bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioinformatic analysis and identification of potential hallmarks in poorly differentiated thyroid cancer
Authors: Chen Xin , Ma Runsheng , Li Hongqiang , Tang Yifeng , Yin Detao 
Published: January 2021

Abstract
Purpose: The accumulation of malignant tumor gene mutations makes differentiated thyroid cancer (DTC) gradually dedifferentiated to poorly differentiated thyroid cancer (PDTC) or anaplastic thyroid cancer (ATC). This study analyzed the gene expression profile in the process of dedifferentiation of thyroid cancer, aiming to explore the molecular mechanism of PDTC and ATC.Methods: Eight series from GEO database are collected for differentially expressed genes (DEGs) of DTC, PDTC and ATC. Then, GO analysis, KEGG pathway analysis, and functional path enrichment analyses are performed by MATESCAPE. Hub-genes are identified by using the method of MNC in protein interaction networks. Moreover, the expression of hub-genes and hub-gene related survival in thyroid cancers are analyzed by GEPIA2. Finally, the functional path enrichment pathways of PDTC are performed by GSEA Java.Results: There are obvious differences among DEGs of DTC, PDTC, and ATC, and 17 cross gene of DEGs were found. The DEGs in PDTC were mainly concentrated in regulation of cytoskeleton organization, cell division, positive regulation of kinase activity. While the DEGs in ATC were mainly in extracellular matrix organization, extracellular structure organization. Furthermore, 6 hub-genes were obtained in the development of PDTC by using Cytoscape: EGF, CCND1, DEPDC1, ANLN, HGF, BCL2L1. The high expression levels of the genes of EGF, DEPDC1, ANLN, HGF were associated with the poor survival of thyroid cancer. While the high expression levels of CCND1 and BCL2L1 were beneficial to the survival of patients with thyroid tumor. Finally, GSEA revealed that two gene sets are significantly enriched, including KEGG_THYROID_CANCER and KEGG_GLIOMA. And CCND1 and EGF have a core gene position in KEGG_GLIOMA.Conclusions: The molecular function (MF), biological processes (BP) and KEGG pathways have changed during the process of malignant transformation of thyroid cancer. Especially, the activation of EGF-EGFR pathway promotes the malignant transformation of thyroid tumor. Furthermore, six hub-genes, especially CCND1 and EGF, could become potential biomarkers of PDTC. This study can serve as a reference to understand the malignant transformation of thyroid cancer.
Development and Validation of an Immune-related Prognostic Signature in Cervical Cancer
Authors: Su Rongjia , Jin Chengwen , Bu Hualei , Wang Xiaoyun , Kuang Menghua , Xiang Jiangdong , jin chengjuan 
Published: January 2021

Abstract
Background: Cervical cancer is the fourth most frequently gynecological malignancy across the world. Immunotherapies have proved to improve prognosis of cervical cancer. However, few studies on immune-related prognostic signature had been reported in cervical cancer. Methods: Raw data and clinical information of cervical cancer samples were download from TCGA and UCSC Xena website. Immunophenoscore of immune infiltration cells in cervical cancer samples was calculated through ssGSEA method using GSVA package. WGCNA, Cox regression analysis, LASSO analysis and GSEA analysis were performed to classify cervical cancer prognosis and explore the biological signaling pathway. Results: There were 8 immune infiltration cells associated with prognosis of cervical cancer. Through WGCNA, 153 genes from 402 immune-related genes were significantly correlated with prognosis of cervical cancer. A 15-gene signature demonstrated powerful predictive ability in prognosis of cervical cancer. GSEA analysis showed multiple signaling pathways containing PD-L1 expression and PD-1 checkpoint pathway differences between high risk and low risk groups. Conclusions: The 15-gene signature was associated with multiple immune cells and immune infiltration in tumor microenvironment. Furthermore, the 15-gene signature is an effective potential prognostic classifier in the immunotherapies and surveillance of cervical cancer.
Assessment of Factors that Contribute to Deforestation in Shabe Sombo Woreda, Jimma Zone, South West Ethiopia
Authors: Weyesa Guta Waktole Waktole 
Published: January 2021

Abstract
Deforestation is the process of removing forest areas and using the land for other uses. Deforestation also has been described as the cutting down of trees without planting others in their place. The causes of deforestation are varied but may broadly be categorized into anthropogenic and natural factors. For the anthropogenic factors, increased wood fuel collection, clearing of forests for agriculture, illegal and poorly regulated timber extraction, social and environmental conflicts, increasing urbanization and industrialization. This study is aimed to assess the deforestation status and contributing factors in making Shabe Sembo woreda, Jimma Zone South West Ethiopia. The main objective of this study is to assess the factors that contribute to deforestation in Shabe sombo woreda, jimma Zone, South West Ethiopia. The study has been conducted in Shabe Sombo woreda located in Jimma Zone, Oromia regional state. A cross sectional study design has been employed. The source of population was all households found in Shabe sombo Woreda. The sample size of this study was 100 householders from 1200 total households. Data were collected by using open and close ended questionnaires for gathering important information used for this study. About 52(54.167%) of the respondents reported that the most factor contributing to deforestation in Shabe Sombo was expansion of agricultural land. Whereas About 28 (29.167%) of the respondents reported as cutting trees for fire wood is one factor contributing to deforestation in shabe Sombo woreda, Jimma zone, Southwest Ethiopia.
Bridgmanite-Predominant Lower Mantle Evidenced from Velocity and Density Profiles across the 660-km Discontinuity
Authors: Fu Suyu , Zhang Yanyao , Okuchi Takuo , Lin Jung-Fu 
Published: January 2021

Abstract
Earth’s mantle composition is essential to our understanding of its physics and dynamics. Here we report single-crystal elasticity (Cij) of (Al,Fe)-bearing bridgmanite, Mg0.88Fe0.1Al0.14Si0.90O3 with Fe3+/∑Fe=~0.65, up to ~82 GPa measured in diamond anvil cells. Together with heat capacity measurements on bridgmanite and ferropericlase, we develop a fully internally-consistent thermoelastic model to simultaneously evaluate lower-mantle mineralogy and geotherm via comparisons of P-wave, S-wave velocities, and density (VP, VS, and ρ) with one-dimensional seismic profiles. Our best-fit model demonstrates the lower mantle consists of ~89 vol% (Al,Fe)-bearing bridgmanite, ~4 vol% ferropericlase, and ~7 vol% CaSiO3 perovskite. A chemically layered mantle with pyrolitic upper mantle and bridgmanite-predominant lower mantle would display ~3.2(±1.5)%, ~5.2(±1.5)%, and ~5.0(±1.0)% jumps in VP, VS, and ρ, respectively, across the 660-km discontinuity, which are well consistent with seismic reflection observations. The lower mantle could have become bridgmanite-predominant via accumulations of ancient silica-rich materials, which helps explain current deep-Earth seismic and geochemical signatures.
A Cassava Common Mosaic Virus Vector for Virus-induced Gene Silencing in Cassava
Authors: Tuo Decai , Zhou Peng , Yan Pu , Liu Yang , Cui Hongguang , Sun Di , Liao Wenbin , Wang He , Yang Xiukun , Li Xiaoying , Shen Wentao 
Published: January 2021

Abstract
Background: Cassava is an important crop for food security and industry in the least-developed and developing countries. The completion of the cassava genome sequence and identification of large numbers of candidate genes by next-generation sequencing provide extensive resources for cassava molecular breeding and increase the need for rapid and efficient gene function analysis systems in cassava. Several plant virus-induced gene silencing (VIGS) systems have been developed as reverse genetic tools for rapid gene function analysis in cassava. However, these VIGS vectors could cause severe viral symptoms or inefficient gene silencing.Results:In this study, we constructed agroinfection-compatible infectious cDNA clones of cassava common mosaic virus strain CM (CsCMV-CM) that causes systemic infection with mild symptoms in cassava. CsCMV-CM was then modified to a viral vector carrying the Nimble cloning frame, which facilitates the rapid and high-throughput cloning of silencing fragments into the viral genome. The CsCMV-based vector successfully silenced phytoene desaturase (PDS) and magnesium chelatase subunit I (ChlI) in different cassava varieties and Nicotiana benthamiana. The silencing of the ChlI gene could persist for more than two months. Conclusions: This CsCMV-based VIGS system provides a new tool for rapid and efficient gene function studies in cassava.
Deep Hierarchical Embedding for Simultaneous Modeling of GPCR Proteins in a Unified Metric Space
Authors: Lee Taeheon , Lee Sangseon , Kang Minji , Kim Sun 
Published: January 2021

Abstract
GPCR proteins belong to diverse families of proteins that are defined at multiple hierarchical levels. Inspecting relationships between GPCR proteins on the hierarchical structure is important, since characteristics of the protein can be inferred from proteins in similar hierarchical information. However, modeling of GPCR families has been performed separately at each level. Relationships between GPCR proteins are ignored in these approaches as they process the information in the proteins with several disconnected models. In this study, we propose a deep learning model to simultaneously learn representations of GPCR family hierarchy from the protein sequences with a unified single model. Novel loss term based on metric learning is introduced to incorporate hierarchical relations between proteins. We tested our approach using a public GPCR sequence dataset. Metric distances in the deep feature space corresponded to the hierarchical family relation between GPCR proteins. Furthermore, we demonstrated that further downstream tasks, like phylogenetic reconstruction and motif discovery, are feasible in the constructed embedding space. These results show that hierarchical relations between sequences were successfully captured in both of technical and biological aspects.
High Expression of PD-L1 is Associated with Better Survival in Pancreatic/Periampullary Cancers and Correlates with Epithelial to Mesenchymal Transition.
Authors: Thakur Nishant , Paik Kwang Yeol , Hwang Gyoyeon , Chong Yosep 
Published: January 2021

Abstract

BackgroundPeriampullary cancers (PACs) are characterised with tumour-infiltrating lymphocytes (TILs), severe fibrosis, and epithelial to mesenchymal transition (EMT). The immune checkpoint marker programmed death-1 (PD-1) and its ligands 1 and 2 have gained popularity in cancers with TILs. Evidence suggests a strong relationship between immune checkpoint markers and EMT in cancers. Here, we evaluated the expression and prognostic significance of immune checkpoint and EMT markers in PAC using an automated image analyser.MethodsFormalin-fixed, paraf-fin-embedded surgically excised PAC tissues from laboratory archives (1998-2014) were evaluated by immunohistochemical staining for PD-1, PD-L1, and PD-L2 in a tissue microarray. ResultsIn total, 115 PAC patients (70 males and 45 female) with an average age of 63 years were analysed. Location, gross type, size, radial resection margin, N-M stage, lymphatic invasion, vascular invasion, peri-neural invasion, histologic well differentiation, severe inflammation, and high PD-L1 expression were significantly associated with recurrence. Higher PD-L1 expression, but not PD-1 and PD-L2, was significantly related to better overall survival (OS) and disease-free survival (DFS). PD-L1 and PD-L2 were significantly related to EMT markers.ConclusionAside from other clinicopathologic parameters, high PD-L1 expression was significantly related to better OS and DFS of PAC patients. Moreover, immune checkpoint markers were significantly associated with EMT markers. Therefore, PD-L1 expression can be a good prognostic marker to guide future immune target-based therapies in PAC patients.
Identification of A 10-Gene Signature To Predict Efficacy of Neoadjuvant Therapy in Patients With HER2 Positive Breast Cancer.
Authors: Wang Yusong , Wang Mozhi , Sun Xiangyu , Yao Litong , Wang Mengshen , Dong Haoran , Li Xinyan , He Mingcong , Xu Yingying 
Published: January 2021

Abstract
Background:Patients with human epidermal growth factor receptor 2 (HER2) positive breast cancer represent a poor prognosis, which are recommended to be treated with neoadjuvant therapy (NAT). Tumor immune microenvironment, especially tumor infiltrating cells (TILs), are proved to predict the efficacy of NAT. However, validated immune-related multi-gene signatures for HER2-positive BC are still lacking.Methods:We collected gene expression arrays of pre-NAT samples from the National Center for Biotechnology Information Gene Expression Omnibus. Totally 4 studies are included in our study (n=295, no. of train=207, no. of validation=95) to construct the signature. Single Sample Gene Set Enrichment Analysis (ssGSEA)and weighted gene co-expression network analysis (WGCNA)were used to quantify immune-infiltrating components in tumor environment and to identify immune related modules. We used spline regression to evaluate non-linear effect of genes and to construct the signature.Results:Immune infiltration status was significantly related to pathological complete response (pCR) (p=0.02). We filtered 80 differential expression genes according to immune infiltration status, and identified two gene modules correlated to pCR and immune infiltration status. CCL5, CD72, PTGDS, CYTIP, PAX5, and estrogen receptor (ER)status were significantly related to pCR in linear multivariate analysis. In spline regression, non-linear aspects of MAP7, IL2RB, CD3G, PTPRC, TRAC were relevant to pCR. We constructed a signature concerning both linear and non-linear effects of genes, which was validated in 5-fold cross validation (AUC=0.81) and an external validation cohort (n=88) (AUC=0.797).Conclusions:In HER2 positive BC, immune infiltration status should be involved into consideration to make optimal regimens. A ten-gene generalized non-linear signature including ER status could predict the efficacy of NAT.
Fast Characteristic of Skin Lesions by Machine-Learning of Raman Spectrum
Authors: Zhang Hua , Wang Danhua , Qu Limei , Xue Ying , Li Xinli , Li Bei , Liu Bin 
Published: January 2021

Abstract
Background: The traditional diagnosis of skin lesions mainly relies on dermoscope and pathological biopsy, of which the former is non-objective and the latter is invasive and time-consuming. It is necessary to find an objective and non-invasive inspection method for the diagnosis of skin cancer which is the most common malignant tumor. Herein, we aimed to fast identify the skin cancers on ultrathin frozen fresh tissue sections by combining Raman spectroscopy detection and machine learning technology. Methods and material: 22 fresh frozen tissue sections including 3 squamous cell carcinomas, 11 basal cell carcinomas, 2 malignant melanomas, 3 seborrheic keratosis, and 3 melanocytic nevi, were included and performed Raman detection. To prevent the discrete Raman data distribution affecting the generalization ability of the learning model, a series of adaptive preprocessing algorithms were first applied to standardize the raw Raman data of five skin lesions. The processed Raman data were performed visualized cluster analysis by principal components analysis (PCA) and t-distributed stochastic neighbor embedding (t-SNE). And, using K-nearest Neighbor (KNN) and support vector machine (SVM) classifiers, two predictive models for diagnose were established and evaluated in the training set and test set by the confusion matrixes and receiver operating characteristic (ROC) curves.Results: The mean variance Raman spectrum graph of 5 skin lesion types were acquired after standardization procession and 4 peak positions with large differences were found. Through dimensionality reduction by PCA and t-SNE, the visual clustering results of Raman data showed heterogeneous intra-cluster homogeneity and inter-cluster dispersion. The test accuracies reached 94.56% and 98.94% in KNN and SVM classifiers respectively. The areas under the ROCs of the two classifiers, in the category dimension and the sample dimension, were all more than 0.99 which is close to the perfect classification effect. Conclusions: Raman spectroscopy is a competitive candidate for the fast and accurate diagnosis of skin lesions and the molecular information provided may be used in the pathological classification, predicting immunotherapy responsiveness and stratifying prognostic risk. Furthermore, the combination of Raman spectroscopy and machine learning methods showed great diagnostic capabilities with high accuracy is a promising tool for the diagnosis of skin lesions.
SLC25A21 Suppresses Cell Growth in Bladder Cancer Via The Reactive Oxygen Species-Mediated Mitochondrion-Dependent Apoptosis Pathway
Authors: Wang Yong , Gao Jiawen , Hu Shasha , Zeng Weiting , Yang Hongjun , Chen Hui , Wang Shuang 
Published: January 2021

Abstract
Background: Bladder cancer (BCa) is a commonly diagnosed malignancy worldwide that has poor survival depending on its intrinsic biologic aggressiveness and a peculiar radio- and chemoresistance features. Gaining a better understanding of tumorigenesis and developing new diagnosis and treatment strategies for BCa is important for improving BCa clinical outcome. SLC25 family member 21 (SLC25A21), a carrier transporting C5-C7 oxodicarboxylates, has been reported to contribute to oxoadipate acidemia. However, the potential role of SLC25A21 in cancer remains absolutely unknown. Methods: The expression levels of SLC25A21 in BCa and normal tissues were examined by real-time PCR and immunohistochemistry. Gain-of- and loss-of-function experiments were performed to detect the biological functions of SLC25A21 in vitro and in vivo by CCK-8 assay, plate colony formation assay, cell migration, invasion assay and experimental animal models. The subcellular distribution of substrate mediated by SLC25A21, mitochondrial membrane potential and ROS production were assessed to explore the potential mechanism of SLC25A21 in BCa.Results: We found that the expression of SLC25A21 was downregulated in BCa tissues compared to normal tissues. A significant positive correlation between decreased SLC25A21 expression and poor prognosis was observed in BCa patients. Overexpression of SLC25A21 significantly inhibited cell proliferation, migration and invasion and induced apoptosis in vitro. Moreover, the enhanced SLC25A21 expression significantly suppressed tumor growth in a xenograft mouse model. Furthermore, we revealed that SLC25A21 suppressed BCa growth by inducing the efflux of mitochondrial α-KG to the cytosol, decreasing to against oxidative stress, and activating the ROS-mediated mitochondrion-dependent apoptosis pathway. Conclusions: Our findings provide the first link between SLC25A21 expression and BCa and demonstrate that SLC25A21 acts as a crucial suppressor in BCa progression, which may help to provide new targets for BCa intervention.
Inflammatory Pseudo Tumor-Like Follicular Dendritic Cell Sarcoma of the Liver with Hepatic Lymphoma History:A Case Report and Literature Review
Authors: Li Jian , Wang Wenqiang , Chen Dong , Akilu Wajeehullahi , Huang Zhiyong , Zhang Erlei 
Published: January 2021

Abstract
Background:Inflammatory Pseudo Tumor (IPT)-like Follicular Dendritic Cell (FDC) Sarcoma of the liver is a very rare disease and occurs mostly in the lymph nodes. Till now, only 19 cases were reported in the English literature. However, the coexistence of IPT-like Sarcoma and Non-Hodgkin’s Lymphoma(NHL) in the same patient has never been reported.Case presentation:We reported a case of a 47-year-old male patient who had a history of Hepatitis B virus (HBV) infection and presented with right upper abdominal discomfort. Nineteen years ago, he underwent liver resection of segment VII for Hepatic Non-Hodgkin Lymphoma (B-cell lymphoma). Serum alpha fetoprotein (AFP) level was normal. However, Imaging studies revealed a well-circumscribed, solid mass in the right hepatic lobe and was diagnosed as (Hepatocellular Carcinoma) HCC or Hepatic Lymphoma preoperatively. Right hemi-hepatectomy was performed on this patient. Histological report showed features of a mixture of chronic inﬂammatory cells and variable amounts of spindle cells. Also, Immuno-Histo-Chemical (IHC) studies demonstrated that all the tumor cells showed strong nuclear in situ labeling for EBV-encoded small RNAs (EBER) and strongly positive stainings with CD21 and CD35. The patient is still disease free after a follow-up of 40 months. Conclusions:To our knowledge, this is the first report demonstrating Hepatic IPT-like FDC Sarcoma in a patient with Primary Hepatic Non-Hodgkin Lymphoma history. In regards to treatment, complete surgical resection should be performed and would acquire excellent long-term outcomes.
Preventive Effect of Resveratrol on Caerulein-induced Acute Pancreatitis in High-fat diet-feeding Mice
Authors: Zhang Xiaoying , Yang Guodong 
Published: January 2021

Abstract
Background: The aim of this study was to investigate the therapeutic effect and the underlying mechanism of resveratrol in high fat diet (HFD) and hyperlipidemia AP (HTG-AP) mice model. Methods: Following successful establishment of the HFD and HTG-AP mice model, resveratrol was administrated. 16sRNA sequencing of gut microbiota in colonic fecal, the LPS, MCP-1, TNF-α, and IL-6 expressions in serum, and MCP-1 expression of the pancreatic tissues were measured in HFD model. The MDA, SOD, T-AOC, TNF-α, and MCP-1 expressions; the NF‑κB proinflammatory signaling pathway‑related proteins in pancreatic tissues were determined. Histopathological examination was evaluated in both models.Results: Resveratrol effectively inhibited pancreatic pathological injury in both models. It reduced the MDA, SOD, T-AOC, TNF-α, and MCP-1 expressions and changed composition of gut microbiota in feces compared with the HFD model. Resveratrol also reduced oxidative stress by decreasing the level of MDA and increasing the levels of SOD and T-AOC. TNF-α and MCP-1 were decreased following the administration of resveratrol. Furthermore, resveratrol suppressed the NF‑κB proinflammatory signaling pathway in pancreatic tissues.Conclusions: The study suggested that resveratrol had therapeutic effect on HFD and HTG-AP mice model by regulating the gut microbiota, promoting antioxidant capacity and inhibiting proinflammatory cytokines via the NF‑κB inflammatory pathway. The results can provide evidence that resveratrol might be regarded as a promising therapeutic agent for HTG-AP.