bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hypermethylation of the glutathione peroxidase 4 gene promoter is associated with the occurrence of immune tolerance phase in chronic hepatitis B
Authors: Su Xing , Wang Zhaohui , Li Jihui , Gao Shuai , Fan Yuchen , Wang Kai 
Published: March 2024

Abstract
Background
Hepatitis B virus (HBV) infection is a public health problem that seriously threatens human health. This study aimed to investigate the clinical significance of glutathione peroxidase 4(GPX4) in the occurrence and development of chronic hepatitis B (CHB).

Methods
A total of 169 participants including 137 patients with CHB and 32 healthy controls (HCs) were recruited. We detected the expression of GPX4 and stimulator of interferon genes (STING) in peripheral blood mononuclear cells (PBMCs) by real-time quantitative polymerase chain reaction (RT-qPCR). The methylation level of GPX4 gene promoter in PBMCs was detected by TaqMan probe-based quantitative methylation-specific PCR (MethyLight). Enzyme-linked immunosorbent assay (ELISA) was performed to detect the serum levels of GPX4, IFN-β, oxidative stress (OS) related molecules, and pro-inflammatory cytokines.

Results
The expression levels of GPX4 in PBMCs and serum of CHB patients were lower than those of HCs, but the methylation levels of GPX4 promoter were higher than those of HCs, especially in patients at the immune tolerance phase. STING mRNA expression levels in PBMCs and serum IFN-β levels of patients at the immune activation phase and reactivation phase of CHB were higher than those at other clinical phases of CHB and HCs. GPX4 mRNA expression level and methylation level in PBMCs from patients with CHB had a certain correlation with STING and IFN-β expression levels. In addition, the methylation level of the GPX4 promoter in PBMCs from patients with CHB was correlated with molecules associated with OS and inflammation.

Conclusions
GPX4 may play an important role in the pathogenesis and immune tolerance of CHB, which may provide new ideas for the functional cure of CHB.
Multiply restimulated human cord blood-derived Tregs maintain stabilized phenotype and suppressive function and predict their therapeutic effects on autoimmune diabetes
Authors: Bi Yuanjie , Kong Ran , Peng Yani , Cai Donghua , Zhang Yu , Yang Fan , Li Xia , Deng Wen , Liu Fang , He Binbin , Cao Chuqing , Deng Chao , Tang Xiaohan , Fan Li , Yu Haibo , Zhou Zhiguang 
Published: March 2024

Abstract
Background
Regulatory T cells (Tregs) are involved in the maintenance of immune homeostasis and immune regulation. Clinical trials on the adoptive transfer of Tregs have been ongoing for > 10 years. However, many unresolved issues remain in the production of readymade Treg products and selection of patients. Hence, this study aimed to develop a method to expand off-the-shelf Tregs derived from umbilical cord blood (UCB-Tregs) in vitro without changing their phenotype and inhibitory function. In addition, the study intended to design an approach to precisely select patients who are more likely to benefit from the adoptive Treg transfer therapy.

Methods
UCB-Tregs were isolated and cultured in a medium containing human recombinant IL-2 and rapamycin and then multiply restimulated with human T-activator CD3/CD28 dynabeads. The phenotype and suppressive capacity of Tregs were assessed on days 18 and 42. The relationship between the suppressive function of UCB-Tregs in vitro and clinical indicators was analyzed, and the ability of the in vitro suppressive capacity to predict the in vivo therapeutic effects was evaluated.

Results
UCB-Tregs expanded 123-fold and 5,981-fold at 18 and 42 days, respectively. The suppressive function of UCB-Tregs on the proliferation of immune cells at 42 days was not significantly different compared with that of UCB-Tregs obtained at 18 days. The suppression rate of UCB-Tregs to PBMCs was negatively correlated with the course of diabetes. Moreover, the high-suppression group exhibited a better treatment response than the low-suppression group during the 12-month follow-up period.

Conclusions
Multiply restimulated UCB-Tregs expanded at a large scale without any alterations in their classical phenotypic features and inhibitory functions. The suppressive function of Tregs in vitro was negatively correlated with the disease duration. The present study revealed the possibility of predicting the in vivo therapeutic effects via the in vitro inhibition assay. Thus, these findings provided a method to obtain off-the-shelf Treg products and facilitated the selection of patients who are likely to respond to the treatment, thereby moving toward the goal of precision treatment.
Explicable prioritization of genetic variants by integration of rule-based and machine learning algorithms for diagnosis of rare Mendelian disorders
Authors: Kim Ho Heon , Kim Dong-Wook , Woo Junwoo , Lee Kyoungyeul 
Published: March 2024

Abstract
Background
In the process of finding the causative variant of rare diseases, accurate assessment and prioritization of genetic variants is essential. Previous variant prioritization tools mainly depend on the in-silico prediction of the pathogenicity of variants, which results in low sensitivity and difficulty in interpreting the prioritization result. In this study, we propose an explainable algorithm for variant prioritization, named 3ASC, with higher sensitivity and ability to annotate evidence used for prioritization. 3ASC annotates each variant with the 28 criteria defined by the ACMG/AMP genome interpretation guidelines and features related to the clinical interpretation of the variants. The system can explain the result based on annotated evidence and feature contributions.

Results
We trained various machine learning algorithms using in-house patient data. The performance of variant ranking was assessed using the recall rate of identifying causative variants in the top-ranked variants. The best practice model was a random forest classifier that showed top 1 recall of 85.6% and top 3 recall of 94.4%. The 3ASC annotates the ACMG/AMP criteria for each genetic variant of a patient so that clinical geneticists can interpret the result as in the CAGI6 SickKids challenge. In the challenge, 3ASC identified causal genes for 10 out of 14 patient cases, with evidence of decreased gene expression for 6 cases. Among them, two genes (HDAC8 and CASK) had decreased gene expression profiles confirmed by transcriptome data.

Conclusions
3ASC can prioritize genetic variants with higher sensitivity compared to previous methods by integrating various features related to clinical interpretation, including features related to false positive risk such as quality control and disease inheritance pattern. The system allows interpretation of each variant based on the ACMG/AMP criteria and feature contribution assessed using explainable AI techniques.
Mussel-inspired resilient hydrogels with strong skin adhesion and high-sensitivity for wearable device
Authors: Kondaveeti Stalin , Choi Geonjun , Veerla Sarath Chandra , Kim Somi , Kim Jaeil , Lee Hee Jin , Kuzhiumparambil Unnikrishnan , Ralph Peter J. , Yeo Junyeob , Jeong Hoon Eui 
Published: March 2024

AbstractStretchable and self-adhesive conductive hydrogels hold significant importance across a wide spectrum of applications, including human–machine interfaces, wearable devices, and soft robotics. However, integrating multiple properties, such as high stretchability, strong interfacial adhesion, self-healing capability, and sensitivity, into a single material poses significant technical challenges. Herein, we present a multifunctional conductive hydrogel based on poly(acrylic acid) (PAA), dopamine-functionalized pectin (PT-DA), polydopamine-coated reduction graphene oxide (rGO-PDA), and Fe3+ as an ionic cross-linker. This hydrogel exhibits a combination of high stretchability (2000%), rapid self-healing (~ 94% recovery in 5 s), and robust self-adhesion to various substrates. Notably, the hydrogel demonstrates a remarkable skin adhesion strength of 85 kPa, surpassing previous skin adhesive hydrogels. Furthermore, incorporating rGO within the hydrogel network creates electric pathways, ensuring excellent conductivity (0.56 S m–1). Consequently, these conductive hydrogels exhibit strain-sensing properties with a significant increase in gauge factor (GF) of 14.6, covering an extensive detection range of ~ 1000%, fast response (198 ms) and exceptional cycle stability. These multifunctional hydrogels can be seamlessly integrated into motion detection sensors capable of distinguishing between various strong or subtle movements of the human body.
Effectiveness and safety of biological and target synthetic drugs treatment for psoriatic arthritis: a systematic review with network meta-analysis
Authors: Montezuma Thais , Probst Livia Fernandes , Almeida Matheus Oliveira 
Published: March 2024

Abstract
Background
Psoriatic arthritis (PA) is a chronic inflammatory systemic arthritis that can result in loss of functional capacity and joint deformation. This systematic review assessed the effectiveness and safety of biological and target synthetic drugs for treating PA.

Methods
We searched for randomized clinical trials (RCTs) that evaluated the use of Adalimumab, Etanercept, Infliximab, Golimumab, Secukinumab, Certolizumab Pegol and Tofacitinib in the main general databases and clinical trial registers databases. The primary outcomes were ACR 50, PsARC, and serious adverse events. Two independent reviewers performed study selection and data extraction. Network meta-analyses were conducted using a random effects model and frequentist approach. The CINeMA software was used to assess the certainty of evidence.

Results
We included 33 RCTs (n = 11,034). The results from the network meta-analysis for the ACR 50 at 6-months follow-up showed that all drugs were superior to placebo, with Secukinumab (high certainty of evidence), Infliximab (very low certainty of evidence) and Adalimumab (high certainty of evidence) ranking the highest. Regarding the PsARC (at 6-months follow-up), all drugs, except for Golimumab (very low certainty of evidence), were superior to placebo, with Etanercept (low certainty of evidence), Infliximab (low certainty of evidence) and Certolizumab Pegol (low certainty of evidence) being the most effective drugs. There were no significant differences in the risk of serious adverse events between the drugs and placebo. Golimumab (very low certainty of evidence), Secukinumab (low certainty of evidence), and Adalimumab (very low certainty of evidence) ranked the highest for safety.

Conclusions
In conclusion, based on the balance between efficacy and safety, Secukinumab and Adalimumab may be the preferred options among the evaluated drugs for treating patients with PsA. However, caution is necessary when interpreting the safety findings, as they are supported by evidence of low to very low certainty. Consequently, the balance between benefits and potential risks may change as new safety evaluation studies become available.

Protocol registration
PROSPERO: CRD42022315577
Isolation and identification of associated endophytic bacteria from barely seeds harbour non-ribosomal peptides and enhance tolerance to salinity stress
Authors: Hussein Walaa , Ramadan Walaa A. , Ibrahim Hayam F. 
Published: March 2024

Abstract
Background
Barely Hordeum vulgare L. is considered one of the most important cereal crops with economic and industrial importance in the world, but its productivity is affected by climate change and abiotic stresses. One of the most recent and important microbiological promising aspects is the use of associated microorganisms, especially the endophytic bacteria producers for non-ribosomal peptides which play an important role in promoting plant growth, productivity, and tolerance to biotic and abiotic stresses. This work aims to identify vertically transferred or inherited endophytic bacterial communities in barely seeds, detect the presence of non-ribosomal peptides from these isolated endophytic strains and study their effect on protein patterns as a response to salinity stress.

Results
From two different tolerant (Giza 126) and sensitive (Giza 123) barely seeds cultivars, six different endophytic bacterial strains were isolated and identified using 16S rRNA. Bacterial strains belonged to Bacillus, Paenibacillus, Staphylococcus and Acinetobacter genera. Three of them have been isolated from both sensitive and tolerant barely cultivar (Uncultured Staphylococcus, Acinetobacter and Priestia endophytica or Bacillus endophyticus), while the other three endophytes have been isolated uniquely from the tolerant barely cultivar (Paenibacillus glucanolyticus, Bacillus cereus and Bacillus sp.). Non-ribosomal peptide synthetases genes NRPs of two lipopeptide families; surfactins and kurstakins have been detected using both bioinformatic analysis and degenerate primers. On the other hand, fragments similar to NRPs genes might be considered new NRPS molecules in Paenibacillus glucanolyticus, Acinetobacter and Priestia endophytica which have been detected using degenerate primers and required whole genome sequencing. The effect of soaking barely seeds exposed to 2.5% NaCl using SDS-PAGE electrophoresis revealed the presence of 24 bands, 10 of them were monomorphic with 41.5%, and 14 were polymorphic with 58.5% polymorphism.

Conclusion
The overnight soaking and co-cultivation of isolated endophytic strains with barely seeds before planting proved their capability in conferring salt stress tolerance to barely seedlings which appeared in protein patterns. We could consider these barely seeds endophytic among the PGPR strains promising to improve plant growth during abiotic stresses.
Performance analysis of deep learning-based object detection algorithms on COCO benchmark: a comparative study
Authors: Tian Jiya , Jin Qiangshan , Wang Yizong , Yang Jie , Zhang Shuping , Sun Dengxun 
Published: March 2024

AbstractThis paper thoroughly explores the role of object detection in smart cities, specifically focusing on advancements in deep learning-based methods. Deep learning models gain popularity for their autonomous feature learning, surpassing traditional approaches. Despite progress, challenges remain, such as achieving high accuracy in urban scenes and meeting real-time requirements. The study aims to contribute by analyzing state-of-the-art deep learning algorithms, identifying accurate models for smart cities, and evaluating real-time performance using the Average Precision at Medium Intersection over Union (IoU) metric. The reported results showcase various algorithms’ performance, with Dynamic Head (DyHead) emerging as the top scorer, excelling in accurately localizing and classifying objects. Its high precision and recall at medium IoU thresholds signify robustness. The paper suggests considering the mean Average Precision (mAP) metric for a comprehensive evaluation across IoU thresholds, if available. Despite this, DyHead stands out as the superior algorithm, particularly at medium IoU thresholds, making it suitable for precise object detection in smart city applications. The performance analysis using Average Precision at Medium IoU is reinforced by the Average Precision at Low IoU (APL), consistently depicting DyHead’s superiority. These findings provide valuable insights for researchers and practitioners, guiding them toward employing DyHead for tasks prioritizing accurate object localization and classification in smart cities. Overall, the paper navigates through the complexities of object detection in urban environments, presenting DyHead as a leading solution with robust performance metrics.
Increasing Annual Cancer Incidence in Patients Age 20-49 Years: A Real-Data Study
Authors: Ribelles Nuria , Pascual Javier , Galvez-Carvajal Laura , Ruiz-Medina Sofía , Garcia-Corbacho Javier , Benitez Jose Carlos , Dominguez-Recio Maria Emilia , Torres Esperanza , Oliva Lucia , Zalabardo Manuel , Rueda Antonio , Alba Emilio 
Published: March 2024

PURPOSE Data from population-based studies have shown an increased incidence of certain types of neoplasms in patients younger than 50 years (early-onset cancer [EOC]); however, little information is derived from other real-world data sources. In a nonpopulation registry, we analyzed changes in the incidence of several neoplasms in successive generations. METHODS This cross-sectional study included all patients with a cancer diagnosis registered in one university hospital in Málaga, Spain, between 1998 and 2021, and 18 neoplasms were analyzed. For each neoplasm, the proportion of patients younger than 50 years and age 50 years and older (late-onset cancer [LOC]) of the total number of patients diagnosed each year was determined. In addition, the age limit was lowered to 45-40 years. Changes in these proportions between each year and the following year were assessed by calculating the annual percentage change (APC), and a final assessment of these changes was performed by determining the average APC (AAPC). RESULTS Of the 24,596 patients, 5,466 (22.2%) had EOC, and 19,130 (77.8%) had LOC. The incidence of all tumors increased throughout the study period in both age groups. The AAPC increase was higher in patients with EOC than in those with LOC for the following neoplasms: head and neck (6.1% v 4.6%), colon (11.0% v 8.2%), testicular (16.3% v –13.1%), non-Hodgkin lymphoma (8.4% v 5.9%), rectum (16.1% v 6.8%), kidney (27.8% v 20.1%), and sarcoma (43.4% v 28.6%). This increase was confirmed in patients younger than 45 years and 40 years. CONCLUSION Our results are consistent with the data published for most tumor sites analyzed. This global public health problem requires the utmost attention to decrease excess cancer in young patients.
Human Papillomavirus–Attributable Head and Neck Cancers in India—A Systematic Review and Meta-Analysis
Authors: Vani Nandimandalam Venkata , Rama Ranganathan , Madhanagopal Rajendran , Vijayalakshmi Ramshankar , Swaminathan Rajaraman 
Published: March 2024

PURPOSE Head and neck cancer accounts for about one third of the global burden in India. Mucosal high-risk human papillomavirus (HPV) has been hypothesized as a contributory risk factor for head and neck cancer (HNC) but its prevalence in Indian patients is not well established. Therefore, this systematic review and meta-analysis aimed to estimate the prevalence of HPV in HNC in India and their attributable fraction by considering the biomarkers of carcinogenesis, p16, and HPV E6/E7 mRNA. METHODS A systematic literature search was done in Medline via PubMed, Embase, Scopus, ScienceDirect, ProQuest, and Cochrane to identify studies on HPV and HNC in the Indian population, published between January 1990 and October 2022. Fifty-four eligible studies were identified and relevant clinical information was collected. Meta-analysis was conducted to estimate the pooled prevalence of HPV DNA, p16INK4a, and E6/E7 mRNA percent positivity by random-effect logistic regression model using Metapreg, STATA 18. RESULTS Thirty-four high-quality studies were taken for meta-analysis. The pooled prevalence of HPV in HNC was 20% (95% CI, 12 to 32) with a high level of heterogeneity ( I2 = 90.79%). The proportion of HPV in oropharyngeal cancer (OPC; 22% [95% CI, 13 to 34]) and laryngeal cancer (LC; 29% [95% CI, 17 to 46]) was higher than in oral cancer (OC; 16% [95% CI, 8 to 30]). The HPV-attributable fraction of OPC, considering the E6/E7 mRNA and p16 positivity, was 12.54% and 9.68%, respectively, almost similar to LC (11.6% and 9.57%), while it was much lower in OC (3.36% and 4%). CONCLUSION The HPV-attributable fraction is considerably lower for OC, suggesting a negligible causative role of HPV in OC. A significant proportion of OPC and LC are attributed to HPV; however, their exact causative role is unclear because of the presence of other known risk factors.
High Concordance of Different Assays in the Determination of Homologous Recombination Deficiency–Associated Genomic Instability in Ovarian Cancer
Authors: Pfarr Nicole , von Schwarzenberg Karin , Zocholl Dario , Merkelbach-Bruse Sabine , Siemanowski Janna , Mayr Eva-Maria , Herold Sylvia , Kleo Karsten , Heukamp Lukas C. , Willing Eva-Maria , Menzel Michael , Lehmann Ulrich , Bartels Stephan , Chakraborty Shounak , Baretton Gustavo , Demes Melanie C. , Döring Claudia , Kazdal Daniel , Budczies Jan , Rad Roland , Wild Peter , Christinat Yann , McKee Thomas , Schirmacher Peter , Horst David , Büttner Reinhard , Stenzinger Albrecht , Sehouli Jalid , Vollbrecht Claudia , Hummel Michael , Braicu Elena I. , Weichert Wilko ,   on behalf of the German HRD assay Harmonization Consortium
Published: March 2024

PURPOSE Poly(ADP-ribose) polymerase inhibitors (PARPi) have shown promising clinical results in the treatment of ovarian cancer. Analysis of biomarker subgroups consistently revealed higher benefits for patients with homologous recombination deficiency (HRD). The test that is most often used for the detection of HRD in clinical studies is the Myriad myChoice assay. However, other assays can also be used to assess biomarkers, which are indicative of HRD, genomic instability (GI), and BRCA1/ 2 mutation status. Many of these assays have high potential to be broadly applied in clinical routine diagnostics in a time-effective decentralized manner. Here, we compare the performance of a multitude of alternative assays in comparison with Myriad myChoice in high-grade serous ovarian cancer (HGSOC). METHODS DNA from HGSOC samples was extracted from formalin-fixed paraffin-embedded tissue blocks of cases previously run with the Myriad myChoice assay, and GI was measured by multiple molecular assays (CytoSNP, AmoyDx, Illumina TSO500 HRD, OncoScan, NOGGO GISv1, QIAseq HRD Panel and whole genome sequencing), applying different bioinformatics algorithms. RESULTS Application of different assays to assess GI, including Myriad myChoice, revealed high concordance of the generated scores ranging from very substantial to nearly perfect fit, depending on the assay and bioinformatics pipelines applied. Interlaboratory comparison of assays also showed high concordance of GI scores. CONCLUSION Assays for GI assessment not only show a high concordance with each other but also in correlation with Myriad myChoice. Thus, almost all of the assays included here can be used effectively to assess HRD-associated GI in the clinical setting. This is important as PARPi treatment on the basis of these tests is compliant with European Medicines Agency approvals, which are methodologically not test-bound.