bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of genes with therapeutic and prognostic values in lung adenocarcinoma microenvironment
Authors: Jiang Xueping , Gao Yanping , Zhang Nannan , Yuan Cheng , Luo Yuan , Sun Wenjie , Zhang Jianguo , Ren Jiangbo , Gong Yan , Xie Conghua 
Published: March 2020

Abstract
Background As the most diagnosed malignancy, lung cancer is also the primary cause of cancer death in the entire world. The therapy of lung adenocarcinoma (LUAD), which is the most prevalent subtype of lung cancer, draw researchers’ increasing attentions. This research aimed to investigate the tumor microenvironment (TME)-related hub genes which might be novel targets for treatment. Materials and methods LUAD-associated data packages, including RNA-Seq information and clinical data of 522 patients, were obtained from The Cancer Genome Atlas (TCGA). For better evaluation of stromal and immune cell components, immune scores, stromal scores and estimate scores were obtained with ESTIMATE algorithm based on gene expression levels in tumors. The R package heatmap and clustering analysis were used to explore interested genes. Differentially expressed genes (DEGs) were identified by Venn diagram. Protein-protein interaction (PPI) network was applied to explore intrinsic connections of DEGs. Kaplan-Meier (K-M) survival curves, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were applied to investigate the prognostic values and intricate biological functions of DEGs. The relationships between 4 survival-related hub genes and 6 types of immune cells were examined using TIMER database. The LinkedOmics database was applied to look for kinase targets of hub genes. Results The immune/stromal/estimate scores were significantly correlated with clinical features, including the grades and sizes of LUAD, distant metastasis and outcomes. A total of 702 DEGs, 589 up-regulated and 113 down-regulated, were identified. GO and KEGG analysis showed that the DEGs had significant correlations with tumor immunology. PPI network suggested that the top 8 nodes were FPR2, C3AR1, MCHR1, CCR5, FPR1, CCL19, CCR2 and CXCL10. K-M survival curves indicated that FPR2, C3AR1, MCHR1 and CCR5, as hub genes, were significantly correlated with the overall survival (OS) of LUAD patients. The expression levels of C3AR1 and CCR5 were positively correlated with immune cell infiltration. LYN, LCK and SYK were the targeted kinases of these hub genes. Conclusion FPR2, C3AR1, MCHR1 and CCR5 were TME-related genes and potential biomarkers for the therapy and prognosis of LUAD.
Socio-economic factors influencing the adoption of low carbon technologies under rice production systems in China
Authors: Chen Zhong-Du , chen fu 
Published: March 2020

Abstract
Rice ( Oryza sativa L.) is the prominent cereal crop in Hunan Province (HP), which is a major rice production area in China. Rice production, such as farmers’ livelihood and the soil quality, has been identified to be influenced by climate change. Low carbon technologies (LCTs) have been identified to tackle agricultural challenges; however, the benefits of LCTs for farmers in rice production are still debatable. The choice of potential LCTs relevant to the case study is based on a literature review of previous empirical studies. Thus, the objective of the study were to 1) investigate the public perception and preferences of LCTs in rice production of HP, and 2) analyze the influences of the factors on farmer’s decision in adopting LCTs in rice production. There were 555 farmer surveys from eight representative rice production counties in HP, both the poisson estimators and multivariate probit approach were applied in the study. Our results show that water-saving irrigation, integrated pest management techniques and planting green manure crops in winter season were the three major LCTs adapted by farmers in rice production in HP. Both the intensity and probability of the adoptions of LCTs were affected by the main factors including farmers’ education level, climate change awareness, machinery ownership, technical support and subsidies. There is a significant correlation among the LCTs, and the adoption of the technologies is interdependent, depicting either complementarities or substitutabilities between the practices. This study suggests that policies enhance the integration of LCTs would be central to farmers’ knowledge, environmental concerns, technical service and financial support in rice production systems in China.
Immunoregulation of PD-1/PD-L1 Inhibitory Pathway on Fetomaternal Tolerance in abortion Triggered by thyroid autoimmunity
Authors: Liu Haixia , Chen Mengya , Shan Zhongyan , Teng Weiping 
Published: March 2020

Abstract
Background: TAI in euthyroid pregnant women is associated with miscarriage. Studies have shown that the PD-1/PD-L1 signaling pathway plays an important role in maternal-fetal tolerance by promoting Treg cells development and inhibition of Th17 cells responses, whereby it is essential for normal pregnancy maintenance. However, whether the PD-1/PD-L1 pathway leads to a Treg/Th17 imbalance has not been fully investigated in TAI. Methods: TAI fetal loss model was established by thyroglobulin (mTg) immunized CBA/J female mice. The frequencies of splenic Th17, Treg, PD-1 and PD-L1 were tested by flow cytometry. IL-17, Foxp3, RORγt, PD-1 and PD-L1 mRNA levels were tested by real-time PCR. Results: Compared with the control group, the number of CD4 + CD25 + Foxp3 + T lymphocyte in the placenta and spleen were significantly reduced (P<0.05) in the experimental group (mTg group), CD4 + IL-17 + T-cell subsets and expression of RORγt and IL-17 mRNA in the placenta were increased (P<0.05), the ratio of Treg/IL-17 in the placenta and spleen was decreased (P<0.05). The expression of PD-1 and PD-L1 in mice immunized with mTg in CD4 + T group decreased the subsetof cells in the placenta and spleen including Tregs. Conclusions: The role of PD-1/PD-L1 pathway in an isolated thyroglobulin antibodies (TgAb) positive mouse abortion model is that it may lead to a peripheral Treg/Th17 imbalance and the maternal-fetal tolerance balance breakdown, which may ultimately result in fetal loss.
Characterization of ocular involvement in patients with Fabry disease
Authors: Wu Yuan , Yao Xuyang , Song Wenjing , Zhao Yawen , Yan Xiaoming , Yuan Yun , Zhang Wei 
Published: March 2020

Abstract
Background Fabry diseas (FD) is an X-linked recessive lysosomal storage disease that is caused by deficient activity of the lysosomal enzyme α-galactosidase A. Ocular abnormalities have been regarded as characteristic, frequent and easily accessed findings in Fabry disease, and have a high diagnostic value. Some of the ocular findings are easy to find using slit lamps. But some are only visible with the imaging devices such as in vivo confocal microscopy (IVCM) and optical coherence topography (OCT) are prone to be ignored. The aim of this study was to examine the prevalence and characteristics of ocular findings in patients with FD. Result 32 FD patients diagnosed by gene test from one medical center were enrolled. Ocular examinations including slit-lamp examination, ophthalmological fundus imaging, in vivo confocal microscopy as well as optical coherence topography were performed. Among these patients, the prevalence of corneal verticillata was 96.8% (31/32). Corneal examination with in vivo confocal microscopy demonstrated hyper-reflective intracellular inclusions located within the basal epithelial cells. There were no obvious abnormalities in the Bowman’s membrane, stroma or endothelium. Conjunctival vessel malformations were observed in 62.5% (20/32) of patients and retinal vessel tortuosity was observed in 68.7% (22/32) of patients. Optical coherence topography showed many strong hyper-reflective foci in the inner retinal layer, in 62.5% (20/32) patients; the foci may be the images of retinal vascular plexi. Spoke-like opacity of lens was only in two patients. An old retinal artery occlusion was observed in one other patient. Conclusions Corneal verticillata, hyper-reflective foci on OCT, retinal vessel tortuosity and conjunctival vessel malformation show a high prevalence in FD. Epithelium deposition and small vessel malformation may be two basic types of all of these ocular involvements. And these ocular manifestations are characteristic and easily accessible, and should be considered diagnostic criteria for Fabry disease.
Risk factors for suicide attempts in patients with bipolar disorder misdiagnosed with major depressive disorder: results from a national survey in China
Authors: Chen Lin , Xu Yu-Yu , Du Jing-Ge , Xin Li-Min , Wang Su-Li , Ji Zhen-Peng , Yang Fu-de , Wang Gang , Fang Yi-Ru , Lu Zheng , Yang Hai-Chen , Hu Jian , Chen Zhi-Yu , Huang Yi , Sun Jing , Wang Xiao-Ping , Li Hui-Chun , Zhang Jin-Bei , Wang Ying , Su Yun’Ai , Si Tian-Mei 
Published: March 2020

Abstract
Background: Bipolar disorder (BD) is a kind of mental disorder with the greatest risk of suicide, but it is often misdiagnosed as major depressive disorder (MDD) clinically. This study aimed to analyze the sociodemographic factors and clinical characteristics associated with suicide attempts (SA) in patients with BD misdiagnosed with MDD in China. Methods: A total of 1487 MDD patients were consecutively enrolled in 13 mental health centers in China. Data on patients’ sociodemographic and clinical characteristics were collected using a standardized protocol. Of these, 306 BD patients were misdiagnosed with MDD according to the Mini International Neuropsychiatric Interview (MINI). Suicide attempters and non-attempters were classified by the suicidality module of the MINI. Multiple logistic regression analyses were performed to assess the association between the independent variables of interest and SA in BD patients misdiagnosed with MDD. Results: Of the 306 BD patients misdiagnosed with MDD, 225 (73.5%) were non-attempters and 81 (26.5%) were attempters. Compared to non-attempters, attempters were older (Z =2.2, p = 0.03) and had more admissions(χ2 =6.1, p = 0.013), more frequent depressive episodes, more atypical characteristics (e.g. increased appetite, weight gain, and more sleep time)(χ2 = 5.8, p = 0.016), more suicidal ideation (χ2 = 27.3, p < 0.001), more psychotic symptoms (χ2 = 7.4, p = 0.006) and more seasonal depressive episodes (χ2 = 5.6, p = 0.018). Multiple logistic regression analyses revealed that attempters were characterized by more suicidal ideation (OR = 5.7, 95% CI: 2.6–12.5) and frequent depressive episodes (OR = 2.4, 95% CI: 1.3–4.6). The limitations of this study include its cross-sectional design and data collection by suicide attempters’ retrospective recall. Conclusions: The findings of this study suggest that BD patients misdiagnosed with MDD are at a higher risk of suicide, and more frequent depressive episodes and suicidal ideation are risk factors for attempted suicide. Early identification of and interventions for these risk factors might reduce the risk of suicide in BD patients misdiagnosed with MDD.
Long non-coding RNA MAFG-AS1 promotes proliferation and metastasis of breast cancer by modulating STC2 pathway
Authors: Di Shihao , Lu Die , Chen Chunni , Ma Tianshi , Zou Zigui , Zhang Zhihong 
Published: March 2020

Abstract
Objective Breast cancer is the most common cancer in Chinese women. A number of studies proposed that long non-coding RNA plays an essential role in the regulation of invasion and metastasis of various forms of malignancy, including lung cancer, gastric cancer and bladder cancer. In this study, a long non-coding RNA MAFG-AS1 was explored in detail to understand the significance in the etiology of breast cancer.Methods Quantitative reverse transcription PCR (qRT-PCR) was used to examine the expression level of LncRNA MAFG-AS1 in tissues and cell lines. The association of LncRNA MAFG-AS1 expression and the postoperative prognosis was analyzed by the Kaplan-Meier method and log-rank test. Cell proliferation was evaluated in vitro and in vivo . Transwell assays were performed to examine the cell migration. Cell cycle and apoptosis was evaluated by flowcytometry analysis. The downstream target gene STC2 of LncRNA MAFG-AS1 was screened using the microarray analysis, which was validated by qRT-PCR, functional analysis, and rescue experiment.Results Expression of LncRNA MAFG-AS1 in the breast cancer tissues was significantly higher than the precancerous lesions. Elevated expression level of LncRNA MAFG-AS1 was correlated to the larger GTV (gross tumor volume), negative expression of ER, PR, Her2, lymph node metastasis, and poor prognosis. The potency of breast cancer proliferation, invasion and metastasis was inhibited in the absence of LncRNA MAFG-AS1.Tumorigenic capacity of breast cancer cells was inhibited in the absence of LncRNA MAFG-AS1. The downstream target gene regulated by LncRNA MAFG-AS1 was screened out by gene chip technology, GO analysis and QRT-PCR ultimately. Disrupted STC2 suppressed the cell proliferation and metastasis when the level of LncRNA MAFG-AS1 elevated.Conclusion The LncRNA MAFG-AS1 triggers tumorigenesis in the breast cancer and regulates breast cancer proliferation and metastasis by modulating the downstream target gene STC2. Results from our study indicates that LncRNA MAFG-AS1 can be used.
Study on correlation between hepatic fibrosis and fat indexes in patients with NAFLD and Type 2 diabetes mellitus
Authors: zhang lingyan , Shao Jianguo , Yao Dengfu , Yao Min , Peng Tingyu , Shi Jiajia , Ji Xiang 
Published: March 2020

Abstract
Background:To analyze the correlation between hepatic fibrosis and fat indexes in patients with non-alcoholic fatty liver disease (NAFLD) and type 2 diabetes mellitus(T2DM). Method: Data of 135 NAFLD patients treated in the outpatient and inpatient department of gastroenterology of the Nantong Third People's Hospital Affiliated to Nantong University from January 2016 to December 2019 were collected and analyzed. The patients were divided into NAFLD group and NAFLD+T2DM group according to medical history, biochemical indexes and B-ultrasound examination results. The fat content and fibrosis degree were detected by FibroTouch instantaneous elastography. Risk factors and protective factors for hepatic fibrosis index were analyzed statistically. Results: (1) Age, fibrosis index, alanine aminotransferase (ALT), aspartate aminotransferase (AST), creatinine, body mass Index(BMI), low density lipoprotein(LDL), hemoglobin A1c(HbA1c) and C-reactive protein (CRP) levels in NAFLD + T2DM group were significantly higher than those in NAFLD group ( P <0.01, Table 1). HDL and peptide C in NAFLD + T2DM group were lower than those in NAFLD group. Step-by-step logistic regression suggested that ALT and LDLC were risk factors, and fibrosis index and peptide C were protective factors. (2）In NAFLD+T2DM group, HDLC and peptide C in the fibrosis subgroup were significantly decreased than compared with those in the non-fibrosis subgroup, and the creatinine, LDLC, HbA1C , Uric acid and BMI in the fibrosis subgroup were significantly increased compared with the non-fibrosis subgroup.（3）Linear regression analysis indicated that HDLC and HbA1C were risk factors and peptide C was protective factor. Conclusion: Hepatic fibrosis is involved in the pathophysiological process of NAFLD and T2DM, and it is extreme importance to prevent hepatic fibrosis.
Using machine learning methods to predict physical activity types with Apple Watch and Fitbit data using indirect calorimetry as the criterion.
Authors: Fuller Daniel , Anaraki Javad Rahimipour , Simango Bo , Dorani Faramarz , Bozorgi Arastoo , Luan Hui , Basset Fabien 
Published: March 2020

Abstract
Background There is considerable promise for using commercial wearable devices for measuring physical activity at the population level. The objective of this study was to examine whether commercial wearable devices could accurately predict lying, sitting, and intensity level of other activities in a lab-based protocol. Methods We recruited a convenience sample of 49 participants (23 men and 26 women) to wear three devices, an Apple Watch Series 2, a Fitbit Charge HR2, and and iPhone 6S. Participants completed a 65-minute protocol consisting of 40 minutes of total treadmill time and 25 minutes of sitting or lying time. Indirect calorimetry was used to measure energy expenditure. The outcome variable for the study was the activity class; lying, sitting, walking self-paced, and running 3 METs, 5 METs, and 7 METs. Minute-by-minute heart rate, steps, distance, and calories from Apple Watch and Fitbit were included in four different machine learning models. Results Our dataset included 3656 and 2608 minutes of Apple Watch and Fitbit data, respectively. We tested decision trees, support vector machines, random forest, and rotation forest models. Rotation forest models had the highest classification accuracies at 82.6% for Apple Watch and 89.3% for Fitbit. Classification accuracies for Apple Watch data ranged from 72.5% for sitting to 89.0% for 7 METs . For Fitbit, accuracies varied between 86.2% for sitting to 92.6% for 7 METs . Conclusion This study demonstrated that commercial wearable devices, Apple Watch and Fitbit, were able to predict physical activity types with a reasonable accuracy. The results support the use of minute-by-minute data from Apple Watch and Fitbit combined with machine learning approaches for scalable physical activity type classification at the population level.
Exosome-mediated radiosensitizing effect on neighboring cancer cells via reactive oxygen species production
Authors: Nakaoka Ai , Nakahana Makiko , Inubushi Sachiko , Akasaka Hiroaki , Salah Mohammed , Kubota Hikaru , Fujita Yoshiko , Hassan Mennaallah , Mukumoto Naritoshi , Nishikawa Ryo , Ishihara Takeaki , Miyawaki Daisuke , Yoshida Kenji , Sasayama Takashi , Sasaki Ryohei 
Published: March 2020

Abstract
Purpose/Objectives: The mechanism of intercellular communication after radiation exposure in cancer cells remains fully undetermined. Exosomes are lipid bilayer-constituted, membrane-enclosed small vesicles that are recognized as mediators transporting a variety of intracellular components including miRNA. Here we identified the novel role of exosomes released from irradiated cells to neighboring cancer cells. Materials/Methods: Human pancreatic cancer cell line MIAPaCa-2 was used in this study. Purified exosome product (PEP) was obtained from cultured media by ultra-centrifugation. PEP was morphologically confirmed by transmission electron microscopy (TEM), and analyzed by NanoSight. Exosome-specific surface markers CD9 and CD63 were evaluated by western blotting. Endocytosis of irradiated exosomes was confirmed by fluorescent microscopy by using the PKH26 dye. Cell survival after irradiation was evaluated by a colony-forming assay. Intracellular reactive oxygen species (ROS) levels were determined using the oxidation-sensitive fluorescent probe dye C-H 2 DCF, and DNA damage was evaluated by detecting phosphorylated histone 2AX (γ-H2AX) foci by immunocytochemistry. MiRNAs were isolated from the exosomes after 5 Gy or 8 Gy of irradiation and comprehensive miRNA expression analysis was performed by miRNA microarray analyses. Expressions of Cu/Zn superoxide dismutase enzyme (SOD1) or Mn superoxide dismutase enzyme (SOD2), catalase, and glutathione peroxidase were studied to determine whether the exosomes received by the neighboring cells may have influence to them and lead to production of ROS or not. Results: Exosome characteristics were confirmed by multiple methods. The uptake of irradiated exosomes was significantly higher than that of nonirradiated exosomes. Notably, nonirradiated neighboring cells with irradiated exosomes induced higher intracellular levels of ROS, and a higher frequency of DNA damage. These neighboring cells also showed greater sensitivity to radiation. Seven upregulated and 5 downregulated miRNAs were identified that correlated with the miRNA microarray analyses results obtained after 5 Gy and 8 Gy radiation. Among them, miR-6823-5p was identified as a possible candidate for SOD1 inhibition, leading to intracellular ROS production and DNA damage. Conclusions : This is the first study to determine that irradiated exosomes can enhance the radiation effect via ROS production in cancer cells. This novel finding may lead to the understanding of the bystander effect of neighboring cancer cells.
Stereotactic Body Radiotherapy for Hepatocellular Carcinoma: Current Evidence and the Feasibility of Radiomics-based Predictive Models
Authors: Dai Yang-Hong , Shen Po-Chien , Chang Wei-Chou , Lo Chen-Hsiang , Yang Jen-Fu , Lin Chun-Shu , Chao Hsing-Lung , Lu Chieh-Sheng , Tu Shu-Ju , Huang Wen-Yen 
Published: March 2020

Abstract
Background : Stereotactic body radiotherapy (SBRT) is an effective but less focused alternative for treatment of hepatocellular carcinoma (HCC). To date, a personalized model for predicting therapeutic response is lacking. This study aimed to review current knowledge and to propose a radiomics-based machine-learning (ML) strategy for local response (LR) prediction. Methods : We searched the literature for studies conducted between January 1993 and August 2019 that used > 100 patients. Additionally, 172 HCC patients in our hospital were retrospectively analyzed between January 2007 and December 2016. In the radiomic analysis, 41 treated tumors were contoured and 46 radiomic features were extracted. Results : The 1-year local control was 85.4% in our patient cohort, comparable with current results (87-99%). The Support Vector Machine (SVM) classifier, based on computed tomography (CT) scans in the A phase processed by equal probability (Ep) quantization with 8 gray levels, showed the highest mean F1 score (0.7995) for favorable LR within 1 year (W1R), at the end of follow-up (EndR), and condition of in-field failure-free (IFFF). The area under the curve (AUC) for this model was 92.1%, 96.3%, and 99.2% for W1R, EndR, and IFFF, respectively. Conclusions : SBRT has high 1-year local control and our study sets the basis for constructing predictive models for HCC patients receiving SBRT.
The occurrence of potentially pathogenic filamentous fungi in recreational surface water as a public health risk
Authors: Góralska Katarzyna , Błaszkowska Joanna , Dzikowiec Magdalena 
Published: March 2020

AbstractMicrofungi occurring in surface water may represent an important health risk. Recreational water reservoirs are a potential reservoir of pathogenic fungi. The aim of the study was to assess the diversity of mycobiota in selected artificial bathing reservoirs with regard to its biosafety for the human population. The studies were conducted during the summer of 2016 in three research seasons (June (I), July and August (II), and September (III)), taking into account the various periods of recreational activities. Filamentous fungi were isolated from water samples collected at five different ponds utilized for recreation. From 162 water samples, 149 fungal taxa of filamentous fungi were identified: 140 were classified to species level and only nine to genus level. Aspergillus fumigatus was the dominant species. The highest species richness (S) was noted in June, with 93 fungal taxa (Menhinick's index from 2.65 to 4.49). Additionally, in season I, the highest diversity of fungal species was revealed (Simpson's diversity index from 0.83 to 0.99). The average number of CFU/1 mL sample ranged between 0.4 and 4.6 depending on the time of sampling and ponds. Of all the isolated species, 128 were clinically relevant (11 from RG-2 and 117 from RG-1), highlighting the need to introduce seasonal mycological monitoring of such reservoirs.This article has been made Open Access thanks to the generous support of a global network of libraries as part of the Knowledge Unlatched Select initiative.