (females: ß = 0.3, p &lt; 0.001; males: ß = 0.4, p &lt; 0.001). An inverse association between osteocalcin and DBP (females: ß = -0.1, p &lt; 0.022; males: ß = -0.1, p = 0.027) was found. CRP levels were also positively associated with DBP levels (females: ß = 2.8, p = 0.001; males: ß = 5.1, p &lt; 0.001).ConclusionWe established age- and sex-specific reference ranges for the serum concentration of DBP. We suggest that BMI, pubertal stages, oral contraceptive use, and inflammation markers need to be considered when interpreting DBP as a stabilizer and regulator of vitamin D metabolism and vitamin D status in children and adolescents.Clinical trial registrationClinicalTrial.gov, identifier NCT02550236.
Association of composite dietary antioxidant index with high risk of prostate cancer in middle-aged and elderly men: insights from NHANES
Authors: Jin Xuefeng , Tong Wenhui , Sun Li , Lu Sujue , Sun Pan , Li Hangxu , Liu Yan 
Published: February 2025

ObjectivesIn the US, the most common type of cancer and the second leading cause of cancer-related death in men is prostate cancer (PCa). Food and lifestyle factors may influence the risk of developing prostate cancer. Therefore, research on dietary components associated with prostate cancer is essential for its prevention. Data from the National Health and Nutrition Examination Survey (NHANES) between 2003 and 2010 was used for this cross-sectional investigation involving 5,658 middle-aged and older American men.MethodsDietary antioxidant vitamins A, C, E, total carotenoids, zinc, and selenium were subtracted from the total mean, divided by the standard deviation, respectively, and then summed to become the CDAI. Participants were categorized as high risk for PCa if they had tPSA greater than 10 ng/mL or tPSA levels between 4 and 10 ng/mL with f/t PSA ratios of 25% or below; the remaining subjects were classified as being at low risk for PCa.ResultsThe sample represented approximately 75,984,602 American men. After multivariate logistic regression, dose-effect analysis and stratified analysis, CDAI was significantly and linearly negatively associated with a high risk of prostate cancer (OR=0.95, P=0.002, P for linear=0.0021). Age moderation analysis showed a significant effect on the inverse relationship between CDAI and prostate cancer risk (B = -0.0097, SE = 0.0034, t = -2.85, P = 0.004). Among the independent effects of CDAI components, zinc and selenium were more strongly negatively associated with prostate cancer (zinc, OR = 0.80, P = 0.008; selenium, OR = 0.78, P&lt; 0.001).ConclusionsCDAI serves as a dietary indicator of prostate cancer risk in middle-aged and older men, and high dietary antioxidant intake has a significant protective effect on prostate cancer risk, especially in the older population of men.
Chaihushugan powder regulates the gut microbiota to alleviate mitochondrial oxidative stress in the gastric tissues of rats with functional dyspepsia
Authors: Liu Xuejiao , Yang Keming , Jia Yuebo , Yeertai Yeliya , Wu Chenheng , Wang Xiangxiang , Jia Qingling , Gu Zhijian , Cong Jun , Ling Jianghong 
Published: February 2025

IntroductionFunctional dyspepsia (FD) is a prevalent functional gastrointestinal disorder associated with oxidative stress (OS) and dysbiosis. Chaihushugan powder (CHSGP) demonstrates efficacy in treating FD; however, the underlying therapeutic mechanism is not yet elucidated. This study aims to investigate the effects of CHSGP on OS and gut microbiota (GM) in FD rats, with a particular emphasis on the role of GM as a potential target for the antioxidant properties of CHSGP.MethodsThe FD rat model was established with a modified tail-clamp stimulation and the administration of the CHSGP decoction at a dosage of 9.6 g/kg via gavage for a duration of 4 weeks. The GM was depleted by the administration of a cocktail of metronidazole (200 mg/kg), ampicillin (200 mg/kg), neomycin sulfate (200 mg/kg), and vancomycin (100 mg/kg). Fecal microbiota transplantation (FMT) was performed with CHSGP-treated fecal supernatant at a dosage of 10 mL/kg. The gastrointestinal motility was measured using the rates of gastric emptying and small intestine propulsion. Hematoxylin and eosin staining was employed to elucidate the pathological changes, while the transmission electron microscope was used to examine the microstructures of the interstitial cells of Cajal (ICC). Chemiluminescence, colorimetric assay, immunofluorescence co-staining, and western blot assay were employed to identify the OS-related markers (ROS, SOD, NOX4, PRDX1, and TRX2). Sequencing of fecal microbiota was performed utilizing 16S rDNA.ResultsThe CHSGP decoction promoted gastrointestinal motility, protected the microstructure of ICC, and reduced OS in FD rats. The GM composition was also regulated by CHSGP. However, these effects disappeared after microbiota depletion. Fortunately, the FMT therapy reinstated them.ConclusionChaihushugan powder decoction might regulate the GM to alleviate mitochondrial OS in the gastric tissues of FD rats.
The incidence of hyperkalemia in patients with secondary hyperparathyroidism after ultrasound-guided radiofrequency ablation vs. parathyroidectomy
Authors: Ren Mian , Liu Yueming , Lin Bo , Zou Wenli , Zhu Bin , Wu Juan 
Published: February 2025

IntroductionThe aim of our study was to compare the incidence of hyperkalemia in maintenance dialysis patients with secondary hyperparathyroidism(SHPT) after parathyroidectomy(PTX) or ultrasound-guided radiofrequency ablation(RFA), and to explore the risk factors and the best preoperative serum potassium threshold.MethodsWe defined hyperkalemia as serum potassium &gt;5.30 mmol/L. Two operation methods were analyzed in subgroups, and the differences in demographic parameters, operation situation and perioperative laboratory indicators were compared between the two groups.ResultsA total of 154 maintenance dialysis patients were included, of which 91 patients received PTX and 63 patients received RFA. 53 patients (34.4%) developed postoperative hyperkalemia. Patients in hyperkalemia group had higher preoperative serum potassium, phosphorus, hemoglobin and 25-hydroxyvitamin D level (p &lt; 0.05). It seemed that males were more prone to suffer hyperkalemia than females, but there was no statistically difference (40.9% vs. 25.8%, p = 0.05). The occurrence of hyperkalemia after the operation was obviously higher in hemodialysis patients. Logistic regression analysis showed that preoperative serum potassium level (OR = 3.269, 95%CI 1.638–6.534, p = 0.001) and PTX (OR = 18.119, 95%CI 5.716–57.438, p &lt; 0.01) were independent risk factors for predicting postoperative hyperkalemia. According to ROC curve analysis, the optimal cutoff value for preoperative serum potassium was 4.66 mmol/L, with a sensitivity of 46.8% and a specificity of 86%.ConclusionHyperkalemia after invasive treatment in patients with severe SHPT was common, and the incidence of hyperkalemia after PTX was significantly higher than that after RFA. Hemodialysis patients were more prone to hyperkalemia, which was related to the preoperative serum potassium level.
Association between early coagulation disorders and the risk of severe acute kidney injury in traumatic brain injury patients: a retrospective cohort study using the MIMIC-IV database
Authors: Gao Yu , Li Yong , Zhou Hai , Wang Xin , Wang Guojun , Zhu Lin 
Published: February 2025

AimAcute kidney injury (AKI) and coagulation disorders are two common complications of traumatic brain injury (TBI) that are associated with poor prognosis. However, the relationship between early coagulation disorders and the risk of severe AKI in TBI patients remains unclear. This study aimed to explore the association between early coagulation disorders and the risk of severe AKI in TBI patients admitted to the intensive care unit (ICU).MethodsIn this retrospective cohort study, adults diagnosed with TBI were selected from the Medical Information Mart for Intensive Care (MIMIC)-IV database. The outcome was the risk of severe AKI within 7 days of ICU admission in TBI patients. Covariates including sociodemographic information, vital signs, scoring systems, and laboratory parameters were extracted from the database. Univariable and multivariable Cox proportional hazard regression models were used to assess the association between early coagulation disorders and the risk of severe AKI within 7 days of admission to the ICU in TBI patients. Subgroup analyses based on age and the Glasgow Coma Scale (GCS) score were further conducted to assess the association.ResultsA total of 846 patients were finally included, of whom 187 (22.10%) had severe AKI. After adjusting for all covariates, the TBI patients with early coagulation disorders had a higher risk of developing severe AKI within 7 days of ICU admission compared to the TBI patients without early coagulation disorders (hazard ratio (HR) = 1.40, 95% confidence interval (CI): 1.04–1.89), particularly among those aged ≥65 years (HR = 1.46, 95%CI: 1.01–2.04) and those with a GCS score ≤ 13 (HR = 1.91, 95%CI: 1.16–3.15).ConclusionTBI patients with early coagulation disorders had a higher risk of developing severe AKI within 7 days of ICU admission. This may serve as a promising biomarker and could be helpful for managing kidney health in TBI patients.
A comparative study of methods for dynamic survival analysis
Authors: de Swart Wieske K. , Loog Marco , Krijthe Jesse H. 
Published: February 2025

IntroductionDynamic survival analysis has become an effective approach for predicting time-to-event outcomes based on longitudinal data in neurology, cognitive health, and other health-related domains. With advancements in machine learning, several new methods have been introduced, often using a two-stage approach: first extracting features from longitudinal trajectories and then using these to predict survival probabilities.MethodsThis work compares several combinations of longitudinal and survival models, assessing their predictive performance across different training strategies. Using synthetic and real-world cognitive health data from the Alzheimer's Disease Neuroimaging Initiative (ADNI), we explore the strengths and limitations of each model.ResultsAmong the considered survival models, the Random Survival Forest consistently delivered strong results across different datasets, longitudinal models, and training strategies. On the ADNI dataset the best performing method was Random Survival Forest with the last visit benchmark and super landmarking with an average tdAUC of 0.96 and brier score of 0.07. Several other methods, including Cox Proportional Hazards and the Recurrent Neural Network, achieve similar scores. While the tested longitudinal models often struggled to outperform simple benchmarks, neural network models showed some improvement in simulated scenarios with sufficiently informative longitudinal trajectories.DiscussionOur findings underscore the importance of aligning model selection and training strategies with the specific characteristics of the data and the target application, providing valuable insights that can inform future developments in dynamic survival analysis.