bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tissue-specific Transcriptome Analysis Reveals Lignocellulose Synthesis Regulation in Elephant Grass (Pennisetum Purpureum Schum.)
Authors: Zhang Wenqing , Zhang Shengkui , Lu Xianqin , Li Can , Liu Xingwang , Dong Geyu , Xia Tao 
Published: July 2020

Abstract
Background:The characteristics of elephant grass, especially its stem lignocellulose, are of great significance for its quality as feed or other industrial raw materials. Because the genome of elephant grass has not been deciphered, the study of its lignocellulose synthesis pathway and key genes is limited. Results:In this study, RNA sequencing (RNA-seq) combining with lignocellulose content analysis and cell wall morphology observation using elephant grass stems from different development stages as materials, were applied to reveal the genes regulating cellulose and lignin synthesis. A total of 3852 differentially expressed genes (DEGs) were identified in three periods of T1, T2 and T3. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the two most abundant metabolic pathways were phenylpropanemetabolism, starch and sucrose metabolism, which closely related to cell wall development, hemicellulose, lignin and cellulose synthesis. Through weighted gene co-expression network analysis (WGCNA) of DEGs, a ‘blue’ module highly correlated with cellulose synthesis and a ‘turquoise’ module highly correlated with lignin synthesis were exhibited. A total of 43 candidate genes were screened, of which 17 had function annotations in other species. In addition, the expression of CesA, PAL, CAD, C4H, COMT, CCoAMT, F5H, CAD and CCR at different development stages were analyzed, and found that the content of lignocellulose was correlated with the expression levels of these structural genes. Conclusions:This study not only provides new insights into the molecular mechanisms of cellulose and lignin synthesis pathways in elephant grass, but also offers a new and extensive list of candidate genes for more specialized functional studies in the future which may promote the development of high-quality elephant grass varieties with high cellulose and low lignin content.
Natural Variation of Physiological Traits, Molecular Markers, and Chlorophyll Catabolic Genes Associated With Heat Tolerance in Perennial Ryegrass Accessions
Authors: Xu Bin , Zhang Jing , Li Hui , Jiang Yiwei , Li Huibin , Zhang Zhipeng , Huang Bingru 
Published: July 2020

Abstract
Background: Identification of genetic diversity in heat tolerance and associated traits is of great importance for improving heat tolerance in cool-season grass species. The objectives of this study were to determine genetic variations in heat tolerance associated with phenotypic and physiological traits and to identify molecular markers associated with heat tolerance in a diverse collection of perennial ryegrass (Lolium perenne L.). Results: Plants of 98 accessions were subjected to heat stress (35/30 ℃, day/night) or optimal growth temperature (25/20 ℃) for 24 d in growth chambers. Overall heattolerance of those accessions was ranked by principal component analysis (PCA) based on eight phenotypic and physiological traits. Among these traits, electrolyte leakage (EL), chlorophyll content (Chl), relative water content (RWC) had high correlation coefficients (−0.858, 0.769, and 0.764, respectively) with the PCA ranking of heat tolerance. We also found expression levels of four Chl catabolic genes (CCGs), including LpNYC1, LpNOL, LpSGR, and LpPPH, were closely related to the heat tolerance of ryegrass accessions. Furthermore, 66 pairs of simple sequence repeat (SSR) markers were used to perform association analysis based on the PCA result. The population structure of ryegrass can be grouped into three clusters, and accessions in cluster C were relatively more heat tolerant than those in cluster A and B. SSR markers significantly associated with above-mentioned traits were identified (R2>0.05, p<0.01)., including two pairs of markers located on chromosome 4 in association with Chl content and another four pairs of markers in association with EL.Conclusion:The result not only identified useful physiological parameters, including EL, Chl content, and RWC, and their associated SSR markers for heat-tolerance breeding of perennial ryegrass, but also highlighted the involvement of Chl catabolism in ryegrass heat tolerance. Such knowledge is of significance for heat-tolerance breeding and heat tolerance mechanisms in perennial ryegrass as well as in other cool-season grass species.
Early-stage predictive markers of critically ill COVID-19 cases
Authors: Zhou Zheng , Yin Shiwei , Xu Jie , Deng Yunfeng , Wang Xinfeng , Ma Xin 
Published: July 2020

Abstract
Background: Severe cytokine storm syndrome (CSS) is considered as the cause of death among critically ill COVID-19 cases. Early identification of the high-risk severe cases is crucial to lower the fatality and healthcare costs.Methods: In this study, we retrospectively analyzed the first and second-week serum levels of IL-6, IL-8, and IL-10 of 50 COVID-19 cases. We calculated the ratios of IL-6/IL-10 and IL-8/IL-10 at 3rd, 6th, 9th, and 12th days of hospitalization. Results: We collected 50 COVID-19 cases (male 54%, mean age 51.2, range 18 - 86), including 39 mild cases (78%), 7 severe/recovered cases (14%), and 4 died cases (8%).The ratios of IL 6/IL-10 and IL-8/IL-10 among mild cases were below 27 (the highest, 26.9) along the 4 testing points of two week hospitalization, while we found that the IL-6/IL-10 and IL-8/IL-10 ratios were as high as 187.51 and 225.3 respectively in the death group on 3rd day with the highest IL-6/IL-10 ratio of 297.28 on the 6th day of hospitalization. Conclusions: Our preliminary results suggest that the ratios of IL-6/IL-10 and IL-8/IL-10 at the early stage (the first two weeks) of COVID-19 could be a predictive marker for the disease prognosis, of which the cut-off lines were suggested below 50 for a mild and recoverable severe cases.
Assessing the Immediate Impact of COVID-19 Lockdown on the Air Quality of Kolkata and Howrah, West Bengal, India
Authors: Sarkar Mohan , Das Anupam , Mukhopadhyay Sutapa 
Published: July 2020

Abstract
The worldwide spread of COVID-19 caused a nationwide lockdown in India from 24th March 2020 and was further extended up to 3rd May 2020 to break off the transmission of novel Coronavirus. The study is designed to assess the changes in air quality from the pre lockdown period to the during lockdown period in Kolkata and Howrah municipal corporation, West Bengal, India. GIS-based techniques include the spatial and temporal distribution of pollutants using interpolation method, on the other hand, statistical methods like Analysis of Variance (ANOVA) was applied to determine the mean differences two phases and correlation matrix helps to understand the changing association of the pollutants in pre and during-lockdown phases. Significant correlations have been found among the pollutants, ANOVA (Two-Way) has shown the significant mean difference of NAQI between the two phases, F (1,611)=465.723, p<0.0001; pairwise comparison for Ballygunj has shown the highest mean difference 108.194 at p<0.0001 significant level between lockdown and pre lockdown phase. Significant positive correlation has been found between PM2.5, PM 10 (0.99*); PM2.5, NO2 (0.81*); PM10, NO2 (0.81*); CO, NO2 (0.77*) and some negative correlations have also been found between O3, NO (-0.15); O3 and NH3 (-0.36) in the pre lockdown phase. The reduction amount of mean concentration from the pre lockdown phase to during lockdown of the main pollutants like PM 2.5, PM10 and NO2 are ~58.71%, ~57.92% and ~55.23%. Near RBU constant emission of PM2.5, 10 and NO2 have been recorded due to the nearby Cossipore thermal power station.
Prediction of Prognosis in Patients with Prostate Cancer by DNA Methylation Classification
Authors: Chen Lei , Pan Deshen , Sha Minglei , Li Deng , Xu Chaoliang , Chen Feiteng , Liu Jiayu , Zheng Danchuan , Lu Jun , Xia Shujie , Shao Yi 
Published: July 2020

Abstract
Background: Prostate cancer is the second most frequently diagnosed cancer and the fifth leading cause of cancer-related death. It is estimated that the incidence of prostate cancer is on the rise worldwide. Epigenetic changes in tumors play an important role in the occurrence and development of prostate cancer. DNA methylation is one of the mechanisms of tumor epigenetic regulation and may be a new biomarker that has great potential in early tumor screening, treatment guidance and prognosis prediction. The purpose of this study was to explore a classification method from the perspective of DNA methylation.Methods: The least absolute shrinkage and selection operator (LASSO) method was used to analyze DNA methylation and RNA-seq data from the Cancer Genome Atlas (TCGA). The methylation sites with small differences were eliminated, and the 21 methylation sites with the most significant differences were retained for analysis. Using their corresponding gene expression levels, a recurrence prediction model for prostate cancer patients was constructed to distinguish high-risk, medium-risk, and low-risk cases. Immune cell abundance analysis, gene enrichment analysis, Tumor burden mutation analysis and gene copy number variation analysis were then used to analyze the differences among these three subtypes and their underlying mechanisms. Results: We observed the difference in disease-free survival (DFS) of the three methylated subtypes in the test set, which was verified in the validation set. We found three subtypes have different proportions of immune cells, especially in memory B cells, M2 macrophages, Treg cells. GSVA and GSEA analysis revealed that the relevant metastasis gene sets of prostate cancer were enriched in high-risk cases. In addition, the mutation frequencies of TP53, TTN and KMT2D were the highest, and gradually increased in the three genotypes according to Tumor burden mutation (TMB) analysis. Gene copy number variation (CNV) showed that AR, LAPTM4B, and MTDH were significantly amplified, while ATP1B2 and FAM92B were significantly deleted. Finally, univariate and multivariate analysis showed that there were statistical differences among the three methylation subtypes, which can be used as an index to predict prostate cancer recurrence.Conclusions: Our study suggests that classification based on DNA methylation is an independent factor for predicting tumor recurrence in patients with prostate cancer.
Tumour-Associated Macrophage Polarisation Promotes Progression of Esophageal Carcinoma
Authors: Yuan Xin , Li Ya , Zhang An Zhi , Jiang Chen Hao , Li Fan Ping , Xie Yu Fang , Li Jiang Fen , Liang Wei Hua , Zhang Hai Jun , Liu Chun Xia , Pang Li Juan , Shen Xi Hua , Li Feng , Hu Jian Ming 
Published: July 2020

Abstract
Background: The immune response mediated by tumour-associated macrophages (TAMs) is vital in tumour progression in many cancers. Fibrinogen-like protein 2 (FGL2) is a critical immunosuppressive factor that regulates the tumour microenvironment. However, no study has yet reported on the relationship between FGL2, tumour-infiltrating lymphocyte recruitment, and prognosis in esophageal carcinoma (ESCA). Methods: Differentially expressed genes (DEGs) in various macrophage phenotypes were analysed using the GEO database. We identified the hub genes involved in affecting ESCA clinical prognosis using Kaplan-Meier plotter. Correlations between hub genes and immune infiltrates were analysed using the Tumour Immune Estimation Resource (TIMER) database, while correlation analysis between FGL2 and cytokine expression was assessed using cBioPortal. In vitro cell co-culture experiments were performed to examine the role of FGL2 in promoting tumorigenesis. Finally, we compared the GO terms and KEGG pathways enriched by the DEGs in M1 and M2 macrophages using DAVID.Results: High FGL2 expression was significantly associated with poorer overall survival and relapse-free survival of esophageal cancer patients. FGL2 expression was positively correlated with immune markers and infiltrating levels of B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils and dendritic cells. In addition, FGL2 expression was strongly correlated to IL-10, MMP9, CCL5, TIM-3, IL-13, VCAM1, M-CSF and FGF-7 expression. Conclusions: M2-like TAMs may regulate the tumour microenvironment by secreting FGL2, thereby inducing the occurrence and progression of ESCA. Reversing TAM polarization may be an effective strategy that reveals new targets for immunotherapy in treating ESCA.
Phenotypic Clusters and Survival Analyses in Interstitial Pneumonia with Myositis-Specific Autoantibodies
Authors: Li Yihua , Yu Shiwen , Fan Yali , Wu Na , Wang Yiran , Ye Qiao 
Published: July 2020

Abstract
Background: Interstitial pneumonia (IP) is one of the common pulmonary complications of idiopathic inflammatory myopathy (IIM), among which myositis-specific autoantibodies (MSA) are specific for IIM diagnosis and prognosis. However, IP patients with MSA (MSA-IP) have not been well described. The study aimed to explore the phenotypic clusters and prognosis of MSA-IP patients.Methods: A total of 124 MSA-IP patients were prospectively enrolled for analysis. Serum MSA were detected using immunoprecipitation. Radiographic patterns of IP were determined according to the classification of idiopathic IPs. The clusters of MSA-IP patients were identified using cluster analysis. Potential risk factors of acute onset and short-term prognosis were also analyzed. Results: There were four clusters of MSA-IP patients. Cluster 1 patients were elders with chronic onset and usual interstitial pneumonia pattern on CT scan. Cluster 2 patients were all positive for anti-aminoacyl-tRNA antibodies, predominantly females and had frequent respiratory symptoms. Patients of cluster 3 showed multi-system involvements with nonspecific interstitial pneumonia pattern. Patients of cluster 4 had severe respiratory symptoms with anti-MDA5. The patients of cluster 3 (OR 6.682, 95% CI 1.560–28.622, P=0.011) or cluster 4 (OR 6.057, 95% CI 1.715–21.388, P=0.005) were susceptible to acute onset. The patients of cluster 4 were prone to disease progression (HR 2.711, 95% CI 1.128–6.519, P=0.034), which was consistent with the Kaplan–Meier curves.Conclusions: Four distinctive clusters were determined by cluster analysis suggesting the characteristics, serological antibodies and prognosis of MSA-IP.
Housing Conditions, Level of Feeding and Presence of Antibiotics in the Feed Shape Rabbit Cecal Microbiota
Authors: Velasco-Galilea María , Guivernau Miriam , Piles Miriam , Viñas Marc , Rafel Oriol , Sánchez Armand , Ramayo-Caldas Yuliaxis , González-Rodríguez Olga , Sánchez Juan P. 
Published: July 2020

Abstract
Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the housing conditions and other animal management aspects, such as the presence of antibiotics in the feed or the level of feeding, is still needed. Characterization of microbial diversity and composition of growing rabbits raised under different conditions could help better understand the role these practices play in cecal microbial communities and how it may result in different animal performance.Results: Four hundred twenty-five meat rabbits raised in two different facilities, fed under two feeding regimes ( ad libitum or restricted) with feed supplemented or free of antibiotics, were selected for this study. A 16S rDNA-based assessment through the MiSeq Illumina sequencing platform was performed on cecal samples collected from these individuals at slaughter. Different univariate and multivariate approaches were conducted to unravel the influence of the different factors on microbial alpha diversity and composition at phylum, genus and OTU taxonomic levels. The animals raised in the facility harboring the most stable environmental conditions had greater, and less variable, microbial richness and diversity. Bootstrap univariate analyses of variance and sparse partial least squares-discriminant analyses endorsed that the farm exerted the largest influence on rabbit microbiota since the relative abundances of many taxa were found differentially represented between both facilities at all taxonomic levels characterized. Furthermore, only five OTUs were needed to achieve a perfect classification of samples according to the facility where animals were raised. The level of feeding and the presence of antibiotics did not modify the global alpha diversity but had an impact on some bacteria relative abundances, albeit in a small number of taxa compared with the farm, which is consistent with the lower sample classification power according to these factors achieved using microbial information.Conclusions: this study reveals different degrees of influence attributable to environment and animal management. It highlights the importance of offering a controlled breeding environment that reduces differences in microbial cecal composition that could be causative of different animal performance.
T-cell lymphoma with a granulomatous lesion of the lungs after autologous hematopoietic stem cell transplantation against Epstein–Barr virus-positive diffuse large B-cell lymphoma: a case report
Authors: Kajimoto Yusuke , Terasaki Yasuhiro , Terasaki Mika , Kunugi Shinobu , Okabe Yugo , Wakita Satoshi , Inokuchi Koiti , Shimizu Akira 
Published: July 2020

Abstract
Background
Post-transplant lymphoproliferative disorders (PTLDs) are serious lymphoid and/or plasmacytic proliferations that occur after undergoing solid organ or hematopoietic stem cell transplantation (HSCT). In the context of HSCT, most reported PTLDs have occurred in patients who received allogenic HSCT (AlloHSCT), but only a few cases have been reported in autologous HSCT (AHSCT) recipients. Primary pulmonary T-cell lymphoma cases are also rare and have been reported mostly in case studies.
Case presentation:
A 53-year-old female patient initially presented with enlargement of the left cervical lymph nodes and was diagnosed as Epstein–Barr virus (EBV)-positive diffuse large B-cell lymphoma (DLBCL). She was treated with R-CHOP, R-ACES, and autologous HSCT (AHSCT) and went into remission. Four years later, computed tomography results revealed multiple lung nodules, and abnormal infiltration and sustained and progressing hypogammaglobulinemia was observed. The pathological specimen of video-assisted thoracoscopic surgical lung biopsy demonstrated extensive invasion of lymphocytes with notable granuloma findings. Flow cytometric immunophenotyping analysis showed that lymphocytes were positive for CD3 and CD5; especially, CD3 was expressed in the cytoplasm. Southern blot analysis revealed rearrangements of the T-cell receptor Cβ1 gene. She was diagnosed with peripheral T-cell lymphoma, regarded as T-cell PTLD accompanied by granulomatous lesion.
Conclusion
Here, we report a rare case of T-cell lymphoma that mainly affected the lungs with the presentation of notable granulomatous findings following AHSCT against EBV-positive DLBCL. This uncommon presentation of rare lung lesions of granulomatous T-cell lymphoma could be related to the manifestation of a PTLD associated with sustained hypogammaglobulinemia.
Genotype Distribution of Human Papillomavirus (HPV) in Iranian Breast Cancer Patients
Authors: Mofrad Morvarid Golrokh , Sadigh Zohreh Azita , Ainechi Sanaz , Faghihloo Ebrahim 
Published: July 2020

Abstract
Background: the role of viruses in the aetiology of breast cancer (BC) have been significantly investigated in recent years. Human papillomavirus (HPV) has been detected in invasive breast carcinomas. Most studies have only focused on the detection of viral DNA therefore the aim of this study was to determine the genotypes of each papillomavirus.Methods: we collected and analyzed 70 blocks of Formalin Fixed Paraffin Embedded (FFPE) including 59 BC samples, and 11 noncancerous samples as control from Iranian patients using nested PCR. Real-time PCR supported nested PCR findings. Genotyping of HPV positive samples was performed, the samples were also subjected to a multiplex PCR to detect herpes simplex-1 (HSV-1), herpes simplex-2 (HSV-2), varicella zoster virus (VZV) and cytomegalovirus (CMV) in BC.Results: Papillomavirus DNA was present in 7 of 59 BC samples (11.8%); while none was detected in control samples. The most prevalent type was HPV18, followed by HPV 6, but we didn’t find HPV16 in cases. All HPV positive patients had high tumor grades (II/ III), and the age range of them were from 33 to 73 years (average was about 51). Most of HPV positive patients had low levels of education. Histologic diagnosis of all positive cases were ductal carcinoma. 5 of 59 BC specimens (8.47%), were positive for HSV-1.Conclusions: Our results suggest that high risk HPVs may play a role in breast carcinogenesis. Also we detected HPV6 and HSV1 in our BC samples, taking into account a carcinogenesis role for low risk HPVs, in addition to high risk HPVs. Further large scale studies are warranted to assess the significance of our findings.
Targeting&nbsp;DNA Methyltransferase 1 Limits Vesicular Stomatitis Virus Through Enhancing IRF3/IFN Signaling
Authors: Zhao Kui , Gao Fei , Lin Ye , Lin Jing , Zhang Bo , Song Deguang , Li Zi , Lan Yungang , Lu Huijun , He Wenqi , Guan Jiyu 
Published: July 2020

Abstract
BackgroundViruses develop strategies to escape from host anti-viral response in many aspects including hijacking host epigenetic factors. However, the relationship between host DNA methyltransferase 1 (DNMT1) and vesicular stomatitis virus (VSV) replication is largely unknown.MethodsIn the present study, we performed Western Blotting, qRT-PCR, RNA interference, Methylation-specific PCR and Cell viability assay to uncover the role of DNMT1 in the process of VSV replication.ResultsWe have observed VSV infection enhances DNMT1 protein accumulation in macrophage cell. Furthermore, DNMT1 functional blocking and gene silencing limit VSV replication. Moreover, loss of DNMT1 increases interferon responses, including Ifnb1 and IFN-stimulated genes (ISGs) upregulation. CpG islands (CGIs) of Irf3 promoter region are demethylated after DNMT1 short-term inhibition with thioguanine, which is accompanied by Irf3 transcript upregulation. Meanwhile, Irf3 silencing largely reversed DNMT1 loss-suppressed VSV replication. What is more, the basal level of endogenous retrovirus (ERV) transcripts is required for thioguanine-induced ISGs.ConclusionsDNMT1 loss-induced IRF3 enhancement leads to interferon responses and subsequent VSV suppression, which provides a potential strategy to inhibit viral replication by targeting DNMT1 with its inhibitor.
The prediction of survival and analysis of microenvironment in patients with sarcoma
Authors: Chen Jiarui , Liu Chong , Liang Tuo , Zhang Zide , Lu Zhaojun , Liao Shian , Jiang Jie , Xu Guoyong , Li Hao , Chen Tianyou , Qin Zhaojie , Liu Huijiang , Cen Jiemei , Zhan Xinli 
Published: July 2020

Abstract
The authors have requested that this preprint be removed from Research Square.