bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global trends in surgically based treatment of anal fistula in Crohn’s disease: a bibliometric and visualization analysis
Authors: Jin Xingtao , Han Ye , Yang Min , Ye Qianqian , Wang Qingming , Zheng De , Mei Zubing 
Published: January 2025

Background:
Crohn’s disease (CD) is a chronic, recurrent gastrointestinal disorder characterized by a complex etiology. Among its perianal complications, anal fistulas represent a challenging comorbidity. With the increase of surgical options, a comprehensive bibliometric analysis was deemed necessary to consolidate the vast array of research in this field.

Methods:
We extracted 1608 articles spanning from 1 January 1994, to 1 May 2024, from the Web of Science Core Collection. Using VOSviewer, CiteSpace, and Scimago Graphica for visual analytics, we synthesized key trends across multiple bibliometric indicators, encompassing geographic and institutional contributions, individual authorship, journal prominence, citation metrics, and thematic prevalence.

Results:
From the delineated corpus, we identified publications from 325 countries and 5110 research institutions, with the US and UK at the forefront of publication volume and academic impact. The data indicated a leading role for institutions like the Cleveland Clinic and Imperial College London. “Diseases of the Colon and Rectum” emerged as a central journal due to its high publication and citation frequency. Distinctly, the analysis uncovered trending keywords, signifying the field’s prioritization on surgical intervention, biologic therapy, imaging modalities, and emerging biological treatments.

Conclusion:
Our findings elucidate a trajectory toward prominent advancements in CD fistula research. This analysis underscores the field’s shift towards integrative treatment strategies, spotlighting the pressing need for comprehensive comparative studies of surgical approaches. It underscores the imperative for robust clinical trials to standardize treatments and extend care to a broader CD patient population.
Extracorporeal shockwave therapy rescued mouse critical limb ischemia via upregulating GPR120 against inflammation and promoting angiogenesis for restoring the blood flow in ischemic zone-experimental study
Authors: Sung Pei-Hsun , Yeh Jui-Ning , Yin Tsung-Cheng , Chai Han-Tan , Chiang John Y. , Huang Chi-Ruei , Chen Yi-Ling , Lee Mel S. , Yip Hon-Kan 
Published: January 2025

Background:
This study tested the hypothesis that extracorporeal shockwave therapy (ECSWT) effectively rescues critical limb ischemia (CLI) in mice through the upregulation of GPR120, which protects against inflammation and angiogenesis to restore blood flow in the ischemic area.

Methods and results:
Compared with the control, ECSWT-induced GPR120-mediated anti-inflammatory effects significantly suppressed the expression of inflammatory signaling biomarkers (TAK1/MAPK family/NF-κB/IL-1β/IL-6/TNF-α/MCP-1) in HUVECs, and these effects were abolished by silencing GPR120 or by the GPR120 antagonist AH7614 (all P < 0.001). C57BL/6 mice (n = 40) were equally categorized into Groups 1 (sham-operated control), 2 (CLI), 3 (CLI + ECSWT), and 4 (CLI + ECSWT + AH7614). By Days 7, 14, and 28 just prior to harvesting the quadriceps muscle, the laser Doppler results showed that the ratio of ischemia to normal blood flow (INBF) in the CLI area was highest in Group 1, lowest in Group 2, and significantly greater in Group 3 than in Group 4 (all P < 0.0001). Endothelial cell markers (CD31/vWF) and GPR120 + cells exhibited identical patterns of INBF among the groups, whereas angiogenesis biomarkers (CXCR4/SDF-1/VEGF/VEGFR2) were significantly and progressively upregulated from Groups 1 to 4 (all P < 0.0001). The protein levels of inflammation (MMP-9, IL-6, and TNF-α) and oxidative stress (NOX-1 and NOX-2) and the cellular levels of inflammation (CD68+)/DNA damage (γ-H2AX+) displayed opposite patterns, whereas the small vessel density in the CLI area displayed an identical pattern of INBF among the groups (all P < 0.0001).

Conclusions:
ECSWT rescued CLI by increasing GPR120-mediated suppression of inflammation and enhancing angiogenesis via activation of VEGFR2.
Students’ Perceptions of Creating Educational Videos as a Teaching and Learning Strategy
Authors: Ramón-Arbués Enrique , Blázquez-Ornat Isabel , Sagarra-Romero Lucía , Benito-Ruiz Eva , Antón-Solanas Isabel , Gómez-Torres Piedad 
Published: January 2025

Background:
The integration of digital technology in nursing education has revolutionized traditional teaching methods. Creating educational videos enhances student engagement and clinical reasoning.

Purpose:
This study evaluated nursing students’ satisfaction and perceptions of creating educational videos as a teaching and learning strategy.

Methods:
A mixed-methods descriptive study was conducted with 150 second-year nursing students enrolled in a Health Education module at San Jorge University (Zaragoza, Spain). Students developed health education videos in groups, and data were collected through a 5-point Likert scale questionnaire and reflective narratives.

Results:
Students produced 33 videos. Quantitative findings showed high satisfaction, with the highest ratings for video applicability. Qualitative data revealed enhanced teamwork, creativity, and information technology skills.

Conclusions:
Video creation is an effective tool in nursing education, fostering engagement and skill development, aligning with modern educational practices.
Enhancing Obstructive Sleep Apnea Screening and Nocturia Treatment: A Quality Improvement Study
Authors: Douglass K. Marie , Laus Katharina , DeAndrade Samantha , Whitaker Taylor , Bernal Lauren , Yazdany Tajnoos , Truong Christina 
Published: January 2025

Importance
Obstructive sleep apnea (OSA) is common but likely underdiagnosed in urogynecology patients with nocturia, and OSA treatment has the potential to improve nocturia symptoms.

Objective
The aim of the study was to assess the effect of implementing a universal screening protocol for OSA in a urogynecology clinic on screening rates, OSA prevalence among patients with nocturia, and symptom improvement following treatment.

Study Design
This was an observational quality improvement study at a urogynecology clinic at a safety-net hospital. Health care providers were asked to screen all new patients with nocturia using the STOP-BANG questionnaire. We assessed screening rates over an 18-month period and followed patients referred for sleep study to determine the percentage who completed evaluation, were identified as having OSA and, if necessary, prescribed treatment, as well as improvement in nocturia symptoms after treatment.

Results
Seventy-eight percent of eligible patients were screened, and screening rates increased substantially over the course of the study. Overall, 20.2% of patients screened positive and were referred for sleep study, and 80.6% of those were ultimately diagnosed with OSA. There were low levels of adherence to the recommended OSA treatment, but patients with OSA who were using the treatment reported better improvement in their symptoms.

Conclusions
Initiation of OSA screening in a urogynecology clinic is a significant and feasible way to address nocturia and has the potential to improve symptoms. Improving rates of OSA testing and adherence to OSA treatment will require a multidisciplinary approach, while systems-level changes are needed to address inequities and other barriers to accessing treatment.
Adjunctive High-Definition Transcranial Direct Current Stimulation in Treatment of Resistant Auditory Verbal Hallucinations in Schizophrenia
Authors: Mahato Apurba Narayan , Munda Sanjay Kumar , Pratap Alok , Mudaliyar Satyanarayanprabhu , Patel Natasha 
Published: January 2025

Background
Resistant auditory verbal hallucination (AVH) remains a disabling symptom in schizophrenia. Transcranial direct current stimulation (tDCS) and its more targeted variant, high-definition tDCS (HD-tDCS), have shown promising results in reducing AVH. We aimed to determine the effects of adjunctive HD-tDCS on various dimensions of AVH in patients with schizophrenia.

Methodology
This randomized controlled trial included 40 patients with schizophrenia with resistant AVH (20 patients each assigned to the active and sham group). A stimulation electrode was placed over the left temporoparietal junction at CP5 according to the 10–10 EEG montage, while return electrodes were positioned at C3, T7, P3, and P7. The active group received 2-mA current for 20 minutes, with a ramp-up and ramp-down of 3 seconds, whereas the sham group received 1-mA current for 30 seconds, with a 3-second ramp-up and ramp-down. AVH severity was assessed using the Psychotic Symptom Rating Scale-Auditory Hallucination at baseline, at the end of HD-tDCS sessions, and 4 weeks after completion.

Results
Within-group comparisons revealed significant improvements in both groups. However, in time*group comparison, the group receiving active HD-tDCS showed a statistically significant improvement only in the frequency dimension of AVH over time (p = 0.011). No other dimensions of AVH improved significantly in the time*group comparison. The effects of HD-tDCS were sustained up to 4 weeks.

Conclusions
Active HD-tDCS over the left temporoparietal junction significantly reduced the frequency of AVH in patients with schizophrenia compared to sham stimulation. However, no significant improvements were observed in other domains of hallucination.
Lentilactobacillus terminaliae sp. nov., isolated from tree bark (Terminalia ivorensis Chev.) and its antioxidant activity
Authors: Phuengjayaem Sukanya , Kingkaew Engkarat , Chamroensaksri Nitcha , Phongsopitanun Wongsakorn , Tanasupawat Somboon 
Published: January 2025

A Gram-stain-positive, facultatively anaerobic, rod-shaped strain, designated SPB1-3T, was isolated from tree bark. This strain exhibited heterofermentative production of dl-lactic acid from glucose. Optimal growth was observed at 25–40 °C, pH 4.0–7.0, and in the presence of 3% (w/v) NaCl. The cell wall peptidoglycan contained lysine and aspartic acid. The predominant fatty acids identified were C16:0 and the Summed feature 7 (C19 :1
ω7c/C19:1
ω6c and/or C19:1
ω6c/ω7c/19cy). The polar lipid profile included phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol, along with two unidentified phospholipids, two unidentified amino lipids and two unidentified lipids. Phylogenetic analysis based on 16S rRNA gene sequences positioned strain SPB1-3T within the genus Lentilactobacillus, showing a close relation to Lentilactobacillus kosonis NBRC 111893T (99.86%) and Lentilactobacillus curieae CCTCC M 2011381T (98.65%). The whole genome of strain SPB1-3T comprised 1 932 998 base pairs with 1955 coding genes and a DNA G+C content of 37.8%. Digital DNA–DNA hybridization between strain SPB1-3T and closely related type strains ranged from 19.50 to 27.20%. The average nucleotide identity ranged from 84.21 to 85.56%, and the average amino acid identity ranged from 57.25 to 85.99%, both falling below the established thresholds for species delineation. Strain SPB1-3T was clearly distinguishable from related Lentilactobacillus species based on its phenotypic and chemotaxonomic characteristics, 16S rRNA gene sequence similarity and whole genome analysis. Additionally, the strain exhibited radical scavenging activity at 66.92% and demonstrated 82.32% inhibition in the tyrosinase inhibitory assay. These findings support the classification of strain SPB1-3T as a novel species within the genus Lentilactobacillus, for which the name Lentilactobacillus terminaliae sp. nov. is proposed. The type strain is SPB1-3T (=JCM 35081T=TISTR 10005T).
High School Science Fair: What Students Say -- Mastery, Performance, and Self-Determination Theory
Authors: Grinnell Frederick , Dalley Simon , Reisch Joan 
Published: January 2025

AbstractBased on free text comments by 1191 students who participated in our national science and engineering fair (SEF) surveys during 2021-22 and 2022-23, we have learned new information about SEF participation and student interest in S&E. The positive reasons that students mentioned most frequently about why SEF participation increased their interest in S&E were: learned new things; experience doing research; enjoyed/fun experience; and career choice. The negative reasons most frequently mentioned by students were: participation was not fun/stressful/boring; not a good project; not interested in science; and required to participate. Overall, students who received coaching and help from scientists made the most positive comments. Students who participated in school-only level SEFs made the most negative. Reasons students gave why SEF participation increased their interest in S&E aligned with mastery criteria. By contrast, reasons students gave in a previous study regarding whether competitive SEFs should be required aligned with performance criteria. Mastery and performance orientations integrate differently with the three elements of self-determination theory: motivation, competence and community engagement. Recognizing these differences in relationship to the interests of high school students who participate in SEFs has the potential to enhance the impact of SEF participation on student STEM interests and knowledge.
RegFormer: A Single-Cell Foundation Model Powered by Gene Regulatory Hierarchies
Authors: Hu Luni , Qiu Ping , Qin Hua , Cao Lei , Jiang Wenjian , Feng Boyu , Zhang Yilin , Chen Qianqian , Shang Yanbang , Xia Tianyi , Deng Ziqing , Xu Xun , Fang Shuangsang , Li Yuxiang , Zhang Yong 
Published: January 2025

AbstractSingle-cell RNA sequencing (scRNA-seq) has significantly advanced our understanding of cellular diversity and the molecular mechanisms underlying biological processes. However, existing computational models often struggle to incorporate essential biological knowledge, handle sparse and noisy data, and scale effectively across large datasets. To address these challenges, we introduce RegFormer, a novel foundation model specifically designed for scRNA-seq analysis. RegFormer integrates hierarchical relationships from gene regulatory networks (GRNs) through an innovative architecture based on Mamba Blocks, enabling more effective modeling of gene interactions and cellular states. Pretrained on a vast dataset of 22 million human cells and comprising approximately 50 million parameters, RegFormer employs dual embeddings to separately capture gene expression levels and gene identities. This approach enhances interpretability by aligning gene expression data with regulatory hierarchies, offering more precise biological insights. Extensive evaluations demonstrate that RegFormer outperforms existing state-of-the-art models, such as scGPT, Geneformer, scFoundation, and scBERT, across a wide range of tasks, including cell annotation, GRN construction, genetic perturbation prediction, and drug response prediction. By combining cutting-edge deep learning techniques with biological knowledge, RegFormer not only improves accuracy and interpretability but also provides deeper insights into cellular processes and regulatory mechanisms, positioning it as a powerful tool for advancing biological discovery.
The TARZN complex bindsde novoenhancer mutations and promotes oncogenic expression in T-ALL
Authors: Zaal Anuar Nurkaiyisah , Goh Chai Yeen , Chua Boon Haow , Tan Shi Hao , Costa Joana R. , Mansour Marc R. , Sanda Takaomi , Kappei Dennis 
Published: January 2025

ABSTRACTTAL1 is overexpressed in 40-60% of T-cell acute lymphoblastic leukemia (T-ALL) cases and forms an oncogenic core regulatory circuit (CRC) with other transcription factors such as LMO1, LMO2 and GATA3. In 5% of T-ALL cases an insertion of a consensus GT dinucleotide (MuTE) is observed upstream of theTAL1gene, driving TAL1 overexpression. Using anin vitroreconstitution DNA pull-down assay combined with quantitative mass spectrometry, we identified proteins that preferentially bound to the MuTE sequence and demonstrated that among the candidates the RNA methyltransferase TARBP1 and the zinc finger proteins ZBTB2, ZBTB25 and ZNF639 form a complex that we term TARZN. Interestingly, the TARZN complex also bound tode novosuper enhancer sites upstream of theLMO1andLMO2genes in T-ALL cells, indicating a putative common mechanism between these different non-coding driver mutations. Furthermore, knock-down of all TARZN members resulted in lower TAL1 protein expression in MuTE-positive but not in MuTE-negative T-ALL cells. Given TARZN’s methyltransferase activity and the lack of concomitantTAL1mRNA level changes, we investigated reduced TAL1 translation and identified reduced neo-synthesised TAL1 protein levels upon TARBP1 knockdown. Overall, these data suggest that the TARZN complex promotes oncogenic expression in T-ALL via co-transcriptional RNA methylation.
AGO1 interacts withNEAT1lncRNA and impacts nuclear compartments
Authors: Shuaib Muhammad , Mannen Taro , Yamazaki Tomohiro , Adroub Sabir Abdu , Ghosheh Yanal , Albawardi Waad , Hirose Tetsuro , Orlando Valerio 
Published: January 2025

AbstractArgonaute 1 (AGO1), a central component of the RNA interference (RNAi) pathway, has recently been implicated in nuclear functions, particularly in chromatin organization and gene regulation. However, the role of AGO1 in lncRNA-driven nuclear compartmentalization remains elusive. In this study, we uncover a novel function for AGO1 in the regulation of nuclear architecture through its interaction with the long non-coding RNA (lncRNA)NEAT1.NEAT1lncRNA is required for the formation of paraspeckles, nuclear substructures involved in multiple cellular processes. We show that AGO1 physically interacts withNEAT1and other key paraspeckle proteins (PSPs) and co-localizes with paraspeckles in the nucleus. AGO1 depletion disrupts expression of bothNEAT1isoforms, reduces the interaction of essential PSPs withNEAT1lncRNA, and leads to impaired paraspeckle formation. Furthermore, depletion ofNEAT1results in the mis-localization of AGO1 from paraspeckles and alters active chromatin compartments. Together, our findings establish a new functional relationship between AGO1 andNEAT1in nuclear compartmentalization and chromatin architecture.
Direct statistical simulation of the Lorenz96 system in model reduction approaches
Authors: Li Kuan , Tobias Steven M. , Marston J. B. 
Published: January 2025

Direct statistical simulation (DSS) of nonlinear dynamical systems bypasses the traditional route of accumulating statistics by lengthy direct numerical simulations by solving the equations that govern the statistics themselves. DSS suffers, however, from the curse of dimensionality as the statistics (such as correlations) generally have higher dimensions than the underlying dynamical variables. Here we investigate two approaches to reduce the dimensionality of DSS, illustrating each method with numerical experiments with the Lorenz96 dynamical system. The forms of DSS chosen here involve approximate closures at second and third order in the equal-time cumulants. We demonstrate significant reduction in computational effort that can be achieved without sacrificing the accuracy of DSS. The methods developed here can be applied to turbulent fluid and magnetohydrodynamical systems.

Published by the American Physical Society
2025
Role of analogies with classical physics in introductory quantum physics teaching
Authors: Rodriguez Luiza Vilarta , van der Veen Jan T. , de Jong Ton 
Published: January 2025

In this study, we explore the use of analogies with classical physics in introductory quantum physics (QP) teaching. This work is part of a larger project in which a learning sequence covering three introductory QP topics was designed, tested, and evaluated in collaboration with high school teachers and physics education researchers. Based on the theoretical foundations of guided inquiry-based learning and collaborative learning, three lessons covering the topics of photoelectric effect, wave-particle duality, and tunneling were developed. For each lesson, a digital inquiry learning space (ILS) was created which implemented a digital laboratory for performing experiments with specific interactive assignments and multimedia material. For this study, each ILS was adapted into two distinct versions, to be applied with students in two experimental conditions: one in which analogies with classical physics were present in the lessons, and one in which such analogies were avoided. Six classes of Dutch upper-secondary students (n=89) were assigned to one of the conditions and followed the respective version of the learning sequence during a period of approximately 6 weeks. Students’ answers to ILS activities were logged and used for a qualitative analysis. Once the learning sequence was finished, students took a post-test covering all three QP topics and scores were compared between the analogy and no analogy conditions. After correcting for students’ overall performance in physics, we found that students in the no analogy condition scored significantly higher on the post-test than the analogy condition for two out of the three QP topics (wave-particle duality and tunneling). An accompanying qualitative analysis suggests that the use of analogies with classical physics might hinder QP learning, as some students manifested difficulties in grasping the limitations of the classical analogies that were used in the materials.

Published by the American Physical Society
2025
PyBibX – a Python library for bibliometric and scientometric analysis powered with artificial intelligence tools
Authors: Pereira Valdecy , Basilio Marcio Pereira , Santos Carlos Henrique Tarjano 
Published: January 2025

PurposeThis paper presents pyBibX, a Python library devised to conduct comprehensive bibliometric and scientometric analyses on raw data files sourced from Scopus, Web of Science and PubMed, seamlessly integrating state-of-the-art artificial intelligence (AI) capabilities into its core functionality.Design/methodology/approachThe library executes a comprehensive exploratory data analysis (EDA), presenting outcomes via visually appealing graphical illustrations. Network capabilities have been deftly integrated, encompassing citation, collaboration and similarity analysis. Furthermore, the library incorporates AI capabilities, including embedding vectors, topic modeling, text summarization and other general natural language processing tasks, employing models such as sentence-BERT, BerTopic, BERT, chatGPT and PEGASUS.FindingsAs a demonstration, we have analyzed 184 documents associated with “multiple-criteria decision analysis” published between 1984 and 2023. The EDA emphasized a growing fascination with decision-making and fuzzy logic methodologies. Next, network analysis further accentuated the significance of central authors and intra-continental collaboration, identifying Canada and China as crucial collaboration hubs. Finally, AI analysis distinguished two primary topics and chatGPT’s preeminence in text summarization. It also proved to be an indispensable instrument for interpreting results, as our library enables researchers to pose inquiries to chatGPT regarding bibliometric outcomes. Even so, data homogeneity remains a daunting challenge due to database inconsistencies.Originality/valuePyBibX is the first application integrating cutting-edge AI capabilities for analyzing scientific publications, enabling researchers to examine and interpret these outcomes more effectively. pyBibX is freely available at https://bit.ly/442wD5z.