bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ferritin microheterogeneity, subunit composition, functional, and physiological implications
Authors: Srivastava Ayush K. , Reutovich Aliaksandra A. , Hunter Nathan J. , Arosio Paolo , Bou-Abdallah Fadi 
Published: November 2023

AbstractFerritin is a ubiquitous intracellular iron storage protein that plays a crucial role in iron homeostasis. Animal tissue ferritins consist of multiple isoforms (or isoferritins) with different proportions of H and L subunits that contribute to their structural and compositional heterogeneity, and thus physiological functions. Using size exclusion and anion exchange chromatography, capillary isoelectric focusing (cIEF), and SDS-capillary gel electrophoresis (SDS-CGE), we reveal for the first time a significant variation in ferritin subunit composition and isoelectric points, in both recombinant and native ferritins extracted from animal organs. Our results indicate that subunits composition is the main determinant of the mean pI of recombinant ferritin heteropolymers, and that ferritin microheterogeneity is a common property of both natural and recombinant proteins and appears to be an intrinsic feature of the cellular machinery during ferritin expression, regulation, post-translational modifications, and post-subunits assembly. The functional significance and physiological implications of ferritin heterogeneity in terms of iron metabolism, response to oxidative stress, tissue-specific functions, and pathological processes are discussed.
SETD5 regulates the OGT-catalyzed O-GlcNAcylation of RNA polymerase II, which is involved in the stemness of colorectal cancer cells
Authors: Cho Hye In , Jo Sora , Kim Min Seong , Kim Han Byeol , Liu Xingzhe , Xuan Yanhua , Cho Jin Won , Jang Yeun Kyu 
Published: November 2023

AbstractThe dosage-dependent recruitment of RNA polymerase II (Pol II) at the promoters of genes related to neurodevelopment and stem cell maintenance is required for transcription by the fine-tuned expression of SET-domain-containing protein 5 (SETD5). Pol II O-GlcNAcylation by O-GlcNAc transferase (OGT) is critical for preinitiation complex formation and transcription cycling. SETD5 dysregulation has been linked to stem cell-like properties in some cancer types; however, the role of SETD5 in cancer cell stemness has not yet been determined. We here show that aberrant SETD5 overexpression induces stemness in colorectal cancer (CRC) cells. SETD5 overexpression causes the upregulation of PI3K-AKT pathway-related genes and cancer stem cell (CSC) markers such as CD133, Kruppel-like factor 4 (KLF4), and estrogen-related receptor beta (ESRRB), leading to the gain of stem cell-like phenotypes. Our findings also revealed a functional relationship between SETD5, OGT, and Pol II. OGT-catalyzed Pol II glycosylation depends on SETD5, and the SETD5-Pol II interaction weakens in OGT-depleted cells, suggesting a SETD5-OGT-Pol II interdependence. SETD5 deficiency reduces Pol II occupancy at PI3K-AKT pathway-related genes and CD133 promoters, suggesting a role for SETD5-mediated Pol II recruitment in gene regulation. Moreover, the SETD5 depletion nullified the SETD5-induced stemness of CRC cells and Pol II O-GlcNAcylation. These findings support the hypothesis that SETD5 mediates OGT-catalyzed O-GlcNAcylation of RNA Pol II, which is involved in cancer cell stemness gain via CSC marker gene upregulation.
The use of Multispectral Radio-Meter (MSR5) data for wheat crop genotypes identification using machine learning models
Authors: Jamil Mutiullah , Rehman Hafeezur , Saqlain Zaheer Muhammad , Tariq Aqil , Iqbal Rashid , Hasnain Muhammad Usama , Majeed Asma , Munir Awais , Sabagh Ayman El , Habib ur Rahman Muhammad , Raza Ahsan , Ajmal Ali Mohammad , Elshikh Mohamed S. 
Published: November 2023

AbstractSatellite remote sensing is widely being used by the researchers and geospatial scientists due to its free data access for land observation and agricultural activities monitoring. The world is suffering from food shortages due to the dramatic increase in population and climate change. Various crop genotypes can survive in harsh climatic conditions and give more production with less disease infection. Remote sensing can play an essential role in crop genotype identification using computer vision. In many studies, different objects, crops, and land cover classification is done successfully, while crop genotypes classification is still a gray area. Despite the importance of genotype identification for production planning, a significant method has yet to be developed to detect the genotypes varieties of crop yield using multispectral radiometer data. In this study, three genotypes of wheat crop (Aas-‘2011’, ‘Miraj-‘08’, and ‘Punjnad-1) fields are prepared for the investigation of multispectral radio meter band properties. Temporal data (every 15 days from the height of 10 feet covering 5 feet in the circle in one scan) is collected using an efficient multispectral Radio Meter (MSR5 five bands). Two hundred yield samples of each wheat genotype are acquired and manually labeled accordingly for the training of supervised machine learning models. To find the strength of features (five bands), Principle Component Analysis (PCA), Linear Discriminant Analysis (LDA), and Nonlinear Discernment Analysis (NDA) are performed besides the machine learning models of the Extra Tree Classifier (ETC), Random Forest (RF), Support Vector Machine (SVM), Decision Tree (DT), Logistic Regression (LR), k Nearest Neighbor (KNN) and Artificial Neural Network (ANN) with detailed of configuration settings. ANN and random forest algorithm have achieved approximately maximum accuracy of 97% and 96% on the test dataset. It is recommended that digital policymakers from the agriculture department can use ANN and RF to identify the different genotypes at farmer's fields and research centers. These findings can be used for precision identification and management of the crop specific genotypes for optimized resource use efficiency.
Global disease burden and its attributable risk factors of peripheral arterial disease
Authors: You Yayu , Wang Zhuo , Yin Zhehui , Bao Qinyi , Lei Shuxin , Yu Jiaye , Xie Xiaojie 
Published: November 2023

AbstractPeripheral arterial disease (PAD) is a prevalent subtype of atherosclerotic cardiovascular diseases. It is crucial to assess the PAD-related burden and its attributable risk factors. We use the Global Burden of Disease study 2019 database to calculate the incidence, prevalence, mortality, disability-adjusted life years (DALY), attributable risk factors and estimated annual percentage change. The disease burden of PAD grows significantly with age accompanied by prominent heterogeneity between male and female. Despite the increase in the absolute numbers of disease burden from 1990 to 2019, the global PAD-related age-standardized death rate (ASDR) and age-standardized disability-adjusted life years rate (ASDALYR) have a mild downward trend from 1990 to 2019, which negatively correlated with sociodemographic index (SDI). Smoking and high systolic blood pressure (SBP) were the primary attributable risk factors for males (ASDR: 33.4%; ASDALYR: 43.4%) and females (ASDR: 25.3%; ASDALYR: 27.6%), respectively. High fasting plasma glucose (FPG) had become the second risk factor for ASDR (males: 28.5%; females: 25.2%) and ASDALYR (males: 29.3%; females: 26.3%) with an upward tendency. Low-middle SDI regions were predicted to have the most remarkable upward trend of PAD-related burden caused by high FPG. Smoking caused more disease burden in males before 85–90 years old and females before 65–70 years old, while high FPG and high SBP caused more burden after that. The patterns of PAD-related burden and its attributable risk factors are heterogeneous across ages, genders, and SDI regions. To reduce disease burden, tailored strategies should be implemented.
Development of an antimicrobial inorganic polymer based on fly ash and metakaolin incorporated by nano-TiO2 for reactive dye removal
Authors: Ahmed Doaa A. , El-Apasery Morsy A. , Ragai Shereen M. 
Published: November 2023

AbstractAdvanced and eco-friendly construction materials are being developed to reduce pollution and improve wastewater treatment efficiency. One such material is a photocatalytic nanocomposite that uses industrial wastes and natural substances to eliminate pollution. A recent study explored using an inorganic polymer composite (FM) made from a mixture of 70% fly ash and 30% metakaolin, with sodium hydroxide and sodium silicate as an alkali activator. The study evaluated the mechanical and hydration characteristics of the FM composite after 28 days in 100% humidity at room temperature. The study also examined the effect of adding 2.5 wt.% of Nano-TiO2 to FM composite and how it affects its properties. Results indicate that adding Nano-TiO2 to FM composite enhances its mechanical, antibacterial, and photocatalytic capabilities. Specifically, FM-TiO2 composite showed 90% removal of reactive blue 19 dye effluent in sunlight after 90 min, making it an excellent choice for sustainable wastewater treatment. This study presents a cost-effective, eco-friendly solution to wastewater treatment, with added antimicrobial properties from Nano-TiO2.
A randomized, blinded study of photobiomodulation in a mouse model of Alzheimer’s disease showed no preventive effect
Authors: Sipion Mélanie , Ferreira Filipa M. , Scholler Jules , Brana Corinne , Gora Michalina , Kouvas George , Barthet Gael , Sobolewski Aleksander 
Published: November 2023

AbstractPhotobiomodulation (PBM), the process of exposing tissue to red or near-infrared light, has become a topic of great interest as a therapy for diverse pathologies, including neurodegenerative disorders. Here, we aimed to evaluate the potential beneficial effect of PBM on Alzheimer’s disease (AD) using behavioral and histological readouts from a well-established transgenic murine AD model (5xFAD mice) in a randomized and fully blinded long-term in-vivo study following GLP (Good Laboratory Practices) guidelines. The heads of the mice were illuminated with no (sham), low or high power 810 nm light, three times a week for 5 months from the first to the sixth month of life corresponding to the prodromal phase of the pathology. The results showed that there were no significant differences between the groups in behavioral tests, including the Morris water maze, novel object recognition, and Y-maze. Similarly, histological analyses showed no differences in amyloid load, neuronal loss or microglial response. In conclusion, under the conditions of our experiment, we were unable to demonstrate any therapeutic effect of PBM for AD. This study calls for further evidence and caution when considering PBM as an effective treatment for AD.
Thermodynamics of continental deformation
Authors: Kumar Ajay , Cacace Mauro , Scheck-Wenderoth Magdalena 
Published: November 2023

AbstractContinental deformation is known to be controlled by the interplay between tectonic and gravitational forces modulated by thermal relaxation-controlled lithospheric strength leading to oscillations around an equilibrium state, or to runaway extension. Using data-driven thermomechanical modelling of the Alpine Himalayan Collision Zone, we demonstrate how deviations from an equilibrium between mantle dynamics, plate-boundary forces, and the thermochemical configuration of the lithosphere control continental deformation. We quantify such balance between the internal energy of the plate and tectonic forces in terms of a critical crustal thickness, that match the global average of present-day continental crust. It follows that thicker intraplate domains than the critical crust (orogens) must undergo weakening due to their increased internal energy, and, in doing so, they dissipate the acquired energy within a diffused zone of deformation, unlike the localized deformation seen along plate boundaries. This evolution is controlled by a dissipative thermodynamic feedback loop between thermal and mechanical relaxation of the driving energy in the orogenic lithosphere. Exponentially growing energy states, leading to runaway extension are efficiently dampened by enhanced dissipation from radioactive heat sources. This ultimately drives orogens with their thickened radiogenic crust towards a final equilibrium state. Our results suggest a genetic link between the thermochemical state of the crust and the tectonic evolution of silicate Earth-like planets.
Agave amica a potential model for the study of agavins metabolism
Authors: Salomé-Abarca Luis Francisco , Márquez-López Ruth Esperanza , López Mercedes G. 
Published: November 2023

AbstractFructans found in agave are called agavins, highly branched neo-fructans. They are essential on the yield and quality of Tequila production. The need for agave specimens with higher accumulation of agavins became essential before the growing demand of such products. To get such specimens, understanding agavins metabolism is a quintessential requirement. For this, a more efficient biological model is required. The recently reclassified Agave amica possesses the potential to gather the requirements for becoming such a model. Therefore, this study dealt with the characterization of carbohydrates in the bulbs of A. amica focusing on fructans. Moreover, it tested and described its feasibility as model for the accelerated study of agavins. Infrared analysis unveiled potential content of fructans in the bulbs of A. amica. Furthermore, high performance thin layer chromatography detected fructooligosaccharides. High performance anion exchange chromatography confirmed a polydisperse mixture of branched fructans. Gas chromatography–mass spectrometry analysis demonstrated agavins like structures in the bulbs of A. amica. Moreover, total fructan content and multivariate data analysis through bulb’s age demonstrated their correlation. Thus, the presence of agavins, their correlation with phenology, and their technical advantages highlighted the feasibility of this species as a potential new biological model for the study of agavins’ metabolism.
Endophytic bacterial communities in ungerminated and germinated seeds of commercial vegetables
Authors: Acuña Jacquelinne J. , Hu Jingming , Inostroza Nitza G. , Valenzuela Tamara , Perez Pablo , Epstein Slava , Sessitsch Angela , Zhang Qian , Jorquera Milko A. 
Published: November 2023

AbstractChile is a prominent seed exporter globally, but the seed microbiome of vegetables (46% of seeds) and its role in the early stages of plant growth have remained largely unexplored. Here, we employed DNA metabarcoding analysis to investigate the composition and putative functions of endophytic bacterial communities in ungerminated and germinated seeds of the commercial vegetables Apiaceae (parsley and carrot), Asteraceae (lettuce), Brassicaceae (cabbage and broccoli), and Solanaceae (tomato). Bacterial quantification showed 104 to 108 copies of the 16S rRNA gene per gram of ungerminated and germinated seeds. Alpha diversity analysis (e.g., Chao1, Shannon, and Simpson indices) did not indicate significant differences (Kruskal–Wallis test) between ungerminated and germinated seeds, except for Solanaceae. However, beta diversity (PCoA) analysis showed distinctions (Adonis test) between ungerminated and germinated seeds, except Apiaceae. Pseudomonadota and Bacillota were identified as the dominant and specialist taxa in both ungerminated and germinated seed samples. Chemoheterotrophy and fermentation were predicted as the main microbial functional groups in the endophytic bacterial community. Notably, a considerable number of the 143 isolated endophytic strains displayed plant growth-promoting traits (10 to 64%) and biocontrol activity (74% to 82%) against plant pathogens (Xanthomonas and Pseudomonas). This study revealed the high variability in the abundance, diversity, composition, and functionality of endophytic bacteria between ungerminated and germinated seeds in globally commercialized vegetables. Furthermore, potential beneficial endophytic bacteria contained in their seed microbiomes that may contribute to the microbiome of the early stages, development, growth and progeny of vegetables were found.
Glutamate receptor genetic variants affected peripheral glutamatergic transmission and treatment induced improvement of Indian ADHD probands
Authors: Chatterjee Mahasweta , Saha Sharmistha , Shom Sayanti , Dutta Nilanjana , Sinha Swagata , Mukhopadhyay Kanchan 
Published: November 2023

AbstractAttention deficit hyperactivity disorder (ADHD), a childhood-onset neurobehavioral disorder, often perturbs scholastic achievement and peer-relationship. The pivotal role of glutamate (Glu) in learning and memory indicated an influence of Glu in ADHD, leading to the exploration of Glu in different brain regions of ADHD subjects. We for the first time analyzed GluR genetic variations, Glu levels, as well as expression of Glu receptors (GluR) in the peripheral blood of eastern Indian ADHD probands to find out the relevance of Glu in ADHD prognosis. After obtaining informed written consent for participation, peripheral blood was collected for analyzing the genetic variants, Glu level, and expression of target genes. Since ADHD probands are often treated with methylphenidate or atomoxetine for providing symptomatic remediation, we have also tested post-therapeutic improvement in the ADHD trait scores in the presence of different GluR genotypes. Two variants, GRM7 rs3749380 “T” and GRIA1 rs2195450 “C”, exhibited associations with ADHD (P ≤ 0.05). A few GluR genetic variants showed significant association with higher trait severity, low IQ, lower plasma Glu level, down-regulated GluR mRNA expression, and poor response to medications. This indicates that down-regulated glutamatergic system may have an effect on ADHD etiology and treatment efficacy warranting further in-depth investigation.
A Weibull process monitoring with AEWMA control chart: an application to breaking strength of the fibrous composite
Authors: Sarwar Muhammad Atif , Noor-ul-Amin Muhammad , Khan Imad , Ismail Emad A. A. , Sumelka Wojciech , Nabi Muhammad 
Published: November 2023

AbstractIn recent times, there has been a growing focus among researchers on memory-based control charts. The Exponentially Weighted Moving Average (EWMA) and Cumulative Sum (CUSUM) charts and the adaptive control charting approaches got the attention. Control charts are commonly employed to oversee processes, assuming the monitored variable follows a normal distribution. However, it's worth noting that this assumption does not hold true in many real-world situations. The use of the algebraic expression for normalization, which can be used for all kinds of skewed distributions with a closed-form distribution function, using the proposed continuous function to adapt a smoothing constant, motivates this study. In the present manuscript, we design an EWMA statistic-based adaptive control chart to monitor the irregular variations in the mean of two parametric Weibull distribution and use Hasting approximation for normalization. The adaptive control charts are used to update the smoothing constant according to the estimated shift. Here we use the proposed continuous function to adapt the smoothing constant. The average run length and standard deviation of run length are calculated under different parameter settings. The effectiveness of the proposed chart is argued in terms of ARLs over the considered EWMA chart through Monte-Carlo (MC) simulation method. The proposed chart is examined, followed by a real data set to demonstrate the design and application procedures.
Plain radiographic indices are reliable indicators for quantitative bone mineral density in male and female patients before total hip arthroplasty
Authors: Rohe Sebastian , Böhle Sabrina , Matziolis Georg , Jacob Benjamin , Brodt Steffen 
Published: November 2023

AbstractOsteoporosis is underdiagnosed in patients undergoing total hip arthroplasty (THA). Bone mineral density measurement by dual-energy X-ray absorptiometry (DXA) is the gold standard, but indices on plain hip radiographs also seemed to be reliable screening tools in female or Asian ethnicities in previous studies. Given the lack of knowledge about male patients and Caucasian ethnicities, this study was conducted to evaluate plane hip radiographic indices as a screening tool for osteopenia and osteoporosis in Caucasian female and also male patients before undergoing THA. A retrospective analysis of 216 elderly patients with pre-existing DXA before hip arthroplasty was performed and four indices were calculated on plain hip radiographs: Canal-Flare-Index (CFI), Canal-Calcar-Ratio (CCR), Canal-Bone-Ratio (CBR) 7 and 10 cm below the lesser trochanter. They were correlated with femoral neck DXA T-scores by Pearson’s correlation and intraclass correlation coefficient, and a ROC analysis was performed. A total of 216 patients (49.5% male) were included. CBR-7 and -10 were highly correlated (p < 0.001) with femoral neck T-score in males (Pearson’s correlation CBR-7 r = − 0.60, CBR-10 r = − 0.55) and females (r = − 0.74, r = − 0.77). CBR-7 and -10 also showed good diagnostic accuracy for osteoporosis in the ROC analysis in males (CBR-7: AUC = 0.75, threshold = 0.51; CBR-10: 0.63; 0.50) and females (CBR-7: AUC = 0.87, threshold = 0.55; CBR-10: 0.90; 0.54). Indices such as the Canal Bone Ratio (CBR) 7 or 10 cm below the lesser trochanter on plain hip radiographs are a good screening tool for osteopenia and osteoporosis on plain hip radiographs and can be used to initiate further diagnostics like the gold standard DXA. They differ between male and female patients.
Bioinformatics analysis of immune cell infiltration patterns and potential diagnostic markers in atherosclerosis
Authors: Ji Haigang , Yuan Ling , Jiang Wenbo , Jiang Yinke , Jiang Mengke , Sun Xuemei , Chen Jing 
Published: November 2023

AbstractThis study aimed to investigate efficient diagnostic markers and molecular mechanisms of atherosclerosis and to analyze the role of immune infiltration through bioinformatics analysis. Expression profile datasets (GSE28829 and GSE43292) of patients with atherosclerosis and healthy controls were downloaded from the GEO database. Glutamine (GLN) metabolism-associated genes were obtained from the Molecular Signatures Database (MSigDB). The limma package in R was used to identify differentially expressed genes (DEGs). Significant modules were filtered using Weighted Gene Co-expression Network Analysis (WGCNA). MSigDB sets were subjected to Gene Set Enrichment Analysis and Gene Set Variation Analysis. The biological functions of DEGs were examined using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. STRING and Cytoscape software were used to identify hub genes and functional modules through protein–protein interaction (PPI) network analysis. The xCell software was adopted to assess the composition patterns of immune and stromal cells. Correlation analyses were performed for key genes and immune cell subtypes. We identified 308 DEGs and GLN-associated genes. Functional enrichment analysis showed that these genes were strongly enriched in muscle contract, muscle tissue development, cutile fiber, mycobacterial, and actin binding. Enriched KEGG pathways comprised dilated cardiomyopathy, hypertrophic cardiomyopathy, and the cAMP signaling pathway. In the PPI network analysis, 27 genes were identified as hub genes. The area under the curve (AUC) values of 27 biomarkers were relatively high, indicating high diagnostic values. The atherosclerosis group exhibited a markedly higher degree of infiltration than the control group. This study identified 27 GLN-associated genes as potential biomarkers for the diagnosis of atherosclerosis. It provides a new perspective on immune responses that facilitates exploration of the molecular mechanisms of atherosclerosis.