bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA N6‐methyladenosine demethylase FTO inhibits glucocorticoid‐induced osteoblast differentiation and function in bone marrow mesenchymal stem cells
Authors: Feng Lingling , Zhao Wei , Fan Yunshan , Yuan Chengcheng , Zhang Xiaohua 
Published: October 2023

AbstractExcess glucocorticoids (GCs) have been reported as key factors that impair osteoblast (OB) differentiation and function. However, the role of RNA N6‐methyladenosine (m6A) in this process has not yet been elucidated. In this study, we report that both the mRNA and protein expression of fat mass and obesity‐associated gene (FTO), a key m6A demethylase, were dose‐dependently downregulated during OB differentiation by dexamethasone (DEX) in bone marrow mesenchymal stem cells (BMSCs), and FTO was gradually increased during OB differentiation. Meanwhile, FTO knockdown suppressed OB differentiation and mineralization, whereas overexpression of wide‐type FTO, but not mutant FTO (mutated m6A demethylase active site), reversed DEX‐induced osteogenesis impairment. Interfering with FTO inhibited proliferation and the expression of Ki67 and Pcna in BMSCs during OB differentiation, whereas forced expression of wide‐type FTO improved DEX‐induced inhibition of BMSCs proliferation. Moreover, FTO knockdown reduced the mRNA stability of the OB marker genes Alpl and Col1a1, and FTO‐modulated OB differentiation via YTHDF1 and YTHDF2. In conclusion, our results suggest that FTO inhibits the GCs‐induced OB differentiation and function of BMSCs.
Development of CeO2–ZrO2 bimetallic oxide catalyst for quinoxaline synthesis
Authors: Anand Samika , Devi K. R. Sunaja 
Published: October 2023

AbstractIn recent years, heterogeneous catalysts have led to environment‐friendly transformations with better yields and reusability. Pd, one of the initial metals employed in heterogeneous organic synthesis, suffered from limitations like its high cost. This justifies the need for development of catalysts with abundant, low‐cost metals, which has been receiving a lot of attention in the scientific community. In this work, a bimetallic oxide catalyst, CeO2–ZrO2, is synthesized by a sol–gel route. The structure and morphology of the catalyst are investigated using X‐ray diffraction, scanning electron microscopy, energy‐dispersive X‐ray analysis, thermogravimetric analysis, Brunauer–Emmett–Teller measurements, and temperature‐programmed desorption. It is utilized for obtaining quinoxaline derivatives at room temperature. 2,3‐Diphenylquinoxaline is obtained via a simple condensation reaction between 1,2‐diaminobenzene and 1,2‐diketones, catalyzed by CeO2(50)–ZrO2(50) with 87% yield in 15 min. Quinoxalines are known for their biological and therapeutic activities; hence, they are essential molecules. The biological activity of the synthesized quinoxaline derivatives has been evaluated against bacterial and fungal strains. © 2023 Society of Chemical Industry.
Diagnostic and prognostic impact of preoperative thrombocytosis in muscle invasive bladder cancer: Any role in clinical practice?
Authors: Sretenovic Milan , Bojanic Nebojsa , Grozdic Milojevic Isidora , Bumbasirevic Uros , Radisavcevic Djordje , Bulat Petar , Sipetic Grujicic Sandra , Milojevic Bogomir 
Published: October 2023

AbstractBackgroundSince earlier research suggested a link between preoperative thrombocytosis and poor oncological outcomes in several cancers, the significance of platelet count abnormalities in bladder carcinoma (BC) demands for further investigation.ObjectiveTo assess the prognostic value of preoperative thrombocytosis (PTC) on survival in patients with bladder carcinoma treated by radical cystectomy (RC).Patients and MethodsAnalytical cohort comprised a single‐center series of 299 patients who underwent RC for bladder carcinoma was evaluated. A platelet count beyond the threshold of 400 × 109/L was considered thrombocytosis. Along with the Kaplan–Meier survival probability, cox proportional hazard regression models were used.ResultsTwenty‐eight (9.4%) patients had preoperative thrombocytosis. PTC was associated with gender, tumor stage, tumor grade, lymphovascular invasion, hydronephrosis, anemia (p < 0.001), and hypoalbuminemia (p < 0.001). Preoperative thrombocytosis was strongly linked to worse overall survival (OS) (p = 0.002), and cancer specific survival (CSS) (p = 0.004), according to the Kaplan–Meier method. Throughout the follow‐up, a total of 198 (66.2%) patients died, including 170 (56.9%) from BC. For this study population 5‐year CSS was 45.8%. Preoperative thrombocytosis was not independently associated with OS (HR 1.168; 95% CI 0.740–1.844; p = 0.504) or CSS (HR 1.060; 95% CI 0.649–1.730; p = 0.816) in multivariate Cox regression analysis. Only tumor stage (HR 2.558; 95% CI 1.675–3.908; p < 0.001), hydronephrosis (HR 1.614; 95% CI 1.173–2.221; p = 0.003), lymph node metastasis (HR 1.555; 95% CI 1.076–2‐2.248; p = 0.019), anemia (HR 1.454; 95% CI 1.034–2.046; p = 0.032) and ASA grade (HR 1.375; 95% CI 1.006–1.879; p = 0.046) were independently associated with CSS.ConclusionsIn a single‐center study of consecutive patients who underwent radical cystectomy for bladder cancer, preoperative thrombocytosis was unable to predict outcomes.
Human red blood cells release microvesicles with distinct sizes and protein composition that alter neutrophil phagocytosis
Authors: de Oliveira Getulio Pereira , Welsh Joshua A. , Pinckney Brandy , Palu Cintia C. , Lu Shulin , Zimmerman Alan , Barbosa Raquel Hora , Sahu Parul , Noshin Maeesha , Gummuluru Suryaram , Tigges John , Jones Jennifer Clare , Ivanov Alexander R. , Ghiran Ionita C. 
Published: October 2023

AbstractExtracellular vesicles (EVs) are membrane‐bound structures released by cells and tissues into biofluids, involved in cell‐cell communication. In humans, circulating red blood cells (RBCs), represent the most common cell‐type in the body, generating daily large numbers of microvesicles. In vitro, RBC vesiculation can be mimicked by stimulating RBCs with calcium ionophores, such as ionomycin and A23187. The fate of microvesicles released during in vivo aging of RBCs and their interactions with circulating cells is hitherto unknown. Using SEC plus DEG isolation methods, we have found that human RBCs generate microvesicles with two distinct sizes, densities and protein composition, identified by flow cytometry, and MRPS, and further validated by immune TEM. Furthermore, proteomic analysis revealed that RBC‐derived microvesicles (RBC‐MVs) are enriched in proteins with important functions in ion channel regulation, calcium homeostasis and vesicular transport, such as of sorcin, stomatin, annexin A7 and RAB proteins. Cryo‐electron microscopy identified two separate pathways of RBC‐MV‐neutrophil interaction, direct fusion with the plasma membrane and internalization, respectively. Functionally, RBC‐MVs decrease neutrophil ability to phagocytose Escherichia coli but do not affect their survival at 24 h. This work brings new insights regarding the complexity of the RBC‐MVs biogenesis, as well as their possible role in circulation.
Genomic instability‐associated two‐miRNA signature as a novel prognostic biomarker in breast cancer
Authors: Zhang Yongming , Chen Yanjia , Liu Tianjun 
Published: October 2023

AbstractBackgroundBreast cancer (BC) is the most common cancer among women worldwide and a leading cause of cancer‐associated deaths among women. However, there is a lack of accurate prognostic biomarkers for BC. In the present study, we aimed to identify a genomic instability (GI)‐associated microRNA signature as a novel potential prognostic biomarker in BC.MethodsWe performed an integrative analysis to investigate the relationship between GI and BC and identify GI‐associated microRNAs (miRNAs). Subsequently, we conducted a discovery and validation study using multicenter cohorts. The GI‐associated miRNA signature was developed in the discovery cohort and independently validated in internal and external cohorts.ResultsGI‐associated miRNAs expression in BC showed heterogeneity and was significantly correlated with BC prognosis. We identified a GI‐associated two‐miRNA signature (miR‐105‐5p and miR‐767‐5p), termed GI2miR, that stratified BC patients into high‐risk and low‐risk groups with significantly different clinical outcomes (log‐rank p = 0.027) in The Cancer Genome Atlas (TCGA) discovery cohort (n = 763). The prognostic value of GI2miR was further validated in internal TCGA validation cohort (n = 253) (log‐rank p = 0.035) and independent GSE22216 cohort (n = 210) (log‐rank p = 0.036). The GI2miR demonstrated independent prognostic value in multivariate Cox proportional hazard regression analyses and stratification analysis.ConclusionsWe have developed a novel prognostic signature based on GI‐associated two miRNAs for BC, which may lay the foundation for BC to improve prognosis prediction.
Clinical and pathological features of omicron variant of SARS‐CoV‐2‐associated kidney injury
Authors: Qi Zhiwen , Yuan Shuguang , Wei Jinying , Xia Shiyu , Huang Yao , Chen Xiaojun , Han Yachun , Li Zheng , Xiao Yang , Peng Fenghua , Fu Xiao , Sun Lin , Liu Hong , Zhu Xuejing 
Published: October 2023

AbstractKidney injury is common in patients with Coronavirus Disease‐19 (COVID‐19), which is related to poor prognosis. We aim to summarize the clinical features, athological types, and prognosis of COVID‐19 associated kidney injury caused by the Omicron strain. In this study, 46 patients with Omicron‐associated kidney injury were included, 38 of whom performed renal biopsy. Patients were divided into two groups: group A for patients with onset of kidney injury after SARS‐CoV‐2 infection; group B for patients with pre‐existing kidney disease who experienced aggravation of renal insufficiency after SARS‐CoV‐2 infection. The clinical, pathological, and prognostic characteristics of the patients were observed. Acute kidney injury (AKI) (35%) was the most common clinical manifestation in group A. Patients in group B mainly presented with chronic kidney disease (CKD) (55%) and nephrotic syndrome (NS) (40%). The pathological type was mainly IgA nephropathy (IgAN) (39% in group A and 45% in group B). Among all of them, one case presenting with thrombotic microangiopathy had worse kidney function at biopsy time. Mean serum C3 levels were 1.2 ± 0.5 and 1.0 ± 0.2 g/L in group A and group B, respectively. In renal tissues, C3 deposits were observed in 71.1% of patients. 11.8% (n = 2) patients experienced deterioration of renal function after treatment, but no patients developed to end‐stage renal disease. In our single‐center study in China, the main clinical manifestations were AKI, CKD, and NS, while the main pathological type was IgAN. Compared with previous strains of SARS‐CoV‐2, patients with the Omicron infection had a favorable prognosis.
Associations between sleep problems and posttraumatic stress symptoms, social functioning, and quality of life in refugees with posttraumatic stress disorder
Authors: Schumm Hannah , Steil Regina , Lechner‐Meichsner Franziska , Morina Nexhmedin , Weise Cornelia , Mewes Ricarda , Kuck Sascha , Reuter Julia , Giesebrecht Julia , Cludius Barbara , Ehring Thomas 
Published: October 2023

AbstractMany patients with posttraumatic stress disorder (PTSD) suffer from sleep problems, leading to impairments in social functioning and quality of life. Refugees are at high risk for sleep problems due to stressful life circumstances and a high PTSD prevalence. However, limited data on the frequency of sleep problems in refugees with diagnosed PTSD exist. This study examined the frequency of sleep problems in refugees with PTSD and their associations with symptoms of PTSD. Additionally, we investigated the contribution of sleep problems to social functioning and quality of life. Participants (N = 70) were refugees from different countries of origin currently living in Germany. All participants met the criteria for PTSD and completed measures of PTSD symptom severity, subjective sleep problems, social impairment, and quality of life. There was a very high frequency of sleep problems in the sample (100%), and sleep problems were significantly associated with both clinician‐rated, r = .47, and self‐rated, r = .30, PTSD symptom severity after controlling for overlapping items. Contrary to expectations, sleep problems did not predict social impairment, d = 0.16, nor quality of life, d = 0.13, beyond the effect of other PTSD symptoms. The findings highlight the widespread frequency of sleep problems among refugees. Future studies should assess the causal nature of the association between sleep problems and measures of psychosocial functioning in more detail and examine its dynamic change over time.
Efficacy of treatments for rosacea in the pediatric population: A systematic review
Authors: Geng Ryan , Bourkas Adrienn , Sibbald R. Gary , Sibbald Cathryn 
Published: October 2023

AbstractThe prevalence of rosacea in the pediatric population is rare and treatment recommendations specific to the pediatric population are lacking. Our objective is to perform a systematic review of the published literature to identify treatments used for rosacea in the pediatric population (age <18 years) and describe their efficacy. Literature searches were performed in four electronic databases: Medline, Embase, CINAHL and EBM Reviews. Data extraction included rosacea subtype, treatment regimen and clinical outcomes. Seventy‐six studies were included, reporting on a total of 389 patients. The most commonly reported treatments included erythromycin, metronidazole, azithromycin, tacrolimus/pimecrolimus and corticosteroids in topical formulations. Isotretinoin and physical treatment modalities were reported to be effective in treating severe recalcitrant cases of rosacea. In our review, we describe the most commonly reported therapies with demonstrated efficacy in treating pediatric rosacea. The evidence supports therapy with topical anti‐inflammatory options initially, with the addition of systemic antibiotics for cases refractory to topical monotherapy.
A missing trophic link: Contribution of the microbial loop to the estimation of the trophic position of pelagic consumers
Authors: Viana Inés G. , García‐Seoane Rita , Bode Antonio 
Published: October 2023

AbstractTrophic position estimation has been a central issue in food web studies. Estimates using compound‐specific isotopic analyses of amino acids were generally based on the trophic enrichment of glutamic acid. However, this trophic position estimation mainly accounts for the trophic steps involving metazoa, as the isotopic fractionation of this amino acid is minimal at trophic steps within the microbial food web. Alternatively, trophic position estimates based on alanine seem to also reflect microbial trophic steps. The difference between these estimations can provide an index of the microbial food web contribution to the trophic position of a particular consumer. Here, we examined the differences between both trophic position estimates through a meta‐analysis of the published data over a large range of marine consumers. The results suggest that the microbial contribution to trophic position decreases as trophic position increases in the marine pelagic food web, showing the lowest values in top consumers. Ureotelic organisms showed the highest microbial contributions. The current data point to an upper limit for the estimation of this index at δ15N values of glutamic acid or alanine of ~ 18.5‰, or trophic positions of 3.9 or 4.7 for fish and ammoniotelic organisms, respectively. Under the stable isotope lens, bacteria and protists may play a key role in the estimation of trophic positions of consumers. However, uncertainties that related both to the microbial loop (e.g., metabolic bacterial pathways) and to metazoan consumers (e.g., influence of the gut microbiome) still obscure the establishment of clear quantitative links between microbial and metazoan food webs.
Ultra‐Tough and Highly Stretchable Dual‐Crosslinked Eutectogel Based on Coordinated and Non‐Coordinated Two Types Deep Eutectic Solvent Mixture
Authors: Yu Kaixuan , Gao Yifeng , Wang Rui , Wu Linlin , Ma Xiaofeng , Fang Ying , Fang Xianli , Dou Qiang 
Published: October 2023

AbstractEutectogels are gaining attention in flexible device applications for their superior ionic conductivity, stability, biocompatibility, and cost‐effectiveness. However, most existing eutectogels suffer from low strength and toughness. Herein, ultra‐tough and highly stretchable polyacrylamide (PAM) eutectogels featuring a dual‐crosslinked network comprising chemical cross‐linking and physical cross‐linking facilitated by metal coordination bonds and hydrogen bonds are developed. This is achieved through a controlled strategy involving polymerization of acrylamide in a coordinated metal salt‐type deep eutectic solvent (DES) combined with a non‐coordinated choline chloride (ChCl)‐type DES mixture. By varying the molar ratio of these two types of DES, exceptional and adjustable mechanical properties of the resulting eutectogel are achieved, including a high tensile strength ranging from 2.9 to 8.2 MPa and elongation at break ranging from 1725 to 747%, at a 70 wt% DES content. Furthermore, the reversible non‐covalent crosslinking in these eutectogels enables self‐recovery and self‐healing capabilities of eutectogels. The prepared eutectogels also exhibit outstanding ionic conductivity (3.56 mS cm−1), making them well‐suited for use as strain sensors in human motion detection. The toughening strategy is universally effective for creating tough eutectogels using coordinated metal salt‐type DES with various metal ions, as well as a diverse range of coordinatable polymers.
Epigenetic regulation in lung cancer
Authors: Ramazi Shahin , Dadzadi Maedeh , Sahafnejad Zahra , Allahverdi Abdollah 
Published: October 2023

AbstractLung cancer is indeed a major cause of cancer‐related deaths worldwide. The development of tumors involves a complex interplay of genetic, epigenetic, and environmental factors. Epigenetic mechanisms, including DNA methylation (DNAm), histone modifications, and microRNA expression, play a crucial role in this process. Changes in DNAm patterns can lead to the silencing of important genes involved in cellular functions, contributing to the development and progression of lung cancer. MicroRNAs and exosomes have also emerged as reliable biomarkers for lung cancer. They can provide valuable information about early diagnosis and treatment assessment. In particular, abnormal hypermethylation of gene promoters and its effects on tumorigenesis, as well as its roles in the Wnt signaling pathway, have been extensively studied. Epigenetic drugs have shown promise in the treatment of lung cancer. These drugs target the aberrant epigenetic modifications that are involved in the development and progression of the disease. Several factors have been identified as drug targets in non‐small cell lung cancer. Recently, combination therapy has been discussed as a successful strategy for overcoming drug resistance. Overall, understanding the role of epigenetic mechanisms and their targeting through drugs is an important area of research in lung cancer treatment.
Neohypoplasticity Revisited
Authors: Mugele Luis , Niemunis Andrzej , Stutz Hans Henning 
Published: October 2023

AbstractThis paper presents further improvements to the neohypoplasticity (NHP), a constitutive model for sand, which overcomes some shortcomings of widely used hypoplastic models. The novelties presented in this paper includes a new description of the additional dilatancy due to the structural variable and the introduction of a new state variable, denoted as , to consider the small strain stiffness in case of a 1D loading reversal. They remove shortcomings of earlier versions of NHP. The new formulations are presented and the performance of NHP is validated with experimental data from Karlsruhe fine sand. Both monotonic and cyclic tests are simulated under drained and undrained conditions. The results demonstrate that the NHP accurately reproduces the observed behaviour in monotonic and cyclic experiments.
DichroPipeline: A suite of online and downloadable tools and resources for protein circular dichroism spectroscopic data analyses, interpretations, and their interoperability with other bioinformatics tools and resources
Authors: Janes Robert W. , Wallace B. A. 
Published: October 2023

AbstractCircular Dichroism (CD) spectroscopy is a widely‐used method for characterizing individual protein structures in solutions, membranes, films and macromolecular complexes, as well as for probing macromolecular interactions, conformational changes associated with binding substrates, and in different functionally‐related environments. This paper describes a series of related computational and display tools that have been developed over many years to aid in those characterizations and functional interpretations. The new DichroPipeline described herein links a series of format‐compatible data processing, analysis, and display tools to enable users to facilely produce the spectra, which can then be made available in the Protein Circular Dichroism Data Bank (https://pcddb.cryst.bbk.ac.uk/) resource, in which the CD spectral and associated metadata for each entry are linked to other structural and functional data bases including the Protein Data Bank (PDB), and the UniProt sequence data base, amongst others. These tools and resources thus provide the basis for a wide range of traceable structural characterizations of soluble, membrane and intrinsically‐disordered proteins.
KEGG tools for classification and analysis of viral proteins
Authors: Jin Zhao , Sato Yoko , Kawashima Masayuki , Kanehisa Minoru 
Published: October 2023

AbstractThe KEGG database and analysis tools (https://www.kegg.jp) have been developed mostly for understanding genes and genomes of cellular organisms. The KO (KEGG Orthology) dataset, which is a collection of functional orthologs, plays the role of linking genes in the genome to pathways and other molecular networks, enabling KEGG mapping to uncover hidden features in the genome. Although viruses were part of KEGG for some time, they were not fully integrated in the KEGG analysis tools, because the KO assignment rate is very low for virus genes. To supplement KOs a new dataset named virus ortholog clusters (VOCs) is computationally generated, covering 90% of viral proteins in KEGG. VOCs can be used, in place of KOs, for taxonomy mapping to uncover relationships of sequence similarity groups and taxonomic groups and for identifying conserved gene orders in virus genomes. Furthermore, selected VOCs are used to define tentative KOs for characterizing protein functions. Here an overview of KEGG tools is presented focusing on these extensions for viral protein analysis.