bluuebunny/crossref_metadata_2025_split huggingface dataset:
SUMO2/3 modification of transcription-associated proteins controls cell viability in response to oxygen and glucose deprivation-mediated stress
Authors: García-Domínguez Mario , Gallardo-Chamizo Francisco , González-Prieto Román , Jafari Vahid , Luna-Peláez Noelia , Vertegaal Alfred 
Published: December 2024

Abstract

Because limited oxygen and glucose supply to tissues is a serious challenge that cells must properly measure to decide between surviving or triggering cell death, organisms have developed accurate mechanisms for sensing and signaling these conditions. In recent years, signaling through posttranslational modification of proteins by covalent attachment of the Small Ubiquitin-like Modifier (SUMO) is gaining notoriety. Enhanced sumoylation in response to oxygen and glucose deprivation (OGD) constitutes a safeguard mechanism for cells and a new avenue for therapeutic intervention. However, indiscriminate global sumoylation can limit the therapeutic potential that a more precise action on selected targets would have. To clear up this, we have conducted a proteomic approach to identify specific SUMO targets responding to OGD and to investigate the potential these targets and their sumoylation have in preserving cells from death. Proteins undergoing sumoylation in response to OGD are mostly related to transcription and RNA processing, and the majority of them are rapidly desumoylated when restoring oxygen and glucose (ROG), confirming the high dynamics of this modification. Since OGD is highly related to brain ischemia we have also studied a cell line differentiated into neurons. However, no major differences have been observed between the SUMO-proteomes of proliferating and differentiated cells. We show that the overexpression of the transcription factor SOX2 or the SUMO ligase PIAS4 has a manifest cell protective effect largely depending on their sumoylation and that maintaining the sumoylation capacity of the coregulator NAB2 is also important to face OGD. Conversely, the sumoylation of the pluripotency factor OCT4, which is a target for the SUMO protease SENP7 after ROG, seems to block its cell survival-promoting capacity. Thus, better outcomes in cell protection would rely on the appropriate combination of sumoylated and non-sumoylated forms of selected factors.
Human health risk assessment of effluent, groundwater, and surface water in Bhakurta Union, Savar, Bangladesh
Authors: Simu Sharmine , shakil abue hasan 
Published: December 2024

Abstract

This study provides an overview of key aspects of water quality assessment in Bhakurta Union, Savar, highlighting the importance of monitoring, the methods employed, and the implications for various stakeholders. A total of 36 samples were collected to evaluate the direct effluent (DE), groundwater (GW), and surface water (SW) quality which involves the measurement and analysis of physiochemical parameters and concentration of trace metallic constituents. Physiochemical parameters include pH, DO, EC, TDS, BOD, and trace metallic constituents including Cr, Cd, Pb, and Zn are assessed in the study. The pH standard range of 6.5 to 8.5 mg/L DoE is where almost all readings fall. The electrical conductivity of direct wastewater is higher than that of groundwater and surface water. Dissolved oxygen (DO) is decreased in the DE (3.80–5.20 mg/L) when the GW and SW levels are below the DoE threshold. TDS mean values in the DE, GW, and SW are 0.53, 0.23, and 0.08 mg/L, respectively, below the DoE threshold. BOD levels are consistently far higher than the DoE standard in all samples. The mean BOD values in the DE, GW, and SW are 50, 56, and 59 mg/L, respectively. The range of Cd values in the DE, GW, and SW is 0-.67, 0-0.1, and 0-0.01 mg/L, respectively. Cr numbers that surpass the DoE standard. Pb levels within acceptable bounds are 0.05 mg/L for DE, GW, and SW, and 0.01–0.05, 0.01–0.06, and 0.01–0.05 mg/L for Pb. All values exceeded the allowed DoE ceiling. Zinc values range from 1.98 to 2.39, 1.35 to 2.22, and 0.66 to 2.08 mg/L. In cases where every data point is within the permissible range, the DoE suggests a zinc content of 5 mg/L. The Pearson correlation matrix showed a significant relationship between them. A positive correlation indicates shared sources, whilst negative correlation indicates distinct sources. Cluster analysis indicates that both natural and manmade sources contribute to the components. The water quality index (WQI) claims that almost all samples are unsafe to eat. The Hazard quotient (HQ) values for Cr are noticeably greater than the levels for Cd, Zn, and Pb, which are lower. Every sample has an adult chronic risk, as indicated by HI values larger than 1. The HQ/HI number for each sample is less than 1, which denotes a low risk of cancer. The results of the entire study indicate that while the water quality of each source is unsafe to drink and presents health hazards, it is not human carcinogenic.
Magnitude and treatment outcome of empyema thoracis in children admitted to St. Paul’s Hospital Millennium Medical College from 2015--2022
Authors: Legesse Eyerusalem , Yeshidinber Abate , Yifru Sisay 
Published: December 2024

Abstract

Background
Empyema thoracis represents a significant clinical challenge in the pediatric population. Its incidence has been increasing in recent years, resulting in increasing morbidity and healthcare costs. The aim of this study was to provide baseline data concerning the incidence, etiological distribution, clinical characteristics, laboratory evaluation, associated factors, treatment practices and outcomes of pediatric patients admitted to the SPHMMC pediatric ER, ward and ICU.
Method
A retrospective chart review over an 8-year period was performed at SPHMMC.
Results
A total of 88 patients diagnosed with empyema thoracis (ET) from January 2015 to December 2022 were included in the final analysis. Of these, 67% were male. The primary symptoms upon presentation were cough, fever, and dyspnea. The incidence of empyema thoracis was found to be 12 per 1000 admissions, representing 5.3% of pneumonia cases, which is higher than previously reported figures. Bacteriological tests indicated that Staphylococcus aureus was the most prevalent causative agent, identified in 50% of patients. All patients received intravenous antibiotics, and closed thoracostomy drainage was performed in 82.9% of cases. One-quarter of the children underwent fibrinolytic therapy, while only three patients had decortication. No in-hospital deaths occurred; however, there were high rates of both local and distant infectious complications. Although binary logistic regression suggested that leukocytosis was linked to improved outcomes, multivariable logistic regression did not identify any independent predictors for the development or outcome of ET in this study.
Conclusion
A significant increase in the incidence of empyema thoracis was noted in children, especially in the last two years. Antibiotic therapy with chest tube drainage insertion ± intrapleural fibrinolysis is an effective treatment for empyema thoracis in children, and surgical intervention is rarely performed. The overall outcome of pediatric empyema thoracis was very good in our setting.
Genome-wide analysis of ascorbate peroxidase and functional characterization of SpAPX249b and SpAPX285c for salt tolerance in Sesuvium portulacastrum
Authors: Zhou Houli , Li Yuxin , Yuan Boxuan , Nie Qinqin , Xiang Zhaozhen , He Lixia , Wang Yongfei , Yang Zhanchao , Wang Juanying , Hui Shugang , Wang Xuchu 
Published: December 2024

Abstract

Ascorbate peroxidase (APX) is a vital antioxidant enzyme, involving in plant development and stress response by scavenging excessive reactive oxygen species (ROS). The APX genes have been characterized in many organisms, however, its role in Sesuvium portulacastrum has not yet to be fully investigated. Here, we identified 33 SpAPXs from the the genome of S. portulacastrum, and found them to be divided into five subgroups across the 16 chromosomes. Cis-element analysis of their promoters indicated that all the detected SpAPXs show potential roles in response to biotic and abiotic stresses as well as phytohormone effects on the plant growth and development. Transcriptomic data of the different tissues revealed that the 9 SpAPX genes were specifically expressed in root and 13 SpAPX genes were specifically expressed in leaves, with SpAPX249b prominently expressed in root and SpAPX285c prominently expressed in leaves. Moreover, quantitative real-time PCR analysis revealed that both SpAPX249b and SpAPX285c genes expressed only after NaCl application and were sharply induced in the high concentration of NaCl treatments. Our findings suggest that SpAPX249b and SpAPX285c may be associated with palnt salt tolerance and can serve as valuable genes for enhancing salt tolerance in other plants.
Diagnosis of Intermittent Fever with Pulmonary Opacities: A Case Report of Pulmonary Primary Intravascular Large B-cell Lymphoma with Aspergillosis and Non-Tuberculous Mycobacterial Pulmonary Disease
Authors: Luan Sichun , Yao Yumeng 
Published: December 2024

Abstract

Background
Intravascular Large B‑cell Lymphoma (IVLBCL) is a rare type of aggressive extranodal non-Hodgkin lymphoma (NHL), characterized by proliferation of B lymphoma cells within blood capillary lumina. Primary pulmonary IVLBCL is a rare sub-type of IVLBCL, presenting symptoms similar to community acquired pneumonia and other pulmonary infectious diseases.
Case Presentation
A 55-year-old women presented to ward with repeated fever. Physical examination found patient had dyspnea and hypoxemia, and laboratory findings showed an increased level of lactate dehydrogenase (1092 U/L) and soluble interleukin-2 receptor (3879 U/mL). Microbiology examinations detected Aspergillus in Bronchoscopy samples, but the fever continued to present after antibiotic treatment. Pathological examination found nests of atypical cells and confirmed IVLBCL after immunohistochemical stain. Further mycobacterial culture reported NTM positive results, and the patient experienced clinical improvement after receiving R-CHOP chemotherapy.
Conclusions: This case described a situation that a patient presenting with fever and pulmonary lesions may actually came with infectious diseases overlapped with unrecognized hematological malignancy, which should be considered in differential diagnoses especially when patients do not respond well to antibiotic treatments. PET-CT plays an important role in diagnosing patients with fever, but may be misled by clinical microbiology results. Primary Pulmonary IVLBCL does not have a specific clinical manifestation, sometimes shows symptoms similar to pulmonary infectious diseases, and is usually confirmed by pathological diagnosis. mNGS has a great sensitivity in detecting microbes in clinical practice, but the diagnosis should always be careful to made before excluding malignant diseases.
Pre-trained Convolutional Neural Networks Identify Parkinson’s Disease from Spectrogram Images of Voice Samples
Authors: Rahmatallah Yasir , Kemp Aaron , Iyer Anu , Pillai Lakshmi , Larson-Prior Linda , Virmani Tuhin , Prior Fred 
Published: December 2024

Abstract

Machine learning approaches including deep learning models have shown promising performance in the automatic detection of Parkinson’s disease. These approaches rely on different types of data with voice recordings being the most used due to the convenient and non-invasive nature of data acquisition. Our group has successfully developed a novel approach that uses convolutional neural network with transfer learning to analyze spectrogram images of the sustained vowel /a/ to identify people with Parkinson’s disease. We tested this approach by collecting a dataset of voice recordings via telephone lines, which have limited bandwidth. This study builds upon our prior results in two major ways: First, we tested the performance of our approach on a larger voice dataset recorded using smartphones with wide bandwidth. Our results show comparable performance between two datasets generated using different recording platforms where we report differences in most important features resulting from the limited bandwidth of telephonic lines. Second, we compared the classification performance achieved using linear-scale and mel-scale spectrogram images and showed a small but statistically significant gain using mel-scale spectrograms. The convolutional neural network with transfer learning approach showed superior performance against conventional machine learning methods that collapse measurements across time to generate feature vectors.
Ultrasound Evaluation of the Optic Nerve in Patients With Severe Symptomatic Hyponatremia
Authors: Bosso Giorgio , Pagano Antonio , Porta Giovanni , Barbato Francesco , Allegorico Enrico , Allocca Roberto , Sansone Gennaro , Serra Claudia , Minerva Valentina , Arbo Paola , Caterino Valeria , Numis Fabio Giuliano 
Published: December 2024

Abstract

Severe hyponatremia can precipitate significant neurological symptoms due to osmotic imbalances that induce intracranial hypertension (ICH). This study investigates the correlation between serum sodium levels and optic nerve sheath diameter (ONSD), measured by ultrasound, in patients presenting with symptomatic severe hyponatremia in the Emergency Department. Sixty-four patients with symptomatic hyponatremia (Na + < 125 mmol/L) and neurological symptoms were enrolled and compared to a matched control group. Serial measurements of serum sodium and ONSD were obtained at 3, 12, and 24 hours post-correction. Results demonstrated a significant inverse correlation between sodium levels and ONSD, with ONSD decreasing as sodium levels were corrected (r = -0.71). ROC analysis confirmed ONSD as a sensitive and specific indicator of elevated intracranial pressure in these patients. This study highlights ultrasound ONSD measurement as a valuable non-invasive tool for monitoring ICH in severe hyponatremia, supporting its role in emergency settings to enhance diagnostic accuracy and therapeutic monitoring. Further research is needed to validate these findings and elucidate prognostic implications.
Proteomic analysis reveals chromatin remodeling as a potential therapeutical target in neuroblastoma
Authors: Liu Zan , Zhao Zitong , Xie Longlong , Xiao Zhenghui , Li Ming , Li Yong , Luo Ting 
Published: December 2024

Abstract

Background
Neuroblastoma (NB) is the most common solid tumor in children, characterized by high recurrence rates, drug resistance, and significant mortality.
Methods
In this study, we analyzed the proteomic profiles of NB tissue samples alongside other pathological categories, including ganglioneuroma (GN) and ganglioneuroblastoma (GNB). Using weighted gene co-expression network analysis (WGCNA), the core prognostic gene models associated with histopathology of NB were identified. Furthermore, by mapping our core prognostic gene models onto drug-perturbed transcriptome profiles from the L1000FWD and CMap databases, repurposing drug candidates were screened and validated for NB.
Results
Our proteomic analysis reveals that pathways associated with the cell cycle and DNA replication are significantly upregulated in NB, while oxidative phosphorylation, pyruvate metabolism, and the TCA cycle are notably downregulated compared to GNB and GN. By applying WGCNA, we identified a core prognostic gene model strongly associated with the unfavorable subtype and high MKI of NB and primarily related to chromatin binding and mRNA metabolic process. Protein-protein interaction network analysis identified 15 hub genes in this core prognostic module: SMARCA4, SMARCA5, SMARCC2, SMARCC1, PBRM1, BRD3, ARID1A, BRD2, ARID1B, KDM1A, TP53BP1, ALYREF, CBX1, SF3B1, and ADNP, which mainly related to chromatin remodeling. Notably, SMARCA4 and ALYREF are also high-risk genes of mortality and validated as potential prognostic biomarkers for NB. Through repurposing drugs screening, mocetinostat and clofarabine were validated as effective treatments in two NB cell lines.
Conclusion
Mocetinostat and clofarabine offer valuable insights for the development of novel targeted therapies in neuroblastoma.
DeEPsnap: human essential gene prediction by integrating multi-omics data
Authors: Zhang Xue , Xiao Weijia , Cochran Brent , Xiao Wangxin 
Published: December 2024

Abstract

Essential genes are necessary for the survival or reproduction of a living organism. The prediction and analysis of gene essentiality can advance our understanding of basic life and human diseases, and further boost the development of new drugs. Wet lab methods for identifying cell essential genes are often costly, time-consuming, and laborious. As a complement, computational methods have been proposed to predict essential genes by integrating multiple biological data sources. Most of these methods are evaluated on model organisms. However, prediction methods for human essential genes are still limited and the relationship between human gene essentiality and different biological information still needs to be explored. In addition, exploring suitable deep learning techniques to overcome the limitations of traditional machine learning methods and improve prediction accuracy is also important and interesting. We propose a snapshot ensemble deep neural network method, DeEPsnap, to predict human essential genes. DeEPsnap integrates sequence features derived from DNA and protein sequence data with features extracted or learned from multiple types of functional data, such as gene ontology, protein complex, protein domain, and protein-protein interaction network. More than 200 features from these biological data are extracted/learned which are integrated together to train a series of cost-sensitive deep neural networks by utilizing multiple deep learning techniques. The proposed snapshot mechanism enables us to train multiple models without increasing extra training effort and cost. The experimental results of 10-fold cross-validation show that DeEPsnap can accurately predict human gene essentiality with an average AUROC (Area Under the Receiver Operating Characteristic curve) of 96.1%, the average AUPRC (Area under the Precision-Recall curve) of 93.82%, the average accuracy of 92.21%, and the average F1 measure about 80.62%. In addition, the comparison of experimental results shows that DeEPsnap outperforms several popular traditional machine learning models and deep learning models. We have demonstrated that the proposed method, DeEPsnap, is effective for predicting human essential genes.
Unveiling Akkermansia muciniphila Akk11: A Comprehensive Genotypic and Phenotypic Safety Assessment
Authors: Wang Xiaowen , Fan Yixuan , Dong Yao , Zuo Huiyu , Xu Yuwei , Han Mei , Zhang Yinan , Gai Zhonghui 
Published: December 2024

Abstract

Background
As a beneficial next-generation microorganism, A. muciniphila is beginning to enter the market as a commercial product and positioning itself as a potential candidate for clinical therapy. This study aims to evaluate the safety and probiotic potential of the Akkermansia muciniphila Akk11 strain isolated from infant feces.
Results
Akk11 was identified as an anaerobic, Gram-negative strain with mucin-degrading capabilities, showing up to 98.36% genomic similarity to the type strain (ATCC BAA-835T) based on average nucleotide identity (ANI) analysis. Genotypic analysis revealed three putative genes, the blaLUS-1 gene encoding class A beta-lactamase, the adeF gene encoding a fusion protein belonging to resistance-nodule-cell division (RND) antibiotic efflux pump system and the elongation factor Tu (Ef-Tu) gene, respectively. These genes were found to be intrinsic, indicating a favorable profile for Akk11. Phenotypic tests showed that Akk11 was highly resistant to gentamicin, kanamycin and streptomycin, while producing no biogenic amines, D-/L-lactic acid or showing negative hemolytic activity. The strain showed good tolerance under gastrointestinal stress conditions, exhibited no cytotoxicity and showed strong adhesion to intestinal cells in vitro. Furthermore, no oral toxicity or genotoxicity was observed in vivo.
Conclusion
The Akk11 strain exhibits a robust safety profile and probiotic potential, with properties comparable to those of the type strain. Our research highlights a novel Akkermansia muciniphila strain, Akk11, which provides a promising new candidate for probiotic applications and warrants further commercial development.
Familiar Name, Unfamiliar Reality: Heat Illness Knowledge Gaps among Junior High and High School Students in Japan
Authors: Matsuo Hiroki , Yamashita Naoyuki 
Published: December 2024

Abstract

Background: Understanding exertional heat illness (EHI) types (heat syncope, heat cramps, exertional heat exhaustion, exertional heat stroke) and related symptoms are necessary for its prevention, and on-site first aid administration reduces its severity. In Japan, junior high and high school students learn about EHI prevention through school health education. However, their recognition and/or understanding of EHI and its related symptoms have not yet been studied. Therefore, the aim of this study was to investigate this, to improve prevention education.
Methods: A self-administered paper-based questionnaire in Japanese was distributed to assess students’ attributes, school club activity habits, and recognition and knowledge of EHI.
Results: We obtained valid responses from 66 junior high school students and 157 high school students. All students recognized the term “(exertional) heat illness,” with most having learned about it in school. However, their understanding of EHI types, symptoms, and severity classifications was limited.
Discussion: Educational content should be enhanced to improve students’ understanding of EHI types and symptoms, enabling better self-management and effective first-aid administration, and contributing to the prevention of severe cases, such as exertional heat stroke.
Conclusion: The present study showed that junior and high school students had low knowledge of EHI types and symptoms, suggesting that school-based heat illness prevention education should emphasise understanding the types of EHI and their symptoms together, as well as etiology, prevention strategies and first aid procedures to reduce the onset and severity of heat illness.