bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metagenomic analysis demonstrates distinct changes in the gut microbiome of Kawasaki diseases children
Authors: Han Linli , Liu Xu , Lan Yue , Hua Yimin , Fan Zhenxin , Li Yifei 
Published: July 2024

BackgroundKawasaki disease (KD) has been considered as the most common required pediatric cardiovascular diseases among the world. However, the molecular mechanisms of KD were not fully underlined, leading to a confused situation in disease management and providing precious prognosis prediction. The disorders of gut microbiome had been identified among several cardiovascular diseases and inflammation conditions. Therefore, it is urgent to elucidate the characteristics of gut microbiome in KD and demonstrate its potential role in regulating intravenous immunoglobulin (IVIG) resistance and coronary artery injuries.MethodsA total of 96 KD children and 62 controls were enrolled in the study. One hundred forty fecal samples had been harvested from KD patients, including individuals before or after IVIG treatment, with or without early coronary artery lesions and IVIG resistance. Fecal samples had been collected before and after IVIG administration and stored at −80°C. Then, metagenomic analysis had been done using Illumina NovaSeq 6000 platform. After that, the different strains and functional differences among comparisons were identified.ResultsFirst, significant changes had been observed between KD and their controls. We found that the decrease of Akkermansia muciniphila, Faecalibacterium prausnitzii, Bacteroides uniformis, and Bacteroides ovatus and the increase of pathogenic bacteria Finegoldia magna, Abiotrophia defectiva, and Anaerococcus prevotii perhaps closely related to the incidence of KD. Then, metagenomic and responding functional analysis demonstrated that short-chain fatty acid pathways and related strains were associated with different outcomes of therapeutic efficacies. Among them, the reduction of Bacteroides thetaiotaomicron, the enrichment of Enterococcus faecalis and antibiotic resistance genes had been found to be involved in IVIG resistance of KD. Moreover, our data also revealed several potential pathogenetic microbiome of that KD patients with coronary artery lesionsConclusionThese results strongly proved that distinct changes in the gut microbiome of KD and the dysfunction of gut microbiomes should be responsible for the pathogenesis of KD and significantly impact the prognosis of KD.
Impact of mitochondrial damage on tumor microenvironment and immune response: a comprehensive bibliometric analysis
Authors: Xing Yichun , Huang Yi , Tang Zhicheng , Lin Ying , Zou Yitong , Huang Yaqiang , He Zhaohui , Huang Qunxiong , Wu Jieying 
Published: July 2024

BackgroundMitochondrial damage contributes to apoptosis, oxidative stress, and inflammation, which collectively impact the immune system’s function and the tumor microenvironment (TME). These processes, in turn, influence tumor cell growth, migration, and response to treatment.ObjectiveWe conducted a bibliometric analysis to elucidate the complex interactions between mitochondrial damage, the immune system, and the TME.MethodsData were sourced from the Science Citation Index Core Collection (WoSCC) and analyzed using advanced tools like VOSviewer and Citespace. Our focus was on literature published between 1999 and 2023 concerning the interactions between mitochondrial damage and the TME, as well as immune responses to tumors. The analysis included regional contributions, journal influence, institutional collaborations, authorship, co-cited authors, and keyword citation bursts.ResultsOur research encompassed 2,039 publications, revealing an increasing trend in annual output exploring the relationship between mitochondrial damage, TME dynamics, and immune responses. China, the United States, and South Korea emerged as the leading contributors. Prominent institutions included Institut National de la Santé et de la Recherche Médicale, University of Texas System, China Medical University, and Sun Yat-sen University. Key journals in this field are the International Journal of Molecular Sciences, Mitochondrion, and the European Journal of Pharmacology. Liang H and Wallace DC were identified as the most productive and co-cited authors, respectively. Keyword analysis highlighted the critical roles of inflammatory responses, oxidative stress, and the immune system in recent research.ConclusionThis bibliometric analysis provides a comprehensive overview of historical and current research trends, underscoring the pivotal role of mitochondrial damage in the TME and immune system.
Comparative analysis of macular characteristics in mCNV and contralateral eyes
Authors: Huang Gongyu , She Xiangjun , Zhang Yun , Zhang Zongduan , Shen Lijun 
Published: July 2024

PurposeTo illustrate the characteristics of perforating scleral vessels in macular regions between mCNV eyes and contralateral eyes in unilateral mCNV patients.MethodsThis was a retrospective study that included patients with unilateral naive mCNV. The study aimed to identify and analyze the distribution of perforating scleral vessels (PSVs) in the macular region of mCNV eyes and contralateral eyes. The central macular choroidal thicknesses (mChT) were measured using optical coherence tomography angiography (OCTA). The grades of myopic atrophic maculopathy (MAM) and macular myopic diffuse chorioretinal atrophy (DCA) were evaluated within groups. The number of PSVs and mChT were compared between contralateral and mCNV eyes based on the grade of DCA. The ROC curves were utilized to explore the diagnostic indexes for mCNV.ResultsA total of 102 eyes from 51 patients with unilateral mCNV were included. There was no significance in the severity of MAM or the grade of DCA between mCNV eyes and contralateral eyes (p = 0.074, p = 0.054, respectively). The mean number of PSVs in mCNV eyes was fewer than the contralateral eyes [1.00 (1.00–2.00) vs. 2.00 (0.75–3.00), p = 0.030]. The mChT in mCNV eyes was thinner than the contralateral eyes [36.00 (25.00–53.75) μm vs. 46.00 (31.00–75.25) μm, p = 0.001]. The mean grade of DCA in mCNV eyes was higher than that in contralateral eyes [3.00 (3.00–3.00) vs. 3.00 (2.00–3.00), p = 0.004]. When DCA involved the macular region, there were more PSVs in contralateral eyes than in mCNV eyes [1.50 (1.00–2.00) vs. 2.00 (1.00–3.00), p = 0.042]. Similarly, when DCA involved the foveal region, there were more PSVs in contralateral eyes than in mCNV eyes [1.50 (1.00–2.00) vs. 3.00 (2.00–4.00), p = 0.004]. The grade of DCA and mChT were valuable factors for predicting mCNV eyes (AUC = 0.6566, p = 0.021; AUC = 0.6304, p = 0.029; respectively). When the extent of DCA exceeded the foveal region, the count of PSVs was a good diagnostic factor for predicting mCNV (AUC = 0.7430, p = 0.003).ConclusionThe mean amount of PSVs was significantly lower in the mCNV eyes compared to the contralateral eyes. When the extent of DCA exceeded the foveal region, the count of PSVs was a good diagnostic factor for predicting mCNV. Myopic eyes with a higher grade of DCA and a thinner mChT were more likely to develop mCNV.
Associations of different inflammatory factors with atherosclerosis among patients with psoriasis vulgaris
Authors: Huong Nguyen Thi Kim , Long Bui , Doanh Le Huu , Thoai Tran Minh , Hang Nguyen Thi , Khoi Le , Nu Pham Thi 
Published: July 2024

BackgroundThis study aimed to measure the associations between different inflammatory factors, namely interleukin (IL)-17A, tumor necrosis factor (TNF)-α, and high-sensitivity C-reactive protein (hs-CRP), and atherosclerosis in patients with psoriasis vulgaris.MethodsA cross-sectional study was conducted at two hospitals in Hanoi, Vietnam. A total of 125 patients with psoriasis vulgaris and 50 healthy controls were recruited. Clinical characteristics and atherosclerosis were assessed. IL-17A, TNF-α, and hs-CRP levels were measured.ResultsPsoriasis vulgaris patients with atherosclerosis had higher levels of hs-CRP (median = 1.22; interquartile range—IQR = 0.34–12.11) and IL-17A (median = 1.30; IQR = 0.43–4.28), but a lower level of TNF-α (median = 0.54; IQR = 0.13–3.41) compared to those without atherosclerosis (p &lt; 0.05). Only LogIL-17A was positively related to atherosclerosis in psoriasis patients (Odds Ratio—OR = 2.16, 95% CI = 1.06–4.38, p &lt; 0.05). After excluding systemically treated patients, LogIL-17A and Log TNF-α were associated with the likelihood of atherosclerosis (p &lt; 0.05).ConclusionThis study suggests a link between elevated levels of IL-17A and TNF-α and subclinical atherosclerosis. Further investigation on a larger scale is required to establish the causality of this relationship.
Impact of concomitant methotrexate on disease activity in patients with rheumatoid arthritis tapering abatacept: results from KOBIO registry
Authors: Park Jun Won , Kim Ju Yeon , Kim Min Jung , Lim Yoo Kyoung , Kim Hyoun-Ah , Kim Jin Hyun , Shin Kichul 
Published: July 2024

ObjectivesTapering biologic agents can be considered for patients with stable disease activity in rheumatoid arthritis (RA). However, the specific strategy for abatacept is uncertain. This study aimed to examine the impact of tapering abatacept on disease activity in RA patients and assess the potential influence of concomitant methotrexate (MTX) treatment.MethodsUsing data from the KOBIO registry, we included 505 1 year intervals from 176 patients with RA that initiated abatacept with concomitant MTX at baseline. The intervals were divided into two groups based on the dose quotient (DQ) of abatacept during each period (i.e., the tapering group (DQ &lt; 1) and control group (DQ = 1)). The primary outcome was achieving DAS28-remission at 1 year intervals. Marginal structural models (MSM) were used to minimize confounding caused by an imbalance in time-varying variables.ResultsAbatacept was tapered at 146 (28.9%) intervals, and the mean DQ was 0.68. DAS28-remission was achieved in 207 (41.8%) intervals. Tapering abatacept did not affect the odds of achieving DAS28-remission compared with the control group (OR 1.04 [0.67–1.62]). The odds remained unaffected in the subgroup that continued MTX (OR 1.42 [0.88–2.30]) but not in the subgroup that discontinued MTX (OR 0.26 [0.10–0.57]). The effects of interaction between tapering abatacept and concomitant MTX use on DAS28 and patient’s functional status showed consistent results. The incidence of adverse events within a 1 year interval was comparable between the two groups.ConclusionWithdrawal of MTX while tapering abatacept may compromise meeting the treatment goal for patients with RA.
Severe community-acquired pneumonia caused by Chlamydia abortus in China: a case report
Authors: Yang Qiong-Fang , Shu Cai-Min 
Published: July 2024

BackgroundChlamydia abortus causes abortions in ruminants; it can also cause miscarriages and stillbirths in pregnant women. However, it rarely causes pneumonia in humans. Here, we report a case of severe community-acquired pneumonia caused by C. abortus.Case presentationOn admission to our hospital, a 74-year-old woman reported that she had had a fever, cough, phlegm in her throat, and shortness of breath for 10 days. In the local hospital, she was initially diagnosed with community-acquired pneumonia and treated with piperacillin–tazobactam for 4 days. However, her condition worsened, and she was therefore transferred to our hospital. On arrival at our emergency department, she was diagnosed with severe community-acquired pneumonia and treated with a high-flow nasal cannula and meropenem; she was then transferred to the Department of Respiratory Medicine. There, her condition continued to worsen despite continued treatment with the high-flow nasal cannula and omadacycline. After 24 h and emergency tracheal intubation, the patient was sent to the intensive care unit (ICU) for further treatment. The doctors in the ICU again adjusted the treatment, this time to meropenem along with mechanical ventilation; they also instituted methylprednisolone, ulinastatin, nadroparin calcium, and human immunoglobulin. In addition, bronchoalveolar lavage fluid was sent for metagenomic next-generation sequencing (mNGS). Subsequent mNGS suggested the presence of C. abortus, sequence number 5072; we therefore discontinued the meropenem and implemented a combination of doxycycline and moxifloxacin. After 8 days of treatment in the ICU, the patient’s condition improved; she was then extubated and, 3 days later, transferred back to the respiratory medicine department. The respiratory physician continued to administer doxycycline and moxifloxacin for 4 days, after which the patient was discharged with medication. A month later, a repeat computed tomography (CT) scan of the chest suggested that the lesions in both lungs had been largely absorbed.ConclusionC. abortus can occasionally cause pneumonia in humans and, rarely, severe, life-threatening pneumonia. mNGS is uniquely suited for the early detection of this unusual infection. The combination of doxycycline and quinolones has been shown to be effective in severe pneumonia caused by C. abortus.
Genome characterization of a multi-drug resistant Escherichia coli strain, L1PEag1, isolated from commercial cape gooseberry fruits (Physalis peruviana L.)
Authors: Molina Diana , Carrión–Olmedo Julio C. , Jarrín–V Pablo , Tenea Gabriela N. 
Published: July 2024

IntroductionFoodborne infections, which are frequently linked to bacterial contamination, are a serious concern to public health on a global scale. Whether agricultural farming practices help spread genes linked to antibiotic resistance in bacteria associated with humans or animals is a controversial question.MethodsThis study applied a long–read Oxford Nanopore MinION-based sequencing to obtain the complete genome sequence of a multi-drug resistant Escherichia coli strain (L1PEag1), isolated from commercial cape gooseberry fruits (Physalis peruviana L.) in Ecuador. Using different genome analysis tools, the serotype, Multi Locus Sequence Typing (MLST), virulence genes, and antimicrobial resistance (AMR) genes of the L1PEag1 isolate were determined. Additionally, in vitro assays were performed to demonstrate functional genes.ResultsThe complete genome sequence of the L1PEag1 isolate was assembled into a circular chromosome of 4825.722 Kbp and one plasmid of 3.561 Kbp. The L1PEag1 isolate belongs to the B2 phylogroup, sequence type ST1170, and O1:H4 serotype based on in silico genome analysis. The genome contains 4,473 genes, 88 tRNA, 8 5S rRNA, 7 16S rRNA, and 7 23S rRNA. The average GC content is 50.58%. The specific annotation consisted of 4,439 and 3,723 genes annotated with KEEG and COG respectively, 3 intact prophage regions, 23 genomic islands (GIs), and 4 insertion sequences (ISs) of the ISAs1 and IS630 families. The L1PEag1 isolate carries 25 virulence genes, and 4 perfect and 51 strict antibiotic resistant gene (ARG) regions based on VirulenceFinder and RGI annotation. Besides, the in vitro antibiotic profile indicated resistance to kanamycin (K30), azithromycin (AZM15), clindamycin (DA2), novobiocin (NV30), amikacin (AMK30), and other antibiotics. The L1PEag1 isolate was predicted as a human pathogen, matching 464 protein families (0.934 likelihood).ConclusionOur work emphasizes the necessity of monitoring environmental antibiotic resistance, particularly in commercial settings to contribute to develop early mitigation techniques for dealing with resistance diffusion.
Mixed planting of subtropical Chinese fir in South China improves microbial carbon source metabolism and functional diversity through the accumulation of nutrients from soil aggregates
Authors: Deng Jiazhen , Hu Jingda , Huang Yongzhen , Wang Shengqiang , Ye Shaoming 
Published: July 2024

IntroductionSoil microbial functional traits are key indicators of soil microbial ecological traits; however, how mixing patterns of Chinese fir and broadleaved trees drive soil microbial functional trait variation at the aggregate scale and how soil microbial functional traits are linked to soil fertility factors have largely not been determined.MethodsIn this study, soil from the 0–20 cm depths in three Chinese fir plantations was collected, and the soil samples were separated into &gt;2 mm (large macro-aggregate), 0.25–2 mm (macro-aggregate) and &lt;0.25 mm (micro-aggregate) by complying with an optimal moisture sieving procedure. The metabolic activities, functional diversity and different carbon sources utilization characteristics of the soil microorganisms were determined by the Biolog Eco microplate method.ResultsIn all Chinese fir plantations, micro-aggregates (&lt;0.25 mm) consistently exhibited the highest levels of microbial metabolic activity, a more uniform carbon source utilisation capacity, and the highest microbial diversity. Micro-aggregates also showed elevated levels of soil organic carbon (OC), total nitrogen (TN), total phosphorus (TP), and higher ratios of C/N and C/P compared to large macro-aggregates and macro-aggregates, indicating that micro-aggregates contain more resources available to soil microorganisms. Soil OC, TN, and TP content were enhanced by integration with Michelia macclurei, suggesting that this combination promotes relatively favourable soil conditions for microbial growth and multiplication. This, in turn, promotes microbial metabolic activity. Furthermore, redundancy and correlation analyses showed that soil OC, TN, and TP were identified as principal determinants of soil microbial functional properties in Chinese fir plantations.DiscussionIn summary, mixed cultivation and aggregate size influenced microbial functional properties via soil nutrient alterations. Consequently, adopting a mixed cultivation approach of Chinese fir and broadleaved trees is advocated in the subtropical regions of Guangxi. Employing a diversity of tree species, including M. macclurei, is recommended for optimal soil quality preservation.
Causal associations among gut microbiota, 1400 plasma metabolites, and asthma: a two-sample Mendelian randomization study
Authors: Wang Lizhu , Lv Zhe 
Published: July 2024

BackgroundEmerging evidence indicates a correlation between imbalances in intestinal microbiota and changes in plasma metabolites in the progression of asthma. However, the causal link between these factors remains unclear.MethodsA two-sample Mendelian randomization (MR) study was employed to evaluate the potential causal connection between gut microbiota, plasma metabolites, and asthma susceptibility. Gut microbiota data from expansive genome-wide genotype studies and 16S fecal microbiome datasets were examined by the MiBioGen Alliance. Asthma data were procured from the FinnGen biobank analysis, while comprehensive Genome-Wide Association Studies (GWAS) summary statistics for plasma metabolites were derived from the NHGRI-EBI GWAS Catalog. Fluctuations in intestinal flora and plasma metabolites in asthma patients were evaluated using the weighted mode method. Additionally, pleiotropic and heterogeneity analyses were performed to ascertain the reliability of the findings.ResultsUpon examining the gut microbiota through MR with the IVW method, alongside tests for heterogeneity and pleiotropy, findings reveal a negative association between the abundance of the Christensenellaceae R.7 group and asthma risk. In contrast, the Bifidobacterium and Prevotella 7 genera exhibit a positive association with asthma risk, indicating they may be potential risk factors (p &lt; 0.05). Furthermore, MR analysis of 1,400 metabolites employing Weighted median, IVW, and Weighted mode methods resulted in p-values below 0.05. Subsequent tests for pleiotropy and heterogeneity showed that the levels of 3,5-dichloro-2,6-dihydroxybenzoic acid have a negative correlation with asthma, whereas the phenylalanine to phosphate ratio has a positive correlation, suggesting their potential as risk factors for asthma (p &lt; 0.05).ConclusionThe current Mendelian randomization study provides evidence supporting a potential causal link between specific gut microbiota taxa, plasma metabolites, and asthma. These findings offer novel perspectives for future research and the development of treatment and prevention strategies for asthma.
Novel insights into causal associations of body mass index or height with pneumothorax: a two-sample Mendelian randomization study
Authors: Liu Gengqiu , Yan Dongqing , Wang Xiaohuai , Liu Anbang , Zhang Junhang 
Published: July 2024

BackgroundObservational studies have reported an association between body mass index (BMI) as well as height and the risk of pneumothorax. However, it has long been unclear whether BMI or height are causally associated with pneumothorax.MethodsGenetic summary data for BMI, height and pneumothorax were retrieved from multiple independent large genome-wide association studies (GWAS). A series of quality control steps were conducted to select instruments. Four independent two-sample Mendelian randomization (MR) analyzes were performed to adequately assess the causal relationship between BMI or height on pneumothorax, and the robustness of the results was assessed by a series of sensitivity analyzes.ResultsHeight increased the risk of pneumothorax with an OR of 1.5181 (95%CI 1.3092–1.7604; p = 3.28e-08); there was no evidence of a causal effect of BMI on the risk of pneumothorax with an OR of 0.8979 (95%CI 0.7417–1.0869; p = 0.269). Height increased the risk of spontaneous pneumothorax with an OR of 1.0010 (95%CI 1.0002–1.0018; p = 0.012); the results showed no significant causal relationship between BMI and spontaneous pneumothorax either with an OR of 0.9992 (95%CI 0.9983–1.0002; p = 0.112).ConclusionOur results supported a genetic association between height and pneumothorax. We found that height increased the risk of pneumothorax. However, no evidence was found to suggest a causal relationship between BMI and pneumothorax risk. The relationship between BMI and pneumothorax requires further in-depth analysis.