bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of an Experiential Learning Curriculum on Systems-Thinking
Authors: Kovaric Kelly , Gingell Gareth 
Published: June 2024

Introduction Though health systems science (HSS) is referred to as the third pillar of medical education along with the pillars of basic science and clinical care, the effects of learning theories used to teach components of HSS including quality improvement/ patient safety (QI/PS), are poorly understood. Experiential learning theory is often referenced in QI/ PS education but its effects on QI/PS education are not well-described. Objective To examine the effects of teaching QI using experiential learning theory on resident systems-thinking. Methods Data was gathered from 30 resident participants in a 3-h QI workshop designed using experiential learning theory. Using a mixed-methods design, aspects of learner systems-thinking were analyzed both before and after the workshop. Learners were asked about their confidence in systems-thinking behaviors, and their QI plans were evaluated qualitatively for themes as well as quantitatively via the QIKAT-R. Results There was a significant increase in self-reported confidence in systems-thinking behaviors post-workshop. Odds ratio of the QI aim statement focusing on the systems-level of the problem after the workshop was 41.4 with a 95% CI of 8.9142 to 192.2721, p-value .0001. Thematic analysis of QI plans revealed a change in residents’ thinking about healthcare problems. They shifted from attributing problems to individual actors to thinking about the problem as lying in the interaction between systems. Conclusion Experiential learning theory can be an effective framework for QI to transform learners into systems-thinkers.
Computed tomography perfusion as an early predictor of malignant cerebral infarction
Authors: Rodríguez-Vázquez Alejandro , Laredo Carlos , Reyes Luis , Dolz Guillem , Doncel-Moriano Antonio , Llansó Laura , Rudilosso Salvatore , Llull Laura , Renú Arturo , Amaro Sergio , Torné Ramón , Urra Xabier , Chamorro Ángel 
Published: June 2024

Introduction: Malignant middle cerebral artery infarction (MCI) needs rapid intervention. This study aimed to enhance the prediction of MCI using computed tomography perfusion (CTP) with varied quantitative benchmarks. Materials and Methods: We retrospectively analyzed 253 patients from a single-center registry presenting with acute, severe, proximal large vessel occlusion studied with whole-brain CTP imaging at hospital arrival within the first 24 h of symptoms-onset. MCI was defined by clinical and imaging criteria, including decreased level of consciousness, anisocoria, death due to cerebral edema, or need for decompressive craniectomy, together with midline shift ⩾6 mm, or infarction of more than 50% of the MCA territory. The predictive accuracy of baseline ASPECTS and CTP quantifications for MCI was assessed by receiver operating characteristic (ROC) area under the curve (AUC) while F-score was calculated as an indicator of precision and sensitivity. Results: Sixty-three out of 253 patients (25%) fulfilled MCI criteria and had worse clinical and imaging results than the non-MCI group. The capacity to predict MCI was lower for baseline ASPECTS (AUC 0.83, F-score 0.52, Youden’s index 6), than with perfusion-based measures: relative cerebral blood volume threshold <40% (AUC 0.87, F-score 0.71, Youden’s index 34 mL) or relative cerebral blood flow threshold <35% (AUC 0.87, F-score 0.62, Youden’s index 67 mL). CTP based on rCBV measurements identified twice as many MCI as baseline CT ASPECTS. Discussion and conclusion: CTP-based quantifications may offer enhanced predictive capabilities for MCI compared to non-contrast baseline CT ASPECTS, potentially improving the monitoring of severe ischemic stroke patients at risk of life-threatening edema and its treatment.
A deep learning framework for predicting disease-gene associations with functional modules and graph augmentation
Authors: Jia Xianghu , Luo Weiwen , Li Jiaqi , Xing Jieqi , Sun Hongjie , Wu Shunyao , Su Xiaoquan 
Published: June 2024

Abstract
Background
The exploration of gene-disease associations is crucial for understanding the mechanisms underlying disease onset and progression, with significant implications for prevention and treatment strategies. Advances in high-throughput biotechnology have generated a wealth of data linking diseases to specific genes. While graph representation learning has recently introduced groundbreaking approaches for predicting novel associations, existing studies always overlooked the cumulative impact of functional modules such as protein complexes and the incompletion of some important data such as protein interactions, which limits the detection performance.

Results
Addressing these limitations, here we introduce a deep learning framework called ModulePred for predicting disease-gene associations. ModulePred performs graph augmentation on the protein interaction network using L3 link prediction algorithms. It builds a heterogeneous module network by integrating disease-gene associations, protein complexes and augmented protein interactions, and develops a novel graph embedding for the heterogeneous module network. Subsequently, a graph neural network is constructed to learn node representations by collectively aggregating information from topological structure, and gene prioritization is carried out by the disease and gene embeddings obtained from the graph neural network. Experimental results underscore the superiority of ModulePred, showcasing the effectiveness of incorporating functional modules and graph augmentation in predicting disease-gene associations. This research introduces innovative ideas and directions, enhancing the understanding and prediction of gene-disease relationships.
Genome-wide identification and evolution of the tubulin gene family in Camelina sativa
Authors: Blume Rostyslav Y. , Rabokon Anastasiia M. , Pydiura Mykola , Yemets Alla I. , Pirko Yaroslav V. , Blume Yaroslav B. 
Published: June 2024

Abstract
Background
Tubulins play crucial roles in numerous fundamental processes of plant development. In flowering plants, tubulins are grouped into α-, β- and γ-subfamilies, while α- and β-tubulins possess a large isotype diversity and gene number variations among different species. This circumstance leads to insufficient recognition of orthologous isotypes and significantly complicates extrapolation of obtained experimental results, and brings difficulties for the identification of particular tubulin isotype function. The aim of this research is to identify and characterize tubulins of an emerging biofuel crop Camelina sativa.

Results
We report comprehensive identification and characterization of tubulin gene family in C. sativa, including analyses of exon-intron organization, duplicated genes comparison, proper isotype designation, phylogenetic analysis, and expression patterns in different tissues. 17 α-, 34 β- and 6 γ-tubulin genes were identified and assigned to a particular isotype. Recognition of orthologous tubulin isotypes was cross-referred, involving data of phylogeny, synteny analyses and genes allocation on reconstructed genomic blocks of Ancestral Crucifer Karyotype. An investigation of expression patterns of tubulin homeologs revealed the predominant role of N6 (A) and N7 (B) subgenomes in tubulin expression at various developmental stages, contrarily to general the dominance of transcripts of H7 (C) subgenome.

Conclusions
For the first time a complete set of tubulin gene family members was identified and characterized for allohexaploid C. sativa species. The study demonstrates the comprehensive approach of precise inferring gene orthology. The applied technique allowed not only identifying C. sativa tubulin orthologs in model Arabidopsis species and tracking tubulin gene evolution, but also uncovered that A. thaliana is missing orthologs for several particular isotypes of α- and β-tubulins.
Mycobiota contaminating some market cake samples with reference to their toxin and enzyme
Authors: Abdelhameed Shimaa M. , Khalifa Basma A. 
Published: June 2024

AbstractFungi can spoil the majority of baked products. Spoilage of cake during storage is commonly associated with fungi. Therefore, this study aimed to assess the quality of different types of cakes sold in the market. The most predominant fungal genera in the tested cake samples (14 samples) were Aspergillus spp., and Penicillium spp. On Potato Dextrose Agar (PDA), the medium fungal total count was 43.3 colonies /g. Aspergillus was the most dominant genus and was isolated from six samples of cake. Aspergillus was represented by 3 species namely, A. flavus, A. niger, and A. nidulans, represented by 13.32, 19.99, and 3.33 colonies /g respectively. On Malt Extract Agar (MEA) Medium, the fungal total count was 123.24 colonies / g. Aspergillus was the most dominant isolated genus from 11 samples of cake and was represented by 5 species, namely, A. flavus, A. niger, A. ochraceous, A. terreus, and A. versicolor (26. 65, 63.29, 3.33, 6.66, and 3.33 colonies / g , respectively). Twenty-four isolates (88.88 %) of the total tested twenty-seven filamentous fungi showed positive results for amylase production. Ten isolates (37.03%) of the total tested filamentous fungi showed positive results for lipase production, and finally eleven isolates (40.74 %) of the total fungal isolates showed positive results for protease production. Aflatoxins B1, B2, G1, G2, and ochratoxin A were not detected in fourteen collected samples of cake. In this study, clove oil was the best choice overpeppermint oil and olive oil for preventing mold development when natural agents were compared. It might be due to the presence of a varietyof bioactive chemical compounds in clove oil, whose major bioactive component is eugenol, which acts as an antifungal reagent. Therefore, freshly baked cake should be consumed within afew days to avoid individuals experiencing foodborne illnesses.
Prognostic value of red blood cell distribution width to albumin ratio for predicting mortality in adult patients meeting sepsis-3 criteria in intensive care units
Authors: Shan Xiaoxi , Li Zhishu , Jiang Jing , Li Wei , Zhan Jingyan , Dong Lixia 
Published: June 2024

Abstract
Background
Patients with sepsis with low albumin levels and high red blood cell distribution width levels have poor prognoses. Red blood cell distribution width to albumin ratio (RAR) has recently attracted attention as an innovative inflammation biomarker. We aimed to explore the association between RAR and the prognosis of patients with sepsis.

Methods
This retrospective observational study included 402 patients meeting the sepsis-3 standards admitted to Yantai Yuhuangding Hospital’s intensive care units (ICUs) between January 2020 and December 2022. The relationship between RAR and mortality in patients with sepsis was examined using regression analysis, Kaplan–Meier analyses, and a receiver operating characteristic curve. Subgroup and sensitivity analyses were conducted to assess the results’ robustness.

Results
RAR, when considered as a continuous variable, was a significant independent in-hospital mortality risk factor (adjusted odds ratio [OR]: 1.383; 95% confidence interval [CI]: 1.164–1.645; P < 0.001). When considering RAR as a categorical variable, the ORs (95% CIs) of hospital mortality for quartile 2 (Q2), Q3, and Q4 compared with Q1 were 1.027 (0.413–2.551), 3.632 (1.579–8.354), and 4.175 (1.625–10.729), respectively, P < 0.001. Similar outcomes were observed for 28- and 90-day mortalities.

Conclusions
RAR may indicate clinical prognosis for patients with sepsis in the ICU, potentially providing a low-cost, easily repeatable, and accessible biomarker for risk categorization for these patients.
CSPG4P12 polymorphism served as a susceptibility marker for esophageal cancer in Chinese population
Authors: Xu Hongxue , Yang Zhenbang , Hu Wenqian , Zhou Xianlei , Zhang Zhi , Zhang Xuemei 
Published: June 2024

Abstract
Background
Chondroitin sulfate proteoglycan 4 pseudogene 12 (CSPG4P12) has been implicated in the pathogenesis of various cancers. This study aimed to evaluate the association of the CSPG4P12 polymorphism with esophageal squamous cell carcinoma (ESCA) risk and to explore the biological impact of CSPG4P12 expression on ESCA cell behavior.

Methods
A case-control study was conducted involving 480 ESCA patients and 480 healthy controls to assess the association between the rs8040855 polymorphism and ESCA risk. The CSPG4P12 rs8040855 genotype was identified using the TaqMan-MGB probe method. Logistic regression model was used to evaluate the association of CSPG4P12 SNP with the risk of ESCA by calculating the odds ratios (OR) and 95% confidence intervals (95%CI ). The effects of CSPG4P12 overexpression on cell proliferation, migration, and invasion were examined in ESCA cell lines. Co-expressed genes were identified via the CBioportal database, with pathway enrichment analyzed using SangerBox. The binding score of CSPG4P12 to P53 was calculated using RNA protein interaction prediction (RPISeq). Additionally, Western Blot analysis was performed to investigate the impact of CSPG4P12 overexpression on the P53/PI3K/AKT signaling pathway.

Results
The presence of at least one rs8040855 G allele was associated with a reduced susceptibility to ESCA compared to the CC genotype (OR = 0.51, 95%CI = 0.28–0.93, P = 0.03). Stratification analysis revealed that the CSPG4P12 rs8040855 C allele significantly decreased the risk of ESCA among younger individuals (≤ 57 years) and non-drinkers (OR = 0.31, 95%CI = 0.12–0.77, P = 0.01; OR = 0.42, 95%CI=0.20–0.87, P = 0.02, respectively). CSPG4P12 expression was found to be downregulated in ESCA tissues compared to adjacent normal tissues. Overexpression of CSPG4P12 in ESCA cells inhibited their proliferation, migration, and invasion capabilities. Furthermore, Western Blot analysis indicated that CSPG4P12 overexpression led to a reduction in PI3K and p-AKT protein expression levels. P53 silencing rescues the inhibitory effect of CSPG4P12 on p-AKT.

Conclusion
The CSPG4P12 rs8040855 variant is associated with reduced ESCA risk and the overexpression of CSPG4P12 inhibited the migration and invasion of ESCA cells by P53/PI3K/AKT pathway. These findings suggest that CSPG4P12 may serve as a novel biomarker for ESCA susceptibility and a potential target for therapeutic intervention.
Basement membrane-associated gene expression as a predictor of survival in oral cancer
Authors: Wang Xu , Liu Chaoge , Wu HuiFang , Gu Yulu , Zhang Le , Xu Rongqing , Lin Qing 
Published: June 2024

Abstract
Background
This study sought to investigate the prognostic value of basement membrane (BM)-associated gene expressions in oral cancer.

Methods
We harvested and integrated data on BM-associated genes (BMGs), the oral cancer transcriptome, and clinical information from public repositories. After identifying differentially expressed BMGs, we used Cox and Lasso regression analyses to create a BMG-based risk score for overall survival at various intervals. We then validated this score using the GSE42743 cohort as a validation set. The prognostic potential of the risk scores and their relations to clinical features were assessed. Further, we conducted functional pathway enrichment, immune cell infiltration, and immune checkpoint analyses to elucidate the immunological implications and therapeutic potential of the BMG-based risk score and constituent genes. To confirm the expression levels of the BMG LAMA3 in clinical samples of oral cancer tissue, we performed quantitative real-time PCR (qRT-PCR) and immunohistochemical staining.

Results
The BMGs LAMA3, MMP14, and GPC2 demonstrated notable prognostic significance, facilitating the construction of a BMG-based risk score. A higher risk score derived from BMGs correlated with a poorer survival prognosis for oral cancer patients. Moreover, the risk-associated BMGs exhibited a significant relationship with immune function variability (P < 0.05), discrepancies in infiltrating immune cell fractions, and immune checkpoint expressions (P < 0.05). The upregulated expression levels of LAMA3 in oral cancer tissues were substantiated through qRT-PCR and immunohistochemical staining.

Conclusion
The BMG-based risk score emerged as a reliable prognostic tool for oral cancer, meriting further research for validation and potential clinical application.
Effect of duloxetine on changes in serum proinflammatory cytokine levels in patients with major depressive disorder
Authors: Gao Wenfan , Gao Yejun , Xu Yayun , Liang Jun , Sun Yanhong , Zhang Yuanyuan , Shan Feng , Ge Jinfang , Xia Qingrong 
Published: June 2024

Abstract
Objective
Accumulating evidence supports the idea that inflammation may contribute to the pathophysiology of major depressive disorder (MDD). Duloxetine, a serotonin-norepinephrine reuptake inhibitor, exhibits anti-inflammatory effects both in vitro and in vivo. In this study, we investigated the impact of duloxetine on changes in serum proinflammatory cytokine levels among individuals diagnosed with MDD.

Methods
A cohort of 23 drug-naïve individuals diagnosed with MDD and 23 healthy controls were included in this study. The severity of depressive symptoms was evaluated using the 24-item Hamilton Depression Scale (HAMD-24). A panel of 7 proinflammatory cytokines, including interleukin-1β (IL-1β), IL-2, IL-6, IL-8, IL-12, tumor necrosis factor-α (TNF-α), and interferon-γ (IFN-γ), were quantified using multiplex Luminex assays. The levels of serum cytokines in healthy controls and patients with MDD were compared at baseline. All patients received duloxetine at a dosage range of 40–60 mg/day for a duration of 4 weeks. The HAMD-24 scores and serum cytokine levels were compared before and after duloxetine treatment.

Results
Compared with healthy controls, patients with MDD had significantly greater levels of IL-2, IL-6, IL-8, IL-12, TNF-α, and IFN-γ (P < 0.05). Moreover, there was a significant decrease in HAMD-24 scores observed pre- and post-treatment (t = 13.161, P < 0.001). Furthermore, after 4 weeks of treatment, the serum levels of IL-8 (t = 3.605, P = 0.002), IL-12 (t = 2.559, P = 0.018), and IFN-γ (t = 3.567, P = 0.002) decreased significantly. However, there were no significant differences in other cytokines, including IL-1β, IL-2, IL-6, and TNF-α, before and after treatment (P > 0.05).

Conclusions
These findings present compelling evidence, potentially for the first time, indicating that duloxetine treatment may effectively reduce the serum concentrations of IL-8, IL-12, and IFN-γ in individuals diagnosed with MDD. However, the precise mechanisms underlying this effect remain unclear and warrant further investigation.
Co-occurrence of obesogenic behaviors and their implications for mental health during the COVID-19 pandemic: a study with university students
Authors: Barbosa Bruna Carolina Rafael , de Deus Mendonça Raquel , Machado Elaine Leandro , Meireles Adriana Lúcia 
Published: June 2024

Abstract
Background
The university years are a critical period for young adults, as they are more exposed to obesogenic behaviors and experience stressful situations that compromise their mental health. This study aims to estimate the prevalence of anxiety and depression symptoms and evaluate the association between the combined occurrence of obesogenic behaviors among university students.

Methods
A cross-sectional study was conducted on students from a public university in Brazil during the COVID-19 pandemic. Data were collected from July to August 2020 using an online questionnaire. The outcome variables (anxiety and depression symptoms) were assessed using the Depression, Anxiety and Stress Scale-21 (DASS-21). The co-occurrence of obesogenic behaviors was measured based on irregular consumption of fruits and vegetables, frequent consumption of ultra-processed foods, physical inactivity during leisure time, and sedentary behavior. A Venn diagram was used for the exploratory analysis. To verify the association between the outcome and explanatory variables, a directed acyclic graph model was constructed, and multivariate logistic regression was performed to calculate odds ratios (ORs) and 95% confidence intervals (95%CIs).

Results
A total of 1,353 students aged 18–24 years participated in this study. Symptoms of anxiety and depression were present in 46.1% and 54.6% of the participants, respectively. The most prevalent combination of obesogenic behaviors was frequent consumption of ultra-processed foods, physical inactivity during leisure time, and sedentary behavior (17.2%). The greater the number of simultaneous obesogenic behaviors, the higher the chance to present symptoms of anxiety [OR: 2.81 (95%CI: 1.77–4.46)] and depression [OR: 3.46 (95%CI: 2.20–5.43)].

Conclusion
These findings reinforce the need to take actions to promote mental health in the university environment in conjunction with programs to promote a healthy lifestyle and improve the physical and mental well-being of students.
Benefits of uric acid-lowering medication after bariatric surgery in patients with gout
Authors: Song Ke , He Ming , Kong Xiangxin , Xian Yin , Zhang Yuan , Xie Xing , Xie Sijun , Jia Aimei , Ren Yixing 
Published: June 2024

Abstract
Background/Purpose
Patients with gout are at risk for increased serum uric acid (SUA) levels and gout attacks in the short term after undergoing bariatric surgery, and the purpose of this study was to evaluate the benefits of short-term treatment with uric acid-lowering medication after bariatric surgery for the control of gout attacks and SUA levels in patients with gout.

Methods
71 patients who underwent SG from January 2020 to December 2022 were prospectively included. These patients were diagnosed with hyperuricemia before surgery and had a history of gout attacks. Patients were classified into a drug-treatment group (DTG, n = 32) and a non-drug-treatment group (NDTG, n = 39) according to whether they took uric acid-lowering medication after surgery. Changes in the number of gout attacks, body mass index (BMI), and SUA levels at 1 week, 1 month, 3 months, and 6 months after bariatric surgery were measured in both groups.

Results
In the DTG, 22 patients (68.8%) experienced an increase in SUA within 1 week, 3 patients (9.4%) had an acute attack of gout within the first month, and no patients had a gout attack thereafter. In the NDTG, 35 patients (89.7%) experienced an increase in SUA within 1 week, 7 patients (17.9%) had an acute gout attack within the first month, and 4 patients (10.3%) experienced gout attacks between month 1 and month 3 postoperatively. Both groups were free of gout attacks between the 3rd and 6th postoperative month and showed a significant decrease in SUA and BMI by the sixth month.

Conclusion
In patients with gout, continued use of uric acid-lowering medication after bariatric surgery is beneficial in reducing the number of gout attacks and the risk of rising SUA.