bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-Wide Analysis of Long Non-Coding RNAs (lncRNAs) in Two Contrasting Soybean Genotypes Subjected to Phosphate Starvation
Authors: zhang jinyu , Zhang Xiangqian , Yang Yuming , Xu Huanqing , Huang Zhongwen , Zhang Dan 
Published: September 2020

Abstract
Background: Phosphorus (P) is essential for plant growth and development, and low-phosphorus (LP) stress is a major factor limiting the growth and yield of soybean. Recently, long noncoding RNAs (lncRNAs) have been reported to be key regulators in response to stress conditions in plants. In soybean, however, how LP stress mediates biogenesis of lncRNAs remains unclear. Results: In this study, to explore the response mechanisms of lncRNAs to LP stress, we used the roots of two representative soybean genotypes with opposite P deficiency responsiveness, a P-sensitive genotype (Bogao) and a P-tolerant genotype (NN94156), to construct RNA sequencing (RNA-seq) libraries. In total, 4,166 novel lncRNAs including 525 differently expressed (DE) lncRNAs were identified across two genotypes at different P levels. GO and KEGG analyses indicated that numerous DE lncRNAs might be involved in diverse biological processes of phosphate, such as lipid metabolic process, catalytic activity, cell membrane formation, signal transduction, nitrogen fixation. Moreover, lncRNA-mRNA-miRNA and lncRNA-mRNA networks were constructed and several promising lncRNAs were identified, which may have highly valuable for further analysis the mechanism in response to LP stress in soybean.Conclusions: These results revealed that LP stress can significantly alter the genome-wide profiles of lncRNAs, especially for P sensitive genotype Bogao. Our findings increase the understanding and provides new insights into the function of lncNRAs responses to P stress in soybean.
CCT6A, a novel prognostic biomarker for Ewing's sarcoma
Authors: Jiang Jie , Liu Chong , Xu Guoyong , Liang Tuo , Yu Chaojie , Qin Zhaojie , Liao Shian , Xue Jiang , Zeng Haopeng , Zhang Zide , Lu Zhaojun , Wang Zequn , Chen Jiarui , Chen Tianyou , Li Hao , Zhan Xinli 
Published: September 2020

Abstract
Background

Ewing's sarcoma (ES) is the second most prevalent malignancy among bone tissue tumors, and there is no adequate prognosis biomarker. The protein encoded by CCT6A is a molecular chaperone. Early studies have suggested that CCT6A is involved in the development of many cancers, however, there is no clear evidence of a role for CCT6A in ES.
Methods

In this study, we performed a bioinformatics analysis of 32 Ewing sarcoma specimens from the GSE17618 dataset for differences in gene expression and overall survival, event-free survival, and gene expression in different subgroups.
Results

After three screenings, we identified CCT6A as highly correlated with Ewing's sarcoma prognosis. Survival analysis showed low overall survival (OS) for CCT6A high expression (P = 0.024). On the other hand, Cox regression analysis showed that CCT6A expression, event-free survival (EFS), and age were strongly associated with the prognosis of Ewing sarcoma, identified as independent poor prognostic biomarkers. (CCT6A: P = 0.015; Age: P-value = 0.026; EFS: P-value = 0.001).
Conclusion

The expression level of CCT6A is strongly associated with the prognosis of Ewing's sarcoma. High expression of the CCT6A gene may serve as a biomarker for poor prognosis in patients with Ewing's sarcoma.
Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages
Authors: Kieft Kristopher , Zhou Zhichao , Anderson Rika , Buchan Alison , Campbell Barbara , Hallam Steven , Hess Matthias , Sullivan Matthew , Walsh David , Roux Simon , Anantharaman Karthik 
Published: September 2020

Abstract
Microbial sulfur metabolism contributes to biogeochemical cycling on global scales. Sulfur metabolizing microbes are infected by phages that can encode auxiliary metabolic genes (AMGs) to alter sulfur metabolism within host cells but remain poorly characterized. Here we identified 191 phages derived from twelve environments that encoded 227 AMGs for oxidation of sulfur and thiosulfate (dsrA, dsrC/tusE, soxC, soxD and soxYZ). Evidence for retention of AMGs during niche-differentiation of diverse phage populations provided evidence that auxiliary metabolism imparts measurable fitness benefits to phages with ramifications for ecosystem biogeochemistry. Gene abundance and expression profiles of AMGs suggested significant contributions by phages to sulfur and thiosulfate oxidation in freshwater lakes and oceans, and a sensitive response to changing sulfur concentrations in hydrothermal environments. Overall, our study provides novel insights on the distribution, diversity and ecology of phage auxiliary metabolism associated with sulfur and reinforces the necessity of incorporating viral contributions into biogeochemical configurations.
Comparative Analysis of Postoperative Sexual Dysfunction and Quality of Life in Type A Aortic Dissection Patients of Different Ages
Authors: Luo Zeng-Rong , Liao Dong-Shan , Chen Liang-Wan 
Published: September 2020

Abstract
Background: To compare postoperative sexual dysfunction (SD) and quality of life (QOL) in Type A Aortic Dissection (AAD) Patients of Different Ages. Methods: From January 2018 to December 2019, 204 AAD postoperative survivors in Union Hospital of Fujian Medical University were selected and were divided into youth group (less than 50 years old) and elderly group (more than 50 years old). We evaluated SD according to the male International Erectile Dysfunction Index (IIEF-5) and female sexual function index (FSFI) . The Short Form 12 Health Survey Questionnaire (SF-12) and Quality of Life Enjoyment and Satisfaction Questionnaire (Q-LES-Q) were used to investigate the QOL, Quick Inventory Depressive Symptomatology-Self Report (QIDS-SR) and the Beck Depression Inventory-II (BDI-II) to investigate depressive symptoms. Results: 175 patients completed all the questionnaire (85.8%). The total SD prevalence rate was 38.9% (68 cases), with 27.4% of the youth (20 cases) and 47.1% of the elderly (48 cases). The age of non-SD and SD patients was 49.0±11.5 and 56.9±10.8 years, respectively (P=0.03). Compared with non-SD patients, the total physical health of SD patients was significantly worse (P=0.04), however, the mental health was not significantly worse (P=0.77); the depressive symptoms did not expressed a significant difference between the SD and non-SD groups (QIDS-SR P=0.15, BDI-Ⅱ P=0.06) . Total physical health in the youth SD group did not show significant better (P = 0.24), however, total mental health showed significantly worse (P=0.04), depressive symptoms scores were significantly higher (QIDS-SR P=0.03, BDI-Ⅱ P=0.04). Conclusion: The postoperative AAD SD prevalence of elderly is higher than that of youth, and the total physical health of SD patients is poorer than those without SD patients. The youth SD patients did not show a significant higher scores than the elderly SD patients, instead, the youth SD patients were more psychologically affected than the elderly SD patients, whose mental health was worse, and depression symptoms were more obvious, suggesting that the factors affecting the QOL of postoperative SD patients are related to physical factors, but the youth postoperative SD patients mainly affected by psychological factors.
Aquaporin 3 Promotes Human Extravillous Trophoblast Migration and Invasion
Authors: Nong Ying-qi , Li Shi-fen , Liu Wen-juan , Zhang Xi-qian , Fan Lin , Chen Ye , Huang Qian-wen , Zhang Qian-yu , Liu Feng-hua 
Published: September 2020

Abstract
Problem: Does aquaporin 3 (AQP3) affect the migration and invasion of human extravillous trophoblast (HTR8/Svneo) cells?Method of Study: A lentivirus infection system was used to construct stable cell lines with either AQP3 knockdown or overexpression. RT-PCR and western blotting were used to verify the efficiencies of AQP3 knockdown or overexpression in HTR8/Svneo cells at mRNA and protein levels, respectively. Cell Counting Kit-8 and flow cytometry assays were used to detect the influence of AQP3 knockdown or overexpression on proliferation and apoptosis of HTR8/Svneo cells. In addition, wound healing and Transwell invasion assays were used to detect the effects of AQP3 knockdown or overexpression on migration and invasion capabilities of HTR8/Svneo cells. An Agilent gene chip was used to screen for significant differentially expressed genes after AQP3 knockdown. Finally, mechanisms by which AQP3 influences the migration and invasion of HTR8/Svneo cells were explored using bioinformatic analysis.Results: Compared with controls, migration and invasion capabilities of HTR8/Svneo cells were significantly reduced after AQP3 knockdown, and significantly increased after AQP3 overexpression. Subsequent bioinformatic analysis of gene chip expression profiles indicated downregulation of genes related to adhesion such as PDGF-B, as well as signaling pathways (such as PIK3/AKT, NF-κB, and TNF) after AQP3 knockdown. Conclusions: AQP3 could significantly promote migration and invasion capabilities of human extravillous trophoblasts, it may mediate embryo invasion and adhesion to endometrium by regulating PDGF-B、PIK3/AKT signaling pathways, although this requires further verification.
How Well Do Documented Goals-of-care Discussions for Patients With Stage IV Cancer Reflect Communication Best Practices?
Authors: Ernecoff Natalie C. , Wessell Kathryn L. , Wood William A. , Winzelberg Gary S. , Collichio Frances A. , Hanson Laura C. 
Published: September 2020

Abstract
Background: Written clinical communication regarding patients’ disease understanding and values may facilitate goal-concordant care, yet little is known about electronic health record (EHR) goals-of-care documentation. We sought to (1) describe frequency of communication best practices in EHR-documented goals-of-care discussions, and (2) assess whether templated notes improve quality of documentation.Methods: We abstracted all EHR-documented goals-of-care discussions for hospitalized patients with Stage IV cancer from admission to 60-days follow-up. Goals-of-care documentation was operationalized to include discussion of: (1) prognosis or illness understanding; and (2) goals or treatment options. Investigators qualitatively coded text based on conceptual frameworks for communication best practices, and noted if a health system template was used. Results: Among 206 of 492 (42%) patients with documented goals-of-care discussions, clinicians frequently communicated cancer progression or incurability (89%), but rarely addressed prognosis for life expectancy (22%). Goals and values were documented for 83%, and a treatment decision for 82% of patients. Treatment preferences were assessed for 98% of patients; options discussed included cancer treatment (62%), hospice (62%), resuscitation (51%), or intensive care (38%). Clinicians made a treatment recommendation for 40% of patients. Attention to emotional and spiritual concerns was uncommon (15%). Use of a template increased documentation of patient goals and values (80% vs. 61%, p<0.01), but did not enhance other communication best practices.Conclusion: Insights from the study can be used to guide future training and research to study and improve the quality of written communication about goal of care, and its impact on goal-concordant care.
"I felt what was happening in our country [USA] with race was so much scarier than the [COVID-19] virus." Black Lives Matter protesters’ beliefs and practices during the COVID-19 pandemic
Authors: Arana-Chicas Evelyn , Jones Brooke D , Cartujano-Barrera Francisco , Cupertino Ana Paula 
Published: September 2020

Abstract
Background: The killing of George Floyd triggered the Black Lives Matter protests against police brutality and social injustices in the midst of the COVID-19 pandemic. No research to date has assessed the COVID-19 prevention practices and beliefs of protesters. The purpose of this study was to assess COVID-19 prevention practices and beliefs of Black Lives Matter protesters in the USA. Methods: A pilot mixed methods study was employed. Participants completed a survey collecting data on their frequency in following COVID-19 recommended guidelines and answered open-ended interview questions to elucidate the results from the survey. Results: Twenty participants completed the study. Participants’ average age was 29 and most participants were female (80%) and black (75%). Most always or almost always properly wore their masks (50% and 25%, respectively) and washed their hands during a protest 2-3 times or more than 3 times (35% and 50%, respectively). Although all believed that COVID-19 testing is important (90%), most had never been tested (85%) and most did not self-quarantine for 14 days after protesting (95%). Moreover, most participants reported never or rarely following social distancing guidelines at a protest (25% and 30%, respectively) and most reported being Not at all or Slightly concerned about COVID-19 while at a protest (25% and 30%, respectively). Qualitative data highlighted the following themes: 1) Fighting for social justice, 2) Protesting being more important than COVID-19, 3) Unable to keep 6 ft distance, 4) Masks worn most of the time, 5) Protests sparked global movement, and 6) Increasing awareness of injustices. Conclusion: Although protesters believe that both the fight for social justice and taking precautions during the COVID-19 pandemic are important, they believe the fight for social justice is more important than the COVID-19 pandemic. However, they understand the importance of COVID-19 and try to practice the recommended guidelines to prevent its spread while protesting. These results make an important contribution for policies for controlling the spread of the disease, and also understanding human behavior of protesting for social justice during a pandemic.
LncRNA MYLK-AS1 facilitates tumor progression and angiogenesis by targeting miR-424-5p/E2F7 axis and activating VEGFR-2 signaling pathway in hepatocellular carcinoma
Authors: Teng Fei , Zhang Ju-Xiang , Chang Qi-Meng , Wu Xu-Bo , Tang Wei-Guo , Wang Jian-Fa , Feng Jin-Feng , Zhang Zi-Ping , Hu Zhiqiu 
Published: September 2020

Abstract
BackgroundLong non-coding RNA is essential for the metastasis, invasion, angiogenesis and progression of hepatocellular carcinoma (HCC). However, their specific mechanisms are still controversial. Here, we found that Lnc-MYLK-AS1 is a potential oncogene. We systematically analyzed the clinical significance and mechanism of Lnc-MYLK-AS1 in HCC metastasis, invasion and angiogenesis.MethodsDetermine research goals through bioinformatics analysis. The expression of MYLK-AS1 in matched tumor and non-tumor tissues of 156 HCC patients was detected by quantitative reverse transcription PCR. The in vitro and in vivo biological functions of MYLK-AS1 were examined through the loss of function and function gain experiments. The use of dual luciferase reporter gene analysis, quantitative PCR, Western blotting, and fluorescence in situ hybridization (FISH) clarified the underlying mechanism of this competitive endogenous RNA (ceRNA). ResultsMYLK-AS1 is up-regulated in HCC cell lines and tumor tissues, which is related to tumor progression and enhancement of angiogenesis. Overexpression of MYLK-AS1 promotes the proliferation, metastasis, invasion, and angiogenesis of HCC cells, while down-regulation of MYLK-AS1 can reverse these effects in vivo and in vitro. Dual analysis of luciferase and RNA immunoprecipitation showed that microRNA miR-424-5p is the direct target of MYLK-AS1, and MYLK-AS1 acts as ceRNA, which can regulate angiogenesis in HCC. Mechanism studies have shown that miR-424-5p specifically targets E2F transcription factor 7 (E2F7), while the complex MYLK-AS1/miR-424-5p activates VEGFR2 signaling through E2F7, thereby promoting tumor proliferation and angiogenesis.ConclusionThe up-regulation of MYLK-AS1 is related to tumor cell proliferation, increased angiogenesis and poor prognosis in HCC patients. MYLK-AS1 regulates E2F7 expression and VEGFR2 signaling by acting as a ceRNA of miR-424-5p.
Serum biomarkers research of tourette’s syndrome children using proteomics techniques--a pilot study
Authors: He WenXiang , Chen YanNi , Wang Duan , Zhang HaiQing , Zhang Hui , Ma YanFang 
Published: September 2020

Abstract
Purpose:This study used proteomics to analyze the changes in serum proteomics between tourette’s syndrome (TS) children and healthy children in order to find serum biomarkers that can distinguish TS children from healthy children.Experimental design: We analyzed the serum proteome of 60 TS children and 30 healthy controls children using magnetic bead-based weak cation exchange (MB-WCX) and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS). Next, we identified candidate biomarkers using liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS). Candidate biomarkers were then validated using ELISA and western blotting.Results: 59 peaks were identified and the expression fold changes of seven peaks in the two groups were greater than 1.9. Two peaks (m/z: 6443.34 Da; m/z: 6642.05 Da;) tended to be upregulated, whilefive peaks (m/z: 863.13 Da; m/z: 2175.98 Da; m/z: 2191.841 Da; m/z: 2277.19 Da;m/z: 2293.11 Da) tended to be down-regulated in TS group. The peak for a 2191.84 Da peptide was identified as FGA (Isoform 1 of the Fibrinogen alpha chain precursor, FGA);The peak for a 2175.98 Da peptide was identified as PKM2 (Isoform M2 of Pyruvate kinase isozymes,PKM2);The peak for a 2277.19 Da peptide was identified as GAPDH (Glyceraldehyde-3-phosphate dehydrogenase,GAPDH);The peak for a 863.13 Da peptide was identified as PROC (Vitamin K-dependent protein C,PROC).Enzyme-linked immunosorbent assay (ELISA) analyses revealed that the expression of FGA and PKM2 were significantly higher in TS children than healthy controls children. Conclusion: FGA and PKM2 may be potential serum biomarkers to distinguish TS children from healthy children.
Variations in Facial Conformation Are Associated With Differences in Nasal Microbiota in Healthy Dogs
Authors: Vangrinsven Emilie , Aline Fastrès , Bernard Taminiau , Billen Frédéric , Georges Daube , Cécile Clercx 
Published: September 2020

Abstract
Background – Extrinsic and intrinsic factors have been shown to influence nasal microbiota (NM) in humans. Very few studies investigated the association between nasal microbiota and factors like facial/body conformation, age, and environment in dogs. Objectives are to investigate variations in NM in healthy dogs with different facial and body conformations and to assess the influence of age and living environment. A total of 46 dogs of different age, living environment and from 3 different breed groups were recruited: 22 meso-/dolichocephalic medium to large breed dogs, 12 brachycephalic dogs and 12 terrier breeds. The nasal bacterial microbiota was assessed through sequencing of 16S rRNA gene (V1-V3 regions) amplicons.Results – We showed major differences in the NM composition together with increased richness and α-diversity in brachycephalic dogs, compared to meso-/dolichocephalic dogs and dogs from terrier breeds. We failed to detect any effect of age or environment.Conclusion – Healthy brachycephalic breeds and their unique facial conformation is associated with a distinct NM profile. Description of the NM in healthy dogs serves as a foundation for future researches assessing the changes associated with disease and the modulation of NM communities as a potential treatment.
Quantitative Assessment of Resting State for Mild Cognitive Impairment Detection: A Functional Near-Infrared Spectroscopy and Deep Learning Approach
Authors: Yang Dalin , Hong Keum-Shik 
Published: September 2020

Abstract
Background: Mild cognitive impairment (MCI) is considered a prodromal stage of Alzheimer’s disease, which is the sixth leading cause of death in the United State. Early diagnosis of MCI can allow for treatment to improve cognitive function and reduce modifiable risk factors. Currently, the combination of machine learning and neuroimaging plays a role in identifying and understanding neuropathological diseases. However, some challenges still remain, and these limitations need to be optimized for clinical MCI diagnosis. Methods: In this study, for stable identification with functional near-infrared spectroscopy (fNIRS) using the minimum resting-state time, nine different measurement durations (i.e., 30, 60, 90, 120, 150, 180, 210, 240, and 270 s) were evaluated based on 30 s intervals using a traditional machine learning approach and graph theory analysis. The machine learning methods were trained using temporal features of the resting-state fNIRS signal and included linear discriminant analysis (LDA), support vector machine, and K-nearest neighbor (KNN) algorithms. To enhance the diagnostic accuracy, feature representation- and classification-based transfer learning (TL) methods were used to detect MCI from the healthy controls through the input of connectivity maps with 30 and 90 s durations. Results: As in the results of the traditional machine learning and graph theory analysis, there was no significant difference among the different time windows. The accuracy of the conventional machine learning methods ranged from 55.76% (KNN, 120 s) to 67.00% (LDA, 90 s). The feature representation-based TL showed improved accuracy in both the 30 and 90 s cases (i.e., mean accuracy of 30 s: 79.37%, mean accuracy of 30 s: 74.05%). Notably, the classification-based TL method achieved the highest accuracy of 97.01% using the VGG19 pre-trained CNN model trained with the 30 s duration connectivity map. Conclusion: The results indicate that a 30 s measurement of the resting state with fNIRS could be used to detect MCI. Moreover, the combination of neuroimaging (e.g., functional connectivity maps) and deep learning methods (e.g., CNN and TL) may be considered as novel biomarkers for clinical computer-assisted MCI diagnosis.
A Chinese Stock Reviews Sentiment Analysis Based on BERT Model
Authors: Mingzheng Li , Lei Chen , Jing Zhao , Qiang Li 
Published: September 2020

Abstract
A huge amount of stock reviews occurred on the Internet due to its rapid development, therefore, the stock reviews sentiment analysis has profound significance for the study of the financial market. Due to the lack of a large amount of labeled data, the accuracy of existing sentiment analysis of Chinese stock reviews remains to be further improved. In this paper, a sentiment analysis algorithm for Chinese stock reviews based on BERT is proposed and it improves the accuracy of sentiment classification. The algorithm uses BERT pre-training language model to perform representation of stock reviews on the sentence level, and then input the obtained feature vector into the classifier layer for classification. In the experiments, we show our method has nearly 8% and 9% improvement than TextCNN and TextRNN in F1, respectively. Our model can obtain the best results via fine-tuning which is proved to be effective in Chinese stock review sentiment analysis.