bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intestinal microbiome changes and mechanisms of maintenance hemodialysis patients with constipation
Authors: Zhang Aiping , Chen Shilei , Zhu Yanqin , Wu Mengqi , Lu Bin , Zhou Xin , Zhu Yan , Xu Xinyu , Liu Hong , Zhu Fenggui , Lin Riyang 
Published: November 2024

BackgroundConstipation is a common symptom in maintenance hemodialysis patients and greatly affects the quality of survival of hemodialysis patients. Fecal microbiota transplantation and probiotics are feasible treatments for functional constipation, but there is still a gap in the research on the characteristics of gut flora in patients with maintenance hemodialysis combined with constipation. The aim of this study is to clarify the characteristics of the intestinal flora and its changes in maintenance hemodialysis patients with constipation.MethodsFecal samples were collected from 45 participants, containing 15 in the maintenance hemodialysis constipation group,15 in the maintenance hemodialysis non-constipation group and 15 in the healthy control group. These samples were analyzed using 16S rRNA gene sequencing. The feature of the intestinal microbiome of maintenance hemodialysis constipation group and the microbiome differences among the three groups were elucidated by species annotation analysis, α-diversity analysis, β-diversity analysis, species difference analysis, and predictive functional analysis.ResultsThe alpha diversity analysis indicated that maintenance hemodialysis constipation group was less diverse and homogeneous than maintenance hemodialysis non-constipation group and healthy control group. At the genus level, the top ten dominant genera in maintenance hemodialysis constipation group patients were Enterococcus, Escherichia-Shigella, Bacteroides, Streptococcus, Bifidobacterium, Ruminococcus_gnavus_group, Lachnospiraceae_unclassified, Faecalibacterium, Akkermansia and UCG-002. Compared with non-constipation group, the Enterococcus, Rhizobiales_unclassified, Filomicrobium, Eggerthella, Allobaculum, Prevotella_7, Gordonibacter, Mitochondria_unclassified, Lachnoanaerobaculum were significantly higher in constipation group (p&lt;0.05). Compared with non-constipation group, the Kineothrix, Rhodopirellula, Weissella were significantly lower in constipation group (p&lt;0.05). The predictive functional analysis revealed that compared with non-constipation group, constipation group was significantly enriched in pathways associated with pyruate metabolism, flavonoid biosynthesis.ConclusionsThis study describes for the first time the intestinal microbiome characteristics of maintenance hemodialysis patients with constipation. The results of this study suggest that there is a difference in the intestinal flora between maintenance hemodialysis patients with constipation and maintenance hemodialysis patients without constipation.
Do clean fuel and trade-openness reduce environmental degradation in China: evidence from asymmetric model
Authors: Shakeel Muhammad , Nobre Catarina 
Published: November 2024

IntroductionThis study investigates the relationship between economic growth, clean fuel utilization, trade, and environmental pollution. By focusing on the potential of clean fuels and trade in reducing pollution, this research aims to understand their role in promoting environmental sustainability in China from 1990 to 2020.MethodsThe study employs the Nonlinear Autoregressive Distributed Lags (NARDL) approach to analyze time series data. This method enables the decomposition of impacts from clean fuels and trade on pollution levels, facilitating an understanding of their distinct contributions to environmental outcomes.ResultsFindings indicate that economic growth is associated with an increase in pollution levels, while clean fuel usage exhibits a modest but significant reduction effect. Nonetheless, the relatively small coefficients highlight the need for a greater share of clean fuels in China’s energy mix. Additionally, trade shows a significant negative relationship with pollution emissions, with data reflecting a gradual decline in pollution over time.DiscussionThese results underscore the benefits of clean fuel adoption and trade promotion as effective measures for mitigating pollution. However, they also highlight the necessity for stronger regulatory policies, public awareness initiatives, and investments in sustainable technologies to ensure China’s long-term environmental sustainability.
Hydrochemical characterization and sustainability assessment of Ismailia canal water, Eastern Nile Delta, Egypt: implications for human health and environmental safety
Authors: El-Said Salem Zenhom , Attiah Abdullah Muhammad , Abu-Alam Tamer 
Published: November 2024

Surface freshwater systems globally face severe stresses due to overpopulation and associated waste. The Ismailia Canal, a crucial freshwater source in the eastern Nile Delta, Egypt, serves multiple purposes and is endangered by various environmental activities. This study characterizes the canal’s water using physicochemical parameters to evaluate its suitability for different uses. Water samples were collected twice in winter and summer seasons of the year 2018 from eight sites distributed along the course of Ismailia Canal. A comprehensive chemical analysis of the samples was carried out. Water chemistry was graphically and statistically assessed. Water qualities were evaluated using WHO guidelines, water quality index (WQI), Pollution indices of metals (PIm) and long- and short-term effect of trace elements on irrigation. Results show that the water is slightly alkaline and moderately hard, with higher salinity in winter than summer. Major cations and anions are higher in winter, whereas NO₃ is higher in summer. The canal water is primarily of the Ca(Mg)-HCO₃ type, influenced mainly by rock-water interactions. While most physicochemical parameters meet drinking water standards, Al, Sb, As, Cd, Fe, Pb, and Tl exceed limits, with significant impacts from Al and Tl year-round, and seasonal impacts from As, Pb, Cd, and Fe. For irrigation, water quality is generally unaffected in winter, but Mo and Se have slight impacts in summer for long-term use. This research is vital for informing sustainable water management practices, which are crucial for Egypt’s research initiatives, economic stability, and environmental sustainability.
Causal impact of gut microbiota on five liver diseases: insights from mendelian randomization and single-cell RNA sequencing
Authors: Li Na , Chen Xuanyi , Xiong Shuai , Cheng Yuxin , Deng Jiali , Zhang Junli , Yu Fei , Hao Liyuan , Li Shenghao , Hu Xiaoyu 
Published: November 2024

BackgroundLiver disease is among the top ten causes of death globally. With studies suggesting a link between gut microbiota (GM) and liver disease.MethodWe selected summary statistics data from the largest available whole-genome association study (n = 13,266) of GM by the MiBioGen consortium as the exposure, and obtained liver disease-related data from IEU Open GWAS and The NHGRI-EBI GWAS Catalog. A two-sample Mendelian Randomization (MR) analysis employing various methods, to establish the causal relationship between GM and five liver diseases. Meanwhile, single-cell RNA sequencing data were used to examine Prevotella-related genes expression under healthy and disease liver.ResultsThe IVW analysis indicate a causal relationship between GM and liver diseases, with Prevotella exhibiting a protective effect in all five liver diseases: Alcoholic liver disease (OR:0.81,95% confidence interval:0.66-1.00,PIVW = 0.0494); Cirrhosis (OR: 0.85,95% confidence interval: 0.73-0.99,PIVW = 0.0397); Hepatic failure, not elsewhere classified (OR:0.60,95% confidence interval:0.37-0.95,PIVW = 0.0305); Benign neoplasm:Liver (OR:0.39,95% confidence interval:0.2-0.75,PIVW = 0.0046); Malignant neoplasm of liver, primary (OR:0.41, 95% confidence interval:0.18-0.93,PIVW = 0.0334). The single-cell results suggest differential expression of Prevotella-related genes between liver disease patients and healthy individuals.ConclusionOur MR results show a causal relationship between the GM and liver disease. Prevotella displays a notable protective effect. This finding may enhance the precision of GM-based therapies and offer new insights for clinical research.
Periodontal ligament tissues support neutrophil differentiation and maturation processes
Authors: Villagómez-Olea Guillermo , Uribe-Querol Eileen , Marichi-Rodríguez Francisco Javier , Meléndez-Zajgla Jorge , Alvaréz-Pérez Marco Antonio , Rosales Carlos 
Published: November 2024

IntroductionPeriodontal ligament is the soft connective tissue joining the roots of teeth with alveolar bone. The periodontal ligament presents significant cellular heterogeneity, including fibroblasts, endothelial cells, cementoblasts, osteoblasts, osteoclasts, and immune cells such as macrophages and neutrophils. These cells have crucial roles for periodontium homeostasis and function. However, certain cell types, such as neutrophils, remain poorly characterized in this tissue, despite their natural abundance and relevance in processes and diseases affecting the periodontal ligament.MethodsIn order to characterize neutrophils present in periodontal ligament, and get some insight into their functions, single-cell RNA sequencing data from published reports was analyzed to integrate and create a comprehensive map of neutrophil heterogeneity within the murine periodontal ligament under steady-state conditions.ResultsFour distinct neutrophil populations were identified based on their unique transcriptional signatures. Comparison and trajectory analysis revealed that these populations represent discrete stages of neutrophils undergoing maturation. These neutrophil populations were also classified, based on their granule content-associated signatures, as azurophil, specific, a transitional stage between specific and gelatinase (specific/gelatinase), and gelatinase. This reflects the sequential order of granule formation during neutrophil development (granulopoiesis) in the bone marrow.DiscussionTogether, our findings indicate that the periodontal ligament may serve as a microenvironment where the ordered and sequential maturation of neutrophils takes place. This suggests that similarly to other niches, the murine periodontal ligament can support, to some extent, hematopoietic processes such as granulopoiesis.
Deciphering differences in microbial community characteristics and main factors between healthy and root rot-infected Carya cathayensis rhizosphere soils
Authors: Fang Wei , Zhu Yiyang , Liang Chenfei , Shao Shuai , Chen Junhui , Qing Hua , Xu Qiufang 
Published: November 2024

IntroductionFusarium-induced root rot of Carya cathayensis (C. cathayensis) is a typical soil-borne disease that has severely damaged the Carya cathayensis industry in China. Understanding the interaction among soil microbial communities, soil characteristics, and pathogenic bacteria is very important for the ecological prevention and control of Carya cathayensis root rot.MethodsWe used Miseq Illumina high-throughput sequencing technology to study the microbial community in the rhizosphere soil of healthy and diseased C. cathayensis, quantified the abundance of bacteria, fungi, and pathogenic fungi, and combined these with soil chemistry and enzyme activity indicators to analyze the characteristics of healthy and diseased rhizosphere soils.ResultsWe found that the pH, soil organic carbon(SOC), available nitrogen (AN), available phosphorus (AP), available potassium (AK),N-acetyl-β-D-glucosaminidase (NAG) β-glucosidase (BG), fungal gene copy number, bacterial community diversity and network complexity of the diseased soil were significantly lower (p &lt; 0.05), while Fusarium graminearum copies number levels increased (p &lt; 0.05). Additionally, the study found that healthy soils were enriched with beneficial bacteria such as Subgroup_7 (0.08%), MND1 (0.29%), SWB02 (0.08%), and Bradyrhizobium (0.09%), as well as potential pathogen-suppressing fungi such as Mortierella (0.13%), Preussia (0.03%), and Humicol (0.37%), were found to be associated with the growth and development of C. cathayensis.DiscussionIn summary, this research comprehensively reveals the differences in environmental and biological factors between healthy and diseased soils, as well as their correlations. It provides a theoretical basis for optimal soil environmental regulation and the construction of healthy microbial communities. This foundation facilitates the development of multifaceted strategies for the prevention and control of C. cathayensis root rot.
Variation and evolution analysis of SARS-CoV-2 using self-game sequence optimization
Authors: Liu Ziyu , Shen Yi , Jiang Yunliang , Zhu Hancan , Hu Hailong , Kang Yanlei , Chen Ming , Li Zhong 
Published: November 2024

IntroductionThe evolution of SARS-CoV-2 has precipitated the emergence of new mutant strains, some exhibiting enhanced transmissibility and immune evasion capabilities, thus escalating the infection risk and diminishing vaccine efficacy. Given the continuous impact of SARS-CoV-2 mutations on global public health, the economy, and society, a profound comprehension of potential variations is crucial to effectively mitigate the impact of viral evolution. Yet, this task still faces considerable challenges.MethodsThis study introduces DARSEP, a method based on Deep learning Associates with Reinforcement learning for SARS-CoV-2 Evolution Prediction, combined with self-game sequence optimization and RetNet-based model.ResultsDARSEP accurately predicts evolutionary sequences and investigates the virus’s evolutionary trajectory. It filters spike protein sequences with optimal fitness values from an extensive mutation space, selectively identifies those with a higher likelihood of evading immune detection, and devises a superior evolutionary analysis model for SARS-CoV-2 spike protein sequences. Comprehensive downstream task evaluations corroborate the model’s efficacy in predicting potential mutation sites, elucidating SARS-CoV-2’s evolutionary direction, and analyzing the development trends of Omicron variant strains through semantic changes.ConclusionOverall, DARSEP enriches our understanding of the dynamic evolution of SARS-CoV-2 and provides robust support for addressing present and future epidemic challenges.
The association between oxidative balance score and sleep duration: a mediation analysis of a cross-sectional study
Authors: Hao Guihua , Zhao Xiaomei , Fu Weiwei , Wu Yiwen , Dai Jingjing , Qian Yifeng , Xie Tian , Hou Lili , Shi Wentao 
Published: November 2024

Study objectivesThe Oxidative Balance Score (OBS), which reflects overall oxidation through diet and lifestyle, has been linked to sleep, but few studies have clarified this relationship. We investigated the association between OBS and sleep duration, and whether oxidative stress (OS) and inflammation mediate the underlying mechanisms.MethodsData were obtained from the National Health and Nutrition Examination Survey spanning the years 2007 to 2018. Multivariable logistic regression analyses were used to evaluate the association between OBS and the risk of sleep duration. Mediation analyses were conducted to investigate the role of OS and inflammatory markers.ResultsA significant negative association was found between OBS and sleep duration (p &lt; 0.01). Meanwhile, compared to participants in OBS tertile 1, the ORs (95% CIs) of incident short sleep duration were 0.78 (0.72–0.86) and 0.72 (0.67–0.79) (both p &lt; 0.01) for OBS tertile 2 and 3, respectively. And the ORs (95% CIs) of incident long sleep duration were 0.83 (0.73, 0.95) and 0.66 (0.57, 0.75) (both p &lt; 0.01) for OBS tertiles 2 and 3 after adjustment for multivariate variables. A linear relationship between OBS and short/long sleep duration (p for non-linearity = 0.69/0.94, both p &lt; 0.01) were revealed. Mediation analysis showed absolute neutrophil count, serum total bilirubin mediated the association between OBS and short/long sleep duration with 5.72, 13.41% proportion of mediation, respectively (both p &lt; 0.001).ConclusionOBS is negatively associated with sleep duration. OS and inflammatory biomarkers mediate the relationship.
Screening high-risk individuals for primary gastric adenocarcinoma: evaluating progression-free survival probability score in the presence and absence of Rictor expression after gastrectomy
Authors: Wang Jian , Li Yifan , Liang Sujiao 
Published: November 2024

ObjectiveDeveloping nomogram-based risk stratification model to determine 3-year and 5-year progression-free survival (PFS) and to identify high-risk patients with gastric adenocarcinoma based on different Rictor statuses.Methods1366 individuals who underwent radical gastric surgery to treat gastric adenocarcinoma at Shanxi Cancer Hospital from May 2002 to December 2020 were analyzed. Cox regression analysis was employed to create the nomograms. The nomograms’ performance was assessed using C-index, time receiver operating characteristic (t-ROC) curves, calibration curves, and decision curve analysis (DCA) curves in training and validation cohorts. Subsequently, patients were categorized into high-risk and low-risk groups based on the nomogram’s risk scores.ResultsThe Rictor (-) nomogram for predicting PFS included variables such as age, number of positive lymph nodes, vascular invasion, maximum diameter of the tumor, omentum metastasis, and expression of MSH2. In the internal validation, the C-index of the Rictor (-) nomogram was 0.760 (95%CI: 0.720-0.799), which was superior to the C-index of the American Joint Committee on Cancer (AJCC) 8th edition TNM staging (0.683, 95%CI: 0.646-0.721). Similarly, the Rictor (+) nomogram for predicting PFS included variables such as gender, age, pT stage, number of positive lymph nodes, neural invasion, maximum diameter of the tumor, omentum metastasis, Clavien-Dindo classification for complications, and CGA expression. The C-index of the Rictor (+) nomogram was 0.795 (95%CI: 0.764-0.825), which outperformed the C-index of the AJCC 8th edition TNM staging (0.693, 95%CI: 0.662-0.723). The calibration curves, t-ROC curves, and decision curve analysis for both nomogram models demonstrated their excellent prediction ability.ConclusionThis study presents the first risk stratification for Rictor status in gastric adenocarcinoma. Our model identifies low-risk patients who may not require additional postoperative treatment, while high-risk patients should consider targeted therapies that specifically target Rictor-positive indicators.
Case report: Radical robotic nephroureterectomy after chemotherapy followed by avelumab in a patient with node-positive UTUC
Authors: Studentova Hana , Student Vladimir , Kurfurstova Daniela , Kopova Andrea , Melichar Bohuslav 
Published: November 2024

IntroductionPlatinum-based chemotherapy followed by the immune checkpoint inhibitor avelumab represents an intensified upfront therapy regimen that may result in significant downstaging and, subsequently, potentially radical robotic nephroureterectomy with a lymph node dissection, an uncommon approach with an unexpectedly favorable outcome.Case presentationWe report a case of a 70-year-old female presented with a sizeable cN2+ tumor of the left renal pelvis and achieved deep partial radiologic response after systemic therapy with four cycles of gemcitabine-cisplatin chemotherapy followed by avelumab maintenance therapy and subsequent robotic resection of the tumor. The patient continued with adjuvant nivolumab therapy once recovered after surgery and remained tumor-free on the subsequent follow-up. The systemic treatment was without any severe adverse reaction.ConclusionWe highlight the feasibility of the upfront systemic therapy with four cycles of gemcitabine-cisplatin chemotherapy followed by avelumab maintenance, robotic-assisted removal of the tumor, and adjuvant immunotherapy with nivolumab. This intensification of the upfront systemic therapy, and the actual treatment sequence significantly increase the chances of prolonged survival or even a cure. This type of personalized therapeutic approach can accelerate future advanced immunotherapeutic strategies.
Surgical management of a large cystic trochlear nerve schwannoma mimicking a brainstem glioma: a case report
Authors: Fimic Miroslav , Haas Patrick , Ortiz Rey Jose Antonio , Tatagiba Marcos 
Published: November 2024

IntroductionIntracranial schwannomas represent a rare group of intracranial tumors, with purely motor nerve schwannomas being the rarest of them. The anatomical proximity of these tumors to the brainstem may present a radiological challenge in differentiating them from intra–axial brainstem tumors, which can influence further decision–making and treatment options.MethodsWe report on a 47–year–old male patient who was diagnosed with a large cystic intracranial tumor with radiological features suggestive of an intrinsic brainstem glioma.ResultsAfter discussing treatment options and risks based on a presumed radiological diagnosis, microsurgical treatment via lateral–suboccipital craniotomy in semi–sitting position, under continuous intraoperative neuromonitoring was performed. Intraoperative findings proved that the tumor was an extra–axial schwannoma originating from the left trochlear nerve. Gross total removal of the lesion was achieved.ConclusionDue to their rarity, non–specific symptoms and the possibility to mimicking intra–axial brainstem tumors on imaging, these tumors may present a diagnostic challenge and should be taken into account during treatment decision-making.
Single and consecutive 10-day remote ischemic preconditioning modify physical performance, post-exercise exerkine levels, and inflammation
Authors: Kochanowicz Magdalena , Brzezinska Paulina , Mieszkowski Jan , Kochanowicz Andrzej , Niespodzinski Bartlomiej , Surmiak Marcin , Reczkowicz Joanna , Borkowska Andzelika , Antosiewicz Jedrzej 
Published: November 2024

PurposeRemote ischemic preconditioning (RIPC) is a method of protection against induced ischemia reperfusion injury, and an increasing number of studies showed some of its inconclusive ergogenic effects in sports. RIPC involves short cycles of cuff inflation followed by its deflation which may affect many body systems. While most of the studies focus on single RIPC effects, there is insufficient data regarding training-like repeated RIPC interventions. Thus, in this study, we analyzed the effect of a single- and consecutive 10-day RIPC procedure on a single leg, focusing on the exerkine levels and changes in inflammation markers following the Wingate Anaerobic Test (WAnT).MethodsTwo single-blinded, sham-controlled protocols were designed to evaluate the 1) single (crossover study) and 2) consecutive 10-day (parallel study) RIPC effects on the WAnT performance and exercise-induced lactate, glucose, exerkine, and inflammation markers (BDNF; IL-6; IL-10; IL-15; LIF; oncostatin M). In each protocol, 37 physically active men (19.98 ± 1.17 years) were randomly assigned into two groups according to a particular study design.ResultsAn increase in participants’ mean (4.81%, p &lt; 0.05) and peak power (6.25%, p &lt; 0.05) during the WAnT was observed only after the consecutive 10-day RIPC. Similarly, a significant 15.5% (p &lt; 0.05) decrease in the IL-6 concentration 120 min after the WAnT was observed only in the consecutive 10-day RIPC protocol, as well as a 12.2% (p &lt; 0.01) increase in oncostatin M 60 min after the WAnT.ConclusionThe results demonstrate the efficacy of the consecutive 10-day RIPC procedure in modulating exercise performance and post-exercise inflammation markers.