bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA-sequencing reveals positional memory of multipotent mesenchymal stromal cells from oral and maxillofacial tissue transcriptomes
Authors: Onizuka Satoru , Yamazaki Yasuharu , Park Sung-Joon , Sugimoto Takayuki , Sone Yumiko , Sjöqvist Sebastian , Usui Michihiko , Takeda Akira , Nakai Kenta , Nakashima Keisuke , Iwata Takanori 
Published: February 2020

Abstract
Background Multipotent mesenchymal stromal cells (MSCs) can be isolated from numerous tissues and are attractive candidates for therapeutic clinical applications due to their immunomodulatory and pro-regenerative capacity. Although the minimum criteria for defining MSCs have been defined, their characteristics are known to vary depending on their tissue of origin.Results We isolated and characterized human MSCs from three different bones (ilium (I-MSCs), maxilla (Mx-MSCs) and mandibular (Md-MSCs)) and proceeded with next generation RNA-sequencing. Furthermore, to investigate the gene expression profiles among other cell types, we obtained RNA-seq data of human embryonic stem cells (ESCs) and several types of MSCs (periodontal ligament-derived MSCs, bone marrow-derived MSCs, and ESCs-derived MSCs) from the Sequence Reads Archive and analyze the transcriptome profile. We found that MSCs derived from tissues of the maxillofacial region, such as the jaw bone and periodontal ligament, were HOX-negative, while those derived from other tissues were HOX-positive. We also identified that MSX1, LHX8, and BARX1 , an essential regulator of craniofacial development, were strongly expressed in maxillofacial tissue-derived MSCs. Although MSCs may be divided into two distinct groups, the cells originated from over the neck or not, on the basis of differences in gene expression profile, the expression patterns of all CD antigen genes were similar among different type of MSCs, except for ESCs.Conclusions Our findings suggest that MSCs from different anatomical locations, despite meeting general characterization criteria, have remarkable differences in gene expression and positional memory. Although stromal cells from different anatomical sources are generally categorized as MSCs, their differentiation potential and biological functions vary. We suggested that MSCs may retain an original tissue memory about the developmental process, including gene expression profiles. This could have an important impact when choosing an appropriate cell source for regenerative therapy using MSCs.
High-throughput profiling of diapause regulated genes from Trichogramma dendrolimi, an important egg parasitoid
Authors: Zhang Xue , Du Wenmei , Zhang Junjie , Zou Zhen , Ruan Changchun 
Published: February 2020

Abstract
Background The parasitoid insect Trichogramma dendrolimi can successfully enter diapause at the prepupal stage. Thus, diapause is an efficient preservation method during the mass production of T. dendrolimi. Previous studies on diapause have focused mostly on ecological characteristics, so the molecular mechanism of diapause in T. dendrolimi is mostly unknown. In this study, we compared transcriptomes of diapause and non-diapause T. dendrolimi to identify genes involved in the development of diapause. Results Transcriptome sequencing was performed using different samples, including diapause prepupae, pupae after diapause, normal prepupae, and pupae. This initially yielded a total of 87,022 unigenes with an average length of 1,604 bp. By removing redundant sequences and those without significant BLAST hits, a non-redundant dataset was generated, containing 7,593 sequences with an average length of 3351 bp. Among the differentially expressed genes, 1,204 were specifically expressed during the diapause stage, and 820 were significantly up-regulated. The result of GO enrichment analysis revealed that binding, oxidation−reduction process, and ribosome biogenesis were significantly affected. Ten genes were selected for validation using a quantitative real-time PCR (qPCR). The changes showed the same trend between the qPCR and RNA-Seq results. Based on previous studies and our data, several genes were identified to be involved in diapause, including UDP-glucuronosyltransferase; Glutathione-S-transferase, ATGs, zinc finger protein genes, cell cycle-related genes, Trehalase, trehalose transporter, hsp68, p53, and DNA damage-regulated gene 1 (pdrg1), and genes related to lipid metabolism were also included. Conclusions In this study, we generated a great amount of transcriptome data from T. dendrolimi, providing a resource for gene function research. The diapause-related genes that we identified establish a valuable basis for future studies on the molecular mechanisms of diapause, not only for T. dendrolimi, but for other species as well.
Genome-wide identification and expression analysis of WRKY transcription factors in pearl millet (Pennisetum glaucum) under dehydration and salinity stress.
Authors: Chanwala Jeky , Satpati Suresh , Dixit Anshuman , Parida Ajay , Giri Mrunmay Kumar , Dey Nrisingha 
Published: February 2020

Abstract
Background: Plants have developed various sophisticated mechanisms to cope up with climate extremes and different stress conditions, especially by involving specific transcription factors (TFs). The members of the WRKY TF family are well known for their role in plant development, phytohormone signaling and developing resistance against biotic or abiotic stresses. In this study, we performed a genome-wide screening to identify and analyze the WRKY TFs in pearl millet ( Pennisetum glaucum; PgWRKY ) , which is one of the most widely grown cereal crop in the semi-arid regions. Results: A total number of 97 putative PgWRKY proteins were identified and classified into three major Groups (I-III) based on the presence of WRKY DNA binding domain and zinc-finger motif structures. Members of Group II have been further subdivided into five subgroups (IIa-IIe) based on the phylogenetic analysis. In-silico analysis of PgWRKYs revealed the presence of various cis-regulatory elements in their promoter region like ABRE, DRE, ERE, EIRE, Dof, AUXRR, G-box, etc., suggesting their probable involvement in growth, development and stress responses of pearl millet. Chromosomal mapping evidenced uneven distribution of identified 97 PgWRKY genes across all the seven chromosomes of pearl millet. Synteny analysis of PgWRKYs established their orthologous and paralogous relationship among the WRKY gene family of Arabidopsis thaliana, Oryza sativa and Setaria italica . Gene ontology (GO) annotation functionally categorized these PgWRKYs under cellular components, molecular functions and biological processes. Further, the differential expression pattern of PgWRKY s was noticed in different tissues (leaf, stem, root) and under both drought and salt stress conditions. The expression pattern of PgWRKY33 , PgWRKY62 and PgWRKY65 indicates their probable involvement in both dehydration and salinity stress responses in pearl millet. Conclusion: Functional characterization of identified PgWRKY s can be useful in delineating their role behind the natural stress tolerance of pearl millet against harsh environmental conditions. Further, these PgWRKY s can be employed in genome editing for millet crop improvement. Keywords : Pearl millet, WRKY Transcription Factors , cis-regulatory elements, Synteny, Abiotic stress
MiR-3613-3p from carcinoma associated fibroblasts exosomes promoted breast cancer cell proliferation and metastasis by regulating SOCS2 expression
Authors: Liu Yonglei , Yang Yanfei , Du Junxian , Lin Dong , Li Feng 
Published: February 2020

Abstract
Background Exosomes carrying microRNA (miRNAs) mediate cell to cell communication which are important regulators in cancer growth and progression. However, the roles and molecular mechanism of the miRNAs in the exosomes from carcinoma associated fibroblasts (CAFs) are still not clear. Methods The targeted gene of miR-3613-3p was predicted by TargetScan and miRanda. The proliferation of cancer cells was conducted by cell counting kit-8 and colony formation assay. Cancer cell migration and invasion were measured by wound healing assay and Transwell assays respectively. Luciferase activity was assayed by dual luciferase assay system. miRNA and mRNA expression was measured by real time RT-PCR. SOCS2 protein levels was assayed by western blotting. Results It was verified that miR-3613-3p was up-regulated in exosomes from fibroblasts educated by TGF-β1, breast cancer cells and breast cancer tissues. Exosomal miR-3613-3p promoted breast cancer cell proliferation and metastasis. Loss-of-function experiments revealed that miR-3613-3p down-regulation in the CAFs exosomes suppressed cell proliferation and drug resistance in breast cancer by targeting SOCS2 expression. The clinical data showed that miR-3613-3p was negatively related to SOCS2 in breast cancer tissues. Conclusion These findings demonstrated that activated fibroblasts exosomes with high levels of miR-3613-3p played an oncogenic role in breast cancer cell survival, metastasis and drug responses, which suggested that the oncogenic role of miR-3613-3p in breast cancer progression.
Whole blood transcriptomic investigation identifies long non-coding RNAs as regulators in sepsis
Authors: Cheng Lixin , Nan Chuanchuan , Kang Lin , Zhang Ning , Liu Sheng , Chen Huaisheng , Hong Chengying , Chen Youlian , Liang Zhen , Liu Xueyan 
Published: February 2020

Abstract
Background: Sepsis is a fatal disease referring to the presence of a known or strongly suspected infection coupled with systemic and uncontrolled immune activation causing multiple organ failure. However, neither pathogenic long non-coding RNAs (lncRNAs) nor biological network analysis in sepsis draws enough attention to the society of sepsis studies. Methods: We performed an in-silico investigation of the gene coexpression pattern for the patients response to all-cause sepsis in consecutive intensive care unit (ICU) admissions. Sepsis coexpression gene modules were identified using WGCNA and enrichment analysis. lncRNAs were determined as sepsis biomarkers based on the interactions among lncRNAs and the identified modules. Results: Twenty-three sepsis modules, including both differentially expressed modules and prognostic modules, were identified from the whole blood RNA expression profilings of sepsis patients. Five lncRNAs, FENDRR, MALAT1, TUG1, CRNDE, and ANCR, were detected as sepsis regulators based on the interactions among lncRNAs and the identified coexpression modules. Furthermore, we found that CRNDE and MALAT1 may act as miRNA sponges of sepsis related miRNAs to regulate the expression of sepsis modules. Ultimately, FENDRR, MALAT1, TUG1, and CRNDE were reannotated using three independent lncRNA expression datasets and validated as differentially expressed lncRNAs. Conclusion: The procedure facilitates the identification of prognostic biomarkers and novel therapeutic strategies of sepsis. Our findings highlight the importance of transcriptome modularity and regulatory lncRNAs in the progress of sepsis.
PREDIRA (PRediction mEdical DevIce for Rheumatoid Arthritis): Scale-up of unique predictive online platform highly improving the quality of life of Rheumatoid Arthritis’ patient by personalized and efficient biotherapies prescription
Authors: Nuñez Dalifer Freites , Baillet Athan , Rodriguez-Rodriguez Luis , Nguyen Minh Vu Chuong , Gonzalez Isidoro , Pablos Jose Luis , Balsa Alejandro , Vazquez Monica , Gaudin Philippe , Fernandez-Gutierrez Benjamín 
Published: February 2020

Abstract
Background: Rheumatoid arthritis (RA) is one of the leading chronic inflammatory rheumatism. First-line therapy with synthetic disease modifying anti-rheumatic drugs (sDMARD) is insufficiently effective in 40% of cases and these patients are treated with biotherapies. The increases use of these drugs each year is becoming a public health issue with considerable economic burden. This cost is 20 times higher than that of sDMARD. However, among patients treated with biotherapies, clinical practice shows that about one-third will not respond to the selected drug. In non-response cases, practitioners currently have no choice but to perform an empirical switching between different treatments, because no tool capable of predicting the response or non-response to these molecules is currently available.Methods : The study is a prospective, phase III, controlled, multicenter, and randomized, single-blind (patient) clinical trial, including RA patients with a previous failure to anti-TNF therapies. The main objective is the analysis of the clinical and pharmacoeconomic impact after 6 months of treatment. Intervention arm: Prescription of biotherapy (rituximab, adalimumab, abatacept) using SinnoTest® software, a prediction software based on proteomic biomarkers. Control arm: Prescription of biotherapy based on current practice, without the SinnoTest® software (any biotherapy). In addition, a sub study will be carried out within this trial to generate a biobank and further analyze the proteomic profile of the patients and their modification throughout the study.Discussion : This clinical trial study will be the first validation study of a biotherapy response prediction software, bringing personalized medicine into the management of RA. We expect that the findings from this study will bring several benefits for the patient and the Health Care System. Trial registration : The study was registered at clincaltrials.gov (NCT04147026). Registered on 31 October, 2019.
Evaluation the efficacy and safety of fire needle compared to filiform needle on knee osteoarthritis: study protocol for a randomised controlled trial
Authors: Gao Yuanjie , Liu Lu , Li Bin , Guo Jing , Liu Huilin , Wang Shaosong , Zhang Fan , Ji Xu , Fu Yuanbo , Wang Yizhan , Sun Jingqing , Yuan Fang 
Published: February 2020

Abstract
Background: Knee osteoarthritis is a common clinical chronic degenerative disease associated with high morbidity and long-term disability. Previous studies have confirmed the efficacy of acupuncture on knee osteoarthritis. Fire needle acupuncture is a combination of heat and acupuncture, which may be more effective than the commonly used filiform needle acupuncture. This study is designed as a randomized controlled trial to evaluate the efficacy and safety of fire needle acupuncture compared to filiform needle acupuncture in knee osteoarthritis patients. Methods and analysis: A total of 100 participants will be randomly assigned to two different groups. Participants will receive fire-needle acupuncture treatment in the fire needle group, while participants in the filiform needle group will be treated with a filiform needle at the same acupuncture points as the fire needle group. All participants will receive a 6-weeks of treatment (2 times per week). The primary outcome is the change of the Western Ontario and McMaster Universities Osteoarthritis Index, and the secondary outcomes include the change of the Visual Analogue Scale, and 12-item Short Form Health Survey from baseline to endpoint. Ethics and dissemination: Ethical approval of this study was granted by the Research Ethical Committee of Beijing Hospital of Traditional Chinese Medicine Affiliated to Capital Medical University (2018SB-066). Written informed consent will be obtained from all participants. Outcomes of the trial will be disseminated through peer-reviewed publications. Trial registration number: ChiCTR1800019579
Effects of perioperative ERAS pathway management VS traditional management on clinical outcomes in laparoscopic-assisted radical resection of distal gastric cancer The GISSG18-01 Randomized Clinical Trial
Authors: Tian Yulong , Cao Shougen , Li Leping , He Qingsi , Xia Lijian , Jiang Lixin , Ding Yinlu , Wang Xinjian , Wang Hao , Mao Weizheng , Hui Xizeng , Shi Yiran , Zhang Huanhu , Chu Xianqun , Kehlet Henrik , Zhou Yanbing 
Published: February 2020

Abstract
Background: As well known, the incidence of gastric cancer in East Asian countries is much higher than the international average. Therefore, improving the prognosis of patients and establishing effective clinical pathways are important topics for the prevention and treatment of gastric cancer. At present, the enhanced recovery after surgery (ERAS) pathway is widely used in the field of gastric surgery. Many RCT studies have proven that the ERAS regimen can not improve the short-term clinical outcomes of gastric cancer patients. However, a prospective study on the effect of the ERAS pathway on the prognosis of gastric cancer patients has not been reported. This trial aims to confirm whether ERAS pathway can improve disease-free survival (DFS) and overall survival (OS) in patients undergoing laparoscopic-assisted radical resection for distal gastric cancer.Methods/design: This study is a prospective, multicenter, randomized controlled trial (RCT). This experiment will include randomly divided groups, the experimental group and the control group, according to a proportion of 1:1. The perioperative period of the experimental group will be managed according to the ERAS pathway, and the control group will be managed according to the traditional management mode. An estimated 400 patients will be enrolled. The main endpoint is to compare the 3-year OS and PFS between the two groups.Discussion: This RCT should demonstrate whether ERAS pathway is superior to traditional treatment on inflammatory indexes, short-term clinical outcome and survival for laparoscopic assisted radical resection of distal gastric cancer.Our data can provide evidence that the ERAS pathway improves survival in patients with gastric cancer.Trial registration: Chinese Clinical Trial Registry, CHiCTR1900022438. Registered on 11 April 2019
Is immediate weight bearing safe for lateral malleolus fracture after surgery?
Authors: Lee Sang-June , Choi Young Rak , Choi SeongJu , Lee Ho Seong , Park Seung-Hwan 
Published: February 2020

Abstract
Introduction Lateral malleolus fracture is one of the most common fractures. However, there is controversy regarding the rehabilitation protocols used after surgery. In particular, the initiation point for weight bearing has not been standardized. In the present study, we investigated the prognostic difference between immediate and delayed weight bearing on lateral malleolus fractures. Materials and Methods The medical records of matched 50 and 41 patients in the immediate and delayed weight-bearing groups were reviewed retrospectively. All patients were treated with open reduction and internal fixation using an anatomical locking compression plate. In the immediate weight-bearing group (IWB), tolerable weight bearing (i.e., can be endured immediately after surgery with crutches) was permitted. In the delayed weight-bearing group (DWB), weight bearing was completely restricted for 4 weeks after surgery. Ankle motion exercise was permitted in both groups starting from the day after surgery. Radiographic assessment data and clinical outcomes were reviewed. Results No significant differences in the radiographic assessments and complications were found between the two groups. Significant differences in shortened length of hospital stay and time to return to work with the IWB rehabilitation protocol were confirmed (IWB group vs. DWB group: 5.7 vs. 8.0 days and 6.0 vs. 8.0 months, respectively). A significant difference in sport factor was observed in the Foot and Ankle Outcome Score at 3 months postoperatively (75.5 vs 68.5). Conclusions We found no significant differences between the two groups with respect to postoperative radiological outcome and complications. The benefits of shortening the time to return to work and length of hospital stay associated with the IWB rehabilitation protocol were confirmed. In conclusion, immediate weight bearing is recommended in patients with lateral malleolus fracture after anatomical reduction and firm fixation by surgery.
Diagnostıc Performance Of Erythropoetin And Erythropoetin Receptor Levels In Patients With Generalized Anxiety Disorder
Authors: Kurutas Ergul Belge 
Published: February 2020

Abstract
Background Generalized anxiety disorder (GAD) is a prevalent psychiatric disorder. Diagnosis of GAD depends on subjective complaints of patients, thus the need for biological markers is constantly emerging. This study aimed, for the first time, to investigate diagnostic value of Erythropoietin (Epo) and its receptor (EpoR) levels in drug-naive patients with GAD. Methods This study included 45 newly diagnosed drug-naive patients with GAD, aged and gender-matched 30 healthy controls. Medical histories were obtained, and physical examinations and laboratory tests were conducted; the Hamilton Anxiety Rating Scale (HAM-A) was also used for all participants. Serum Epo and EpoR levels were measured by ELISA. Results HAM-A score was significantly higher in GAD patients versus the controls (p< 0.05). While the levels of Epo in patients with GAD were lower than the control patients, EpoR levels were increased in these patients (p<0.05). Epo/EpoR ratios were significantly lower in the patients with GAD than in the control subjects (p<0.05). A positive significant correlation was observed between the EpoR level and the HAM-A score (r= 0.755, p<0.001). However, there was a negative significant correlation between Epo levels and HAM-A score (r= -0.749, p<0.001). ROC analysis revealed both sensitivity and specificity of 100%, respectively, for the presence of anxiety when the serum Epo value was 7.64 ng/mL (the area under the curve was 1.000) and EpoR value was 0.97 ng/mL (the area under the curve was 1.000). Conclusion Our findings showed that Epo/EpoR ratio may be an important biomarker for GAD. Epo may be a good choice for GAD treatment.
Clinical Implications of 37 Childhood Cases with 2019-nCoV Infection in Shenzhen, China
Authors: Wang Yanrong , LIU Yingxia , Yang Yang , WANG Xianfeng , LIU Lei 
Published: February 2020

Abstract
Background 2019-nCoV was first identified in December 2019 in samples obtained from a 61 years old man who died of acute respiratory failure in the city of Wuhan, China with a subsequent outbreak in China. Till now, there were rare reports about childhood patients with 2019-nCoV infection.Methods We report 37 children diagnosed with 2019-nCoV infection admitted in the Third People’s hospital of Shenzhen from December 11, 2019 to February 11, 2020.Results There were 9 mild cases, 20 common cases and 1 severe case and 7 cases with asymptomatic infection. The age ranged from 7 months to 18 years old and the median age was 7 years old. The common clinical features were fever (29.7%, 11/37) and cough (32.4%, 12/37). No death occurred among our patients. 86.5% (32/37) children were infected with 2019-nCoV after their family members (parents or grandparents). 1 child was identified with 2019-nCoV infection after 3 times testing. The majority (78.4%) of cases occurred in those children who travelled to Hubei Province. The percentage of cases in preschool and in schools was 21.6% and 54.1% (P<0.05) respectively.Conclusions Family cluster transmission of 2019-nCoV was suspected in 86.5% of patients. Timely continuous 2019-nCoV pathogen testing is recommended. More attention should be paid to school children.