bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncovering Endothelial to mesenchymal transition drivers in atherosclerosis via multi-omics analysis
Authors: Huang Qingyan , Gan Yuhong , Zheng Xiaoqi , Yu Zhikang , Huang Qionghui , Huang Mingfeng 
Published: November 2024

Abstract

Purpose:This study aimed to identify novel candidates that regulate Endothelial to mesenchymal transition（EndMT）in atherosclerosis by integrating multi-omics data.
Methods: The single-cell RNA sequencing (scRNA-seq) dataset GSE159766, bulk RNA-seq dataset GSE118446 and microarray dataset GSE56309 were obtained from the Gene Expression Omnibus (GEO) database. The uniform manifold approximation and projection (UMAP) were used for downscaling and cluster identification. Differentially expressed genes (DEGs) from GSE118446 and GSE56309 were analyzed using limma package. Functional enrichment analysis was applied by DAVID functional annotation tool. Quantitative real-time polymerase chain reaction (qPCR) and western blotting were used for further validation.
Results: Nine endothelial cell (EC) clusters were identified in human plaques, with EC cluster 5 exhibiting an EndMT phenotype. The intersection of genes from EC cluster 5 and common DEGs in vitro EndMT models revealed seven mesenchymal candidates: PTGS2, TPM1, SERPINE1, FN1, RASD1, SEMA3C, and ESM1. Validation of these findings was carried out through qPCR analysis.
Conclusion: Through the integration of multi-omics data using bioinformatics methods, our study identified seven novel EndMT candidates: PTGS2, TPM1, SERPINE1, FN1, RASD1, SEMA3C, and ESM1.
Transcriptional activation and coactivator binding by yeast Ino2 and its human ortholog proto-oncoprotein c-Myc
Authors: Wendegatz Eva-Carina , Lettow Julia , Wierzbicka Wiktoria , Schüller Hans-Joachim 
Published: November 2024

Abstract

Basic helix-loop-helix domains in yeast regulatory proteins Ino2 and Ino4 mediate formation of a heterodimer which binds to and activates expression of phospholipid biosynthetic genes. The human proto-oncoprotein c-Myc (Myc) and its binding partner Max activate genes important for cellular proliferation and contain functional domains structure and position of which strongly resembles Ino2 and Ino4. Since Ino2 – Myc and Ino4 – Max may be considered as orthologs we performed functional comparisons in yeast. We demonstrate that Myc and Max could be stably synthesized in S. cerevisiae and together significantly activated a target gene of Ino2/Ino4 but nevertheless were unable to functionally complement an ino2 ino4 double mutant. We also map two efficient transcriptional activation domains in the N-terminus of Myc (TAD1: aa 1–41 and TAD2: aa 91–140), corresponding to TAD positions in Ino2. We finally show that coactivators such as TFIID subunits Taf1, Taf4, Taf6, Taf10 and Taf12 as well as ATPase subunits of chromatin remodelling complexes Swi2, Sth1 and Ino80 previously shown to interact with TADs of Ino2 were also able to bind TADs of Myc, supporting the view that heterodimers Ino2/Ino4 and Myc/Max are evolutionary related but have undergone transcriptional rewiring of target genes.
Patient and staff acceptability of remote mentoring of new endoscopists undertaking conscious colonoscopy – a UK prospective, feasibility study using surveys and clinical outcomes
Authors: Dostert Klara , Vogel Irene , Smith Laurie , Ansell James , Horwood James , Hawkes Neil , Davies Lynne , White Judith , Withers Kathleen , Cornish Julie , Torkington Jared 
Published: November 2024

Abstract

Background
Training future endoscopists is challenging due to limited resources in UK endoscopy services. Telementoring, facilitated by platforms like Proximie®, offers a potential solution by enabling remote guidance and training. This study aims to investigate the feasibility and acceptability of using the Proximie® system for telementoring in colonoscopy for both patients and staff.
Methods
A single-centre, prospective feasibility study was conducted with 28 patients undergoing colonoscopy over 10 training lists. Six trainees and six mentors (4 remote, 6 on-site) participated. Clinical outcomes were assessed using key performance indicators, and questionnaires were used to evaluate patient and staff experiences.
Results
Caecal intubation was achieved in 68.4% of cases by trainees, increasing to 95% with on-site mentor intervention. Splenic flexure intubation was successful in 87.5% of cases, reaching 100% with assistance. No complications occurred during any procedures, and no patients required repeat colonoscopy at three months. Patient satisfaction was high, with 91.3% finding it reassuring to have remote support, and all patients willing to have telementoring in future procedures. Staff feedback was generally positive. Most trainees (80%) found remote supervision acceptable as an alternative to on-site mentoring, with 60% rating it excellent and 40% as good. The majority (90%) expressed interest in using telementoring in the future. On-site mentors (60%) and remote mentors (83.3%) also found telementoring acceptable and expressed strong interest in its future use.
Conclusion
Telementoring using Proximie® was well-received by both staff and patients, with minimal technical issues and no negative impact on clinical outcomes. The system was reassuring for patients, and telementoring shows potential as a safe, additional training tool in colonoscopy. Further research is needed to compare its educational benefits with traditional methods.
Designing and implementing the flipped Classroom Model for teaching first aids course and evaluating it with the Kirkpatrick model
Authors: Ahmady Soleiman , Kohan Noushin , Zazoly Atefeh Zabihi , Gorji Ali Morad Heidari 
Published: November 2024

Abstract

Background
The use of interactive teaching patterns and appropriate educational design approaches is an essential requirement emphasized in medical education, especially for courses such as first aids. Therefore, the purpose of this study was to design, implement, and evaluate the presentation of a first aid course using the flipped Classroom Model.
Methods
This scholarly study was conducted for the first aids course in the field of occupational health and safety engineering at Mazandaran University of Medical Sciences, Sari, Iran. For course design, the instructional design model proposed in the study by Elmagzoub and Eltahir (2017) was used, which was a combination of the flipped classroom model and the ADDIE instructional design model stages. Therefore, the study included 5 stages: "planning and needs assessment, programming, coaching, assessing and evaluating, and revising". The first two steps of the Kirkpatrick model were used to evaluate course.
Results
The results showed that the average student satisfaction score (51.60 ± 3.09) was at a satisfactory level. The results of the independent t-test showed that there was no significant difference in satisfaction scores based on gender, marital status, and age (P > 0.05). Also, the average score of the students in the post-test was 17.75 ± 1.56. Comparing the students' scores in the pre-test and post-test using the paired t-test showed that the average score of the students in the post-test was higher than the pre-test, and the difference between the students' scores was statistically significant (P < 0.05).
Conclusion
Based on the results of the evaluation and the needs assessment data, it can be inferred that having an educational design appropriate for each generation, using interactive teaching approaches, and involving learners in their own learning is both a demand of students and leads to desirable outcomes. Therefore, it is a positive step in improving the quality of education and it is recommended to be included in the educational planning of practical courses as well.
Myocardial infarction creates a critical time window for AAV-based cardiac gene transfer
Authors: Guo Yuxuan , Chen Gonglie , Zhang Yueyang , Liu Zhanzhao , Chen Zhan , Yang Luzi , Gao Fei , Dong Erdan 
Published: November 2024

Abstract

Developing approaches to enhance adeno-associated virus (AAV)-based cardiac gene transfer is the key to successful cardiac gene therapy, but factors influencing AAV transduction remains poorly investigated. This study showed that myocardial infarction (MI) enhanced AAV transduction peaking at the third day post MI in mice. This excessive AAV enriched at the border zone potentially due to local vascular permeabilization and metabolic remodeling. This effect could be harnessed to boost cardiac base editing and improve the outcome of gene therapy for MI. Thus, heart disease itself is a non-negligible factor that alters AAV behavior and influence cardiac gene therapy.
Serial chemical crystallography for autonomous quantitative phase analysis in an electron microscope
Authors: Yang Taimin , Waterman David , Chu Zheting , Beilsten-Edmands James , Huang Zhehao , Zou Xiaodong 
Published: November 2024

Abstract

Recent advancements in robotics and artificial intelligence have accelerated the development of autonomous workflows for material discovery. Powder X-ray diffraction (PXRD) remains the primary method for characterizing crystal structures in these workflows. However, its limitations become apparent when peak overlapping becomes severe. To address this, we present serial electron diffraction with tilt (t-SerialED), a method for fast autonomous phase and structural analysis of beam-sensitive, nano-sized polycrystalline materials. t-SerialED incorporates 3D reciprocal space information into SerialED, ensuring reliable quantitative phase analysis for complex mixtures that are difficult to analyze by traditional techniques. Conducted in a standard electron microscope without specialized hardware, t-SerialED enables high-throughput analysis of beam-sensitive, multi-phase mixtures across a wide range of materials, from nanoporous frameworks to pharmaceutical compounds. By resolving key challenges in serial crystallography such as indexing and preferred orientation, this method enables precise structure determination, including the visualization of disordered guest molecules and non-covalent interactions like hydrogen bonding network and proton charge transfer. t-SerialED expands the capabilities of serial chemical crystallography and it can become a complementary method to traditional crystallography methods, offering a robust solution for routine quantitative phase analysis and structure determination.
Identification of Novel Drug Target Genes in Inflammatory Bowel Disease through Mendelian Randomization Study and Single-Cell Analysis
Authors: He Xidong , Bai Xiaoyin , Wang Beiming , Yu Ziqing , Cao Yubin , Yang Hong 
Published: November 2024

Abstract

Background and Objectives: Despite the availability of numerous drugs for treating Inflammatory Bowel Disease (IBD), managing the condition remains challenging. Mendelian randomization (MR) research, a widely utilized methodology in various diseases, has proven effective in identifying new therapeutic drug targets. The primary objective of our study is to uncover novel drug target genes for IBD through the application of MR. Methods: IBD-associated genes were systematically screened using the Gene Expression Omnibus (GEO) database. We performed Gene Ontology (GO) and Kyoto Encyclopedia of Gene Genomes (KEGG) pathway enrichment analysis on the differentially expressed genes. Subsequently, MR was employed to assess the causal impact of expression Quantitative Trait Loci (eQTL) on IBD. Colocalization analysis was then conducted to identify key genes with druggable potential in the context of IBD. Single-cell analysis was subsequently performed on the identified druggable target genes. Results: Our study identified 600 differential genes through screening the GEO database. GO and KEGG pathway enrichment analysis showed that differentially expressed genes were mainly enriched in inflammatory response pathways. MR analysis further pinpointed the causal relationship between eQTLs corresponding to seven genes and IBD outcomes. Colocalization analysis identified four key genes (EPB41L3, IL1R2, PVALB, SLC22A4) sharing the same causal variant with IBD. Single-cell analysis of these genes showed predominant expression in cell types related to inflammation. Conclusion: Our investigation furnishes genetic evidence supporting the potential therapeutic benefits of four druggable genes (EPB41L3, IL1R2, PVALB, SLC22A4) in the treatment of IBD. These findings contribute to advancing research on IBD drug development.
Unlocking the Potential of Basalt Quarry Dust for Sustainable Removal of Toxic Malachite Green Dye: Characterization, Adsorption Behaviour and Optimization Analysis Using Soft Computing-Based Modeling
Authors: Chaware Chirag Yogender , Nayak Ashish Kumar , Khobragade Moni Udhaorao 
Published: November 2024

Abstract

Amidst the increasing problems of water scarcity and textile pollution, the wastewater treatment industry is in dire need of affordable adsorbents. The textile industry needs to find cost-effective ways to mitigate its environmental impact, as it is a major cause of water pollution. Since water stress is increasing globally, affordable adsorbents are crucial for providing sustainable and approachable solutions to pollution problems, guaranteeing efficient water treatment, and encouraging environmental preservation in the face of growing concerns. The purpose of this study is to determine how well waste basalt quarry dust (BQD) works as an adsorbent to remove malachite green (MG) dye, a cationic dye that is a major source of dye pollution. The characterization of BQD reveals a zeta potential of -23.3 mV, which is a promising indication of MG adsorption. According to BET analysis, the surface area of BQD is 8.731 m2/g, the pore volume is 0.015 cc/g, and the pore width is 3.794 nm. Various kinetic and equilibrium models are used to investigate the adsorption process. The adsorption kinetics show a well-fitted pseudo-first-order non-linear model with an adjusted R2 value of 0.99415. This shows how effective and reliable the BQD is an adsorbent. The Sips isotherm is an excellent fit with an adjusted R2 value of 0.9827, demonstrating the robustness of the adsorption process. Thermodynamic studies emphasize the spontaneity and exothermic nature of the adsorption process. In addition to these, the response surface methodology is used for optimising the removal efficiency, and the quadratic model of the central composite design is well-fitted to the adsorption process, exhibiting a predicted R2 value of 0.9917, which is greater than that of the artificial neural network model (R2 = 0.9698). Desorption studies also demonstrate the remarkable resilience of the adsorbent, maintaining 85% of its effectiveness after five cycles using 0.5 M HCl as an eluent. This study highlights the potential for long-term sustainable reuse of BQD, supporting the circular economy by advancing the development of affordable adsorption processes that are environmentally friendly, and utilizing byproducts from one industry as resources to treat waste from another.
Influence of temperature and nutrients on the inhibitory effects of the submerged macrophyte Egeria densa on the growth and saxitoxin production of the cyanobacterium Raphidiopsis raciborskii
Authors: Cabral Jefferson Vitor Melo , Severiano Juliana dos Santos , Santos-Silva Ranielle Daiana dos , Nery Aline Maria Bezerra , Araújo-Silva Mateus Santos , Otogo Regina Anya , Chia Mathias Ahii , Barbosa José Etham Lucena 
Published: November 2024

Abstract

The role of nutrients and temperature in competition-driven allelopathic interactions between macrophytes and cyanobacteria is overlooked in assessing the potential of macrophytes to control harmful cyanobacterial blooms. This study aimed to evaluate the inhibitory effects of the submerged macrophyte Egeria densa— in its physical presence and through its extracts—on the growth and saxitoxin (SXT) production of the cyanobacterium Raphidiopsis raciborskii under varying temperatures (24°C, 28°C, and 32°C) and enriched levels of phosphorus and nitrogen. The results demonstrated that the inhibitory effects of E. densa on R. raciborskii were influenced by the type of macrophyte exposure, temperature, and nutrient concentration. The physical presence of E. densa generally exerted a significant suppressive effect on the cyanobacterium than its extracts; however, increasing temperatures and nutrient levels favored cyanobacterial growth, reducing the macrophyte's inhibitory power, especially at 28°C. Notably, the inhibitory effect of the extracts was more pronounced at 32°C, regardless of nutrient concentration. Saxitoxin concentrations were generally positively correlated with R. raciborskii biomass but decreased when the cyanobacterium was exposed to the macrophyte. During exposure to the physical presence of E. densa at 24°C and to its extracts at 32°C, toxin levels were negatively related to biomass, suggesting a possible physiological response to stress induced by the macrophyte or toxin release due to cell death and lysis. These findings indicate that temperature and nutrients complicate allelopathic interactions between macrophytes and cyanobacteria, and that E. densa extracts hold promise for controlling toxic blooms of R. raciborskii in a warmer and more eutrophic future.
Synergistic Effects of Urban Mitigation and Adaptation Pilot Policies in China: An Analysis Based on Low-Carbon Resilience
Authors: WANG DI , Chen Shiwei 
Published: November 2024

Abstract

Low-carbon cities and climate resilient cities represent urban development models in China aimed at achieving urban mitigation and adaptation objectives. This study focuses on the dual pilot policy of low-carbon cities and climate resilient cities, establishing a comprehensive evaluation index system for urban low-carbon resilience that encompasses ecological, economic, social, and institutional dimensions. Utilizing panel data from 286 prefecture-level cities and above in China from 2005 to 2021, this study employs Difference-in-Differences, K-means clustering, Double Machine Learning, and a tri-dimensional policy analysis framework of "policy instruments—policy pathways—policy objectives." It provides an in-depth assessment of the dual pilot policy's impact through policy synergy effects, policy tool analysis, and key case studies, supplemented by heterogeneity analysis, mechanism analysis, and cluster analysis. Results indicate that the dual pilot policy significantly enhances the low-carbon resilience of pilot cities, outperforming the effects seen in cities with a singular pilot policy. The policy effects vary among different types of pilot cities, with notably significant impacts in cities facing high temperatures, low temperatures, heavy rainfall, and high disaster risks. Cities characterized by higher levels of low-carbon resilience (categorized as MMHM) manifest more consistent policy synergy effects, whereas cities with lower levels of resilience (classified as LLLL) exhibit some disparities. The study also identifies the strengthening of green technology innovation, human capital development, and communication infrastructure construction as key factors enhancing policy effectiveness. Ultimately, this research underscores the importance of the diversity and combination of policy tools, as well as the multidimensionality and synergy of policy objectives, for effective climate action. It recommends that urban managers consider the synergistic effects of climate change mitigation and adaptation measures when formulating climate policies.
Disease Burden of Non-COVID-19 Lower Respiratory Infections, Risk Factors, and Aetiologies in China 1990-2021: insights from the Global Burden of Disease Study 2021
Authors: Guo Baojun , Chen Guowen , Chen Miaolian , Huang Ruixia , Mo Jinliang , Lu Zhongman , Ji Qingling , Liao Xiangqing , Liao Jianjun 
Published: November 2024

Abstract

Background
Lower respiratory infections (LRI) are the highest mortality diseases among infectious diseases globally, with China ranking second in the incidence and mortality of lower respiratory infections in 2021. This study, based on GBD 2021, investigates the burden of lower respiratory infections, risk factors, and etiologies in China from 1990 to 2021.
Methods
This study analyzes the trends in the disease burden of lower respiratory infections in China from 1990 to 2021, categorized by gender, age, and year, and explores the attributable mortality and disability-adjusted life years (DALYs) rates related to the risk factors and aetiologies associated with lower respiratory infections.
Results
Compared to 1990, the age-standardized incidence rate (ASIR), age-standardized mortality rate (ASMR), and age-standardized DALY rate (ASDAR) of lower respiratory infections in China decreased by 48%, 77%, and 89% in 2021. Ambient particulate matter pollution surpassed household air pollution from solid fuels to become the leading risk factor. Despite the significant decline, Streptococcus pneumoniae remains the primary pathogen associated with lower respiratory infections.
Conclusion
The disease burden of lower respiratory infections in China has significantly decreased over the past 32 years, but there is still a need to strengthen air pollution control, enhance tobacco regulation, and focus on the health of the elderly population. In response to the changes in the pathogen spectrum, it is necessary to improve detection capabilities and develop new antimicrobial drugs and vaccines.
Assessing the Macroeconomic Impact of COVID-19 Pandemic on the Nigerian Economy through the Lens of SIR-Macro Model
Authors: Nwosu Chinedu , Marcus Samuel 
Published: November 2024

Abstract

This study focused on assessing the impact of COVID-19 pandemic on Nigerian economy through the lens of SIR-macro model. We implemented the SIR-macro model developed by Eichenbaum et al. (2021) to study the interaction between agents’ economic decisions and COVID-19 epidemic. We calibrated the parameters of the models based on the characteristics of Nigeria’s economic structure and analyzed the implications of containment policies on the severity of economic recession as well as the dynamics of the epidemics. We found that government containment policies were effective in reducing the severity of the epidemic in terms of the spread of the disease and number of deaths. The containment policies on the other hand exacerbated the severity of the economic recession. We concluded that the predictions of the model are qualitatively sufficient in explaining the macroeconomic outcomes in Nigeria during this period. We suggest that government should consider socio-demographic characteristics of the country in the selection of policies in an epidemic condition. The government should strengthen the health care system with adequate infrastructure to prevent large case fatalities.
JEL Code:C51, C63,E71,I12, I18