bluuebunny/crossref_metadata_2025_split huggingface dataset:
The prevalence of patients suffering from chronic spontaneous urticaria, in whom omalizumab cannot be stopped even after six years
Authors: Schichter-Konfino V. , Mubariki R. , Toubi E. , Vadasz Z. 
Published: October 2024

BackgroundOmalizumab (OMA) was the first FDA-approved biological drug for severe chronic spontaneous urticaria (CSU), and until today is the only beneficial and truly safe one. The objectives were: To assess the prevalence of CSU patients in whom OMA cannot be stopped over time. We also asked if biomarkers (e.g., anti-TPO antibodies and total IgE) could assist in anticipating this issue.MethodsWe used our prospective registry of 93 patients, which included CSU disease duration, the onset of OMA treatment, Urticaria Activity Score (UAS7) during follow-up, co-morbidities, serum IgE levels and the presence of anti-TPO antibodies. Finally, we assessed the response to OMA during a period of six years.ResultsOut of the 93 treated CSU patients, OMA was stopped in ten patients after six months being defined as failures. In another ten patients, OMA was discontinued after 2–4 years of therapy, achieving a remission. Seventy-three patients are still treated between 2 and 6 years, having different degrees of response. Of these, in thirty-eight (52%) patients, we could not stop OMA even after six years due to CSU relapses. The prevalence of lower serum IgE levels and anti-TPO antibody positivity was significantly higher in CSU patients in whom OMA could not be stopped.ConclusionThis is the first study where OMA-treated CSU patients were followed up to six years. In half of them, long-term therapy of six years is still required.
Variational Bayes latent class analysis for EHR-based phenotyping with large real-world data
Authors: Buckley Brian , O'Hagan Adrian , Galligan Marie 
Published: October 2024

IntroductionBayesian approaches to patient phenotyping in clinical observational studies have been limited by the computational challenges associated with applying the Markov Chain Monte Carlo (MCMC) approach to real-world data. Approximate Bayesian inference via optimization of the variational evidence lower bound, variational Bayes (VB), has been successfully demonstrated for other applications.MethodsWe investigate the performance and characteristics of currently available VB and MCMC software to explore the practicability of available approaches and provide guidance for clinical practitioners. Two case studies are used to fully explore the methods covering a variety of real-world data. First, we use the publicly available Pima Indian diabetes data to comprehensively compare VB implementations of logistic regression. Second, a large real-world data set, Optum™ EHR with approximately one million diabetes patients extended the analysis to large, highly unbalanced data containing discrete and continuous variables. A Bayesian patient phenotyping composite model incorporating latent class analysis (LCA) and regression was implemented with the second case study.ResultsWe find that several data characteristics common in clinical data, such as sparsity, significantly affect the posterior accuracy of automatic VB methods compared with conditionally conjugate mean-field methods. We find that for both models, automatic VB approaches require more effort and technical knowledge to set up for accurate posterior estimation and are very sensitive to stopping time compared with closed-form VB methods.DiscussionOur results indicate that the patient phenotyping composite Bayes model is more easily usable for real-world studies if Monte Carlo is replaced with VB. It can potentially become a uniquely useful tool for decision support, especially for rare diseases where gold-standard biomarker data are sparse but prior knowledge can be used to assist model diagnosis and may suggest when biomarker tests are warranted.
Improvement of the gait deviation index for spinal cord injury to broaden its applicability: the reduced gait deviation index for spinal cord injury (rSCI-GDI)
Authors: Herrera-Valenzuela Diana , Sinovas-Alonso Isabel , Reyes Ana de los , Gil-Agudo Ángel , del-Ama Antonio J. 
Published: October 2024

BackgroundThe SCI-GDI is an accurate and effective metric to summarize gait kinematics in adults with SCI. It is usually computed with the information registered with a photogrammetry system because it requires accurate information of pelvic and hip movement in the three anatomic planes, which is hard to record with simpler systems. Additionally, due to being developed from the GDI, the SCI-GDI is built upon nine joint movements selected for a pediatric population with cerebral palsy, for which the GDI was originally developed, but those nine movements are not necessarily as meaningful for adults with SCI. Nevertheless, pelvic movement and hip rotation have been proven to have low reliability even when acquired with gold-standard photogrammetry systems. Additionally, the use of photogrammetry is limited in real-life scenarios and when used with rehabilitation technologies, which limits the use of the SCI-GDI to evaluate gait in alternative scenarios to gait laboratories and to evaluate technologies for gait assistance. This research aimed to improve the SCI-GDI to broaden its applicability beyond the use of photogrammetry.MethodsAn exploration of the mathematical relevance of each joint movement included in the original GDI for the performance of the metric is performed. Considering the results obtained and the clinical relevance of each of the 9 joints used to compute the SCI-GDI in the gait pattern of the SCI population, a more adaptable SCI-GDI is proposed using four joint movements that can be precisely captured with simpler systems than photogrammetry: sagittal planes of hip, knee and ankle and hip abduction/adduction.ResultsThe reduced SCI-GDI (rSCI-GDI) effectively represents gait variability of adults with SCI as does the SCI-GDI, while providing more generalizable results and equivalent or stronger correlations with clinical tests validated in the population. During the derivation of the improved index, it was demonstrated that pelvic movements, hip rotation, and foot progression angle introduce high variability to the dataset of gait patterns of the adult population with SCI, but they have low relevance to characterize gait kinematics of this population. The rSCI-GDI can be calculated using the 14-feature vectorial basis included in the electronic addendum provided.
Factors related to cardiac rupture after acute myocardial infarction
Authors: Gao Xue , Guo Ying , Zhu Xiaoting , Du Chunlei , Ma Beibei , Cui Yinghua , Wang Shuai 
Published: October 2024

BackgroundCardiac rupture (CR) after acute myocardial infarction (AMI) is a fatal mechanical complication. The early identification of factors related to CR in high-risk cases may reduce mortality. The purpose of our study was to discover relevant risk factors for CR after AMI and in-hospital mortality from CR.MethodsIn this study, we enrolled 1,699 AMI cases from October 2013 to May 2020. A total of 51 cases were diagnosed with CR. Clinical diagnostic information was recorded and analyzed retrospectively. We randomly matched these cases with AMI patients without CR in a 1:4 ratio. Univariate and multivariate logistic regression and stratifying analysis were used to identify risk factors for CR. Univariate and multivariate Cox regression hazard analysis and stratifying analysis were used to assess predictors of in-hospital mortality from CR.ResultsThe incidence of CR after AMI was 3.0% and in-hospital mortality was approximately 57%. Multivariate logistic regression analysis identified that white blood cell count, neutrophil percentage, anterior myocardial infarction, a Killip class of &gt;II, and albumin level were independently associated with CR (p &lt; 0.05). Stratifying analysis showed that age, systolic blood pressure, and bicarbonate were independent risk factors for female CR (p &lt; 0.05) but not male CR. Triglyceride and cardiac troponin I were independent risk factors for male CR (p &lt; 0.05) but not female CR. Anterior myocardial infarction, a Killip class of &gt;II, and neutrophil percentage were independent risk factors for male and female CR (p &lt; 0.05). Multivariate Cox regression analysis showed that the time from symptom to CR and the site of CR were independent predictors for in-hospital mortality from CR (p &lt; 0.05). Stratification analysis indicated that risk factors did not differ based on gender, but platelet counts were predictors for in-hospital mortality in female and male CR.ConclusionLow albumin, a high white blood cell count, neutrophil percentage, anterior myocardial infarction, and a Killip class of &gt;II were independent and significant predictors for CR. However, risk factors are different in male and female CR. The time from symptom to CR, the site of CR, and platelet counts were independent predictors for in-hospital mortality from CR. These may be helpful in the early and accurate identification of high-risk patients with CR and the assessment of prognosis. In addition, gender differences should be considered.
Examining the causal association between moderate alcohol consumption and cardiovascular risk factors in the Taiwan Biobank: a Mendelian randomization analysis
Authors: Chien Pei-Shan , Wong Tzu-Jung , Tai An-Shun , Shr Yau-Huo , Yu Tsung 
Published: October 2024

BackgroundThe Mendelian randomization approach uses genetic variants as instrumental variables to study the causal association between the risk factors and health outcomes of interest. We aimed to examine the relation between alcohol consumption and cardiovascular risk factors using two genetic variants as instrumental variables: alcohol dehydrogenase 1B (ADH1B) rs1229984 and aldehyde dehydrogenase 2 (ALDH2) rs671.MethodsUsing data collected in the Taiwan Biobank—an ongoing, prospective, population-based cohort study—our analysis included 129,032 individuals (46,547 men and 82,485 women) with complete data on ADH1B rs1229984 and ALDH2 rs671 genotypes and alcohol drinking status. We conducted instrumental variables regression analysis to examine the relationship between alcohol drinking and body mass index (BMI), systolic blood pressure (SBP), diastolic blood pressure (DBP), fasting glucose, glycated hemoglobin (HbA1c), triglycerides, high-density lipoprotein cholesterol (HDLc), and low-density lipoprotein cholesterol (LDLc).ResultsIn the rs1229984-instrumented analysis, alcohol drinking was only associated with higher levels of SBP in men and lower levels of DBP in women. In the rs671-instrumented analysis, alcohol drinking was associated with higher levels of BMI, SBP, DBP, fasting glucose, triglycerides, HDLc and lower levels of LDLc in men; alcohol drinking was associated with higher levels of HDLc and lower levels of SBP, HbA1c, and triglycerides in women.ConclusionUsing Mendelian randomization analysis, some of our study results among men echoed findings from the previous systematic review, suggesting that alcohol drinking may be causally associated with higher levels of BMI, SBP, DBP, fasting glucose, triglycerides, HDLc, and lower levels of LDLc. Although alcohol drinking is beneficial to a few cardiovascular risk factors, it is detrimental to many others. The assumptions that underlie the Mendelian randomization approach should also be carefully examined when interpreting findings from such studies.
Global hotspots and trends in gut mycological research: a visual analytics and bibliometric approach
Authors: Zhu Wenhao , Chi Jiayu , Zhang Yongde , Wu Dongliang , Xia Xinyu , Liao Xingyu , Xu Kexin , Shi Wenying , Hu Haowen , Wang Wei , Lu Zhiyuan , Zhang Zixu , Liu Yang 
Published: October 2024

BackgroundRecent findings highlight the significant impact of intestinal fungi on the complex makeup of the gut microbiota and human health, challenging past oversights. However, a lack of thorough systematic and quantitative analyses remains. This study aims to address this gap by thoroughly examining the current research on gut fungi. Through analyzing developments and unique features in this area, our goal is to foster a deeper understanding and identify future research pathways.MethodsWe performed an extensive bibliometric analysis on documents from 2000 to 2023, sourced from the Web of Science Core Collection (WoSCC). Utilizing advanced visualization tools such as VOSviewer, CiteSpace, and Bibliometrix R, we meticulously examined and illustrated the data in scientific landscapes and networks.ResultsA total of 1434 papers were analyzed, revealing a substantial increase in publication volume over the past two decades, particularly in 2020. Contributions came from 67 countries, 2178 institutions, and 8,479 authors. China led in publication output with 468 articles, followed by the University of California with 84 articles, and ZHANG F as the most prolific author with 17 articles. Emerging research areas such as “Fungal-Bacteria Interactions,” “Gut Fungus and Gut-Brain Axis,” and “Gut Fungus and Immunity” are expected to attract growing interest in the future.ConclusionThis extensive bibliometric analysis offers a current overview of scholarly efforts concerning intestinal fungi, highlighting the predominant landscape in this field. These insights can assist scholars in identifying appropriate publication avenues, forming collaborative relationships, and enhancing understanding of key themes and emerging areas, thereby stimulating future research endeavors.
Circular RNA TAF4B targeting MFN2 accelerates cell growth in bladder cancer through p27 depression and AKT activation
Authors: Zhang Xiaoting , Xu Jia , Zhuang Guangzhen , Wang Yiting , Li Xiaofeng , Zhu Xiaohui 
Published: October 2024

IntroductionBladder cancer (BCa) is a common malignancy in the urinary tract. It has high recurrence rates and often requires microscopic examination, which presents significant challenges in clinical treatment. Previous research has shown that circular TAF4B (circTAF4B) is significantly upregulated in BCa and is associated with a poor prognosis. However, the specific targets and molecular mechanisms by which circTAF4B functions in BCa are still not well - understood.MethodsIn this study, an RNA pull - down assay and mass spectrometry were utilized to identify MFN2 as a binding protein of circTAF4B. Additionally, siRNA was used to silence MFN2 to observe the amplification of the inhibitory effects of circTAF4B overexpression on cell growth and migration in BCa cells. Moreover, circTAF4B shRNA lentiviral particles were employed to study their impact on BCa progression by examining the regulation of p27 and the blocking of AKT signaling.ResultsIt was found that MFN2 is a binding protein of circTAF4B. Silencing MFN2 with siRNA enhanced the inhibitory effects of circTAF4B overexpression on cell growth and migration in BCa cells. Also, circTAF4B shRNA lentiviral particles inhibited BCa progression by upregulating p27 and blocking AKT signaling.DiscussionIn conclusion, the physical binding of circTAF4B to MFN2 is a crucial process in the tumorigenesis and progression of BCa. Targeting circTAF4B or its complexes may have potential as a therapeutic strategy for BCa diagnosis and treatment.
Understanding long COVID: prevalence, characteristics, and risk factors in the Eastern Province of Saudi Arabia
Authors: Aldhawyan Adam F. , BuSaad Mohammed A. , Almaghlouth Nawaf E. , Alnasser Abdullah H. , Alnasser Jomana A. , Almansour Abdulelah H. , AlHarkan Khalid S. 
Published: October 2024

BackgroundThe COVID-19 pandemic has significantly raised public health concerns and efforts to limit its spread, impacting societies and health systems worldwide. As challenges persist, the emergence of Long COVID (LC) marks a turning point in understanding the pandemic’s long-term effects.AimThis study aimed to determine the prevalence of LC in the Eastern Province of the Kingdom of Saudi Arabia (KSA) and explore factors contributing to its persistence.MethodsThis descriptive, cross-sectional, questionnaire-based study was carried out between December 1, 2023, and March 1, 2024, involving 1,355 patients who recovered from COVID-19. Participants were conveniently chosen and information was gathered through in-person interviews in public settings after obtaining consent.ResultsA majority of the patients (N = 1,355; 47.5% female; 93.8% Saudis; mean Age ± SD 33.13 ± 12.60 years) had received three COVID-19 vaccine doses (89.5%). Women experienced 17.4% more LC symptoms than men (p &lt; 0.001). The risk of having a higher symptom count increased by 42.5% 12 months after acute COVID-19 infection compared with baseline (&lt;3 months, p &lt; 0.001). A higher body mass index (BMI) was associated with more symptoms (1.1% increase per unit, p = 0.004). More acute-phase symptoms correlated with more LC symptoms (p &lt; 0.001). Higher educational attainment reduced LC risk by 33% (p &lt; 0.001). Finally, age and vaccination status had no effect on LC symptoms count (p &gt; 0.05).ConclusionSociodemographic and clinical factors contribute differently to the chances of having LC and the count of symptoms. Awareness of such factors could provide insight into improving management, leading to better health outcomes.
The causal relationship between gut microbiota and lower extremity deep vein thrombosis combined with pulmonary embolism
Authors: Xu Qiyang , Fang Jihong , Wang Yi , Lang Dehai , Xu Bin 
Published: October 2024

BackgroundOver the years, numerous studies have explored the relationship between gut microbiota and lower extremity deep vein thrombosis (LEDVT) and pulmonary embolism (PE). The present study utilized Mendelian randomization (MR) to assess the causal link between gut microbiota and LEDVT combined with PE.MethodsHuman gut microbiota genome-wide association study (GWAS) summary data from the MiBioGen consortium (n = 18,340) were utilized. Summary-level data on LEDVT (2,116 cases and 359,078 controls) and LEDVT combined with PE (4,319 cases and 356,875 controls) were obtained from the IEU Open GWAS project. MR analysis was conducted using the inverse variance weighted (IVW) method as the primary analysis. Additionally, MR-Egger, weighted median, weighted mode, and simple mode were employed as supplementary methods. Sensitivity analyses, including tests for heterogeneity and horizontal pleiotropy, were performed. Lastly, reverse MR analysis was performed.ResultsThe IVW analyses revealed seven causal relationships between genetic liability in the gut microbiota and LEDVT and five causal relationships between genetic liability in the gut microbiota and LEDVT combined with PE. The intersection of these outcomes identified that the genus Butyricicoccus reduced the risk of both LEDVT and LEDVT combined with PE, while the genus Clostridium innocuum increased the risk for both conditions.ConclusionThis study demonstrates that the gut microbiota is causally associated with LEDVT and LEDVT combined with PE. Our findings provide valuable insights into the underlying mechanisms and suggest potential avenues for further clinical investigations of these conditions.
Proteomics fingerprinting reveals importance of iron and oxidative stress in Streptomyces scabies–Solanum tuberosum interactions
Authors: Giroux Lauriane , Isayenka Iauhenia , Lerat Sylvain , Beaudoin Nathalie , Beaulieu Carole 
Published: October 2024

IntroductionThe Gram-positive actinobacterium Streptomyces scabies is the major causal agent of potato common scab. The main pathogenicity factor is thaxtomin A, a phytotoxin that causes atypical cell death, although other secondary metabolites have been described to play a role in S. scabies virulence. Despite this, many aspects of the interaction between S. scabies and its primary host Solanum tuberosum L. remain to be elucidated.MethodsIntracellular proteins of S. scabies EF-35 grown in the presence of in vitro produced tubers (microtubers) of the Russet Burbank and Yukon Gold potato cultivars were extracted and analysed by electrospray mass spectrometry (ES MS/MS). Based on the results of proteomic analysis, iron quantification by ICP-MS and nitrite quantification using Griess reagent in growth media as well as RT-qPCR analysis of the siderophore pyochelin gene expression were performed in the presence and absence of microtubers. Hydrogen peroxide accumulation was also determined in the nutrient medium used for co-cultivation of bacteria and potato microtubers.ResultsPotato microtubers caused an increase in the content of bacterial proteins involved in stress and defense, secondary metabolism, and cell differentiation, as well as secreted proteins. Co-cultivation with potato microtubers induced the accumulation of S. scabies proteins implicated in siderophore pyochelin biosynthesis, nitrite production and oxidative stress perception and response. The increase in the abundance of proteins related to pyochelin biosynthesis was consistent with a significant decrease in the iron content in the culture medium, as well as with induction of expression of pyochelin biosynthesis genes. Elevated nitrite/sulfite reductase protein levels were associated with increased nitrite excretion by S. scabies cells in the presence of host microtubers. The increase in the levels of proteins associated with signaling and oxidative stress response could have been caused by the accumulation of ROS, in particular hydrogen peroxide, detected in the studied system.DiscussionThese findings show that interactions of S. scabies with living potato microtubers induce the production of secondary metabolites, defense responses, and protection from oxidative stress. This study suggests the importance of iron during host - S. scabies interactions, resulting in competition between pathogen and its host.
Genetically predicted 486 blood metabolites in relation to risk of esophageal cancer: a Mendelian randomization study
Authors: Jia Caiyan , Yi Dan , Ma Mingze , Xu Qian , Ou Yan , Kong Fanming , Jia Yingjie 
Published: October 2024

Background and ObjectiveEnhancing therapy choices for varying stages of esophageal cancer and improving patient survival depend on timely and precise diagnosis. Blood metabolites may play a role in either causing or preventing esophageal cancer, but further research is needed to determine whether blood metabolites constitute a genetic risk factor for the disease. In order to tackle these problems, we evaluated the causal association between esophageal cancer and 486 blood metabolites that functioned as genetic proxies using a two-sample Mendelian randomization (MR) study.MethodsWe utilized two-sample MR analyses to evaluate the causal links between blood metabolites and esophageal cancer. For the exposure, we used a genome-wide association study (GWAS) of 486 metabolites, and a GWAS study on esophageal cancer from Sakaue et al. was used for preliminary analyses. Causal analyses employed randomized inverse variance weighted (IVW) as the main method, supplemented by MR-Egger and weighted median (WM) analyses. Sensitivity analyses included the MR-Egger intercept test, Cochran Q test, MR-PRESSO, and leave-one-out analysis. Additionally, independent esophageal cancer GWAS data were utilized for replication and meta-analysis. FDR correction was applied to discern features with causal relationships. For conclusive metabolite identification, we conducted Steiger tests, linkage disequilibrium score regression, and colocalization analyses. Moreover, we utilized the program MetaboAnalyst 5.0 to analyze metabolic pathways.ResultsThis study found an important association between esophageal cancer and three metabolites: 1-linoleoylglycerophosphoethanolamine* [odds ratio (OR) = 3.21, 95% confidence interval (CI): 1.42–7.26, p &lt; 0.01], pyroglutamine* (OR = 1.92, 95% CI: 1.17–3.17, p &lt; 0.01), and laurate (12:0) (OR = 3.06, 95% CI: 1.38–6.78, p &lt; 0.01).ConclusionThis study establishes a causal link between three defined blood metabolites and esophageal cancer, offering fresh insights into its pathogenesis.