bluuebunny/crossref_metadata_2025_split huggingface dataset:
Findings on serial thigh MRI can identify individuals with inflammatory myositis who recover sub-optimally: A 6-month follow-up study
Authors: Gorijavolu Mamatha , Kavadichanda Chengappa G , Gopal Aishwarya , Ananthakrishnan Ramesh , Naik Dhukhabandhu , Mariaselvam Christina Mary , Thabah Molly Mary , Negi Vir Singh 
Published: November 2024

Background: Magnetic resonance imaging (MRI) of the thigh is used in diagnosis of idiopathic inflammatory myositis (IIM) diagnosis due to its high sensitivity in detecting muscle oedema and to localize the site for muscle biopsy. At the same time, dual energy absorptiometry (DXA) is an accepted method in clinical practice to measure muscle mass and change in body composition. In this longitudinal study of patients with active IIM we sought to correlate muscle findings on serial thigh MRI and body composition assessed using DXA with six-month clinical outcomes, we also studied correlation of thigh MRI scores with body composition parameters. Methods: A single-centre prospective study involving 20 active IIM patients. Clinical outcomes, muscle enzymes, MRI of the thigh scores and body composition were periodically assessed over 6 months. Results: Muscle oedema score significantly decreased from baseline (median 17.7) to 3 months (0.7) and 6 months (0) ( p < 0.001). Fatty infiltration increased significantly from baseline (8.8) to 3 months (13.3; p < 0.001) and remained stable. Muscle atrophy score did not change significantly from baseline to 3 or 3 to 6 months. Body composition indices showed significant changes over 6 months, with increases in both lean mass indices and adiposity measures ( p < 0.05). Muscle oedema score significantly correlated with manual muscle testing-8 (MMT-8) at baseline ( r = −0.64). At 6 months MMT-8 showed a significant negative correlation with muscle atrophy ( r = −0.562) and fatty infiltration ( r = −0.478) but not with muscle oedema. Multivariate regression model revealed muscle oedema scores at 3 months ( p = 0.03) and baseline muscle atrophy ( p = 0.02) as significant predictors of MMT-8 at 6 months. Conclusion: Thigh MRI correlated with clinical outcomes both cross-sectionally and longitudinally. Higher baseline muscle atrophy and fatty infiltration, and higher muscle oedema at 3 months predict suboptimal clinical outcomes at 6 months. Intramuscular fatty infiltration scores on thigh MRI did not correlate with lower limb fat indices but correlated with overall fat indices on DXA scan.
Outcomes of Proximal Row Carpectomy With Interposition Arthroplasty for Advanced Wrist Arthritis
Authors: Adenikinju Abidemi , Wu Kitty Y. , Karim Kristin , Carlsen Brian , Kakar Sanjeev 
Published: November 2024

Background: This study aimed to evaluate and compare the outcomes of proximal row carpectomy (PRC) with interposition arthroplasty using dorsal wrist capsule interposition, lateral meniscus allograft, or dermal allograft in patients with lunate facet/capitate degeneration. Methods: Patients who underwent PRC with interposition arthroplasty between 2010 and 2022 at a single institution were identified. Preoperative and postoperative visual analog scale (VAS) pain, functional outcomes, and complications were recorded. Results: Twenty-one patients (11 dorsal capsule, 6 meniscus, 4 dermal matrix) were identified with a mean follow-up of 65.8 months. Postoperative pain and functional outcome scores significantly improved. The mean postoperative Quick Disabilities of the Arm, Shoulder, and Hand score was 20.3. In total, 89.5% of patients returned to work, including 75% of manual laborers. Conclusions: No significant differences were found between dorsal capsular flap versus allograft groups. Proximal row carpectomy with interposition arthroplasty is an effective motion-sparing procedure for patients with proximal capitate and/or lunate fossa arthritis, improving pain and function.
UFO registry: final analysis of baseline data from patients with advanced prostate cancer in Asia
Authors: Ye Dingwei , Kanesvaran Ravindran , Chiong Edmund , Lojanapiwat Bannakij , Pu Yeong-Shiau , Rawal Sudhir Kumar , Aik Ong Teng , Zeng Hao , Chung Byung Ha , Ashani Md Yusoff Noor , Ohyama Chikara , Kim Choung Soo , Hu Zhiquang , Tsai Yuh-Shyan , Razack Azad Hassan Abdul , Singh Anildeep , Liu Yanfang , Uemura Hirotsugu 
Published: November 2024

Background: The incidence of prostate cancer (PC) is increasing in Asian countries. The epidemiology of PC, its treatment including the use of novel therapeutic options, impacts on quality of life, and clinical outcomes of patients with PC in Asia, are not well documented. Objectives: To describe the demographic and disease features of the full cohort of patients enrolled in the United in Fight against prOstate cancer (UFO) registry. Design: The UFO registry was a multi-national, longitudinal, observational study of patients with PC presenting to participating tertiary care hospitals in eight Asian countries/regions. Methods: Patients with high-risk localized PC (HRL), non-metastatic biochemically recurrent, or metastatic PC were consecutively enrolled from September 14, 2015 until September 1, 2020 and followed for up to 5 years. Results: Among the full cohort of 3635 patients, 425 had HRL, 389 had non-metastatic biochemically recurrent, and 2821 had metastatic PC. Median follow-up time was 4.2, 4.2, and 2.6 years, respectively. At first diagnosis, the mean age ranged from 65.7 to 69.1 years, 38.5% had extra-capsular tumor extension, 34.0% had regional lymph node metastases, and 65.1% had distant metastases. Quality-of-life scores at enrollment were significantly worse in patients with metastatic disease. Decisions to start therapy were mainly driven by treatment guidelines and disease progression. The decision to discontinue hormonal therapy was often due to disease progression. Few patients received novel hormonal therapies despite their availability. Conclusion: The UFO registry provides a detailed, contemporary picture of the characteristics, treatment, and outcomes of patients with PC in Asia. There is an unmet medical need to improve access to novel agents in Asia, aiming to improve quality of life and clinical outcomes. Trial registration: Clinicaltrials.gov Identifier: NCT02546908, Registry Identifier: NOPRODPCR4001.
The safety and efficiency of SMART coil for brain aneurysm: A systematic review and meta-analysis
Authors: Habibi Mohammad Amin , Mirjnani Mohammad Sina , Zafari Rasa , saadat Zahra , Zahedinasab Bahareh , Delbari Pouria , Zare Amir Hessam , Sheipouri Amirmahdi , Mobader Sani Sheida 
Published: November 2024

Background The SMART coil system is a relatively new generation of embolic coils consisting of a bare platinum coil, a detachment pusher, and a detachment handle. This study investigated the safety and efficiency of the SMART coil system in treating cerebral aneurysms. Method PubMed/Medline, Embase, Web of Science, and Scopus were searched until October, 1st 2023. Non-English language, non-human studies, and non-original studies were excluded. Results A total of 7 studies were included. The results of our study reflected complete aneurysm occlusion (mRRC1) rate of 45% (95% CI, 0.35–0.56), neck remnant aneurysm (mRRC2) rate of 36% (95% CI, 0.30–0.42), and residual aneurysm (mRRC3) rate of 22% (95% CI, 0.12–0.38) during post-procedural assessment. Moreover, considering longest follow-up, our study showed complete aneurysm occlusion (mRRC1) rate of 66% (95% CI, 0.43–0.84), neck remnant aneurysm (mRRC2) rate of 27% (95% CI, 0.13–0.49), and residual aneurysm (mRRC3) rate of 9% (95% CI, 0.04–0.20). In addition, recanalization and retreatment rates were reported 10% (95% CI, 0.06–0.17) and 9% (95% CI, 0.06–0.12), respectively. The rates of adverse and serious adverse events were 9% (95% CI, 0.07–0.10) and 6% (95% CI, 0.01–0.22), respectively. Three studies reported a stroke rate which was 2% (95% CI, 0.00–0.13), and five studies reported a mortality rate which was 6% (95% CI, 0.03–0.11). Conclusion The findings suggested that the SMART coil can be a safe and efficient treatment in patients with intracranial aneurysms compared to other available treatment methods.
Calculated haemorheological profile and laboratory parameters in new diagnosed multiple myeloma patients: retrospective analysis according to survival
Authors: Carlisi Melania , Lo Presti Rosalia , Spoto Corinne , Mancuso Salvatrice , Siragusa Sergio , Caimi Gregorio 
Published: November 2024

Background: Multiple myeloma is a malignant haematological neoplasm characterised by clonal proliferation of plasma cells, with a complex clinical picture, and a significant impact on patient survival, in which the prognosis evaluation of patients is of great importance. Objectives: In this single-centre retrospective analysis, performed in a group of newly diagnosed multiple myeloma patients, we examined several clinical and laboratory parameters in order to evaluate their trend according to survival of patients. Design: We collected data from 190 newly diagnosed multiple myeloma evaluated at the Hematology Division of the ‘Paolo Giaccone’ University Hospital of Palermo from 1 January 2017 to 30 September 2022. Specifically, we performed our analysis in the entire cohort of patients and also in the specific disease isotype. Methods: We evaluated simple and low-cost laboratory and haemorheological parameters, the latter obtained in a calculated way. The primary endpoint was to evaluate the trend and the differences of these parameters in the study population, divided into two specific groups, deceased and survivors after a specific observation period of almost 7 years. Results: In the entire cohort of multiple myeloma patients, we observed a mortality rate of 40%, of whom 36.4% were men and 43.1% were women. Among the patients who died, in comparison with those who survived, it is significantly evident the increase in age, in red cell distribution width (RDW), RDW%/albumin ratio and in the RDW%/haemoglobin ratio; moreover, in the same patients subgroup, we observed a reduction in haematocrit, total serum protein, calculated whole blood viscosity (evaluated according to the de Simone formula), serum albumin, albumin/fibrinogen ratio and in haemoglobin levels. Conclusion: The obtained data can represent a possible starting point for subsequent targeted analyses, aimed at studying the prognostic value of each individual parameter considered, favouring an increasingly complete and immediate prognostic evaluation of patients.
Rescue immune tolerance induction with a recombinant factor Fc-fused VIII: prospective ReITIrate study of clinical, humoral and cellular immune responses
Authors: Königs Christoph , Meeks Shannon L. , Nolan Beatrice , Schmidt Anja , Löfqvist Malin , Dumont Jennifer , Leickt Lisa , Nayak Sushrusha , Lethagen Stefan 
Published: November 2024

Background: Immune tolerance induction (ITI) is the gold standard for inhibitor eradication to restore the clinical efficacy of factor replacement therapy in haemophilia. However, as ITI often requires frequent administration over extended periods, it can be considered burdensome for patients and healthcare resources. Therefore, there is a need to optimise ITI treatment, particularly in patients who failed previous ITI attempts. Objectives: The ReITIrate study aimed to prospectively evaluate rescue ITI with efmoroctocog alfa, an extended half-life recombinant FVIII Fc fusion protein (herein rFVIIIFc), within a limited 60-week timeframe in patients with severe haemophilia A and inhibitors who failed previous ITI attempts. Design: ReITIrate was a phase IV, open-label, single-arm, interventional, multicentre study. Methods: Primary endpoint was ITI success (negative titre, <0.6 BU/mL; incremental recovery >66%; elimination half-life ⩾7 hours) within 60 weeks. Exploratory immunophenotype analyses were performed to characterise anti-drug antibodies (ADA) and cellular immune responses. Results: Nine of 16 enrolled subjects completed the ITI period during ReITIrate, of which one subject attained all 3 ITI success criteria after 46 weeks with no relapse. Two subjects achieved partial success (one subject met 2/3 success criteria; one met all criteria, but not simultaneously, with inhibitor recurrence). One additional subject (ITI failure) achieved negative inhibitor titre. Across these four subjects, median (range) time to negative titre was 19 (11–60) weeks. No new safety concerns were identified. IgG4 was the major contributor to the ADA IgG response. Subjects with partial/complete ITI success had fewer IgG subclasses involved than those who failed/withdrew. Immunophenotyping indicated an increase in regulatory T-cells (CD4+CD25+CD127low), supporting the ability to perform sensitive blood sampling to identify immune tolerance markers. Conclusion: This study demonstrates that ITI with rFVIIIFc given within a limited timeframe has potential benefit in a difficult-to-treat inhibitor haemophilia population who failed previous ITI attempts. Trial registration: NCT03103542.
Identifying Areas of High Vulnerability for Rural Veteran Food Insecurity
Authors: Bradley Sarah E. , Heuer Jacquelyn , Hahm Bridget , Pettey Kristin , Besterman-Dahan Karen 
Published: November 2024

Introduction/Objectives: Americans, including veterans, living in rural areas experience higher rates of food insecurity than the general population in the United States, but rural veteran food insecurity remains an understudied subject. Due to a lack of data on the subject, this project aimed to use geographic information systems (GIS) mapping of proxy variables for rural veteran food insecurity in order to identify areas of high vulnerability where future research could be targeted. Methods: Key factors which may indicate vulnerability to rural veteran food insecurity were identified in a review of the literature. These factors were mapped in ArcGIS Pro, including veteran population, community health, county rurality, and locations of food deserts. Results: After areas were identified that met search criteria, 3 sites were identified which serve a highly rural patient population and whose population has the highest vulnerability to rural veteran food insecurity based on search criteria. Conclusions: This project demonstrates how GIS mapping can be used to identify regions in the United States at high vulnerability for rural veteran food insecurity. Findings from this project will be used by the project team to develop interventions for rural veteran food insecurity which can be implemented at the local or national level.
Expression of senescence-related CD161 promotes extranodal NK/T cell lymphoma by affecting T cell phenotype and cell cycle
Authors: Jin Chengxun , Li Xin , Zhang Chaohe 
Published: November 2024

Abstract
Purpose
The intention of this work is to probe the role of senescence-related gene CD161 in extranodal NK/T cell lymphoma (ENKTL).

Methods
This study used H2O2 to establish three distinct in vitro oxidative stress aging models (NKL, SNT-8, and YT). Western blotting was employed to assess the levels of two iconic aging proteins, MMP1 and P53, and flow cytometry was utilized to investigate cell cycle and the expressions of CD4, CD8, and CD161. Cell viability was evaluated via the CCK-8 assay. The transcriptome analysis assessed the differential gene expression between the control and aging group of NKL. In vivo, we established a BALB/c mice aging tumor model. After 15 days, the mice were euthanized to harvest tumors. ELISA was employed to measure aging indicators in the mouse tissues. Flow cytometry was utilized to assess the levels of CD4, CD8, and CD161 in tumor samples. Hematoxylin-eosin (HE) staining was performed to evaluate the structure and cellular morphology of the tumor tissue.

Results
In the NKL, SNT-8 and YT aging models, the levels of MMP1 and P53 proteins were significantly increased. Flow cytometry results indicated that all three cell types exhibited marked arrest in the G1 phase. Compared with the control group, the expressions of CD4 and CD161 in the aging group were significantly increased, while the expression of CD8 was decreased. Transcriptome analysis revealed 2,843 differentially expressed genes (DEGs) between the control and aging groups, with 2,060 up-regulated and 783 down-regulated genes identified. Following CD161 knockdown, cell viability of three cell types in the aging group was significantly reduced compared to the control group. The G1 phase of the cells was significantly interrupted. The expressions of CD4 and CD161 were significantly increased, and the expression of CD8 was decreased. However, in the aging + si-CD161 group, a partial alleviation of oxidative stress was observed with a reduction in CD161 expression levels. Animal experiments demonstrated that knockout of CD161 can inhibit tumor progression and partially mitigate oxidative stress.

Conclusions
CD161 may inhibit ENKTL tumor development by regulating cell cycle and T-cell phenotype.
Co-culture of human AT2 cells with fibroblasts reveals a MUC5B phenotype: insights from an organoid model
Authors: Yao Yiwen , Ritzmann Felix , Miethe Sarah , Kattler-Lackes Kathrin , Colakoglu Betül , Herr Christian , Kamyschnikow Andreas , Brand Michelle , Garn Holger , Yildiz Daniela , Langer Frank , Bals Robert , Beisswenger Christoph 
Published: November 2024

AbstractImpaired interaction of fibroblasts with pneumocytes contributes to the progression of chronic lung disease such as idiopathic pulmonary fibrosis (IPF). Mucin 5B (MUC5B) is associated with IPF. Here we analyzed the interaction of primary fibroblasts and alveolar type 2 (AT2) pneumocytes in the organoid model. Single-cell analysis, histology, and qRT-PCR revealed that fibroblasts expressing high levels of fibrosis markers regulate STAT3 signaling in AT2 cells, which is accompanied by cystic organoid growth and MUC5B expression. Cystic growth and MUC5B expression were also caused by the cytokine IL-6. The PI3K-Akt signaling pathway was activated in fibroblasts. The drug dasatinib prevented the formation of MUC5B-expressing cystic organoids. MUC5B associated with AT2 cells in samples obtained from IPF patients. Our model shows that fibrotic primary fibroblasts induce impaired differentiation of AT2 cells via STAT3 signaling pathways, as observed in IPF patients. It can be used for mechanistic studies and drug development.
Mbnl1-mediated alternative splicing of circMlxipl regulates Rbbp6-involved ChREBP turnover to inhibit lipotoxicity-induced β-cell damage
Authors: Gong Yingying , Wei Meilin , Cao Xiaopei , Xu Changliu , Jin Jiewen , Pei Ling , Li Yanbing , Xiao Haipeng , Wu Liting 
Published: November 2024

Abstract
Background
Diabetes, a global epidemic, is the leading cause of mortality globally. The aim of this study is to get better understanding of pathophysiology of diabetes.

Methods
Palmitic acid (PA)-treated β-cells, db/db mice and high fat diet (HFD)-fed mouse model of type 2 diabetes were established. H&E was used to assess the histological changes of pancreas. IHC, FISH, western blot or qRT-PCR was employed to detect the expression of key molecules in primary islets or lipotoxic β-cells. Cell behaviors were detected by MTT, EdU incorporation assay, TUNEL assay and glucose-induced insulin secretion (GSIS). The associations among circMlxipl, Mbnl1 and Rbbp6 were validated by RIP and RNA pull-down assays, and the direct binding between Hdac3 and Mbnl1 promoter was examined by ChIP and luciferase assays. Co-IP was employed to assess the interaction between ChREBP and Rbbp6, as well as the ubiquitination of ChREBP.

Results
Hdac3 and ChREBP were upregulated, but Mbnl1 and circMlxipl were downregulated in islets from diabetic mice and lipotoxic β-cells. Mbnl1 overexpression protected against PA-induced impairments in lipotoxic β-cells through modulating back-splicing of circMlxipl and suppressing ChREBP. Hdac3 served as a transcriptional repressor of Mbnl1, and it was implicated in circMlxipl-mediated protection via regulating ChREBP expression in lipotoxic β-cells. Lack of circMlxipl inhibited Rbbp6-mediated ubiquitin-proteasomal degradation of ChREBP in lipotoxic β-cells. In vivo studies revealed that Hdac3 knockdown or Mbnl1 overexpression alleviated diabetes symptoms through circMlxipl-regulated ChREBP in diabetic mice.

Conclusion
Mbnl1-mediated alternative splicing of circMlxipl regulates Rbbp6-involved ChREBP turnover to inhibit lipotoxicity-induced β-cell damage.
PIPETS: a statistically informed, gene-annotation agnostic analysis method to study bacterial termination using 3′-end sequencing
Authors: Furumo Quinlan , Meyer Michelle M. 
Published: November 2024

Abstract
Background
Over the last decade the drop in short-read sequencing costs has allowed experimental techniques utilizing sequencing to address specific biological questions to proliferate, oftentimes outpacing standardized or effective analysis approaches for the data generated. There are growing amounts of bacterial 3′-end sequencing data, yet there is currently no commonly accepted analysis methodology for this datatype. Most data analysis approaches are somewhat ad hoc and, despite the presence of substantial signal within annotated genes, focus on genomic regions outside the annotated genes (e.g. 3′ or 5′ UTRs). Furthermore, the lack of consistent systematic analysis approaches, as well as the absence of genome-wide ground truth data, make it impossible to compare conclusions generated by different labs, using different organisms.

Results
We present PIPETS, (Poisson Identification of PEaks from Term-Seq data), an R package available on Bioconductor that provides a novel analysis method for 3'-end sequencing data. PIPETS is a statistically informed, gene-annotation agnostic methodology. Across two different datasets from two different organisms, PIPETS identified significant 3'-end termination signal across a wider range of annotated genomic contexts than existing analysis approaches, suggesting that existing approaches may miss biologically relevant signal. Furthermore, assessment of the previously called 3′-end positions not captured by PIPETS showed that they were uniformly very low coverage.

Conclusions
PIPETS provides a broadly applicable platform to explore and analyze 3′-end sequencing data sets from across different organisms. It requires only the 3′-end sequencing data, and is broadly accessible to non-expert users.
Moderate benefit of escape room game on learning outcome in medicine
Authors: Fedorcsak Peter 
Published: November 2024

Abstract
Background
Well-designed escape room games engage students with complex problems and challenge clinical and teamwork skills, but their impact on learning has been uncertain. This study aimed to estimate the effect size of escape room game on performance in a broad knowledge test.

Methods
During clinical rotation in reproductive endocrinology and infertility (REI), medical students participated in a 3-hour small-group class. For 2 semesters, groups had traditional patient visits and case discussions, and for 3 semesters, patient visits and an escape room game including debrief. The game was set up in the outpatient clinic, the puzzles were taken from clinical problems in REI, and challenges included operating an ultrasound scanner on a mannequin. Mid-semester, students completed a test of general knowledge in REI. To estimate the effect of small group class on declarative knowledge, test scores of students who had already had the class (exposed) were compared to scores of those who had not yet had the class (control).

Results
Students were highly satisfied with gamified teaching. Those who attended the small group class without the escape room game achieved similar scores on knowledge test than control students (Cohen’s d = 0.05, 95%CI -0.58 to 0.68, n = 71). Students who played the escape room game achieved marginally higher score than respective controls (Cohen’s d = 0.22, 95%CI -0.1 to 0.53, n = 182).

Conclusions
Escape room game may improve learning outcome of a traditional small group class, but the effect of a single game session on declarative knowledge is modest and is unlikely to exceed related instructional methods like simulation.