bluuebunny/crossref_metadata_2025_split huggingface dataset:
Case report: A clinical case study of six patients with Chlamydia psittaci pneumonia
Authors: Dai Jinmeng , Lian Xue , Mo Juanfen , Li Xiaosi , Mo Weiqiang , Wang Haiqin , Jiang Jianping 
Published: February 2023

ObjectiveTo investigate the clinical features, diagnosis, and treatment of Chlamydia psittaci (C. psittaci) pneumonia.MethodsWe retrospectively analyzed the clinical data of six patients with C. psittaci pneumonia who were admitted to the Division of Pulmonary and Critical Care Medicine of the Second Hospital of Jiaxing from December 2021 to September 2022.ResultsAll patients reported a fever and other accompanying symptoms, including cough (5/6), chest tightness (1/6), fatigue (2/6), and headache (1/6). Laboratory results showed that all patients had high levels of C-reactive protein (CRP≥70 mg/L), procalcitonin (PCT; 2 patients with PCT levels ≥0.5 ng/L), and erythrocyte sedimentation rate (ESR). Lactate dehydrogenase (LDH) and aspartate aminotransferase (AST) levels were elevated in 3/6 and of 2/6 patients, respectively. Chest computed tomography (CT) of most patients showed patchy, high-density shadows with partial consolidation, accompanied by air bronchogram signs and pleural effusion. Six patients were diagnosed with C. psittaci pneumonia using metagenomic next-generation sequencing (mNGS). They showed favorable outcomes following immediate adjustment of the regimen to doxycycline-based therapy and hydration, nutrition, and other follow-up treatments. In the imaging findings obtained at one-two month, the lesions were completely cleared, suggesting a favorable prognosis.ConclusionPatients with C. psittaci pneumonia commonly present sepsis and rapidly progressing disease. Early diagnosis is critical for C. psittaci pneumonia using mNGS, which can lead to favorable prognoses via immediate adjustment therapies.
End-of-treatment anti-HBs levels and HBeAg status identify durability of HBsAg loss after PEG-IFN discontinuation
Authors: Guo Yifei , Han Jiajia , Zhang Yongmei , Jin Chengmeng , Zhang Yao , He Jingjing , Chen Shiqi , Guo Yue , Lin Yanxue , Li Fahong , Yang Feifei , Shen Zhongliang , Mao Richeng , Zhu Haoxiang , Zhang Jiming 
Published: February 2023

BackgroundHepatitis B surface antigen (HBsAg) loss, namely, the functional cure, can be achieved through the pegylated interferon (PEG-IFN)-based therapy. However, it is an unignorable fact that a small proportion of patients who achieved functional cure develop HBsAg reversion (HRV) and the related factors are not well described.MethodsA total of 112 patients who achieved PEG-IFN-induced HBsAg loss were recruited. HBV biomarkers and biochemical parameters were examined dynamically. HBV RNA levels were assessed in the cross-sectional analysis. The primary endpoint was HRV, defined as the reappearance of HBsAg after PEG-IFN discontinuation.ResultsHRV occurred in 17 patients during the follow-up period. Univariable analysis indicated that hepatitis B e antigen (HBeAg) status, different levels of hepatitis B surface antibody (anti-HBs), and hepatitis B core antibody (anti-HBc) at the end of PEG-IFN treatment (EOT) were significantly associated with the incidence of HRV through using the log-rank test. Additionally, time-dependent receiver operating characteristic (ROC) analysis showed that the anti-HBs was superior to anti-HBc in predictive power for the incidence of HRV during the follow-up period. Multivariable Cox proportional hazard analysis found that anti-HBs ≥1.3 log10IU/L (hazard ratio (HR), 0.148; 95% confidence interval (CI), 0.044-0.502) and HBeAg negativity (HR, 0.183; 95% CI, 0.052-0.639) at EOT were independently associated with lower incidence of HRV. Cross-sectional analysis indicated that the HBV RNA levels were significantly correlated with the HBsAg levels in patients with HRV (r=0.86, p=0.003).ConclusionsEOT HBeAg negativity and anti-HBs ≥1.3 log10IU/L identify the low risk of HRV after PEG-IFN discontinuation.
Systematic analysis of myocardial immune progression in septic cardiomyopathy: Immune-related mechanisms in septic cardiomyopathy
Authors: Ma Dunliang , Qin Xianyu , Zhong Zhi-an , Liao Hongtao , Chen Pengyuan , Zhang Bin 
Published: February 2023

BackgroundThe immune infiltration and molecular mechanisms underlying septic cardiomyopathy (SC) have not been completely elucidated. This study aimed to identify key genes related to SC and elucidate the potential molecular mechanisms.MethodsThe weighted correlation network analysis (WGCNA), linear models for microarray analysis (LIMMA), protein-protein interaction (PPI) network, CIBERSORT, Kyoto Encyclopedia of Genes and Genomes pathway (KEGG), and gene set enrichment analysis (GSEA) were applied to assess the key pathway and hub genes involved in SC.ResultsWe identified 10 hub genes, namely, LRG1, LCN2, PTX3, E LANE, TCN1, CLEC4D, FPR2, MCEMP1, CEACAM8, and CD177. Furthermore, we used GSEA for all genes and online tools to explore the function of the hub genes. Finally, we took the intersection between differential expression genes (DEGs) and hub genes to identify LCN2 and PTX3 as key genes. We found that immune-related pathways played vital roles in SC. LCN2 and PTX3 were key genes in SC progression, which mainly showed an anti-inflammatory effect. The significant immune cells in cardiomyocytes of SC were neutrophils and M2 macrophages.ConclusionThese cells may have the potential to be prognostic and therapeutic targets in the clinical management of SC. Excessive anti-inflammatory function and neutrophil infiltration are probably the primary causes of SC.
Quantifying the contributions of climate factors and human activities to variations of net primary productivity in China from 2000 to 2020
Authors: Li Zijian , Chen Jiangping , Chen Zhanpeng , Sha Zongyao , Yin Jianhua , Chen Zhaotong 
Published: February 2023

Net primary productivity (NPP) plays a vital role in the globe carbon cycle. Quantitative assessment of the effects of climate changes and human activities on net primary productivity dynamics is vital for understanding the driving mechanisms of vegetation change and sustainable development of ecosystems. This study investigates the contributions of climatic factors and human activities to vegetation productivity changes in China from 2000 to 2020 based on the residual trend analysis (RESTREND) method. The results showed that the annual average net primary productivity in China was 325.11 g C/m2/year from 2000 to 2020 and net primary productivity showed a significantly increasing trend (p&lt;0.05) at a rate of 2.32 g C/m2/year. Net primary productivity increased significantly (p&lt;0.05) across 40.90% of China over the study period, while only 1.79% showed a significantly declining trend (p&lt;0.05). The contributions of climatic factors and human activities to net primary productivity increase were 1.169 g C/m2/year and 1.142 g C/m2/year, respectively. Climate factors contributed positively mainly in Sichuan Basin, the Loess Plateau, the Mongolian Plateau, and Northeast China Plain. Positive contributions of human activities to net primary productivity mainly occurred in the Loess Plateau, Central China, and the Greater Khingan Mountains. The effects of climatic factors and human activities on net primary productivity changes varied among sub-regions. In Tropical Monsoon Climate Region and Subtropical Monsoon Climate Region, human activities had greater impacts on net primary productivity increase than climate factors, while climate factors were the dominant factor for net primary productivity recovery in other sub-regions. In addition, during 2000–2020, net primary productivity was dominated by both climate factors and human activities in 49.84% of China, while areas dominated solely by climate factors and human activities accounted for 13.67% and 10.92%, respectively. Compared to changed land cover types, the total net primary productivity as well as the increase of total net primary productivity in China was mostly contributed by unchanged land cover types, which contributed more than 90%.
A rare homozygous variant of MC2R gene identified in a Chinese family with familial glucocorticoid deficiency type 1: A case report
Authors: Liu ShuPing , Zeng Ting , Luo Cheng , Peng DanXia , Xu Xuan , Liu Qin , Wu Qiong , Lu Qin , Huang FuRong 
Published: February 2023

BackgroundMelanocortin-2 receptor (MC2R), a member of the G protein-coupled receptor family, is selectively activated by adrenocorticotropic hormone (ACTH). variants in MC2R are associated with family glucocorticoid deficiency 1 (FGD1).Case presentationWe first reported a Chinese family with two affected siblings with a homozygotic variant of c.712C&gt;T/p.H238Y in MC2R, presenting with skin hyperpigmentation, hyperbilirubinemia, and tall stature. These individuals showed novel clinical features, including congenital heart defects, not been found in other FGD1 patients.ConclusionsWe reported a Chinese family with affected siblings having a homozygotic variant of c.712C&gt;T/p.H238Y in MC2R.Our report may expand the genetic and clinical spectrum of FGD1.
Clinical symptoms, thyroid dysfunction, and metabolic disturbances in first-episode drug-naïve major depressive disorder patients with suicide attempts: A network perspective
Authors: Peng Pu , Wang Qianjin , Lang Xiaoe , Liu Tieqiao , Zhang Xiang-Yang 
Published: February 2023

BackgroundsCo-occurrence of thyroid dysfunction, metabolic disturbances, and worsening clinical symptoms in major depressive disorder (MDD) patients with suicidal attempts (SA) are common. However, their relationship in SA patients remains unexplored. We aimed to (1) determine the independent association of thyroid dysfunction, clinical symptoms, and metabolic disturbances with SA; and (2) identify their interactions in SA patients via the network approach.Methods1718 FEDN MDD patients were recruited. Depressive, anxiety, and psychotic symptoms were assessed by the Hamilton Rating Scale for Depression (HAMD), the Hamilton Rating Scale for Anxiety (HAMA), and the Positive and Negative Syndrome Subscale positive subscale, respectively. The serum levels of thyroid hormones and other metabolic parameters were assessed. Logistic regression model was applied to determine the correlates of SA. Network analysis was applied to determine the interaction between thyroid dysfunction, clinical symptoms, and metabolic disturbances.ResultsSA patients had significant worse metabolic disturbances, thyroid dysfunction, and clinical symptoms than non-SA patients. Thyroid peroxidases antibody, thyroid stimulating hormone (TSH), HAMD scores, HAMA scores, and systolic blood pressure was independently associated with SA. Network analysis suggested that TSH was the hub of the network, exhibiting substantial associations with metabolic disturbances, anxiety, and psychotic symptoms in SA patients.ConclusionsOur work highlights the predominant role of serum TSH levels in the pathophysiology of SA. Regular thyroid function tests might help early detect SA. Targeting increased TSH levels may help reduce metabolic disturbances and clinical symptoms in SA patients.
A cuproptosis-related LncRNA signature: Integrated analysis associated with biochemical recurrence and immune landscape in prostate cancer
Authors: Ren Lei , Yang Xu , Wang Weifeng , Lin Hansen , Huang Guankai , Liu Zixiong , Pan Jincheng , Mao Xiaopeng 
Published: February 2023

Background: As a new form of regulated cell death, cuproptosis differs profoundly from apoptosis, ferroptosis, pyroptosis, and necroptosis. The correlation between cuproptosis and long non-coding RNAs (lncRNAs) has been increasingly studied recently. In this study, a novel cuproptosis-related lncRNA prognostic signature was developed to investigate biochemical recurrence (BCR) and tumor immune landscape in prostate cancer (PCa).Methods and Materials: The transcriptome data and clinicopathologic information of PCa patients were downloaded from The Cancer Genome Atlas (TCGA). Pearson’s correlation analysis was applied to identify lncRNAs associated with cuproptosis. Based on Cox regression analysis and the least absolute shrinkage and selection operator (LASSO) regression analysis, we developed a cuproptosis-related lncRNA prognostic model (risk score) to predict the BCR of PCa patients. Additionally, we also constructed a nomogram with the risk score and clinicopathologic features. The biological function, tumor mutation burden (TMB), immune cell infiltration, expression levels of immune checkpoint genes, and anti-cancer drug sensitivity were investigated.Results: We constructed and validated the cuproptosis-related lncRNA signature prognostic model (risk score) by six crlncRNAs. All patients were divided into the low- and high-risk groups based on the median risk score. The Kaplan–Meier (KM) survival analysis revealed that the high-risk group had shorter BCR-free survival (BCRFS). The risk score has been proven to be an independent prognostic factor of BCR in PCa patients. In addition, a nomogram of risk scores and clinicopathologic features was established and demonstrated an excellent predictive capability of BCR. The ROC curves further validated that this nomogram had higher accuracy of predicting the BCR compared to other clinicopathologic features. We also found that the high-risk group had higher TMB levels and more infiltrated immune cells. Furthermore, patients with high TMB in the high-risk group were inclined to have the shortest BCRFS. Finally, patients in the high-risk group were more susceptible to docetaxel, gefitinib, methotrexate, paclitaxel, and vinblastine.Conclusion: The novel crlncRNA signature prognostic model shows a greatly prognostic prediction value of BCR for PCa patients, extends our thought on the association of cuproptosis and PCa, and provides novel insights into individual-based treatment strategies for PCa.
Revisiting fall armyworm population movement in the United States and Canada
Authors: Tessnow Ashley E. , Nagoshi Rodney N. , Meagher Robert L. , Fleischer Shelby J. 
Published: February 2023

IntroductionBiophysical approaches validated against haplotype and trap catch patterns have modeled the migratory trajectory of fall armyworms at a semi-continental scale, from their natal origins in Texas or Florida through much of the United States east of the Rocky Mountains. However, unexplained variation in the validation analysis was present, and misalignments between the simulated movement patterns of fall armyworm populations and the haplotype ratios at several locations, especially in the northeastern US and Canada, have been reported.MethodsUsing an expanded dataset extending into Canada, we assess the consistency of haplotype patterns that relate overwintered origins of fall armyworm populations to hypothesized dispersal trajectories in North America and compare the geographic distribution of these patterns with previous model projections.Results and discussionWe confirm the general accuracy of previous modeling efforts, except for late in the season where our data suggests a higher proportion of Texas populations invading the northeast, extending into eastern Canada. We delineate geographic limits to the range of both overwintering populations and show that substantial intermixing of the Texas and Florida migrants routinely occurs north of South Carolina. We discuss annual variation to these migratory trajectories and test the hypothesis that the Appalachian Mountains influence geographic patterns of haplotypes. We discuss how these results may limit gene flow between the Texas and Florida natal populations and limit the hereditary consequences of interbreeding between these populations.
Effects of altitude on the gut microbiome and metabolomics of Sanhe heifers
Authors: Zhang Xinyu , Wang Wei , Cao Zhijun , Yang Hongjian , Wang Yajing , Li Shengli 
Published: February 2023

IntroductionExtreme environments at high altitudes pose a significant physiological challenge to animals. We evaluated the gut microbiome and fecal metabolism in Sanhe heifers from different altitudes.MethodsTwenty Sanhe heifers (body weight: 334.82 ± 13.22 kg, 15-month-old) selected from two regions of China: the Xiertala Cattle Breeding Farm in Hulunbeier, Inner Mongolia [119°57′ E, 47°17′ N; approximately 700 m altitude, low altitude (LA)] and Zhizhao Dairy Cow Farm in Lhasa, Tibet [91°06′ E, 29°36′ N; approximately 3,650 m altitude, high altitude (HA)], were used in this study. Fecal samples were collected and differences in the gut microbiota and metabolomics of Sanhe heifers were determined using 16S rRNA gene sequencing and metabolome analysis.Results and discussionThe results showed that altitude did not significantly affect the concentrations of fecal volatile fatty acids, including acetate, propionate, butyrate, and total volatile fatty acids (p &gt; 0.05). However, 16S rRNA gene sequencing showed that altitude significantly affected gut microbial composition. Principal coordinate analysis based on Bray–Curtis dissimilarity analysis revealed a significant difference between the two groups (p = 0.001). At the family level, the relative abundances of Peptostreptococcaceae, Christensenellaceae, Erysipelotrichaceae, and Family_XIII were significantly lower (p &lt; 0.05) in LA heifers than in HA heifers. In addition, the relative abundances of Lachnospiraceae, Domibacillus, Bacteroidales_S24-7_group, Bacteroidales_RF16_group, Porphyromonadaceae, and Spirochaetaceae were significantly higher in HA heifers than in LA heifers (p &lt; 0.05). Metabolomic analysis revealed the enrichment of 10 metabolic pathways, including organismal systems, metabolism, environmental information processing, genetic information processing, and disease induction. The genera Romboutsia, Paeniclostridium, and g_unclassified_f_Lachnospiraceae were strongly associated with the 28 differential metabolites. This study is the first to analyze the differences in the gut microbiome and metabolome of Sanhe heifers reared at different altitudes and provides insights into the adaptation mechanism of Sanhe heifers to high-altitude areas.
Development of Candida autochthonous starter for cigar fermentation via dissecting the microbiome
Authors: Jia Yun , Liu Yuanfa , Hu Wanrong , Cai Wen , Zheng Zhaojun , Luo Cheng , Li Dongliang 
Published: February 2023

IntroductionThe main goal of tobacco fermentation technology is to minimize the alkaloid content while improving flavor substance content.MethodsThis study revealed the microbial community structure and their metabolic functions during cigar leaf fermentation by high-throughput sequencing and correlation analysis, and evaluated the fermentation performance of functional microbes based on in vitro isolation and bioaugmentation fermentation.ResultsThe relative abundance of Staphylococcus and Aspergillus increased first but then decreased during the fermentation, and would occupy the dominant position of bacterial and fungal communities, respectively, on the 21st day. Correlation analysis predicted that Aspergillus, Staphylococcus and Filobasidium could contribute to the formation of saccharide compounds, Bacillus might have degradation effects on nitrogenous substances. In particular, Candida, as a co-occurring taxa and biomarker in the later stage of fermentation, could not only degrade nitrogenous substrates and synthesize flavor substances, but also contribute to maintaining the stability of microbial community. Moreover, based on in vitro isolation and bioaugmentation inoculation, it was found that Candida parapsilosis and Candida metapsilosis could significantly reduce the alkaloids content and increase the content of flavor components in tobacco leaves.DiscussionThis study found and validated the critical role of Candida in the fermentation of cigar tobacco leaves through high-throughput sequencing and bioaugmentation inoculation, which would help guide the development of microbial starters and directional regulation of cigar tobacco quality.
Intestinal microbiota changes pre- and post-fecal microbiota transplantation for treatment of recurrent Clostridioides difficile infection among Iranian patients with concurrent inflammatory bowel disease
Authors: Gholam-Mostafaei Fahimeh Sadat , Azimirad Masoumeh , Naseri Kaveh , Nabavi-Rad Ali , Asadzadeh Aghdaei Hamid , Shahrokh Shabnam , Ebrahimi Daryani Nasser , Yadegar Abbas , Zali Mohammad Reza 
Published: February 2023

IntroductionPatients with inflammatory bowel disease (IBD) are at a greater risk for the recurrence of Clostridioides difficile infection (rCDI) that is triggered by intestinal microbiota dysbiosis. Fecal microbiota transplantation (FMT) has emerged as a highly effective therapeutic option for this complication. However, little is known about the impact of FMT on intestinal microbiota alterations in rCDI patients suffering from IBD. In this study, we aimed to investigate post-FMT intestinal microbiota alterations in Iranian rCDI patients with underlying IBD.MethodsA total of 21 fecal samples were collected including 14 samples pre- and post-FMT and 7 samples from healthy donors. Microbial analysis was performed by quantitative real-time PCR (RT-qPCR) assay targeting the 16S rRNA gene. The pre-FMT profile and composition of the fecal microbiota were compared to the microbial changes of samples collected 28 days after FMT.Results and discussionOverall, the fecal microbiota profile of recipients was more similar to donor samples after the transplantation. We observed a significant increase in the relative abundance of Bacteroidetes post-FMT, compared to the pre-FMT microbial profile. Furthermore, there were remarkable differences between the microbial profile of pre-FMT, post-FMT, and healthy donor samples by PCoA analysis based on the ordination distance. This study demonstrates FMT as a safe and effective approach to restore the indigenous composition of the intestinal microbiota in rCDI patients and ultimately results in the treatment of concurrent IBD.
Small target detection with remote sensing images based on an improved YOLOv5 algorithm
Authors: Pei Wenjing , Shi Zhanhao , Gong Kai 
Published: February 2023

IntroductionSmall target detection with remote sensing images is a challenging topic due to the small size of the targets, complex, and fuzzy backgrounds.MethodsIn this study, a new detection algorithm is proposed based on the YOLOv5s algorithm for small target detection. The data enhancement strategy based on the mosaic operation is applied to expand the remote image training sets so as to diversify the datasets. First, the lightweight and stable feature extraction module (LSM) and C3 modules are combined to form the feature extraction module, called as LCB module, to extract more features in the remote sensing images. Multi-scale feature fusion is realized based on the Res 2 unit, Dres 2, and Spatial Pyramid Pooling Small (SPPS) models, so that the receptive field can be increased to obtain more multi-scale global information based on Dres2 and retain the obtained feature information of the small targets accordingly. Furthermore, the input size and output size of the network are increased and set in different scales considering the relatively less target features in the remote images. Besides, the Efficient Intersection over Union (EIoU) loss is used as the loss function to increase the training convergence velocity of the model and improve the accurate regression of the model.Results and discussionThe DIOR-VAS and Visdrone2019 datasets are selected in the experiments, while the ablation and comparison experiments are performed with five popular target detection algorithms to verify the effectiveness of the proposed small target detection method.