bluuebunny/crossref_metadata_2025_split huggingface dataset:
Associations in cell type-specific hydroxymethylation and transcriptional alterations of pediatric central nervous system tumors
Authors: Lee Min Kyung , Azizgolshani Nasim , Zhang Ze , Perreard Laurent , Kolling Fred W. , Nguyen Lananh N. , Zanazzi George J. , Salas Lucas A. , Christensen Brock C. 
Published: April 2024

AbstractAlthough intratumoral heterogeneity has been established in pediatric central nervous system tumors, epigenomic alterations at the cell type level have largely remained unresolved. To identify cell type-specific alterations to cytosine modifications in pediatric central nervous system tumors, we utilize a multi-omic approach that integrated bulk DNA cytosine modification data (methylation and hydroxymethylation) with both bulk and single-cell RNA-sequencing data. We demonstrate a large reduction in the scope of significantly differentially modified cytosines in tumors when accounting for tumor cell type composition. In the progenitor-like cell types of tumors, we identify a preponderance differential Cytosine-phosphate-Guanine site hydroxymethylation rather than methylation. Genes with differential hydroxymethylation, like histone deacetylase 4 and insulin-like growth factor 1 receptor, are associated with cell type-specific changes in gene expression in tumors. Our results highlight the importance of epigenomic alterations in the progenitor-like cell types and its role in cell type-specific transcriptional regulation in pediatric central nervous system tumors.
Evolution of triclosan resistance modulates bacterial permissiveness to multidrug resistance plasmids and phages
Authors: Yang Qiu E. , Ma Xiaodan , Li Minchun , Zhao Mengshi , Zeng Lingshuang , He Minzhen , Deng Hui , Liao Hanpeng , Rensing Christopher , Friman Ville-Petri , Zhou Shungui , Walsh Timothy R. 
Published: April 2024

AbstractThe horizontal transfer of plasmids has been recognized as one of the key drivers for the worldwide spread of antimicrobial resistance (AMR) across bacterial pathogens. However, knowledge remain limited about the contribution made by environmental stress on the evolution of bacterial AMR by modulating horizontal acquisition of AMR plasmids and other mobile genetic elements. Here we combined experimental evolution, whole genome sequencing, reverse genetic engineering, and transcriptomics to examine if the evolution of chromosomal AMR to triclosan (TCS) disinfectant has correlated effects on modulating bacterial pathogen (Klebsiella pneumoniae) permissiveness to AMR plasmids and phage susceptibility. Herein, we show that TCS exposure increases the evolvability of K. pneumoniae to evolve TCS-resistant mutants (TRMs) by acquiring mutations and altered expression of several genes previously associated with TCS and antibiotic resistance. Notably, nsrR deletion increases conjugation permissiveness of K. pneumoniae to four AMR plasmids, and enhances susceptibility to various Klebsiella-specific phages through the downregulation of several bacterial defense systems and changes in membrane potential with altered reactive oxygen species response. Our findings suggest that unrestricted use of TCS disinfectant imposes a dual impact on bacterial antibiotic resistance by augmenting both chromosomally and horizontally acquired AMR mechanisms.
Mitochondrial genome transfer drives metabolic reprogramming in adjacent colonic epithelial cells promoting TGFβ1-mediated tumor progression
Authors: Guan Bingjie , Liu Youdong , Xie Bowen , Zhao Senlin , Yalikun Abudushalamu , Chen Weiwei , Zhou Menghua , Gu Qi , Yan Dongwang 
Published: April 2024

AbstractAlthough nontumor components play an essential role in colon cancer (CC) progression, the intercellular communication between CC cells and adjacent colonic epithelial cells (CECs) remains poorly understood. Here, we show that intact mitochondrial genome (mitochondrial DNA, mtDNA) is enriched in serum extracellular vesicles (EVs) from CC patients and positively correlated with tumor stage. Intriguingly, circular mtDNA transferred via tumor cell-derived EVs (EV-mtDNA) enhances mitochondrial respiration and reactive oxygen species (ROS) production in CECs. Moreover, the EV-mtDNA increases TGFβ1 expression in CECs, which in turn promotes tumor progression. Mechanistically, the intercellular mtDNA transfer activates the mitochondrial respiratory chain to induce the ROS-driven RelA nuclear translocation in CECs, thereby transcriptionally regulating TGFβ1 expression and promoting tumor progression via the TGFβ/Smad pathway. Hence, this study highlights EV-mtDNA as a major driver of paracrine metabolic crosstalk between CC cells and adjacent CECs, possibly identifying it as a potential biomarker and therapeutic target for CC.
Combined pretreatment neutrophil-lymphocyte ratio and platelet-lymphocyte ratio predicts survival and prognosis in patients with non-metastatic nasopharyngeal carcinoma: a retrospective study
Authors: Yang Dong , Li Pian , Meng Zhen , Hu Xueying , Huang Zichong , Huang Heqing , Dong Huan , Qin Yating , Chen Cong , Chen Xinghua , Li Zhiru , Zhou Ziyan , Li Yi , Kang Min 
Published: April 2024

AbstractThe clinical significance of the combination of neutrophil–lymphocyte ratio (NLR) and platelet-lymphocyte ratio (PLR) is unclear. This study investigated the predictive value of pretreatment NLR (pre-NLR) combined with pretreatment PLR (pre-PLR) for the survival and prognosis of nasopharyngeal carcinoma (NPC). A total of 765 patients with non-metastatic NPC from two hospitals were retrospectively analyzed. The pre-NLR-PLR groups were as follows: HRG, high pre-NLR and high pre-PLR. MRG, high pre-NLR and low pre-PLR or low pre-NLR and high pre-PLR. LRG, neither high pre-NLR nor high pre-PLR. Receiver operating characteristic (ROC) curves were used to identify the cutoff-value and discriminant performance of the model. We compared survival rates and factors affecting the prognosis among different groups. The 5-year overall survival (OS), local regional recurrence-free survival (LRRFS) and distant metastasis-free survival (DMFS) of NPC patients in HRG were significantly poorer than those in MRG and LRG. The pre-NLR-PLR score was positively correlated with T stage, clinical stage, ECOG, and pathological classification. Multivariate cox regression analysis showed that pre-NLR-PLR scoring system, ECOG, pre-ALB, pre-CRP and pre-LMR were independent risk factors affecting 5-year OS, LRRFS and DMFS. The ROC curve showed that area under the curve (AUC) values of pre-NLR-PLR of 5-year OS, LRRFS and DMFS were higher than those of pre-NLR and pre-PLR. pre-NLR-PLR is an independent risk factor for the prognosis of NPC. The pre-NLR-PLR scoring system can be used as an individualized clinical assessment tool to predict the prognosis of patients with non-metastatic NPC more accurately and easily.
Diet of moulting Swainson's Thrushes (Catharus ustulatus) and Tennessee Warblers (Leiothlypis peregrina) at a stopover site during fall migration measured with fecal DNA metabarcoding
Authors: Blanc-Benigeri Ana , Poirier Vanessa , Narango Desiree , Elliott Kyle H. , Frei Barbara 
Published: April 2024

AbstractMoult and migration are energetically demanding and require adequate nutrition. In some species, individuals may interrupt their fall migration to moult at discrete stopover locations outside of their breeding grounds (i.e., moult-migration) leading to competing nutritional demands for moult and migration. Here, we use DNA barcoding of fecal samples to compare the diet of moulting and actively migrating (post-moult) Swainson’s Thrushes (Catharus ustulatus) and Tennessee Warblers (Leiothlypis peregrina) during their fall migration stopover at a large urban greenspace in Montreal, Canada. Diet differed according to moult status, species, and seasonality. Swainson’s Thrushes had a broad diet with frequent detections of both insects and berry-producing shrubs; while detections in Tennessee Warblers’ diets were mainly arthropods. For both species, more actively migrating individuals consumed fleshy-fruiting plants than moulting individuals. A higher proportion of moulting birds consumed arthropods compared to active migrants, due to either arthropod availability or a dietary preference for proteinaceous foods to grow feathers. Both species and moult classes consumed more native plants than non-native plants later in the season. We show the importance of managing urban greenspaces with native plants and diverse food sources that can provide for the different dietary needs of migratory birds.
Deep-learning based 3D birefringence image generation using 2D multi-view holographic images
Authors: Kim Hakdong , Jun Taeheul , Lee Hyoung , Chae Byung Gyu , Yoon MinSung , Kim Cheongwon 
Published: April 2024

AbstractRefractive index stands as an inherent characteristic of a material, allowing non-invasive exploration of the three-dimensional (3D) interior of the material. Certain materials with different refractive indices produce a birefringence phenomenon in which incident light is split into two polarization components when it passes through the materials. Representative birefringent materials appear in calcite crystals, liquid crystals (LCs), biological tissues, silk fibers, polymer films, etc. If the internal 3D shape of these materials can be visually expressed through a non-invasive method, it can greatly contribute to the semiconductor, display industry, optical components and devices, and biomedical diagnosis. This paper introduces a novel approach employing deep learning to generate 3D birefringence images using multi-viewed holographic interference images. First, we acquired a set of multi-viewed holographic interference pattern images and a 3D volume image of birefringence directly from a polarizing DTT (dielectric tensor tomography)-based microscope system about each LC droplet sample. The proposed model was trained to generate the 3D volume images of birefringence using the two-dimensional (2D) interference pattern image set. Performance evaluations were conducted against the ground truth images obtained directly from the DTT microscopy. Visualization techniques were applied to describe the refractive index distribution in the generated 3D images of birefringence. The results show the proposed method’s efficiency in generating the 3D refractive index distribution from multi-viewed holographic interference images, presenting a novel data-driven alternative to traditional methods from the DTT devices.
Comparative study on convolutional neural network and regression analysis to evaluate uniaxial compressive strength of Sandy Dolomite
Authors: Wang Meiqian , Liu Wenlian , Liu Haiming , Xie Ting , Wang Qinghua , Xu Wei 
Published: April 2024

AbstractSandy Dolomite is a kind of widely distributed rock. The uniaxial compressive strength (UCS) of Sandy Dolomite is an important metric in the application in civil engineering, geotechnical engineering, and underground engineering. Direct measurement of UCS is costly, time-consuming, and even infeasible in some cases. To address this problem, we establish an indirect measuring method based on the convolutional neural network (CNN) and regression analysis (RA). The new method is straightforward and effective for UCS prediction, and has significant practical implications. To evaluate the performance of the new method, 158 dolomite samples of different sandification grades are collected for testing their UCS along and near the Yuxi section of the Central Yunnan Water Diversion (CYWD) Project in Yunnan Province, Southwest of China. Two regression equations with high correlation coefficients are established according to the RA results, to predict the UCS of Sandy Dolomites. Moreover, the minimum thickness of Sandy Dolomite was determined by the Schmidt hammer rebound test. Results show that CNN outperforms RA in terms of prediction the precision of Sandy Dolomite UCS. In addition, CNN can effectively deal with uncertainty in test results, making it one of the most effective tools for predicting the UCS of Sandy Dolomite.
Fmoc-FF hydrogels and nanogels for improved and selective delivery of dexamethasone in leukemic cells and diagnostic applications
Authors: Gallo Enrico , Diaferia Carlo , Smaldone Giovanni , Rosa Elisabetta , Pecoraro Giovanni , Morelli Giancarlo , Accardo Antonella 
Published: April 2024

AbstractDexamethasone (DEX) is a synthetic analogue of cortisol commonly used for the treatment of different pathological conditions, comprising cancer, ocular disorders, and COVID-19 infection. Its clinical use is hampered by the low solubility and severe side effects due to its systemic administration. The capability of peptide-based nanosystems, like hydrogels (HGs) and nanogels (NGs), to serve as vehicles for the passive targeting of active pharmaceutical ingredients and the selective internalization into leukemic cells has here been demonstrated. Peptide based HGs loaded with DEX were formulated via the “solvent-switch” method, using Fmoc-FF homopeptide as building block. Due to the tight interaction of the drug with the peptidic matrix, a significant stiffening of the gel (G′ = 67.9 kPa) was observed. The corresponding injectable NGs, obtained from the sub-micronization of the HG, in the presence of two stabilizing agents (SPAN®60 and TWEEN®60, 48/52 w/w), were found to be stable up to 90 days, with a mean diameter of 105 nm. NGs do not exhibit hemolytic effects on human serum, moreover they are selectively internalized by RS4;11 leukemic cells over healthy PBMCs, paving the way for the generation of new diagnostic strategies targeting onco-hematological diseases.
Body mass index is an overlooked confounding factor in existing clustering studies of 3D facial scans of children with autism spectrum disorder
Authors: Schwarz Martin , Geryk Jan , Havlovicová Markéta , Mihulová Michaela , Turnovec Marek , Ryba Lukáš , Martinková Júlia , Macek Milan , Palmer Richard , Kočandrlová Karolína , Velemínská Jana , Moslerová Veronika 
Published: April 2024

AbstractCluster analyzes of facial models of autistic patients aim to clarify whether it is possible to diagnose autism on the basis of facial features and further to stratify the autism spectrum disorder. We performed a cluster analysis of sets of 3D scans of ASD patients (116) and controls (157) using Euclidean and geodesic distances in order to recapitulate the published results on the Czech population. In the presented work, we show that the major factor determining the clustering structure and consequently also the correlation of resulting clusters with autism severity degree is body mass index corrected for age (BMIFA). After removing the BMIFA effect from the data in two independent ways, both the cluster structure and autism severity correlations disappeared. Despite the fact that the influence of body mass index (BMI) on facial dimensions was studied many times, this is the first time to our knowledge when BMI was incorporated into the faces clustering study and it thereby casts doubt on previous results. We also performed correlation analysis which showed that the only correction used in the existing clustering studies—dividing the facial distance by the average value within the face—is not eliminating correlation between facial distances and BMIFA within the facial cohort.
Innovative decision making tools using discrete mathematics for stress urinary incontinence treatment
Authors: Okui Nobuo 
Published: April 2024

AbstractIn this study, we applied graph theory to clinical decision-making for Stress Urinary Incontinence (SUI) treatment. Utilizing discrete mathematics, we developed a system to visually understand the shortest path to the desired treatment outcomes by considering various patient variables. Focusing on women aged 35–50, we examined the effectiveness of Tension-free Vaginal Tape (TVT) surgery and Vaginal Erbium Laser (VEL) treatment for over 15 years. The TVT group consisted of 102 patients who underwent surgery using either the Advantage Fit mid-urethral sling system (Boston Scientific Co., MA, USA) or the GYNECARE TVT retropubic system (Ethicon Inc., NJ, USA). The VEL group included 113 patients treated with a non-ablative Erbium: YAG laser (FotonaSmooth™ XS; Fotona d.o.o., Ljubljana, Slovenia), and there were 112 patients in the control group. We constructed a network diagram analyzing the correlations between health, demographic factors, treatment methods, and patient outcomes. By calculating the shortest path using heuristic functions, we identified significant correlations and treatment effects. This approach supports patient decision making by choosing between TVT and VEL treatments based on individual objectives. Our findings provide new insights into SUI treatment, highlighting the value of a data-driven personalized approach for clinical decision-making. This interdisciplinary study bridges the gap between mathematics and medicine, demonstrating the importance of a data-centric approach in clinical decisions.
Prediction and causal inference of hyperuricemia using gut microbiota
Authors: Miyajima Yuna , Karashima Shigehiro , Mizoguchi Ren , Kawakami Masaki , Ogura Kohei , Ogai Kazuhiro , Koshida Aoi , Ikagawa Yasuo , Ami Yuta , Zhu Qiunan , Tsujiguchi Hiromasa , Hara Akinori , Kurihara Shin , Arakawa Hiroshi , Nakamura Hiroyuki , Tamai Ikumi , Nambo Hidetaka , Okamoto Shigefumi 
Published: April 2024

AbstractHyperuricemia (HUA) is a symptom of high blood uric acid (UA) levels, which causes disorders such as gout and renal urinary calculus. Prolonged HUA is often associated with hypertension, atherosclerosis, diabetes mellitus, and chronic kidney disease. Studies have shown that gut microbiota (GM) affect these chronic diseases. This study aimed to determine the relationship between HUA and GM. The microbiome of 224 men and 254 women aged 40 years was analyzed through next-generation sequencing and machine learning. We obtained GM data through 16S rRNA-based sequencing of the fecal samples, finding that alpha-diversity by Shannon index was significantly low in the HUA group. Linear discriminant effect size analysis detected a high abundance of the genera Collinsella and Faecalibacterium in the HUA and non-HUA groups. Based on light gradient boosting machine learning, we propose that HUA can be predicted with high AUC using four clinical characteristics and the relative abundance of nine bacterial genera, including Collinsella and Dorea. In addition, analysis of causal relationships using a direct linear non-Gaussian acyclic model indicated a positive effect of the relative abundance of the genus Collinsella on blood UA levels. Our results suggest abundant Collinsella in the gut can increase blood UA levels.
Factors influencing the intention to use the ICD-11 among medical record officers (MROs) and assistant medical record officers (AMROs) in Ministry of Health, Malaysia
Authors: Ooi Erwyn Chin Wei , Isa Zaleha Md , Manaf Mohd Rizal Abdul , Fuad Ahmad Soufi Ahmad , Ahmad Azman , Mustapa Mimi Nurakmal , Marzuki Nuraidah Mohd 
Published: April 2024

AbstractThe transition of ICD has never been a straightforward initiative. As nations transition to ICD-11, ensuring its acceptance among the users is essential. To our knowledge, there are limited studies about the instrument and ICD-11 adoption. Therefore, the purpose of this study was to design an instrument and investigate the factors influencing the intention to use the ICD-11 among medical record officers (MROs) and assistant medical record officers (AMROs) at Ministry of Health (MOH) Malaysia facilities. Based on the current literature, a model based on the decomposed theory of planned behaviour (DTPB) was proposed. The model consisted of 13 dimensions and 12 hypotheses identified from previous studies. Using PLS-SEM, 185 survey data points were analysed. The study findings showed that ten factors have a significant impact on the suggested model. Users' subjective norm was the most influential factor in their intention to use ICD-11. Unexpectedly, perceived usefulness and was found to have no significant influence. This study is important for policymakers in strategising ICD-11 implementation efforts. This study's novelty lies in applying a DTPB theory model in the context of the intention to use ICD-11.
Effects of washing agents on the mechanical and biocompatibility properties of water-washable 3D printing crown and bridge resin
Authors: Liu Yunqi , Jin Gan , Lim Jung-Hwa , Kim Jong-Eun 
Published: April 2024

AbstractThree-dimensional (3D) printing, otherwise known as additive manufacturing in a non-technical context, is becoming increasingly popular in the field of dentistry. As an essential step in the 3D printing process, postwashing with organic solvents can damage the printed resin polymer and possibly pose a risk to human health. The development of water-washable dental resins means that water can be used as a washing agent. However, the effects of washing agents and washing times on the mechanical and biocompatibility properties of water-washable resins remain unclear. This study investigated the impact of different washing agents (water, detergent, and alcohol) and washing time points (5, 10, 20, and 30 min) on the flexural strength, Vickers hardness, surface characterization, degree of conversion, biocompatibility, and monomer elution of 3D printed samples. Using water for long-term washing better preserved the mechanical properties, caused a smooth surface, and improved the degree of conversion, with 20 min of washing with water achieving the same biological performance as organic solvents. Water is an applicable agent option for washing the 3D printing water-washable temporary crown and bridge resin in the postwashing process. This advancement facilitates the development of other water-washable intraoral resins and the optimization of clinical standard washing guidelines.
Colostrum as a source of ESBL-Escherichia coli in feces of newborn calves
Authors: Bachmann Lisa , Weber Laura , Liermann Wendy , Hammon Harald M. , Delling Cora , Dengler Franziska , Schaufler Katharina , Schwabe Michael , Eger Elias , Becker Karsten , Schütz Anne , Homeier-Bachmann Timo 
Published: April 2024

AbstractThe aim of the present study was to determine if colostrum and the equipment for harvesting and feeding colostrum are sources of fecal ESBL/AmpC-producing Escherichia coli (ESBL/AmpC-E. coli) in calves. Therefore, 15 male calves fed with pooled colostrum on a dairy farm and held individually in an experimental barn, the colostrum pool and the equipment for harvesting and feeding colostrum were sampled and analyzed for the occurrence of ESBL/AmpC-E. coli. The ESBL-AmpC-E. coli suspicious isolates were subjected to whole-genome sequence analysis. Forty-three of 45 fecal samples were tested positive for ESBL/AmpC-E. coli. In the colostrum sample and in the milking pot, we also found ESBL/AmpC-E. coli. All 45 E. coli isolates were ESBL-producers, mainly commensal sequence type (ST) 10, but also human-extraintestinal pathogenic E. coli ST131 and ST117 were found. The clonal identity of six fecal isolates with the ESBL-E. coli isolate from the colostrum and of five fecal isolates with the strain from the milking pot demonstrates that the hygiene of colostrum or the colostrum equipment can play a significant role in the spread of ESBL-E. coli. Effective sanitation procedures for colostrum harvesting and feeding equipment are crucial to reduce the ESBL-E. coli shedding of neonatal dairy calves.