bluuebunny/crossref_metadata_2025_split huggingface dataset:
An approach to the diagnosis of lumbar disc herniation using deep learning models
Authors: Prisilla Ardha Ardea , Guo Yue Leon , Jan Yih-Kuen , Lin Chih-Yang , Lin Fu-Yu , Liau Ben-Yi , Tsai Jen-Yung , Ardhianto Peter , Pusparani Yori , Lung Chi-Wen 
Published: September 2023

Background:In magnetic resonance imaging (MRI), lumbar disc herniation (LDH) detection is challenging due to the various shapes, sizes, angles, and regions associated with bulges, protrusions, extrusions, and sequestrations. Lumbar abnormalities in MRI can be detected automatically by using deep learning methods. As deep learning models gain recognition, they may assist in diagnosing LDH with MRI images and provide initial interpretation in clinical settings. YOU ONLY LOOK ONCE (YOLO) model series are often used to train deep learning algorithms for real-time biomedical image detection and prediction. This study aims to confirm which YOLO models (YOLOv5, YOLOv6, and YOLOv7) perform well in detecting LDH in different regions of the lumbar intervertebral disc.Materials and methods:The methodology involves several steps, including converting DICOM images to JPEG, reviewing and selecting MRI slices for labeling and augmentation using ROBOFLOW, and constructing YOLOv5x, YOLOv6, and YOLOv7 models based on the dataset. The training dataset was combined with the radiologist’s labeling and annotation, and then the deep learning models were trained using the training/validation dataset.Results:Our result showed that the 550-dataset with augmentation (AUG) or without augmentation (non-AUG) in YOLOv5x generates satisfactory training performance in LDH detection. The AUG dataset overall performance provides slightly higher accuracy than the non-AUG. YOLOv5x showed the highest performance with 89.30% mAP compared to YOLOv6, and YOLOv7. Also, YOLOv5x in non-AUG dataset showed the balance LDH region detections in L2-L3, L3-L4, L4-L5, and L5-S1 with above 90%. And this illustrates the competitiveness of using non-AUG dataset to detect LDH.Conclusion:Using YOLOv5x and the 550 augmented dataset, LDH can be detected with promising both in non-AUG and AUG dataset. By utilizing the most appropriate YOLO model, clinicians have a greater chance of diagnosing LDH early and preventing adverse effects for their patients.
Identification of CHMP7 as a promising immunobiomarker for immunotherapy and chemotherapy and impact on prognosis of colorectal cancer patients
Authors: Guo Yu , Wang Shu , Liang Feng , Wang Min 
Published: September 2023

Introduction: ESCRT is a molecular machine involved in various important physiological processes, such as the formation of multivesicular bodies, cellular autophagy, and cellular membrane repair. CHMP7 is a regulatory subunit of ESCRT-III and is necessary for the proper functioning of ESCRT. In this study, public databases were exploited to explore the role of CHMP7 in tumors.Methods: The research on CHMP7 in oncology is rather limited. In this study, the differential expression of CHMP7 in multiple tumor tissues was analyzed with information from public databases and clinically collected colorectal cancer tissue samples. Subsequently, the mutational landscape of CHMP7, methylation levels, and the relationship between its expression levels and genomic instability were resolved. The immune microenvironment is a compelling emerging star in tumor research. The correlation of CHMP7 with various infiltrating immune cell types in TME was analyzed by online datasets and single-cell sequencing. In terms of clinical treatment, the impact of CHMP7 expression levels on chemotherapy and immunotherapy and the evaluation of small molecule drugs related to CHMP7 were assessed.Results:CHMP7 has a predictive value for the prognosis of patients with tumors and is highly involved in tumor immunity. The downregulation of CHMP7 may lead to genomic instability. A strong correlation between CHMP7 and TME immune cell infiltration has been observed, participating in the formation of suppressive TME and promoting tumor progression. The expression level of CHMP7 is significantly lower in the non-responder group of multiple chemotherapeutic agents. CHMP7 can potentially serve as a new biomarker for predicting the efficacy of tumor chemotherapy and immunotherapy.Conclusion: As a gene of interest, CHMP7 is expected to provide novel and promising targets for further treatment of patients with tumor.
Tricuspid annular and right atrial volume changes are associated in healthy adults—insights from the three-dimensional speckle-tracking echocardiographic MAGYAR-Healthy Study
Authors: Nemes Attila , Kormányos Árpád , Rácz Gergely , Ruzsa Zoltán , Achim Alexandru , Ambrus Nóra , Lengyel Csaba 
Published: September 2023

IntroductionThe tricuspid valve and its annulus (TA) and the right atrium (RA) play a significant role in regulating blood flow in the right heart. However, their effect on each other is not fully understood even in normal circumstances. Three-dimensional (3D) speckle-tracking echocardiography (3DSTE) is able to simultaneously assess TA and RA at the same time in a non-invasive way. The present study aimed to examine associations between tricuspid annular (TA) dimensions and right atrial (RA) volumes in healthy adults by 3DSTE.MethodsThe present study comprised 144 healthy subjects (mean age: 34.4 ± 12.6 years, 72 males), who participated in this study on a voluntary basis for screening between 2011 and 2015. In all subjects, electrocardiography, two-dimensional Doppler echocardiography and 3DSTE have been performed.ResultsWith increasing end-systolic maximum RA volume, all end-systolic and end-diastolic TA dimensions showed simultaneous increase, but in various degrees resulting in (non-significant) reduction of TA functional properties. Similarly, with increasing diastolic pre-atrial contraction and minimum RA volumes, TA dimensions increased simultaneously (except end-diastolic TA diameter), but in various degrees resulting in reduced TA fractional shortening and fractional area change. With increasing RA dimensions, end-systolic and end-diastolic TA dimensions showed simultaneous increase, but in different, sometimes not significant degrees. While RA stroke volumes showed increasing pattern with TA dilation, RA emptying fractions have not changed substantially.Conclusions3DSTE is suitable for non-invasive assessment of TA dimensions and RA volumes at the same time using the same 3D echocardiographic dataset. Significant associations between TA size and RA volumes exist in healthy circumstances. Strong associations in case of dilation of TA in the presence of higher RA volumes could partly explain functional tricuspid regurgitation later developing in subjects in sinus rhythm.
Thoracic endovascular aortic repair under venoarterial extracorporeal membrane oxygenation for acute aortic dissection patients: a case report
Authors: Zhu Leilei , Dong Pingping , Du Liwen , Xun Kai , Liu Peng , Lu Xiaozhen , Shi Yongwei 
Published: September 2023

BackgroundOpen repair and replacement of the diseased aorta is still the standard treatment for type A aortic dissection (TAAD) in most patients. In endovascular treatment alone, ensuring adequate blood supply to the brain while covering the dissection with a stent is difficult.Case presentationThis study includes a 71-year-old male patient with type A aortic dissection presented at a recent follow-up examination after having undergone thoracic endovascular aortic repair (TEVAR) plus left subclavian artery chimney stent reconstruction for descending aortic dissection 5 years ago. Preoperative computed tomographic angiography, computed tomographic perfusion, and transcranial Doppler showed an intact cerebral arterial ring and good collateral circulation. We successfully performed an endovascular repair of the thoracic aorta with venoarterial extracorporeal membrane oxygenation (V-A ECMO) to protect the craniocerebral blood supply, greatly increase the safety of the operation, and ensure a good prognosis.ConclusionTEVAR under V-A ECMO protection is beneficial for patients with TAAD because of its minimal trauma, rapid recovery, few complications, and low mortality.
Bibliometric research on analysis of links between periodontitis and cardiovascular diseases
Authors: Tang Kuangyun , Wu Yongjia , Zheng Qianhan , Chen Xuepeng 
Published: September 2023

BackgroundPeriodontitis (PD) and cardiovascular diseases (CVD) rank among the most prevalent pathologies worldwide, and their correlation has been a subject of prolonged investigation. Numerous studies suggest shared etiological factors; however, a definitive causal connection remains unestablished. The objective of this study was to employ bibliometric and visual analyses in order to comprehensively examine the overarching characteristics, focal areas of research, and prospective trends pertaining to the PD-CVD relationship.MethodsWe sourced articles, reviews, and online publications on PD- and CVD- research from the Web of Science Core Collection (WoSCC) spanning from January 1, 1993, to May 15, 2023. A triad of analytical tools (R-Bibliometrix, VOSviewer 1.6.19, and CiteSpace 6.2.R3) were utilized to facilitate collaboration network analysis, co-citation analysis, co-occurrence analysis, and citation burst detection.ResultsOut of the 1,116 publications that fulfilled the eligibility criteria in the WoSCC database, the comprehensive characteristics analysis divulged a sustained growth trend in publication frequency. In the cluster analysis of reference co-citation and keyword co-occurrence, prominent themes such as “periodontitis”, “cardiovascular diseases”, “inflammation”, “Porphyromonas gingivalis”, and “atherosclerosis” consistently emerged. Contemporary topics such as “peri-implantitis,” “COVID-19”, “cardiovascular risk factors,” and “endocarditis” were pinpointed as burgeoning research hotspots.ConclusionBased on this bibliometric study, in the field of association studies between PD and CVD, the etiologic mechanisms of both diseases have been intensively studied in the last three decades. Periodontal pathogens might serve as potential initiating factors linking PD and CVD. Inflammation may constitute a significant etiological factor shared by both diseases. Several emerging topics, such as COVID-19 and peri-implantitis, exhibit promising potential. This exhaustive overview casts light on pivotal research arenas, augmenting the field's understanding and stimulating further scholarly investigations.
Assessing the potential for the Surface Water and Ocean Topography (SWOT) mission for constituent flux estimations
Authors: Gehring Jaclyn , Beighley Edward , Stubbins Aron 
Published: September 2023

The recently launched Surface Water and Ocean Topography (SWOT) satellite will simultaneously measure river surface water widths, elevations, and slopes. These novel observations combined with assumptions for unobserved bathymetry and roughness enable the derivation of river discharge. Derived discharge data will not be available until the fall of 2023, despite the satellite having completed approximately 6 months of observations for validation and calibration and transitioning into the nominal orbit phase. SWOT has an irregular flyover frequency, ranging from roughly 1 to 10 times per 21 days. Here, we present how best to use SWOT data when it becomes live, including consideration of how best to accommodate or utilize the irregular flyover frequency of SWOT as it intersects with river reaches. We investigate the predicted capabilities of SWOT for several major rivers using synthetic/theoretical SWOT time series data and evaluate how the characteristics of river discharge dynamics and SWOT sampling frequency impact discharge estimates. This analysis indicates the irregular frequency of SWOT best captures the hydrology of larger, more stable, rivers but presents challenges in smaller, flashier rivers, particularly when sampling frequency decreases (i.e., falls to once per 21 days). Further, the use of SWOT discharge for quantifying constituent fluxes is considered. We provide recommendations concerning how to best use SWOT data for applications related to hydrology and biogeochemistry, including how to design studies to accommodate its irregular orbit cycle.
Prevalence of vitamin B12 deficiency in type 2 diabetic patients taking metformin, a cross-sectional study in primary healthcare
Authors: Al Quran Thekraiat , Khader Ateka , Allan Hadeel , Al-Momani Rua’a , Aqel Hamzeh T. , Alsaleh Mu’taz , Bataineh Ziad 
Published: September 2023

BackgroundSeveral studies documented that metformin use contributes to vitamin B12 deficiency in patients with type 2 diabetes mellitus (T2DM). However, there has been a lack of data assessing this issue in Jordan.AimsAssess the vitamin B12 serum levels, frequency of vitamin B12 deficiency, and related factors among Jordanian patients with T2DM patients treated with metformin.Methodsa total of 447 subjects attending a primary health care center were included in this cross-sectional study consisting of T2DM patients who use metformin and a control group of non-diabetics. Serum B12 levels were evaluated and B12 deficiency was defined as serum B12 levels ≤ 200 pmol/L. Associations of B12 serum levels or B12 deficiency with other factors like gender, age, and duration of T2DM were analyzed.ResultsThere was no significant difference in serum B12 levels nor the frequency of vitamin B12 deficiency between T2DM metformin-treated patients and control groups. Among metformin-treated patients there was no difference relating to age, type 2 diabetes mellitus duration, proton pump inhibitors use, and metformin use (duration, dose) between patients with or without B12 deficiency.ConclusionThe prevalence of vitamin B12 deficiency among T2DM patients on metformin treatment in this study was high (48.9%). However, the treatment with metformin and the dose of metformin use was not associated with vitamin B12 deficiency.
Automatic recognition of complementary strands: lessons regarding machine learning abilities in RNA folding
Authors: Chasles Simon , Major François 
Published: September 2023

Introduction: Prediction of RNA secondary structure from single sequences still needs substantial improvements. The application of machine learning (ML) to this problem has become increasingly popular. However, ML algorithms are prone to overfitting, limiting the ability to learn more about the inherent mechanisms governing RNA folding. It is natural to use high-capacity models when solving such a difficult task, but poor generalization is expected when too few examples are available.Methods: Here, we report the relation between capacity and performance on a fundamental related problem: determining whether two sequences are fully complementary. Our analysis focused on the impact of model architecture and capacity as well as dataset size and nature on classification accuracy.Results: We observed that low-capacity models are better suited for learning with mislabelled training examples, while large capacities improve the ability to generalize to structurally dissimilar data. It turns out that neural networks struggle to grasp the fundamental concept of base complementarity, especially in lengthwise extrapolation context.Discussion: Given a more complex task like RNA folding, it comes as no surprise that the scarcity of useable examples hurdles the applicability of machine learning techniques to this field.
Immunological correlates of protection afforded by PHV02 live, attenuated recombinant vesicular stomatitis virus vector vaccine against Nipah virus disease
Authors: Monath Thomas P. , Nichols Richard , Feldmann Friederike , Griffin Amanda , Haddock Elaine , Callison Julie , Meade-White Kimberly , Okumura Atsushi , Lovaglio Jamie , Hanley Patrick W. , Clancy Chad S. , Shaia Carl , Rida Wasima , Fusco Joan 
Published: September 2023

IntroductionImmune correlates of protection afforded by PHV02, a recombinant vesicular stomatitis (rVSV) vector vaccine against Nipah virus (NiV) disease, were investigated in the African green monkey (AGM) model. Neutralizing antibody to NiV has been proposed as the principal mediator of protection against future NiV infection.MethodsTwo approaches were used to determine the correlation between neutralizing antibody levels and outcomes following a severe (1,000 median lethal doses) intranasal/intratracheal (IN/IT) challenge with NiV (Bangladesh): (1) reduction in vaccine dose given 28 days before challenge and (2) challenge during the early phase of the antibody response to the vaccine.ResultsReduction in vaccine dose to very low levels led to primary vaccine failure rather than a sub-protective level of antibody. All AGMs vaccinated with the nominal clinical dose (2 × 107 pfu) at 21, 14, or 7 days before challenge survived. AGMs vaccinated at 21 days before challenge had neutralizing antibodies (geometric mean titer, 71.3). AGMs vaccinated at 7 or 14 days before challenge had either undetectable or low neutralizing antibody titers pre-challenge but had a rapid rise in titers after challenge that abrogated the NiV infection. A simple logistic regression model of the combined studies was used, in which the sole explanatory variable was pre-challenge neutralizing antibody titers. For a pre-challenge titer of 1:5, the predicted survival probability is 100%. The majority of animals with pre-challenge neutralizing titer of ≥1:20 were protected against pulmonary infiltrates on thoracic radiograms, and a majority of those with titers ≥1:40 were protected against clinical signs of illness and against a ≥fourfold antibody increase following challenge (indicating sterile immunity). Controls receiving rVSV-Ebola vaccine rapidly succumbed to NiV challenge, eliminating the innate immunity stimulated by the rVSV vector as a contributor to survival in monkeys challenged as early as 7 days after vaccination.Discussion and conclusionIt was concluded that PHV02 vaccine elicited a rapid onset of protection and that any detectable level of neutralizing antibody was a functional immune correlate of survival.
Causal relationships between CD25 on immune cells and hip osteoarthritis
Authors: Luo Hao , Zhu Yong , Guo Bin , Ruan Zhe , Liu Zhi , Fan Zhihua , Zhao Shushan 
Published: September 2023

ObjectivesPrevious research has indicated a potential association between immune factors and osteoarthritis (OA), but the causal relationship between CD25 expression on immune cells and hip OA remains enigmatic. To shed light on this relationship, this study utilized the two-sample Mendelian Randomization (MR) method.MethodsLeveraging genome-wide association studies (GWAS) data from the UK Biobank and arcOGEN, the investigation encompasses a substantial European cohort comprising 15,704 hip OA cases and 378,169 controls. Genetic insights into CD25 stem from a subgroup of 3,757 individuals with European ancestry, encompassing 77 CD25-related traits. Several MR methods were applied, and robustness was assessed through heterogeneity and sensitivity analysis.ResultsAmong the 77 traits examined, 66 shared the same single nucleotide polymorphisms (SNPs) with hip OA. Of these, 7 CD25-related traits were found to be causally associated with hip OA (adjusted P&gt;&lt;0.05), with F-statistics ranging from 33 to 122. These traits are specifically related to CD4+CD25+ T cells, exhibiting odds ratios (OR) and 95% confidence intervals (CI) less than 1. Notably, no causal link was discerned with the CD8+CD25+ T cell subset. Within absolute count (AC) and relative count (RC) trait types, a significant causal relationship was observed solely between CD4+CD25+ T cells and hip OA, without subtype localization. A more intricate examination of CD25 expression levels within the CD4+CD25+ T cell subset revealed a correlation with the CD39+ regulatory T (Treg) subset and hip OA, particularly within the CD39+ activated Treg subset. Furthermore, a notable causal relationship emerged between CD25 expression levels in the CD45RA- not Treg subset and hip OA. However, no significant causal link was established with any subsets of B cells.ConclusionThe genetic prediction suggests that CD25, particularly within the realm of CD4+CD25+ T cells, may exert a protective influence against the development of hip OA. These findings provide a novel therapeutic approach for the prevention and treatment of hip OA.
Improvement in neoantigen prediction via integration of RNA sequencing data for variant calling
Authors: Nguyen Bui Que Tran , Tran Thi Phuong Diem , Nguyen Huu Thinh , Nguyen Thanh Nhan , Pham Thi Mong Quynh , Nguyen Hoang Thien Phuc , Tran Duc Huy , Nguyen Vy , Tran Thanh Sang , Pham Truong-Vinh Ngoc , Le Minh-Triet , Phan Minh-Duy , Giang Hoa , Nguyen Hoai-Nghia , Tran Le Son 
Published: September 2023

IntroductionNeoantigen-based immunotherapy has emerged as a promising strategy for improving the life expectancy of cancer patients. This therapeutic approach heavily relies on accurate identification of cancer mutations using DNA sequencing (DNAseq) data. However, current workflows tend to provide a large number of neoantigen candidates, of which only a limited number elicit efficient and immunogenic T-cell responses suitable for downstream clinical evaluation. To overcome this limitation and increase the number of high-quality immunogenic neoantigens, we propose integrating RNA sequencing (RNAseq) data into the mutation identification step in the neoantigen prediction workflow.MethodsIn this study, we characterize the mutation profiles identified from DNAseq and/or RNAseq data in tumor tissues of 25 patients with colorectal cancer (CRC). Immunogenicity was then validated by ELISpot assay using long synthesis peptides (sLP).ResultsWe detected only 22.4% of variants shared between the two methods. In contrast, RNAseq-derived variants displayed unique features of affinity and immunogenicity. We further established that neoantigen candidates identified by RNAseq data significantly increased the number of highly immunogenic neoantigens (confirmed by ELISpot) that would otherwise be overlooked if relying solely on DNAseq data.DiscussionThis integrative approach holds great potential for improving the selection of neoantigens for personalized cancer immunotherapy, ultimately leading to enhanced treatment outcomes and improved survival rates for cancer patients.