bluuebunny/crossref_metadata_2025_split huggingface dataset:
Triple therapy for Helicobacter pylori eradication and the risk of hypoglycemia in patients with diabetes: a population-based cohort study
Authors: Chang Anne , Chang Anna , Chen Wan-Ting , Chan Lung , Hong Chien-Tai , Chien Li-Nien 
Published: September 2023

AbstractThe incidence of type 2 diabetes mellitus has risen globally, from 108 million cases in 1980 to 422 million cases in 2014. Although controlling glycemic levels in patients with diabetes is crucial, insulin and sulfonylureas can cause hypoglycemic episodes and even potentially fatal events such as comas, seizures, life-threatening arrhythmias, and myocardial infarctions. Several antibiotics have been documented to cause hypoglycemic episodes; the use of antibiotics along with insulin or sulfonylureas might further increase the risk of hypoglycemia. Therefore, researchers must determine which antibiotics carry a risk of inducing severe hypoglycemic events. The prevalence of H. pylori infection remains high in most countries, and the infection is often treated with triple therapy involving amoxicillin, clarithromycin, and a proton pump inhibitor (PPI). Several case reports have reported that hypoglycemia can occur when used with patients who also take diabetes medication. Therefore, we hypothesized that patients with diabetes have an increased risk of hypoglycemic episodes when being treated with triple therapy for H. pylori infection. By analyzing medical records from Taiwan’s National Health Insurance Research Database, we found a significant association between hypoglycemia and triple therapy treatment for diabetic patients with peptic ulcer disease. Prescribing triple therapy to patients with diabetes and peptic ulcers significantly increased the risk of a hypoglycemic episode (adjusted odds ratio [aOR] = 1.75, 95% confidence interval [CI]: 1.64 to 1.88, P < 0.001). Similarly, the highest aOR (5.77, 95% CI 4.82 to 6.92) was found in patients with diabetes and peptic ulcers who had hypoglycemic episodes within 30 days after triple therapy treatment. Many patients with diabetes require H.pylori eradication for peptic ulcer treatment, and vigilance toward the risk of hypoglycemia in this population is thus necessary.
Predicting mortality among patients with severe COVID-19 pneumonia based on admission vital sign indices: a retrospective cohort study
Authors: Udompongpaiboon Piyaphat , Reangvilaikul Teeraphat , Vattanavanit Veerapong 
Published: September 2023

Abstract
Background
Coronavirus disease 2019 (COVID-19) pneumonia remains a major public health concern. Vital sign indices—shock index (SI; heart rate [HR]/systolic blood pressure [SBP]), shock index age (SIA, SI × age), MinPulse (MP; maximum HR–HR), Pulse max index (PMI; HR/maximum HR), and blood pressure–age index (BPAI; SBP/age)—are better predictors of mortality in patients with trauma compared to traditional vital signs. We hypothesized that these vital sign indices may serve as predictors of mortality in patients with severe COVID-19 pneumonia. This study aimed to describe the association between vital sign indices at admission and COVID-19 pneumonia mortality and to modify the CURB-65 with the best performing vital sign index to establish a new mortality prediction tool.

Methods
This retrospective study was conducted at a tertiary care center in southern Thailand. Adult patients diagnosed with COVID-19 pneumonia were enrolled in this study between January 2020 and July 2022. Patient demographic and clinical data on admission were collected from an electronic database. The area under the receiver operating characteristic (AUC) curve analysis was used to assess the predictive power of the resultant multivariable logistic regression model after univariate and multivariate analyses of variables with identified associations with in-hospital mortality.

Results
In total, 251 patients with COVID-19 pneumonia were enrolled in this study. The in-hospital mortality rate was 27.9%. Non-survivors had significantly higher HR, respiratory rate, SIA, and PMI and lower MP and BPAI than survivors. A cutoff value of 51 for SIA (AUC, 0.663; specificity, 80%) was used to predict mortality. When SIA was introduced as a modifier for the CURB-65 score, the new score (the CURSIA score) showed a higher AUC than the Acute Physiology and Chronic Health Evaluation II and CURB-65 scores (AUCs: 0.785, 0.780, and 0.774, respectively) without statistical significance.

Conclusions
SIA and CURSIA scores were significantly associated with COVID-19 pneumonia mortality. These scores may contribute to better patient triage than traditional vital signs.
Updated recommendations on the therapeutic role of extracorporeal shock wave therapy for peyronie’s disease: systematic review and meta-analysis
Authors: Wang Xiaofeng , Liu Hongquan , Tang Gonglin , Wu Gang , Chu Yongli , Wu Jitao , Cui Yuanshan 
Published: September 2023

Abstract
Background
The therapeutic role of extracorporeal shockwave therapy (ESWT) for Peyronie’s disease (PD) has been controversial in a long term. We aimed to further evaluate the therapeutic effect of ESWT for PD on the basis of available high-quality studies.

Methods
The PubMed, CENTRAL and Embase databases were searched for articles published from January 1st, 2000 to December 31, 2022. Only randomized controlled trials (RCTs) using ESWT to treat PD were included. Meta-analysis and forest plots were carried out using Review Manager 5.4.1 software, and outcomes were reviewed by 2 authors independently. Using the Risk of Bias assessment form (ROB-2) by Cochrane Collaboration for quality assessment. PRISMA 2020 guidelines were used in this article to achieve the quantitative and qualitative synthesis of data.

Results
A total of four RCTs were included. 151 patients in the ESWT group and 150 patients in the control group. The meta-analysis results showed that ESWT could significantly reduce plaque size (OR 2.59, 95%CI 1.15 to 5.85, P = 0.02) and relieve pain (MD -1.55, 95%CI -2.46 to -0.64, P = 0.0008); but it has no significant effect on reducing the penile curvature (OR 1.93, 95%CI 0.87–4.26, P = 0.11) and improving sexual function (MD 2.6, 95%CI -1.63 to 6.83, P = 0.23), there is also no significant difference in complication rates between groups (OR 2.94, 95%CI 0.66 to 13.03, P = 0.16). The risk of bias of results is low. The limitations of this study are that the number of included studies is too small, some experimental outcomes are missing, and the expression of outcomes is not unified.

Conclusions
For PD, ESWT can be considered as a safe short-term treatment, which can reduce plaque size and relieve pain, but cannot improve penile curvature and sexual function. Its long-term efficacy remains to be discussed.

Registration number
PROSPERO (ID: CRD42023436744).
The mediating role of coping styles in the relationship between second victim experience and professional quality of life among nurses: a cross-sectional study
Authors: Li Xizhao , Che Chong Chin , Li Yamin , Wang Ling , Chong Mei Chan 
Published: September 2023

Abstract
Background
Studies have shown that second-victim experiences could increase risks of the compassion fatigue while support from individuals and organisations is most often protection. However, the risk for poor compassion satisfaction and increased compassion fatigue in nurses aroused by adverse events remains an underestimated problem, meanwhile, litter known about the role of positive and negative coping styles among nurses suffering from adverse events. This study aims to investigate the effect of second-victim experiences on the professional quality of life among nurses and to determine the mediating role of coping styles in the relationship between second-victim experiences and professional quality of life.

Methods
Multistage sampling was used to recruit registered nurses from Hunan province in China. Registered nurses who identified themselves as experiencing adverse events from nine tertiary hospitals were included in this study. Participants were recruited to complete a survey on the second victim experience and support tool, the simplified coping style questionnaire, and the professional quality of life scale. The stress coping theory was used to develop the framework in this study. The structural equation modelling approach was used for conducting the mediating effects analysis via IBM SPSS Statistics 26.0 and Mplus 8.3.

Results
In total, 67% (n = 899) of nurses reported a second victim experience during their careers. In a bivariate analysis, both second-victims experiences and coping styles were significantly associated with their professional quality of life. The results showed that the effects of second victim experiences on their professional quality of life were fully mediated by coping styles. A total of 10 significantly indirect pathways were estimated, ranging from -0.243 to 0.173.

Conclusions
Second-victim experiences are common among nurses in this study. Since the mediating effects of coping styles were clarified in this study, it is imperative to promote the perception of negative coping styles and encourage nurses to adopt more positive coping styles with adequate support systems.
Diversity of RNA viruses in the cosmopolitan monoxenous trypanosomatid Leptomonas pyrrhocoris
Authors: Macedo Diego H. , Grybchuk Danyil , Režnarová Jana , Votýpka Jan , Klocek Donnamae , Yurchenko Tatiana , Ševčík Jan , Magri Alice , Dolinská Michaela Urda , Záhonová Kristína , Lukeš Julius , Servienė Elena , Jászayová Alexandra , Serva Saulius , Malysheva Marina N. , Frolov Alexander O. , Yurchenko Vyacheslav , Kostygov Alexei Yu. 
Published: September 2023

Abstract
Background
Trypanosomatids are parasitic flagellates well known because of some representatives infecting humans, domestic animals, and cultural plants. Many trypanosomatid species bear RNA viruses, which, in the case of human pathogens Leishmania spp., influence the course of the disease. One of the close relatives of leishmaniae, Leptomonas pyrrhocoris, has been previously shown to harbor viruses of the groups not documented in other trypanosomatids. At the same time, this species has a worldwide distribution and high prevalence in the natural populations of its cosmopolitan firebug host. It therefore represents an attractive model to study the diversity of RNA viruses.

Results
We surveyed 106 axenic cultures of L. pyrrhocoris and found that 64 (60%) of these displayed 2–12 double-stranded RNA fragments. The analysis of next-generation sequencing data revealed four viral groups with seven species, of which up to five were simultaneously detected in a single trypanosomatid isolate. Only two of these species, a tombus-like virus and an Ostravirus, were earlier documented in L. pyrrhocoris. In addition, there were four new species of Leishbuviridae, the family encompassing trypanosomatid-specific viruses, and a new species of Qinviridae, the family previously known only from metatranscriptomes of invertebrates. Currently, this is the only qinvirus with an unambiguously determined host. Our phylogenetic inferences suggest reassortment in the tombus-like virus owing to the interaction of different trypanosomatid strains. Two of the new Leishbuviridae members branch early on the phylogenetic tree of this family and display intermediate stages of genomic segment reduction between insect Phenuiviridae and crown Leishbuviridae.

Conclusions
The unprecedented wide range of viruses in one protist species and the simultaneous presence of up to five viral species in a single Leptomonas pyrrhocoris isolate indicate the uniqueness of this flagellate. This is likely determined by the peculiarity of its firebug host, a highly abundant cosmopolitan species with several habits ensuring wide distribution and profuseness of L. pyrrhocoris, as well as its exposure to a wider spectrum of viruses compared to other trypanosomatids combined with a limited ability to transmit these viruses to its relatives. Thus, L. pyrrhocoris represents a suitable model to study the adoption of new viruses and their relationships with a protist host.
Genome and whole-genome resequencing of Cinnamomum camphora elucidate its dominance in subtropical urban landscapes
Authors: Li Danqing , Lin Han-Yang , Wang Xiuyun , Bi Bo , Gao Yuan , Shao Lingmei , Zhang Runlong , Liang Yuwei , Xia Yiping , Zhao Yun-Peng , Zhou Xiaofan , Zhang Liangsheng 
Published: September 2023

Abstract
Background
Lauraceae is well known for its significant phylogenetic position as well as important economic and ornamental value; however, most evergreen species in Lauraceae are restricted to tropical regions. In contrast, camphor tree (Cinnamomum camphora) is the most dominant evergreen broadleaved tree in subtropical urban landscapes.

Results
Here, we present a high-quality reference genome of C. camphora and conduct comparative genomics between C. camphora and C. kanehirae. Our findings demonstrated the significance of key genes in circadian rhythms and phenylpropanoid metabolism in enhancing cold response, and terpene synthases (TPSs) improved defence response with tandem duplication and gene cluster formation in C. camphora. Additionally, the first comprehensive catalogue of C. camphora based on whole-genome resequencing of 75 accessions was constructed, which confirmed the crucial roles of the above pathways and revealed candidate genes under selection in more popular C. camphora, and indicated that enhancing environmental adaptation is the primary force driving C. camphora breeding and dominance.

Conclusions
These results decipher the dominance of C. camphora in subtropical urban landscapes and provide abundant genomic resources for enlarging the application scopes of evergreen broadleaved trees.
A bifactor model supports unidimensionality of the International Knee Documentation Committee Subjective Knee Form in young active patients with anterior cruciate ligament tears: a retrospective analysis of a randomized controlled trial
Authors: Marmura Hana , Tremblay Paul F. , Getgood Alan M. J. , Bryant Dianne M. 
Published: September 2023

Abstract
Background
The International Knee Documentation Committee Subjective Knee Form (IKDC) is the most highly recommended patient reported outcome measure for assessing patients with anterior cruciate ligament (ACL) injuries and those undergoing ACL reconstruction (ACLR) surgery. The IKDC was developed as a unidimensional instrument for a variety of knee conditions. Structural validity, which determines how an instrument is scored, has not been definitively confirmed for the IKDC in respondents with ACL injuries, and in fact an alternative two-factor/subscale structure has been proposed in this population. The purpose of this study was to determine the most appropriate structure and scoring system for the IKDC in young active patients following ACL injury.

Methods
In total, 618 young patients deemed at high risk of graft rupture were randomized into the Stability 1 trial. Of the trial participants, 606 patients (98%) completed a baseline IKDC questionnaire used for this analysis. A cross sectional retrospective secondary data analysis of the Stability 1 baseline IKDC data was completed to assess the structural validity of the IKDC using exploratory and confirmatory factor analyses. Factor analyses were used to test model fit of the intended one-factor structure, a two-factor structure, and alternative four-factor and bifactor structures (i.e., a combination of a unidimensional factor with additional specific factors) of the IKDC, in a dataset of young active ACL patients.

Results
The simple one-factor and two-factor structures of the IKDC displayed inadequate fit in our dataset of young ACL patients. A bifactor model provided the best fit. This model contains one general factor that is substantially associated with all items, plus four secondary, more specific content factors (symptoms, activity level, activities of daily living, and sport) with generally weaker associations to subsets of items. Although the single-factor model did not provide unambiguous support to unidimensionality of the IKDC based on fit indices, the bifactor model supports unidimensionality of the IKDC when covariance between items with similar linguistic structure, response options, or content are acknowledged.

Conclusions
Overall, findings of a bifactor model with evidence of a reliable general factor well defined by all items lends support to continue interpreting and scoring this instrument as unidimensional. This should be confirmed in other samples. Clinically, based on these findings, the IKDC can be represented by a single score for young active patients with ACL tears. A more nuanced interpretation would also consider secondary factors such as sport and activity level.

Trial registration
The Stability 1 trial for which these data were collected was registered on ClinicalTrial.gov (NCT02018354).
Unravelling the impact of dental workforce training and education programmes on policy evolution: a mixed-method study protocol
Authors: Lin Galvin Sim Siang , Goh Shu Meng , Halil Mohd Haikal Muhamad 
Published: September 2023

Abstract
Background
The dental workforce plays a crucial role in delivering quality oral healthcare services, requiring continuous training and education to meet evolving professional demands. Understanding the impact of dental workforce training and education programmes on policy evolution is essential for refining existing policies, implementing evidence-based reforms and ensuring the growth of the dental profession. Therefore, this study protocol aims to assess the influence of dental workforce training and education programmes on policy evolution in Malaysia.

Methods
A mixed-method research design will be employed, combining quantitative surveys and qualitative interviews. Stakeholder theory and policy change models will form the theoretical framework of the study. Participants from various stakeholder groups will be recruited using purposive sampling. Data collection will involve surveys and one-on-one semi-structured interviews. Descriptive statistics, inferential analysis and thematic analysis will be used to analyse the data. Integration of quantitative and qualitative data will be used to provide a comprehensive understanding of the data.

Discussion
This study will shed light on factors influencing policy decisions related to dental education and workforce development in Malaysia. The findings will inform evidence-based decision-making, guide the enhancement of dental education programmes and improve the quality of oral healthcare services. Challenges related to participant recruitment and data collection should be considered, and the study’s unique contribution to the existing body of knowledge in the Malaysian context will be discussed.
Exploration of the radiosensitivity-related prognostic risk signature in patients with glioma: evidence from microarray data
Authors: Zhang Xiaonan , Ren Qiannan , Li Zhiyong , Xia Xiaolin , Zhang Wan , Qin Yue , Wu Dehua , Ren Chen 
Published: September 2023

Abstract
Background
Gene expression signatures can be used as prognostic biomarkers in various types of cancers. We aim to develop a gene signature for predicting the response to radiotherapy in glioma patients.

Methods
Radio-sensitive and radio-resistant glioma cell lines (M059J and M059K) were subjected to microarray analysis to screen for differentially expressed mRNAs. Additionally, we obtained 169 glioblastomas (GBM) samples and 5 normal samples from The Cancer Genome Atlas (TCGA) database, as well as 80 GBM samples and 4 normal samples from the GSE7696 set. The “DESeq2” R package was employed to identify differentially expressed genes (DEGs) between the normal brain samples and GBM samples. Combining the prognostic-related molecules identified from the TCGA, we developed a radiosensitivity-related prognostic risk signature (RRPRS) in the training set, which includes 152 patients with glioblastoma. Subsequently, we validated the reliability of the RRPRS in a validation set containing 616 patients with glioma from the TCGA database, as well as an internal validation set consisting of 31 glioblastoma patients from the Nanfang Hospital, Southern Medical University.

Results
Based on the microarray and LASSO COX regression analysis, we developed a nine-gene radiosensitivity-related prognostic risk signature. Patients with glioma were divided into high- or low-risk groups based on the median risk score. The Kaplan–Meier survival analysis showed that the progression-free survival (PFS) of the high-risk group was significantly shorter. The signature accurately predicted PFS as assessed by time-dependent receiver operating characteristic curve (ROC) analyses. Stratified analysis demonstrated that the signature is specific to predict the outcome of patients who were treated using radiotherapy. Univariate and multivariate Cox regression analysis revealed that the predictor was an independent predictor for the prognosis of patients with glioma. The prognostic nomograms accompanied by calibration curves displayed the 1-, 2-, and 3-year PFS and OS in patients with glioma.

Conclusion
Our study established a new nine-gene radiosensitivity-related prognostic risk signature that can predict the prognosis of patients with glioma who received radiotherapy. The nomogram showed great potential to predict the prognosis of patients with glioma treated using radiotherapy.
A diagnostic model for sepsis-induced acute lung injury using a consensus machine learning approach and its therapeutic implications
Authors: Zheng Yongxin , Wang Jinping , Ling Zhaoyi , Zhang Jiamei , Zeng Yuan , Wang Ke , Zhang Yu , Nong Lingbo , Sang Ling , Xu Yonghao , Liu Xiaoqing , Li Yimin , Huang Yongbo 
Published: September 2023

Abstract
Background
A significant proportion of septic patients with acute lung injury (ALI) are recognized late due to the absence of an efficient diagnostic test, leading to the postponed treatments and consequently higher mortality. Identifying diagnostic biomarkers may improve screening to identify septic patients at high risk of ALI earlier and provide the potential effective therapeutic drugs. Machine learning represents a powerful approach for making sense of complex gene expression data to find robust ALI diagnostic biomarkers.

Methods
The datasets were obtained from GEO and ArrayExpress databases. Following quality control and normalization, the datasets (GSE66890, GSE10474 and GSE32707) were merged as the training set, and four machine learning feature selection methods (Elastic net, SVM, random forest and XGBoost) were applied to construct the diagnostic model. The other datasets were considered as the validation sets. To further evaluate the performance and predictive value of diagnostic model, nomogram, Decision Curve Analysis (DCA) and Clinical Impact Curve (CIC) were constructed. Finally, the potential small molecular compounds interacting with selected features were explored from the CTD database.

Results
The results of GSEA showed that immune response and metabolism might play an important role in the pathogenesis of sepsis-induced ALI. Then, 52 genes were identified as putative biomarkers by consensus feature selection from all four methods. Among them, 5 genes (ARHGDIB, ALDH1A1, TACR3, TREM1 and PI3) were selected by all methods and used to predict ALI diagnosis with high accuracy. The external datasets (E-MTAB-5273 and E-MTAB-5274) demonstrated that the diagnostic model had great accuracy with AUC value of 0.725 and 0.833, respectively. In addition, the nomogram, DCA and CIC showed that the diagnostic model had great performance and predictive value. Finally, the small molecular compounds (Curcumin, Tretinoin, Acetaminophen, Estradiol and Dexamethasone) were screened as the potential therapeutic agents for sepsis-induced ALI.

Conclusion
This consensus of multiple machine learning algorithms identified 5 genes that were able to distinguish ALI from septic patients. The diagnostic model could identify septic patients at high risk of ALI, and provide potential therapeutic targets for sepsis-induced ALI.