bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tumorigenesis of basal muscle invasive bladder cancer was mediated by PTEN protein degradation resulting from SNHG1 upregulation
Authors: Li Tengda , Huang Maowen , Sun Ning , Hua Xiaohui , Chen Ruifan , Xie Qipeng , Huang Shirui , Du Mengxiang , Zhao Yazhen , Lin Qianqian , Xu Jiheng , Han Xiaoyun , Zhao Yunping , Tian Zhongxian , Zhang Yu , Chen Wei , Shen Xian , Huang Chuanshu 
Published: February 2024

AbstractBackgroundPhosphatase and tensin homolog deleted on chromosome ten (PTEN) serves as a powerful tumor suppressor, and has been found to be downregulated in human bladder cancer (BC) tissues. Despite this observation, the mechanisms contributing to PTEN’s downregulation have remained elusive.MethodsWe established targeted genes’ knockdown or overexpressed cell lines to explore the mechanism how it drove the malignant transformation of urothelial cells or promoted anchorageindependent growth of human basal muscle invasive BC (BMIBC) cells. The mice model was used to validate the conclusion in vivo. The important findings were also extended to human studies.ResultsIn this study, we discovered that mice exposed to N-butyl-N-(4-hydroxybu-tyl)nitrosamine (BBN), a specific bladder chemical carcinogen, exhibited primary BMIBC accompanied by a pronounced reduction in PTEN protein expression in vivo. Utilizing a lncRNA deep sequencing high-throughput platform, along with gain- and loss-of-function analyses, we identified small nucleolar RNA host gene 1 (SNHG1) as a critical lncRNA that might drive the formation of primary BMIBCs in BBN-treated mice. Cell culture results further demonstrated that BBN exposure significantly inducedSNHG1in normal human bladder urothelial cell UROtsa. Notably, the ectopic expression ofSNHG1alone was sufficient to induce malignant transformation in human urothelial cells, whileSNHG1knockdown effectively inhibited anchorage-independent growth of human BMIBCs. Our detailed investigation revealed thatSNHG1overexpression led to PTEN protein degradation through its direct interaction with HUR. This interaction reduced HUR binding to ubiquitin-specific peptidase 8 (USP8) mRNA, causing degradation of USP8 mRNA and a subsequent decrease in USP8 protein expression. The downregulation of USP8, in turn, increased PTEN polyubiquitination and degradation, culminating in cell malignant transformation and BMIBC anchorageindependent growth. In vivo studies confirmed the downregulation of PTEN and USP8, as well as their positive correlations in both BBN-treated mouse bladder urothelium and tumor tissues of bladder cancer in nude mice.ConclusionsOur findings, for the first time, demonstrate that overexpressedSNHG1competes with USP8 for binding to HUR. This competition attenuates USP8 mRNA stability and protein expression, leading to PTEN protein degradation, consequently, this process drives urothelial cell malignant transformation and fosters BMIBC growth and primary BMIBC formation.
Synthesis and biological evaluation of titanium dioxide/thiopolyurethane composite: anticancer and antibacterial effects
Authors: El Sadda Rana R. , Eissa Mai S. , Elafndi Rokaya K. , Moawed Elhossein A. , El-Zahed Mohamed M. , Saad Hoda R. 
Published: February 2024

AbstractNanocomposites incorporating titanium dioxide (TiO2) have a significant potential for various industrial and medical applications. These nanocomposites exhibit selectivity as antimicrobial and anticancer agents. Antimicrobial activity is crucial for medical uses, including applications in food processing, packaging, and surgical instruments. Additionally, these nanocomposites exhibit selectivity as anticancer agents. A stable nanocomposite as a new anticancer and antibacterial chemical was prepared by coupling titanium dioxide nanoparticles with a polyurethane foam matrix through the thiourea group. The titanium dioxide/thiopolyurethane nanocomposite (TPU/TiO2) was synthesized from low-cost Ilmenite ore and commercial polyurethane foam. EDX analysis was used to determine the elemental composition of the titanium dioxide (TiO2) matrix. TiO2NPs were synthesized and were characterized using TEM, XRD, IR, and UV–Vis spectra. TiO2NPs and TPU foam formed a novel composite. The MTT assay assessed Cisplatin and HepG-2 and MCF-7 cytotoxicity in vitro. Its IC50 values for HepG-2 and MCF-7 were 122.99 ± 4.07 and 201.86 ± 6.82 µg/mL, respectively. The TPU/TiO2 exhibits concentration-dependent cytotoxicity against MCF-7 and HepG-2 cells in vitro. The selective index was measured against both cell lines; it showed its safety against healthy cells. Agar well-diffusion exhibited good inhibition zones against Escherichia coli (12 mm), Bacillus cereus (10 mm), and Aspergillus niger (19 mm). TEM of TPU/TiO2-treated bacteria showed ultrastructure changes, including plasma membrane detachment from the cell wall, which caused lysis and bacterial death. TPU/TiO2 can treat cancer and inhibit microbes in dentures and other items. Also, TPU/TiO2 inhibits E. coli, B. cereus, and A. niger microbial strains.
Sea cucumbers: an emerging system in evo-devo
Authors: Perillo Margherita , Sepe Rosa Maria , Paganos Periklis , Toscano Alfonso , Annunziata Rossella 
Published: February 2024

AbstractA challenge for evolutionary developmental (evo-devo) biology is to expand the breadth of research organisms used to investigate how animal diversity has evolved through changes in embryonic development. New experimental systems should couple a relevant phylogenetic position with available molecular tools and genomic resources. As a phylum of the sister group to chordates, echinoderms extensively contributed to our knowledge of embryonic patterning, organ development and cell-type evolution. Echinoderms display a variety of larval forms with diverse shapes, making them a suitable group to compare the evolution of embryonic developmental strategies. However, because of the laboratory accessibility and the already available techniques, most studies focus on sea urchins and sea stars mainly. As a comparative approach, the field would benefit from including information on other members of this group, like the sea cucumbers (holothuroids), for which little is known on the molecular basis of their development. Here, we review the spawning and culture methods, the available morphological and molecular information, and the current state of genomic and transcriptomic resources on sea cucumbers. With the goal of making this system accessible to the broader community, we discuss how sea cucumber embryos and larvae can be a powerful system to address the open questions in evo-devo, including understanding the origins of bilaterian structures.
Calcific bursitis of the Gruberi bursa: a case report
Authors: Patel Nikhil N. , Jose Jean , Pravia Cristina 
Published: February 2024

Abstract
Background
Bursitis is the inflammation of a synovial bursa, a small synovial fluid-filled sac that acts as a cushion between muscles, tendons, and bones. Further, calcific bursitis results from calcium deposits on the synovial joint that exacerbates pain and swelling. The Gruberi bursa is located dorsolaterally in the ankle, between the extensor digitorium longus and the talus. Despite limited literature on its pathophysiology, the aim of this case is to discuss the bursa’s association with calcific bursitis and its management via a case presented to our clinic.

Case presentation
A 47-year-old Caucasian female with no past medical or family history presents with acute right ankle pain following a minor injury 3 months prior with no improvement on analgesic or steroid therapy. Imaging demonstrated incidental calcium deposits. The day prior to presentation, the patient stated she used 1-pound ankle weights that resulted in mild swelling and gradual pain to the right dorsoanterior ankle. Physical exam findings displayed a significant reduction in the range of motion limited by pain. Imaging confirmed calcification within the capsule of the talonavicular joint, consistent with Gruberi bursitis. Initial management with prednisone yielded minimal improvement, requiring an interventional approach with ultrasound-guided barbotage that elicited immediate improvement.

Conclusion
The presented case report highlights a rare and unique instance of acute ankle pain and swelling caused by calcific Gruberi bursitis in a young female. Although the Gruberi bursa is a relatively new discovery, it contains inflammatory components that may predispose it to calcification and should be considered in the differential of ankle swelling. Therefore, utilizing a systematic approach to a clinical presentation and considering all differential diagnoses is essential.
Addressing the challenges of reconstructing systematic reviews datasets: a case study and a noisy label filter procedure
Authors: Neeleman Rutger , Leenaars Cathalijn H. C. , Oud Matthijs , Weijdema Felix , van de Schoot Rens 
Published: February 2024

AbstractSystematic reviews and meta-analyses typically require significant time and effort. Machine learning models have the potential to enhance screening efficiency in these processes. To effectively evaluate such models, fully labeled datasets—detailing all records screened by humans and their labeling decisions—are imperative. This paper presents the creation of a comprehensive dataset for a systematic review of treatments for Borderline Personality Disorder, as reported by Oud et al. (2018) for running a simulation study. The authors adhered to the PRISMA guidelines and published both the search query and the list of included records, but the complete dataset with all labels was not disclosed. We replicated their search and, facing the absence of initial screening data, introduced a Noisy Label Filter (NLF) procedure using active learning to validate noisy labels. Following the NLF application, no further relevant records were found. A simulation study employing the reconstructed dataset demonstrated that active learning could reduce screening time by 82.30% compared to random reading. The paper discusses potential causes for discrepancies, provides recommendations, and introduces a decision tree to assist in reconstructing datasets for the purpose of running simulation studies.
Multiple objectives dynamic VM placement for application service availability in cloud networks
Authors: Alahmad Yanal , Agarwal Anjali 
Published: February 2024

AbstractEnsuring application service availability is a critical aspect of delivering quality cloud computing services. However, placing virtual machines (VMs) on computing servers to provision these services can present significant challenges, particularly in terms of meeting the requirements of application service providers. In this paper, we present a framework that addresses the NP-hard dynamic VM placement problem in order to optimize application availability in cloud computing paradigm. The problem is modeled as an integer nonlinear programming (INLP) optimization with multiple objectives and constraints. The framework comprises three major modules that use optimization methods and algorithms to determine the most effective VM placement strategy in cases of application deployment, failure, and scaling. Our primary goals are to minimize power consumption, resource waste, and server failures while also ensuring that application availability requirements are met. We compare our proposed heuristic VM placement solution with three related algorithms from the literature and find that it outperforms them in several key areas. Our solution is able to admit more applications, reduce power consumption, and increase CPU and RAM utilization of the servers. Moreover, we use a deep learning method that has high accuracy and low error loss to predict application task failures, allowing for proactive protection actions to reduce service outage. Overall, our framework provides a comprehensive solution by optimizing dynamic VM placement. Therefore, the framework can improve the quality of cloud computing services and enhance the experience for users.
Concentration strategies for spiked and naturally present biomarkers in non-invasively collected first-void urine
Authors: Téblick Laura , Lipovac Marijana , Burdier F. Ricardo , De Smet Annemie , Bell Margo , van den Borst Eef , Matheeussen Veerle , Vorsters Alex 
Published: February 2024

Abstract
Background
First-void urine (FVU) provides a non-invasive method for collecting a wide range of biomarkers found in genital tract secretions. To optimize biomarker collection in FVU, this study investigated the impact of naturally present and supplemented precipitating agents: uromodulin (UMOD) and polyethylene glycol (PEG), on the concentration of human papillomavirus (HPV) pseudovirions (PsV), cell-free DNA (cfDNA), and cellular genomic DNA (gDNA) through centrifugation.

Methods
FVU samples from ten healthy female volunteers, along with a control sample, were spiked with seal herpesvirus 1 (PhHV-1) DNA, HPV16 plasmid DNA, and HPV16 PsV with an enhanced green fluorescent protein (EGFP) reporter. The samples were subjected to various concentration protocols involving PEG precipitation, low-speed centrifugation (5 min at 1000×g), and medium-speed centrifugation (1 h at 3000×g). Subsequently, quantitative PCR (qPCR) was used to assess cellular and cell-free glyceraldehyde-3-phosphate dehydrogenase (GAPDH) DNA, cell-free PhHV-1 and HPV16 DNA, and PsV (EGFP) DNA. In addition, UMOD levels were measured.

Results
The findings revealed that PEG significantly increased the concentration of cfDNA and gDNA in the pellet after centrifugation, with the most pronounced effect observed for cfDNA. Moreover, low-speed centrifugation without PEG effectively depleted cellular gDNA while preserving cfDNA in the supernatants. Pseudovirions were consistently pelleted, even with low-speed centrifugation, and a positive but not significant effect of PEG on PsV (EGFP) DNA yield in the pellet was observed. Additionally, a significant correlation was observed between UMOD and GAPDH, HPV16, and PsV (EGFP) DNA quantities in the pellet. Furthermore, large variations among the FVU samples were observed.

Conclusions
With this study, we provide novel insights into how various biomarker precipitation protocols, including both the properties of FVU and the use of PEG as a precipitating agent, influence the concentration of cfDNA, cellular gDNA, and pseudovirions.
Long noncoding RNA and messenger RNA profiling in epicardial adipose tissue of patients with new-onset postoperative atrial fibrillation after coronary artery bypass grafting
Authors: Peng Yuanshu , Su Pixiong , Zhao Lei 
Published: February 2024

Abstract
Background
Postoperative atrial fibrillation (POAF) constitutes a significant complication following coronary artery bypass graft surgery (CABG), potentially linked to epicardial adipose tissue (EAT). This investigation seeks to elucidate the association between POAF and EAT at the genetic level.

Methods
EAT and clinical data from patients undergoing CABG were systematically acquired, adhering to established inclusion and exclusion criteria. Patients were categorized into POAF and Non-POAF groups based on the presence or absence of POAF. High-throughput sequencing data of EAT were subjected to differential expression analysis and gene function assessment. A random selection of long noncoding RNAs (lncRNAs) underwent quantitative real-time polymerase chain reaction (qRT-PCR) for validation of the high-throughput sequencing findings. Coexpression analysis was employed to elucidate the interactions between lncRNAs and messenger RNAs (mRNAs).

Results
RNA sequencing yielded a total of 69,685 transcripts (37,740 coding and 31,945 noncoding sequences), representing 16,920 genes. Within this dataset, 38 mRNAs and 12 lncRNAs exhibited differential expression between the POAF and Non-POAF groups (P < 0.05, fold change > 1.5). The qRT-PCR results for lncRNAs corroborated the sequencing findings (P < 0.01). Functional enrichment analysis of genes and the coexpression network indicated that these differentially expressed RNAs were primarily implicated in processes such as cell growth, differentiation, signal transduction, as well as influencing tissue fibrosis and ion transmembrane transport.

Conclusions
This study unveils a potential association between myocardial fibrosis and ion channels co-regulated by mRNAs and lncRNAs, closely linked to the emergence of new-onset POAF, after accounting for clinical risk factors. This discovery holds promise for further advances in clinical and fundamental research.
Langerhans cell histiocytosis of the skull in 23 children
Authors: Wei Min , Jiang Wenbin , Wang Rui , Xiao Bo , Zhan Qijia 
Published: February 2024

Abstract
Objective
To explore the clinical features, diagnosis, treatment and prognosis of Langerhans cell histiocytosis (LCH) of the skull in children.

Methods
This study retrospectively summarized the clinical manifestations, treatment methods and follow-up status of children with skull LCH who were admitted to the Department of Neurosurgery of Shanghai Children’s Hospital from January 2014 to June 2021.

Results
A total of 23 patients confirmed by histology as LCH received hospitalization treatment, including 14 males and 9 females, aged (5.76 ± 3.86) years old. The clinical manifestations were mostly incidentally discovered head masses that gradually enlarged (19 cases, 82.61%). Only 2 cases are affected by multiple systems, while the rest are affected by single systems. 9 patients were involved in multiple skull lesions, and 14 patients had local skull lesions. All patients underwent surgical intervention, with 17 patients undergoing total resection and 6 patients undergoing biopsy. 21 patients received chemotherapy after surgery. The median follow-up was 2.46 years (range 0.33–6.83 years). 21 patients had their symptoms and signs under control or even resolved, and 2 patients experienced recurrence during follow-up. The overall control rate reached 91.30%.

Conclusion
Personalized treatment plans according to different clinical types. Regular outpatient follow-up is crucial to monitor disease recurrence and late effects.
Association of triglyceride glucose index with cardiovascular events: insights from the Isfahan Cohort Study (ICS)
Authors: Rafiee Hamed , Mohammadifard Noushin , Nouri Fatemeh , Alavi Tabatabaei Ghazaal , Najafian Jamshid , Sadeghi Masoumeh , Boshtam Maryam , Roohafza Hamidreza , Haghighatdoost Fahimeh , Hassannejad Razieh , Sarrafzadegan Nizal 
Published: February 2024

Abstract
Background
There is limited evidence regarding the evaluation of the association between the triglyceride glucose (TyG) index, an indicator of insulin resistance, and the incident risk of cardiovascular disease (CVD). Therefore, we aimed to examine the relationship between the TyG index and CVD incidence in a cohort of Iranian adults.

Methods
This study was performed in the framework of the Isfahan Cohort Study (ICS). The study population included 5,432 individuals aged ≥ 35 years. CVD events, including acute myocardial infarction (MI), stroke, and unstable angina (UA), were diagnosed by physicians. The TyG index was calculated as Ln [fasting triglycerides (mg/dL) × fasting plasma glucose (mg/dL)/2]. The relationship between the TyG index and CVD events was investigated using Cox regression models. Receiver operating characteristics (ROC) curve analysis was used to determine the best cut-off for the TyG index for predicting CVD outcomes.

Results
During a median follow-up period of 11.2 years, a total number of 819 CVD, 164 MI, 172 stroke, and 384 UA were recorded. Following adjustment for multiple confounders, elevated TyG levels were associated with a higher risk of CVD (HR = 1.48; 95% CI 1.22–1.79; p < 0.001), MI (HR = 2.24; 95% CI 1.42–3.52; p < 0.001), stroke (HR = 1.45; 95% CI 0.96–2.19; p = 0.042), but not UA (HR = 1.28; 95% CI 0.96–1.69). The optimal TyG index cut-off was 8.91 for predicting CVD (sensitivity 58%; specificity 58%), 9.04 for predicting MI (sensitivity 57%; specificity 65%), 8.92 for predicting stroke (sensitivity 57%; specificity 57%), and 8.98 for predicting UA (sensitivity 53%; specificity 61%).

Conclusion
We found a robust, direct association between the TyG index and the incidence of CVD events. This emphasizes the significance of observing the TyG index as an indicator of the occurrence of CVD events.
Gut microbiota contributes to bisphenol A-induced maternal intestinal and placental apoptosis, oxidative stress, and fetal growth restriction in pregnant ewe model by regulating gut-placental axis
Authors: Zhang Hao , Zha Xia , Zhang Bei , Zheng Yi , Elsabagh Mabrouk , Wang Hongrong , Wang Mengzhi 
Published: February 2024

Abstract
Background
Bisphenol A (BPA) is an environmental contaminant with endocrine-disrupting properties that induce fetal growth restriction (FGR). Previous studies on pregnant ewes revealed that BPA exposure causes placental apoptosis and oxidative stress (OS) and decreases placental efficiency, consequently leading to FGR. Nonetheless, the response of gut microbiota to BPA exposure and its role in aggravating BPA-mediated apoptosis, autophagy, mitochondrial dysfunction, endoplasmic reticulum stress (ERS), and OS of the maternal placenta and intestine are unclear in an ovine model of gestation.

Results
Two pregnant ewe groups (n = 8/group) were given either a subcutaneous (sc) injection of corn oil (CON group) or BPA (5 mg/kg/day) dissolved in corn oil (BPA group) once daily, from day 40 to day 110 of gestation. The maternal colonic digesta and the ileum and placental tissue samples were collected to measure the biomarkers of autophagy, apoptosis, mitochondrial dysfunction, ERS, and OS. To investigate the link between gut microbiota and the BPA-induced FGR in pregnant ewes, gut microbiota transplantation (GMT) was conducted in two pregnant mice groups (n = 10/group) from day 0 to day 18 of gestation after removing their intestinal microbiota by antibiotics. The results indicated that BPA aggravates apoptosis, ERS and autophagy, mitochondrial function injury of the placenta and ileum, and gut microbiota dysbiosis in pregnant ewes. GMT indicated that BPA-induced ERS, autophagy, and apoptosis in the ileum and placenta are attributed to gut microbiota dysbiosis resulting from BPA exposure.

Conclusions
Our findings indicate the underlying role of gut microbiota dysbiosis and gut-placental axis behind the BPA-mediated maternal intestinal and placental apoptosis, OS, and FGR. The findings further provide novel insights into modulating the balance of gut microbiota through medication or probiotics, functioning via the gut-placental axis, to alleviate gut-derived placental impairment or FGR.
Effect of onions tunic extract on sodium oxalate-induced acute kidney injury
Authors: Olayeriju Olanrewaju Sam , Omoboyowa Damilola Alex 
Published: February 2024

AbstractAcute kidney injury (AKI) is one of the global health concerns afflicting the human population and urolithiasis (kidney stone), especially the calcium oxalate stone is the most prominent amongst the stone formers with a huge recurrence rate. This study elucidates the ameliorative potential of the tunic of onions against Wistar kidney rats toxified with sodium oxalate.Ethylacetate extract of the tunic of onions otherwise regarded as Onions peel extract (OPE) in this study was prepared to get the flavonol-rich extracts. Adult male Wistar rats received 70 mg/kg body weight sodium oxalate with or without co-treatment with OPE, quercetin or cystone. Biochemical analyses were carried out on the plasma and urine, followed by a histopathological assessment of the kidney. Intoxication with sodium oxalate brought about electrolyte imbalance, nephrotic syndrome (high concentrations of total protein and albumin in the urine and low concentrations in the plasma) reduced renal function (low renal clearance of creatinine and urea) and damage to the kidney as well as fluid accumulation. Treatment with flavonol extract from onion tunic mitigated these deleterious changes as a result of sodium oxalate intoxication. The finding suggests that onion peel has the potential to prevent damage arising from oxalate toxicity in the kidney.
Graphical Abstract