bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Epigenetic Changes in a Rat Model of Post-traumatic Stress Disorder Controlled by Valproic Acid
Authors: Akpınar Gökçe , Ketenci Sema , Sarıdoğan Gökçe E. , Aydın Banu , Tekin Nurdan , Cabadak Hülya , Gören M. Zafer 
Published: October 2023

Abstract
Valproic acid (VPA) is a potent non-selective histone deacetylase (HDAC) inhibitor. HDAC inhibitors and histone proteins have been studied extensively in the literature. They have been proven effective in the learning and memory processes in psychiatric conditions, including post-traumatic stress disorder (PTSD). However, the exact mechanisms and significance of different epigenetic modulations are far less clarified.
Traumatic stress results in different rates of PTSD development in clinical studies, mainly attributed to different trauma types experienced by the individuals. The treatment responses to trauma to pharmacological agents may change drastically according to gender differences. As the hippocampus has a crucial role in the memory and fear circuitry, with this study, we aimed to observe the role of HDAC inhibitor VPA on hippocampal epigenetic changes and early immediate gene activation marked by c-Fos protein in a PTSD rat model where behavioral parameters of both sexes were also considered. Our study demonstrated that freezing time and anxiety indexes were affected differently by traumatic stress in males and females; however, stress had more prominent outcomes in the female gender in both parameters. H3 acetylation was observed to be higher in saline-treated female rats than the male rats, and H4 acetylation increased in the VPA-administered stressed male rats, suggesting a possible explanation for better outcomes compared to saline-treated rats after the predator stress is applied to both groups. These results suggest that VPA positively effects learning and memory in the PTSD model, and this may be attributed to various mechanisms along with epigenetic changes.
Characterization of Fungal Microbiome Structure in Leaf Litter Compost through Metagenomic Profiling of the Nuclear Ribosomal Internal Transcribed Spacer Region
Authors: Mahongnao Sophayo , Sharma Pooja , Nanda Sarita 
Published: October 2023

Abstract
This study addressed the significant but understudied role of fungal communities in leaf litter and organic waste compost ecosystems, using advanced ITS metagenomic profiling. The research aims to comprehensively characterize these fungal communities to better understand their diversity, composition, and potential functions, with practical implications for optimizing composting processes and promoting sustainable waste management practices. Various compost samples were collected, including leaf litter composts and other matured organic waste composts, from different sources in Delhi-National Capital Region, India. DNA was extracted from these samples and amplified using PCR to obtain the DNA sequence of the fungal internal transcribed spacer (ITS) region. It was followed by sequencing and bioinformatics analysis to characterize the fungal microbiome and assess diversity within the compost ecosystems. Results revealed that leaf litter composts and cow dung manure had the highest fungal read counts, while kitchen waste compost had the lowest. Alpha diversity indices, including Chao1 and Shannon, exhibited differences in species richness and diversity among composts, though statistical significance was limited. The study also identified dominant fungal phyla such as Ascomycota, Basidiomycota, Mucoromycota, and Zoopagomycota, across the composts. The presence of beneficial fungal genera like Pichia, Trichoderma, Mortierella, Basidiobolus, as well as pathogenic viz. Alternaria, Fusarium, and Acremonium, in these composts underscored the need for proper composting practices and source selection to optimize soil fertility and minimize disease risks in agriculture. Overall, these findings contribute to optimizing composting processes, advancing waste management practices, and enhancing the use of compost as a bio-organic fertilizer. The results also highlighted the significance of monitoring compost quality and its impact on soil health for sustainable agricultural practices.
Phosphogypsum’s impact on growth and nutrient acquisition in carob trees (Ceratonia siliqua L.) inoculated with native microbiota
Authors: Khassali Hamza , Jadrane Issam , Geoffroy Alexandre , Duponnois Robin , Ouahmane Lahcen 
Published: October 2023

Abstract
Phosphogypsum (PG) management is one of the major challenges of the phosphate industries in Morocco and worldwide. Its efficient management and valorization at a low-cost and without additional treatment are highly desirable. The purpose of this study is to evaluate the effects of Moroccan PG on the growth and development of carob tree (Ceratonia siliqua) in the presence and absence of its native microbiota. The analysis of the native microbiota revealed that the bacterial community was primarily dominated by Actinobacteria and Proteobacteria, while the fungal community was mainly composed of Ascomycota and Basidiomycota. In the absence of the consortium microbiota, the heights, root dry weights, shoot dry weights and leaflet numbers increased significantly (p < 0.05) in carob plants grown on soil substrates amended with PG at a ratio of 2 % compared to those grown without PG (0 %). Micronutrient (Zn, Fe, Cu, Mn, Ni and Co) contents also increased with PG doses in both the roots and leaves although toxic elements (As, Cd and Pb) were also detected, especially in carob plants grown at 10 and 20 % PG. Inoculation with consortium microbiota in combination with PG had similar beneficial effects on the different physiological parameters measured in the carob plants. The most significant growth was recorded in carob seedlings grown under PG doses of 1 and 2 % and these plants also displayed a better performance against toxic elements. In fact, toxic element concentrations in inoculated carob seedlings grown in PG amended soil were lower compared to non-inoculated plants and far below ranges considered phytotoxic for vascular plants for both inoculum treatments. Our results open up exciting perspectives for the valorization and more widespread use of phosphogypsum in combination with native microorganisms in crop cultivation particularly in regions with difficult soil conditions.
Acquiring of photosensitivity by Mycobacterium tuberculosis in vitro and inside infected macrophages due to accumulation of endogenous Zn-porphyrins
Authors: Savitsky Alexander , Shleeva Margarita , Linge Irina , Gligonov Ivan , Vostroknutova Galina , Shashin Denis , Tsedilin Andrey , Apt Alexander , Kaprelyants Arseny 
Published: October 2023

Abstract
Mycobacterium tuberculosis (Mtb) is able to transition into a dormant state, causing the latent state of tuberculosis. Dormant mycobacteria acquire resistance to all known antibacterial drugs and can survive in the human body for decades before becoming active. In the dormant forms of M. tuberculosis, the synthesis of porphyrins and Zn-complexes significantly increased when 5-aminolevulinic acid (ALA) was added to the growth medium. Transcriptome analysis revealed a certain activation of genes involved in the metabolism of tetrapyrroles during the transition of Mtb into a dormant state, which may lead to the observed accumulation of free porphyrins. Dormant Mtb viability was reduced by more than 99.99% under illumination for 30 minutes (300 J/cm2) with 565 nm light that correspond for Zn-porphyrin and coproporphyrin absorptions. We did not observe any PDI effect using active bacteria in vitro. However, after accumulation of active cells in lung macrophages and their persistence within macrophages for several days in the presence of ALA, a significant sensitivity of active Mtb cells (ca. 99.99%) to light exposure was developed. These findings create a perspective for the treatment of latent and multidrug-resistant tuberculosis by the eradication of the pathogen in order to prevent recurrence of this disease.
Novel prognostic nomograms for postoperative patients with oral squamous cell carcinoma in the central region of China
Authors: Cheng Hao , Xu Jin-Hong , He Jia-Qi , Xu Xue-Lian 
Published: October 2023

Abstract
Background
Oral squamous cell carcinoma (OSCC) is the most common pathological type in oral tumors. This study intends to construct a novel prognostic nomogram model based on China populations for these resectable OSCC patients, and then validate these nomograms.
Methods
A total of 607 postoperative patients with OSCC diagnosed between June 2012 and June 2018 were obtained from two tertiary medical institutions in Xinxiang and Zhengzhou. Then, 70% of all the cases were randomly assigned to the training group and the rest to the validation group. The endpoint time was defined as overall survival (OS) and disease-free survival (DFS). The nomograms for predicting the 3-, and 5-year OS and DFS in postoperative OSCC patients were established based on the independent prognostic factors, which were identified by the univariate analysis and multivariate analysis. A series of indexes were utilized to assess the performance and net benefit of these two newly constructed nomograms. Finally, the discrimination capability of OS and DFS was compared between the new risk stratification and the American Joint Committee on Cancer (AJCC) stage by Kaplan-Meier curves.
Results
607 postoperative patients with OSCC were selected and randomly assigned to the training cohort (n = 425) and validation cohort (n = 182). The nomograms for predicting OS and DFS in postoperative OSCC patients had been established based on the independent prognostic factors. Moreover, dynamic nomograms were also established for more convenient clinical application. The C-index for predicting OS and DFS were 0.691, 0.674 in the training group, and 0.722, 0.680 in the validation group, respectively. Besides, the calibration curve displayed good consistency between the predicted survival probability and actual observations. Finally, the excellent performance of these two nomograms was verified by the NRI, IDI, and DCA curves in comparison to the AJCC stage system.
Conclusion
The newly established and validated nomograms for predicting OS and DFS in postoperative patients with OSCC perform well, which can be helpful for clinicians and contribute to clinical decision-making.
A patient with concurrent endobronchial leiomyoma and uterine leiomyoma: A case report
Authors: Wang Zilin , Hou Gang 
Published: October 2023

Abstract
Background: Benign endobronchial tumors are uncommon, accounting for 2% of all pulmonary tumors. Primary endobronchial leiomyomas are extremely rare, accounting for approximately 0.66% of all benign pulmonary tumors.
Case presentation: In this report, we describean uncommon case of a female patient with concurrent endobronchial and uterine leiomyomas who underwent radial endobronchial ultrasound, electrocautery snaring, and argon plasma coagulation for bronchoscopic resection of the endobronchial lesion.
Conclusions: Primary endobronchial leiomyomas are rare and diagnosed based on the pathological results, which excluded malignant lung cancer and other spindle-cell tumors. A differential diagnosis of BML could not be ignored in this patient because of her history of uterine leiomyoma.
Correlation among occupational stress, job burnout and depressive symptoms in 2,083 manufacturing workers of China
Authors: Li Xiaoyi , Chen Huiqing , Liao Xiqing , Huang Manqi , Liu Xiaoman , Guo Yao , Chen Jiabin , Li Shuang 
Published: October 2023

Abstract
Background
This study aims to investigate the correlation among occupational stress, job burnout, and depressive symptoms in manufacturing workers of China.
Methods
A total of 2,083 workers from two manufacturing enterprises in Beijing and four manufacturing enterprises in Guangdong Province were selected as study subjects using judgment sampling method. The occupational stress, job burnout, and depression symptoms were accessed using the Core Occupational Stress Measurement Scale, Maslach Burnout Inventory General Survey and Patient Health Questionnaire Depression Scale.
Results
A total of 2,311 questionnaires were distributed, and 2,083 valid questionnaires were collected, with a valid questionnaire recovery rate of 90.1%. The average score of occupational stress among the study subjects was 45.0, and the detection rate of occupational stress was 29.5% (615/2,083). The average score of job burnout was 1.8, and the detection rate of job burnout was 55.8% (1,163/2,083). The average score of depressive symptoms was 6.0, and the detection rate was 15.7% (327/2,083). The depression symptom scores of the study subjects were positively correlated with the organization and reward dimensions, the demand and effort dimensions of occupational stress, and the emotional exhaustion and depersonalization dimensions of job burnout (rS were 0.299, 0.266, 0.648 and 0.637, respectively, all P < 0.01). They were negatively correlated with the dimension scores of social support and autonomy in occupational stress, and low personal sense of achievement sense in job burnout (rS were-0.254, །0.019and །0.138, respectively, all P < 0.01). The four dimensions of occupational stress explained 15.9% of variation in depressive symptoms (P < 0.01). The inclusion of the three dimensions of job burnout on the above basis could explain 29.3% of the variation in depressive symptoms (P < 0.01).
Conclusions
Occupational stress among 2,083 manufacturing workers in China not only affected job burnout, but also indirectly affected depressive symptoms. Reducing their occupational stress and job burnout levels could help alleviate their depressive symptoms.
Causal association between type 2 diabetes and risk of pulmonary tuberculosis: A Mendelian randomization study
Authors: Cui Kunping , Teng Xiangnan , Feng Shuang , Xu Shanling , Bai Lang 
Published: October 2023

Abstract

Objective: This study examined whether T2D is causally associated with the risk of PTB.
Methods: Genome-wide association studies (GWASs) of type 2 diabetes (T2D) and pulmonary tuberculosis (PTB) were performed using a Mendelian randomization (MR)-based platform. We used publicly available summary statistics datasets from GWAS meta-analyses of T2D in individuals of East Asian descent (n = 191764) as the exposure and a GWAS dataset for PTB included in Biobank Japan (n = 212453) as the outcome. Two-sample Mendelian randomization (MR) analysis using the inverse variance-weighted (IVW), weighted median, and MR-Egger regression methods was performed to examine the causal relationship between T2D and PTB risk.
Results: We selected 81 single-nucleotide polymorphisms (SNPs) with genome‐wide significance from GWASs on T2D as the instrumental variables. Consistent associations between T2D and PTB were observed with all three methods, which suggests that T2D is positively associated with an increased risk of PTB. Moreover, the findings showed no evidence that the observed causal effect between T2D and the risk of PTB was affected by genetic pleiotropy (MR-Egger intercept = -0.024, P = 0.188).
Conclusion: MR analysis provided strong evidence indicating that T2D may be causally associated with an increased risk of PTB.
Investigating into microbiota in the uterine cavity of the unexplained recurrent spontaneous abortion patients in early pregnancy
Authors: Bai Shiyu , Xu Guocai , Mo Hanjie , Qi Tianyuan , Fu Shuai , Zhu Liqiong , Huang Bingqian , Zhang Jianping , Chen Hui 
Published: October 2023

Abstract
Introduction
The majority of unexplained recurrent spontaneous abortion (URSA) cases have been attributed to immune abnormalities. Inappropriate changes in microbiota could lead to immune disorders. However, the specific role of uterine cavity microbiota in URSA remains unclear, and only a limited number of related studies are available for reference.
Methods
We utilized double-lumen embryo transfer tubes to collect uterine cavity fluid samples from pregnant women in their first trimester. Subsequently, we conducted 16S rRNA sequencing to analyze the composition and abundance of the microbiota in these samples.
Results
For this study, we enlisted 10 cases of URSA and 28 cases of induced miscarriages during early pregnancy. Microbial communities were detected in all samples of the URSA group (100%, n = 10), whereas none were found in the control group (0%, n = 28). Among the identified microbes, Lactobacillus and Curvibacter were the two most dominant species.
Conclusions
This study revealed that during early pregnancy, Lactobacillus and Curvibacter were the predominant colonizers in the uterine cavity of URSA patients and were associated with URSA. Consequently, alterations in the dominant microbiota may lead to adverse pregnancy outcomes.
Mitochondrial respiratory function is strongly associated with progressive glaucomatous vision loss
Authors: Petriti Bledi , Rabiolo Alessandro , Chau Kai-Yin , Williams Pete , Montesano Giovanni , Lascaratos Gerassimos , Garway-Heath David 
Published: October 2023

Abstract

Intraocular pressure (IOP) has been the only modifiable risk factor for glaucoma. However, glaucoma develops with high IOP (high tension glaucoma; HTG) and normal IOP (normal tension glaucoma; NTG) and many lose vision despite IOP-lowering treatment, suggesting other factors confer susceptibility. We demonstrate that lymphocyte/monocyte mitochondrial oxygen consumption rate (OCR) is lower in glaucoma patients than in controls (P < 0.001), is lower in NTG than HTG (P < 0.01) and lower OCR is strongly associated with faster visual field (VF) progression in patients treated by lowering IOP (P < 0.001), explaining 13% of variance in the rate of progression. In a reference cohort of untreated glaucoma patents, IOP explained 16% of VF progression variance. Lymphocyte/monocyte nicotinamide adenine dinucleotide (NAD) levels are lower in glaucoma patients (P < 0.001) and strongly associated with OCR (P < 0.001). Our results support mitochondrial OCR and NAD levels as new biomarkers for glaucoma progression susceptibility and new targets for treatment.
Mechanism of Cationic Lipid-Induced DNA Condensation: Lipid-DNA Coordination and Divalent Cation Charge Fluctuations
Authors: Kirmizialtin Serdal , He Weiwei 
Published: October 2023

Abstract
The condensation of nucleic acids by lipids is a widespread phenomenon in biology with crucial implications for drug delivery. However, due to the challenges in measuring and assessing the contribution of each component in the lipid-DNA-cation system, the intricate physical mechanisms underlying the assembly of DNAs in lipid bilayers remain insufficiently understood. Specifically, the role of divalent cations in the like-charge attraction of DNA pairs remains a topic of debate. This study utilizes all-atom molecular dynamics simulations and free energy calculations to investigate the condensation of DNA duplexes in cationic lipid bilayers. Our exhaustive exploration of the thermodynamic factors inducing DNA condensation reveals unique roles for phospholipid head groups and cations. We observed that bridging cations between the lipid head groups and DNA, drastically reduce DNA charges, while mobile magnesium cations ping-ponging between DNA double strands, create charge fluctuations. While the first factor stabilizes the DNA-lipid complex, the latter creates attractive forces to induce the condensation of DNA pairs. This novel mechanism not only sheds light on the current data regarding cationic lipid-induced DNA condensation but also provides potential design strategies for creating efficient gene delivery vectors for drug delivery.
Single-cell RNA sequencing reveals osteosarcoma microenvironment differences between chemotherapy and without chemotherapy
Authors: Wang Peigeng , Wu Hao , Yao Xiguan , Ye Dongping 
Published: October 2023

Abstract
Background: Osteosarcoma(OS) is considered to be the most common primary bone tumor in adolescents. Currently, the main treatment for osteosarcoma is a combined neoadjuvant chemotherapy-surgery-adjuvant chemotherapy model. Unfortunately, this effective treatment regimen appears to have entered a bottleneck over the past 10 years, and the key mechanisms and mysteries triggered by osteosarcoma before and after chemotherapy have not been elucidated. This study aims to investigate the effects of osteosarcoma microenvironment between chemotherapy and without chemotherapy.
Methods: We obtained data on 8 osteosarcoma cases that had undergone single-cell sequencing from a public database, including 4 cases each with and without chemotherapy. The single-cell expression profile of the degenerated nucleus pulposus was constructed by software analysis for cell filtering, data normalization, cell subcluster analysis, and cell type identification procedures, and marker genes for cell subclusters were obtained. The effects of different cell subclusters on the immune microenvironment of osteosarcoma with and without chemotherapy were further investigated by gene function analysis and pseudo time analysis.
Results: The 8 osteosarcoma cases contained a total of about 100,000 single cells, and after quality control screening, a total of 80,552 cells were obtained and 8 major cell types were identified for subsequent analysis. The osteoblastic OS cells had the highest proportion of the eight major cell types, followed by the myeloid cells, osteoclasts, the proliferative OS cells, T and NK cells, endothelial cells, macrophages, and osteoblasts. Moreover, compared with the non-chemotherapy group, the heterogeneity exhibited by the chemotherapy group was also mainly reflected in several cell clusters with a high proportion.
Conclusion: Revealed that oxidative phosphorylation, epithelial-mesenchymal transition, and angiogenesis are closely associated with anti-osteosarcoma deterioration, metastasis, and chemoresistance. In addition, hypoxia related genes (RGS5, CYGB, C1qtnf3) upregulated in chemotherapy have been found to be closely related to proliferation, migration, invasion and angiogenesis of osteosarcoma cells. MMP9 and MMP13 can indirectly promote tumor angiogenesis, and down-regulation of MMP9 and MMP13 may be one of the markers of prognosis in osteosarcoma patients. Downregulation of MHCI may lead to immune escape of tumor cells. Heat shock proteins (HSP) are involved in the activation and inhibition of osteosarcoma-associated pathways. These results present a deeper single-cell atlas of the tumor microenvironment for osteosarcoma and provide potential therapeutic targets for future treatment of osteosarcoma.