bluuebunny/crossref_metadata_2025_split huggingface dataset:
The exposure to volatile organic chemicals associates positively with rheumatoid arthritis: a cross-sectional study from the NHANES program
Authors: Lei Ting , Qian Hu , Yang Junxiao , Hu Yihe 
Published: June 2023

IntroductionRheumatoid arthritis (RA) is an autoimmune disease and closely associated with both genetic and environmental factors. Volatile organic chemicals (VOC), a common environment pollutant, was associated with some autoimmune diseases, while whether VOC exposure or which VOC leads to RA is yet clarified.MethodsA cross-sectional study using data from the 6 survey cycles (2005-2006, 2011-2012, 2013-2014, 2015-2016, 2017-2018, 2017-2020) of NHANES program was performed. The RA or non-arthritis status of participant was identified through a questionnaire survey. The quantile logistic regression method was used for correlation analysis between VOC metabolites (VOCs) in urine and RA. The covariates included age, gender, race, educational level, marital status, total energy intake, physical activity, smoking, hypertension, diabetes, urine creatinine, albumin and marihuana use.ResultsA total of 9536 participants (aged 20 to 85) with 15 VOCs, comprising 618 RA and 8918 non-arthritis participants, was finally included for analysis. Participants in the RA group showed higher VOCs in urine than that in the non-arthritis group. A positive association between 2 VOCs (AMCC: Q4: OR=2.173, 95%CI: 1.021, 4.627. 3HPMA: Q2: OR=2.286, 95%CI: 1.207 - 4.330; Q4: OR=2.663, 95%CI: 1.288 -5.508.) and RA was detected in the model 3, which was independent of all the covariates. The relative parent compounds of the two VOCs included N,N-Dimethylformamide and acrolein.DiscussionThese findings suggested that the VOC exposure significantly associated with RA, providing newly epidemiological evidence for the establishment that environmental pollutants associated with RA. And also, more prospective studies and related experimental studies are needed to further validate the conclusions of this study.
Transcriptome sequencing and single-cell sequencing analysis identify GARS1 as a potential prognostic and immunotherapeutic biomarker for multiple cancers, including bladder cancer
Authors: Nie Jianqiang , Liu Taobin , Mao Taotao , Yang Hailang , Deng Wen , Liu Xiaoqiang , Fu Bin 
Published: June 2023

BackgroundGlycyl-tRNA synthetase 1 (GARS1) belongs to the aminoacyl-tRNA synthetase family, playing a crucial role in protein synthesis. Previous studies have reported a close association between GARS1 and various tumors. However, the role of GARS1 in human cancer prognosis and its impact on immunology remain largely unexplored.MethodsIn this study, we comprehensively analyzed GARS1 expression at the mRNA and protein levels, examined genetic alterations, and assessed its prognostic implications in pan-cancer, with a specific emphasis on the immune landscape. Furthermore, we investigated the functional enrichment of genes related to GARS1 and explored its biological functions using single-cell data. Finally, we conducted cellular experiments to validate the biological significance of GARS1 in bladder cancer cells.ResultsIn general, GARS1 expression was significantly upregulated across multiple cancer types, and it demonstrated prognostic value in various cancers. Gene Set Enrichment Analysis (GSEA) revealed the association of GARS1 expression with multiple immune regulatory pathways. Moreover, GARS1 exhibited significant correlations with immune infiltrating cells (such as DC, CD8+T cells, Neutrophils, and Macrophages), immune checkpoint genes (CD274, CD276), and immune regulatory factors in tumors. Additionally, we observed that GARS1 could effectively predict the response to anti-PD-L1 therapy. Notably, Ifosfamide, auranofin, DMAPT, and A-1331852 emerged as potential therapeutic agents for GARS1-upregulated tumors. Our experimental findings strongly suggest that GARS1 promotes the proliferation and migration of bladder cancer cells.ConclusionGARS1 holds promise as a potential prognostic marker and therapeutic target for pan-cancer immunotherapy, offering valuable insights for the development of more precise and personalized approaches to tumor treatment in the future.
Single cell transcriptome profiling reveals cutaneous immune microenvironment remodeling by photodynamic therapy in photoaged skin
Authors: Yan Yu , Yan Guorong , Cao Zhi , Wang Bo , Zeng Qingyu , Shi Lei , Chang Qihang , Chen Chengqian , Zhang Linglin , Liao Caihe , Jin Shengkai , Sun Xiaofei , Zhang Guolong , Wang Peiru , Wang Xiuli 
Published: June 2023

BackgroundThe immune microenvironment plays a critical role in maintaining skin homeostasis, which is closely related to the dysfunction in photoaged skin such as autoimmunity and tumorigenesis. Several recent studies have demonstrated the efficacy of 5-aminolevulinic acid photodynamic therapy (ALA-PDT) in alleviating photoaging and skin cancer. However, the underlying immune mechanisms and the immune microenvironment change by ALA-PDT remain largely unknown.MethodsTo illustrate the effects of ALA-PDT on immune microenvironment in photoaged skin, single cell RNA sequencing (scRNA-seq) analysis of photoaged skin on the extensor side of the human forearm before and after ALA-PDT was performed. R-packages of Seurat, clusterProfiler, Monocle, CellChat were used for cell clustering, differentially expressed genes analysis, functional annotation, pseudotime analysis and cell-cell communication analysis. The gene sets related to specific functions were extracted from the MSigDB database, which were used to score the functions of immune cells in different states. We also compared our result with published scRNA-seq data of photoaged skin of the eyelids.ResultsThe increase score of cellular senescence, hypoxia and reactive oxygen species pathway in immune cells and the decrease of immune receptor activity function and proportion of naive T cells were found in skin photoaging. Moreover, the function of T cell ribosomal synthesis was also impaired or down regulated and function of G2M checkpoint was up regulated. However, ALA-PDT showed promising results in reversing these effects, as it improved the above functions of T cells. The ratio of M1/M2 and percentage of Langerhans cells also decreased with photoaging and increased after ALA-PDT. Additionally, ALA-PDT restored the antigen presentation and migration function of dendritic cells and enhanced cell-cell communication among immune cells. These effects were observed to last for 6 months.ConclusionALA-PDT has potential to rejuvenate immune cells, partially reversed immunosenescence and improved the immunosuppressive state, ultimately remodelling the immune microenvironment in photoaged skin. These results provide an important immunological basis for further exploring strategies to reverse skin photoaging, chronological aging and potentially systemic aging.
Identification and validation of aging-related gene signatures and their immune landscape in diabetic nephropathy
Authors: Liang Yingchao , Liang Zhiyi , Huang Jinxian , Jia Mingjie , Liu Deliang , Zhang Pengxiang , Fang Zebin , Hu Xinyu , Li Huilin 
Published: June 2023

BackgroundAging and immune infiltration have essential role in the physiopathological mechanisms of diabetic nephropathy (DN), but their relationship has not been systematically elucidated. We identified aging-related characteristic genes in DN and explored their immune landscape.MethodsFour datasets from the Gene Expression Omnibus (GEO) database were screened for exploration and validation. Functional and pathway analysis was performed using Gene Set Enrichment Analysis (GSEA). Characteristic genes were obtained using a combination of Random Forest (RF) and Support Vector Machine Recursive Feature Elimination (SVM-RFE) algorithm. We evaluated and validated the diagnostic performance of the characteristic genes using receiver operating characteristic (ROC) curve, and the expression pattern of the characteristic genes was evaluated and validated. Single-Sample Gene Set Enrichment Analysis (ssGSEA) was adopted to assess immune cell infiltration in samples. Based on the TarBase database and the JASPAR repository, potential microRNAs and transcription factors were predicted to further elucidate the molecular regulatory mechanisms of the characteristic genes.ResultsA total of 14 differentially expressed genes related to aging were obtained, of which 10 were up-regulated and 4 were down-regulated. Models were constructed by the RF and SVM-RFE algorithms, contracted to three signature genes: EGF-containing fibulin-like extracellular matrix (EFEMP1), Growth hormone receptor (GHR), and Vascular endothelial growth factor A (VEGFA). The three genes showed good efficacy in three tested cohorts and consistent expression patterns in the glomerular test cohorts. Most immune cells were more infiltrated in the DN samples compared to the controls, and there was a negative correlation between the characteristic genes and most immune cell infiltration. 24 microRNAs were involved in the transcriptional regulation of multiple genes simultaneously, and Endothelial transcription factor GATA-2 (GATA2) had a potential regulatory effect on both GHR and VEGFA.ConclusionWe identified a novel aging-related signature allowing assessment of diagnosis for DN patients, and further can be used to predict immune infiltration sensitivity.
Study on diversity, nitrogen-fixing capacity, and heavy metal tolerance of culturable Pongamia pinnata rhizobia in the vanadium-titanium magnetite tailings
Authors: Shen Tian , Jin Ruimin , Yan Jing , Cheng Xiran , Zeng Lan , Chen Qiang , Gu Yunfu , Zou Likou , Zhao Ke , Xiang Quanju , Penttinen Petri , Ma Menggen , Li Shuangcheng , Zou Ting , Yu Xiumei 
Published: June 2023

IntroductionThe diversity, nitrogen-fixing capacity and heavy metal tolerance of culturable rhizobia in symbiotic relationship with Pongamia pinnata surviving in vanadium (V) - titanium (Ti) magnetite (VTM) tailings is still unknown, and the rhizobia isolates from the extreme barren VTM tailings contaminated with a variety of metals would provide available rhizobia resources for bioremediation.MethodsP. pinnata plants were cultivated in pots containing the VTM tailings until root nodules formed, and then culturable rhizobia were isolated from root nodules. The diversity, nitrogen-fixing capacity and heavy metal tolerance of rhizobia were performed.ResultsAmong 57 rhizobia isolated from these nodules, only twenty strains showed different levels of tolerance to copper (Cu), nickel (Ni), manganese (Mn) and zinc (Zn), especially strains PP1 and PP76 showing high tolerance against these four heavy metals. Based on the phylogenetic analysis of 16S rRNA and four house-keeping genes (atpD, recA, rpoB, glnII), twelve isolates were identified as Bradyrhizobium pachyrhizi, four as Ochrobactrum anthropic, three as Rhizobium selenitireducens and one as Rhizobium pisi. Some rhizobia isolates showed a high nitrogen-fixing capacity and promoted P. pinnata growth by increasing nitrogen content by 10%-145% in aboveground plant part and 13%-79% in the root. R. pachyrhizi PP1 showed the strongest capacity of nitrogen fixation, plant growth promotion and resistance to heavy metals, which provided effective rhizobia strains for bioremediation of VTM tailings or other contaminated soils. This study demonstrated that there are at least three genera of culturable rhizobia in symbiosis with P. pinnata in VTM tailings.DiscussionAbundant culturable rhizobia with the capacity of nitrogen fixation, plant growth promotion and resistance to heavy metals survived in VTM tailings, indicating more valuable functional microbes could be isolated from extreme soil environments such as VTM tailings.
Gut microbiota and chronic obstructive pulmonary disease: a Mendelian randomization study
Authors: Wei Yi , Lu Xuechao , Liu Chao 
Published: June 2023

BackgroundA growing number of studies implies a strong association between gut microbiota and chronic obstructive pulmonary disease (COPD). However, the causal impact between gut microbiota and COPD remains unclear. As a result, we used a two-sample Mendelian randomization (MR) method to investigate the connection between gut microbiota and COPD in this study.MethodsThe largest available genome-wide association study (GWAS) of gut microbiota was obtained from the MiBioGen consortium. Summary-level dataset for COPD were obtained from the FinnGen consortium. The main analysis method for determining the causal link between gut microbiota and COPD was inverse variance weighted (IVW). Subsequently, pleiotropy and heterogeneity tests were performed to determine the reliability of the results.ResultsIVW method identified 9 bacterial taxa nominally associated with the risk of COPD. Class Actinobacteria (p = 0.020), genus Allisonella (p = 0.024), genus Coprococcus2 (p = 0.002) and genus Oscillospira (p = 0.018) were protective against COPD. In addition, order Desulfovibrionales (p = 0.011), family Desulfovibrionaceae (p = 0.039), family Peptococcaceae (p = 0.020), family Victivallaceae (p = 0.012) and genus Marvinbryantia (p = 0.017) were associated with a higher risk of COPD. No pleiotropy or heterogeneity were found.ConclusionAccording to the findings of this MR analysis, a causal relationship exists between certain gut microbiota and COPD. New insights into the mechanisms of COPD mediated by gut microbiota are provided.
Evaluation of fMRI activation in post-stroke patients with movement disorders after repetitive transcranial magnetic stimulation: a scoping review
Authors: Cheng Siman , Xin Rong , Zhao Yan , Wang Pu , Feng Wuwei , Liu Peng 
Published: June 2023

BackgroundMovement disorders are one of the most common stroke residual effects, which cause a major stress on their families and society. Repetitive transcranial magnetic stimulation (rTMS) could change neuroplasticity, which has been suggested as an alternative rehabilitative treatment for enhancing stroke recovery. Functional magnetic resonance imaging (fMRI) is a promising tool to explore neural mechanisms underlying rTMS intervention.ObjectOur primary goal is to better understand the neuroplastic mechanisms of rTMS in stroke rehabilitation, this paper provides a scoping review of recent studies, which investigate the alteration of brain activity using fMRI after the application of rTMS over the primary motor area (M1) in movement disorders patients after stroke.MethodThe database PubMed, Embase, Web of Science, WanFang Chinese database, ZhiWang Chinese database from establishment of each database until December 2022 were included. Two researchers reviewed the study, collected the information and the relevant characteristic extracted to a summary table. Two researchers also assessed the quality of literature with the Downs and Black criteria. When the two researchers unable to reach an agreement, a third researcher would have been consulted.ResultsSeven hundred and eleven studies in all were discovered in the databases, and nine were finally enrolled. They were of good quality or fair quality. The literature mainly involved the therapeutic effect and imaging mechanisms of rTMS on improving movement disorders after stroke. In all of them, there was improvement of the motor function post-rTMS treatment. Both high-frequency rTMS (HF-rTMS) and low-frequency rTMS (LF-rTMS) can induce increased functional connectivity, which may not directly correspond to the impact of rTMS on the activation of the stimulated brain areas. Comparing real rTMS with sham group, the neuroplastic effect of real rTMS can lead to better functional connectivity in the brain network in assisting stroke recovery.ConclusionrTMS allows the excitation and synchronization of neural activity, promotes the reorganization of brain function, and achieves the motor function recovery. fMRI can observe the influence of rTMS on brain networks and reveal the neuroplasticity mechanism of post-stroke rehabilitation. The scoping review helps us to put forward a series of recommendations that might guide future researchers exploring the effect of motor stroke treatments on brain connectivity.
Insulin-like growth factor 1 supplementation supports motor coordination and affects myelination in preterm pigs
Authors: Christiansen Line I. , Ventura Gemma C. , Holmqvist Bo , Aasmul-Olsen Karoline , Lindholm Sandy E. H. , Lycas Matthew D. , Mori Yuki , Secher Jan Bojsen-Møller , Burrin Douglas G. , Thymann Thomas , Sangild Per T. , Pankratova Stanislava 
Published: June 2023

IntroductionPreterm infants have increased risk of impaired neurodevelopment to which reduced systemic levels of insulin-like growth factor 1 (IGF-1) in the weeks after birth may play a role. Hence, we hypothesized that postnatal IGF-1 supplementation would improve brain development in preterm pigs, used as a model for preterm infants.MethodsPreterm pigs delivered by cesarean section received recombinant human IGF-1/IGF binding protein-3 complex (rhIGF-1/rhIGFBP-3, 2.25 mg/kg/day) or vehicle from birth to postnatal day 19. Motor function and cognition were assessed by monitoring of in-cage and open field activities, balance beam test, gait parameters, novel object recognition and operant conditioning tests. Collected brains were subject to magnetic resonance imaging (MRI), immunohistochemistry, gene expression analyses and protein synthesis measurements.ResultsThe IGF-1 treatment increased cerebellar protein synthesis rates (both in vivo and ex vivo). Performance in the balance beam test was improved by IGF-1 but not in other neurofunctional tests. The treatment decreased total and relative caudate nucleus weights, without any effects to total brain weight or grey/white matter volumes. Supplementation with IGF-1 reduced myelination in caudate nucleus, cerebellum, and white matter regions and decreased hilar synapse formation, without effects to oligodendrocyte maturation or neuron differentiation. Gene expression analyses indicated enhanced maturation of the GABAergic system in the caudate nucleus (decreased NKCC1:KCC2 ratio) with limited effects in cerebellum or hippocampus.ConclusionSupplemental IGF-1 during the first three weeks after preterm birth may support motor function by enhancing GABAergic maturation in the caudate nucleus, despite reduced myelination. Supplemental IGF-1 may support postnatal brain development in preterm infants, but more studies are required to identify optimal treatment regimens for subgroups of very or extremely preterm infants.
High unhealthy food and beverage consumption is associated with poor diet quality among 12–35-month-olds in Guédiawaye Department, Senegal
Authors: Vanderkooy Anna , Ferguson Elaine L. , Sy Ndèye Yaga , Kane Rosenette , Diagne Maty , Mbodji Aminata , Pries Alissa M. 
Published: June 2023

BackgroundHigh consumption of unhealthy foods and beverages (UFB) during early childhood is cause for concern, with growing evidence from low- and middle-income countries finding associations with poor diet quality and malnutrition. Research from sub-Saharan Africa remains limited, with no studies quantifying the contribution of UFB to total energy intakes among young children or exploring the relationship between such intakes and diet quality or anthropometric outcomes.ObjectivesAssess UFB consumption patterns and their contribution to total energy intake from non-breastmilk foods/beverages (TEI-NBF), assess the association between high UFB consumption and dietary/nutrition outcomes, and explore drivers of unhealthy food choice among young children in Guédiawaye Department, Senegal.MethodsWe conducted a cross-sectional study of a representative sample of 724 primary caregivers and their 12–35.9-month-old children. The study included a questionnaire, a quantitative four-pass 24-h dietary recall, and anthropometric measurements. The contribution of UFB to TEI-NBF was calculated and terciles generated. Logistic and linear models were used to compare outcomes of high versus low UFB consumption terciles.ResultsUFB contributed on average 22.2% of TEI-NBF, averaging 5.9% for the lowest tercile and 39.9% for the highest. Diets of high UFB consumers, as compared to low, were significantly less dense in protein, fiber, and seven of the 11 micronutrients assessed and significantly denser in total fat, saturated fat, and total sugar. No associations were found with anthropometric outcomes. High UFB consumers were older and more likely to be living in food insecurity. The most common drivers of commercial UFB consumption were related to child preference, the use of these products as behavior management tools, treats, or gifts, and the sharing of these products by someone else eating them.ConclusionHigh UFB consumption is associated with poor diet quality among 12–35-month-olds in Guédiawaye Department, Senegal. Addressing high UFB consumption during this critical developmental period should be prioritized in young child nutrition research, programming, and policy development.
Risk factors and a new nomogram for predicting brain metastasis from lung cancer: a retrospective study
Authors: Wu Bo , Zhou Yujun , Yang Yong , Zhou Dong 
Published: June 2023

ObjectiveThis study aims to establish and validate a new nomogram for predicting brain metastasis from lung cancer by integrating data.Methods266 patients diagnosed as lung cancer between 2016 and 2018 were collected from Guangdong Academy of Medical Sciences. The first 70% of patients were designated as the primary cohort and the remaining patients were identified as the internal validation cohort. Univariate and multivariable logistics regression were applied to analyze the risk factors. Independent risk factors were used to construct nomogram. C-index was used to evaluate the prediction effect of nomogram.100 patients diagnosed as lung cancer between 2018 and 2019 were collected for external validation cohorts. The evaluation of nomogram was carried out through the distinction and calibration in the internal validation cohort and external validation cohort.Results166 patients were diagnosed with brain metastasis among the 266 patients. The gender, pathological type (PAT), leukocyte count (LCC) and Fibrinogen stage (FibS) were independent risk factors of brain metastasis. A novel nomogram has been developed in this study showed an effective discriminative ability to predict the probability of lung cancer patients with brain metastasis, the C-index was 0.811.ConclusionOur research provides a novel model that can be used for predicting brain metastasis of lung cancer patients, thus providing more credible evidence for clinical decision-making.