bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction of a lncRNA-Associated ceRNA Network and Identification of A Potential Six-lncRNA Prognostic Signature for Esophageal Cancer
Authors: Hu Jun , Wang Fang , Liu Logen , Ning Wenfeng 
Published: June 2020

Abstract
BACKGROUND: Mounting evidence has shown that long noncoding RNAs (lncRNAs) can function as competing endogenous RNAs (ceRNAs) which participate in the initiation and progression of cancers. In the ceRNA network, lncRNAs, microRNAs (miRNAs) and mRNAs, communicate with and co-regulate each other. Rarely there is a systematic lncRNA-mediated ceRNA network and potential specific ceRNA pairs or triples of esophageal cancer (EC). In this study, we investigate the lncRNA-mediated ceRNA network in EC and screen the potential prognostic lncRNA biomarkers.METHODS: We obtained mRNA, miRNA, and lncRNA expression data and relevant clinical features on patients with EC from The Cancer Genome Atlas (TCGA), and used the edgR package to identify differentially expressed mRNAs, lncRNAs and miRNAs between EC samples and normal samples. The EC ceRNA network was constructed based on miRNA target prediction through the databases of miRcode, miRDB, miRTarBase and TargetScan. And then Pearson’s correlation analysis was adopted to identify co-expression mRNA-lncRNA pairs. Finally, the robust likelihood-based survival analysis and Cox regression models were used to identify prognosis-related lncRNAs, which was evaluated by Kaplan-Meier and receiver operating characteristic (ROC) curve analysis.RESULTS: A total of 3,200 mRNAs, 131 miRNAs and 1,338 lncRNAs were identified as significantly differentially expressed in EC, of which, 30 mRNAs, 15 lncRNAs, and 8 miRNAs were incorporated in the ceRNA network. According to the ceRNA network node degrees, lncRNA MAGI2-AS3, hsa-mir-93 and TGFBR2 were the key genes. Also, the ceRNA network revealed some important ceRNA pairs and triples, such as SNX29P2-TGFBR2 and MAGI2-AS-hsa-mir-143-COL1A1. Finally, we developed a six-lncRNA signature (ZNF341-AS1, AC130324.2, AC027271.1, AL591212.1, AL732314.4 and LOC105372352), with improved diagnostic potential for EC with the area under the ROC curve of 0.93.CONCLUSIONS: our present work sheds new light on the tumorigenesis roles of lncRNA-mediated ceRNA network in EC and identifies a six‐lncRNA model that could be used as candidate prognostic signature.
Investigation of Leishmania infection and blood sources analysis in Phlebotomus chinensis (Diptera: Psychodidae) along extension region of the Loess Plateau, China
Authors: Chen Hanming , Chen Huiying , Tao Feng , Gao Jingpeng , Li Kaili , Shi Hua , Peng Heng , Ma Yajun 
Published: June 2020

Abstract
BackgroundVisceral leishmaniasis (VL) was one of the most important parasitic diseases in China, caused by Leishmania protozoans and transmitted by sandflies. Recently VL cases have reappeared in China, including the extension region of the Loess Plateau. The purpose of this study was to detect the infection rate of Leishmania and analyze the blood sources of the sandflies vectors to guide the development of prevention and control measures. MethodsSandflies were collected by light traps from rural areas in Shanxian, Henan, China in 2015, as well as in Wuxiang and Yangquan, Shanxi, China in 2017. The blood sources of sandflies were analyzed by PCR detecting the host-specific mitochondrial cytochrome b (mtDNA Cyt b) gene fragments. Leishmania infection in sandflies was detected by amplifying and sequencing ribosomal DNA internal transcribed spacer 1 (ITS1). The Leishmania specific antibodies in the sera of local dogs were detected by ELISA. ResultsBlood sources showed diversity in the extension region of the Loess Plateau, including human, chicken, dog, cattle, pig and goat. Multiple blood sources within a sandfly individual were observed in samples from Yangquan (17/118, 14.4%) and Wuxiang (12/108, 11.1%). Leishmania DNA was detected in sandflies collected from Yangquan, of which 8.5% pooled and 1.9% individual samples were positive. The ITS1 sequences were conserved with the Leishmania donovani complex. The positive rate of Leishmania specific antibodies in dogs was 5.97%. ConclusionThis study detected the blood sources and Leishmania parasites infection of sandflies by molecular methods in the extension region of Loess Plateau, China. A high epidemic risk of leishmaniasis is currently indicated by the results as the infection of Leishmania in sandflies, the extensive blood sources of sandflies including humans, and positive antibody of Leishmania in local dog sera. Given the recent increase of VL cases, asymptomatic patients, dogs and other potential infected animals should be screened and treated. Furthermore, the density of sandflies needs to be controlled and personal protection should be strengthened.
Readmission rate after epilepsy surgery: A systematic review and meta-analysis
Authors: Mir Soheila , Jor Anis , Salarzaei Morteza 
Published: June 2020

Abstract
ObjectiveToday, quality of care has become a central issue with regard to redesigning health care delivery. For improvement of quality of care, measurement and analysis of outcomes is essential. the aim of this study is to evaluate the 30 day readmission rate of epilepsy surgery.Material and MethodsA systematic literature review was performed in April 2020. We reviewed MEDLINE/PubMed, Cochrane Library, and ClinicalTrials.gov for citation or ongoing trials from January 2010 to March 2020. The search criteria were limited to human studies published in English language. The Medical Subject Headings terms used for the search in PubMed were ‘epilepsy surgery’ ,’readmission’, ’reoperation ’ and ‘neurological surgery’. We used random-effects meta-analyses to estimate pooled risk ratios and 95% confidence intervals for early readmissionResultsIn the 7trials reporting readmission rates, the overall prevalence of readmission and re-operation within 30 days was 10% and 9%. The most common cause of re-admission was seizure(31.6%). The overall mean Elixhauser index among readmitted patients after epilepsy surgery was 8.05.ConclusionMinimizing factors that contribute to readmission in various patient populations and procedures becomes important for patient care, resource utilization, and physician reimbursement.understanding about a readmission rate of 10% can be useful to health systems designing quality improvement efforts.Awareness of the reasons for readmission is important for patient counseling and surgical decision making.In epilepsy surgery, although our study did not show a significant difference but ,readmissions might be reduced with optimization of pre-existing comorbidities
Atraumatic Restorative Treatment compared to the Hall Technique for occluso-proximal carious lesions in primary molars; 36-month follow-up of a randomised control trial in a school setting
Authors: Araujo Mariana Pinheiro , Innes Nicola Patricia , Bonifácio Clarissa Calil , Hesse Daniela , Olegário Isabel Cristina , Mendes Fausto Medeiros , Raggio Daniela Prócida 
Published: June 2020

Abstract
Background: Atraumatic Restorative Treatment (ART) and the Hall Technique (HT) are both minimally invasive, non-aerosol generating procedures (non-AGPs). They seem to have never been directly compared, nor has the HT been studied in a non-clinical setting. This study compared the HT and ART restorations placed in a school setting after 36 months.Methods: Children (5-10 yo) who had a primary molar with an occluso-proximal carious lesion were allocated to the ART or HT arms. Primary outcome: restoration survival over 36-months (using Kaplan-Meier survival analysis, log rank test, and Cox regression). Secondary outcomes: 1) occlusal vertical dimension (OVD) (1, 2, 3, 4 weeks) and 2) child self-reported discomfort; 3) treatment acceptability (immediately following interventions); 4) Child Oral Health Related Quality of Life (OHRQoL), before treatment and after 6 months and 5) a post-hoc analysis of time to tooth exfoliation (1, 6, 12, 18, 24, 30, 36 months).Results: One-hundred and thirty-one children (ART=65; HT=66) were included (mean age=8.1±1.2). At 36 months, 112 (85.5%) children were followed-up. Primary outcome: restoration survival rates ART=32.7% (SE=0.08; 95%CI=0.17-0.47); HT=93.4% (0.05; 0.72-0.99), p<0.001; Secondary outcomes: 1) OVD returned to pre-treatment state within 4 weeks; 2) treatment discomfort was higher for the HT (p=0.018); 3) over 70% of children and parents showed a high acceptability for treatments, with crown aesthetics being a concern for around 23% of parents; 4) Child OHRQoL improved after six months; and 5) teeth treated with the HT exfoliated earlier than those in the ART group (p=0.007).Conclusions: Both ART and the HT were acceptable to child participants and their parents and all parents thought both restorations protected their child’s tooth. However, the crown appearance concerned almost a quarter of parents in the HT arm. Children experienced less discomfort in the ART group. Although both treatments can be performed in a non-clinical setting and have the advantage of being non-aerosol generating procedures (non-AGPs), the HT had almost three times higher survival rates (93.4%) for restoring primary molar occluso-proximal cavities compared to ART (32.7%).Trial registration: This trial was registered in ClinicalTrials.gov (NCT02569047), 5th October 2015. https://clinicaltrials.gov/ct2/show/study/NCT02569047?cond=Hall+Technique+Atraumatic+Restorative+Treatment&draw=2&rank=2
A new classification of cross-sectional root canal shape changes, a cone-beam computed tomography study
Authors: Razumova Svetlana , Brago Anzhela , Barakat Haydar , Howijieh Ammar , Kozlova Yuliya , Baykulova Malina 
Published: June 2020

Abstract
Background: The root canal system is considering the most important factor in endodontic treatment, due to the complexity of its anatomy and morphology. The aim of this study was to present a new classification of root canal shape changes in three thirds (coronal, middle, apical) in different age groups using cone-beam computed tomography scanning.Materials and methods: 300 CBCT scans for patient aged 20-70 were evaluated to study the morphology of the cross-sectional root canal shape in coronal, middle and apical thirds among three age groups; young (20-44), middle (45-59) and elderly (60-70). The root canal shape was classified as follow: round, oval, ribbon. Results: The cross-sectional root canal shape was identified in two groups: canals with an unchanging (constant) shape and canals with changing shape. In turn, in canals with changing shape, the change could be identified in the region of the middle or apical thirds of the canal. The results showed that root canal shape changes in two cases: 1) the presence of one or more canals in the root (with or without isthmus between them), 2) with age, as it was observed that the cross-sectional shape of the root canal becomes round in the apical third with age.Conclusion: A new classification of the changes of root canal shape in three thirds (coronal, middle, apical) was presented in this study.
Lower Collagen Area and Contralateral Lymph Node Metastasis Type Associated with Lower Disease-Free Survival in Thyroid Papillary Carcinoma
Authors: Dou Chengyun , Tang Fen , Li Jianping , Zhao Qiang , Cao Chuangjie 
Published: June 2020

Abstract
Objectives: To introducing a novel prognostic risk scheme which based on collagen area and lymph node metastasis type in thyroid papillary carcinoma (PTC).Method: Tumor collagen area and lymph node matastasis type as well as several other histomorphological factors with disease-free survival (DFS) were investigated in a corhort of 101 PTC patients. Results: Median follow-up time of DFS was 76 months(inter quartile range: 71–83 months). Low collagen area and contralateral lymph node matastasis type were associated with dismal patient disease-free survival (DFS) significantly. While tumors with high collagen area showed a mean DFS of 77.37 months, gradually decreased to 76.53 months for tumors with moderate collagen area and to 66.67 months for tumors with low collagen area (p =0.028). Negtive, central and ipsilateral lymph node metastasis showed mean DFS of 72.72, 74.8 and 72.81 months respectively, decreased to 62.17 months with bilateral lymph node metastasis and 59.43 months with contralateral lymph node metastasis (p=0.029). In the cohort, uinivariate statistical analysis of the novel risk scheme revealed that the hazard ratio (HR) for DFS was 5.18 for R2 and 15.53 for R3 tumors compared to R1 PTC (p=0.003). Disease free survival dropped from 77.74 months for R1 tumors to 68.7 months for R2 and 56.38 months for R3. Multivariate statistical analysis of the novel risk scheme revealed that the HR for DFS was 3.259 (95% confident interval [CI] 1.122–9.469, p=0.03).Conclusion: Our novel risk algorithm incorporating tumor collagen area and lymph node matastasis type allows strongly prognostic stratification of PTC. We suggest this risk algorithm as a morphology-based parameter for the routine diagnostic assessment of this tumor entity.
An Ultrasensitive Immunoassay Strip for Simultaneously Detecting Cyproheptadinehydrochloride and Six Phenothiazinesin Feedstuffs Based on a Monoclonal Antibody
Authors: Na Guanqiong , Hu Xiaofei , Sun Yaning , Tang Liang , Xing Guangxu , Xing Yunrui , Zhang Gaiping 
Published: June 2020

Abstract
Background: An antihistamine cyproheptadine (CPH) and phenothiazines (PZs)sedative hypnoticshave a similar tricyclic structure, these drugs are often illegally added to food animal feedstuffs due to their price advantage and significant effect in promoting growth and improving meat quality. However, the abuse of these drugs may lead totheir residues in animal products, thereby causing harmful effects such as allergies and dermatological reactions on human health.To supervise the use of prohibited drugs and ensure food safety, it is necessary to establish a simple and effective screening method to detect CPH and PZs.In this research, an artificial antigen against cyproheptadine(CPH) was successfully synthesized by bromoacetic acid substitution method. An ultrasensitive and broad-specific monoclonal antibody (mAb) able to recognize CPH and six phenothiazines (PZs) was produced. Based on the gold-labeled mAb, an immunochromatographic strip (ICS) was established.Results:The 50% inhibition concentration (IC50) of the produced mAb against CPH was identified as 0.036 ng mL-1 by ELISA, and the cross-reactivities for six PZs were from 6.33% to 63.16%. The visual detection limits(cut-off values) of the developed ICS ranged from 5 to 100ngg-1 in feedstuffs. Take a reading by strip reader, the IC50 was from 0.570 to 7.750ng g-1. In addition,a recovery experiment was carried out to verify the reliability of the ICS. The intra-assay recoveries were from 79.83% to 103.38% with the highest coefficient of variation (CV) of 11.31%. The inter-assay recoveries were from 79.00% to 96.63% with the highest CV of 12.66%.Conclusions: We have successfully produced a broad-spectrum monoclonal antibody and established an ICS for simultaneouslydetecting CPH and six PZs drugs.In brief, the proposed ICS was considered suitable for qualitatively and quantitatively monitoring CPH and PZs in feedstuffs.
Transcriptomic profiling of germinating seeds under cold stress and characterization of the cold-tolerant gene LTG5 in rice
Authors: Pan yinghua , Liang Haifu , Gao Lijun , Dai Gaoxing , Chen Weiwei , Yang Xinghai , Qing Dongjin , Gao Ju , Wu Hao , Huang Juan , Zhou Weiyong , Huang Chengcui , Liang Yuntao , Deng Guofu 
Published: June 2020

Abstract
Background: Wild rice ( Oryza rufipogon Griff.) is an important germplasm resource for rice improvement. It has superior tolerance for many abiotic stresses including cold stress, but little is known about the mechanism underlying its resistance to cold. Low temperature is one of the most prevalent factors that limit rice productivity and geographical distribution.Results: This study aimed to elucidate the molecular genetic mechanisms of wild rice in tolerating low temperature. Comprehensive transcriptome profiles of two rice genotypes (cold-sensitive ce 253 and cold-tolerant Y12-4) at the germinating stage under cold stress were comparatively analyzed. A total of 42.44–68.71 million readings were obtained, resulting in the alignment of 29128 and 30131 genes in genotypes 253 and Y12-4, respectively. Many common and differentially expressed genes (DEGs) were analyzed in cold-sensitive and cold-tolerant genotypes. Results showed more upregulated DEGs in cold-tolerant genotypes than in cold-sensitive genotypes at four stages under cold stress. Gene ontology enrichment analyses indicated more upregulated genes than downregulated ones in cold-tolerant genotypes based on cellular process, metabolic process, response stimulus, membrane part, and catalytic activity. To confirm the RNA Sequencing (RNA-seq) data, Quantitative real time polymerase chain reaction (qRT-PCR) was performed on seven randomly selected DEGs. These genes showed similar expression patterns corresponding with the RNA-Seq method. We also explored a gene for cold tolerance LTG5 , encoding a UDP-glucosyltransferase. The overexpression of LTG5 gene conferred cold tolerance to indica rice.Conclusion: Overall, our results suggested that gene resources related to cold stress from wild rice can be valuable for improving the cold tolerance of crop plants.
Humic-acid-driven escape from eye parasites revealed by RNA-seq and target-specific metabarcoding
Authors: Noreikiene Kristina , Ozerov Mikhail , Ahmad Freed , Kõiv Toomas , Kahar Siim , Gross Riho , Sepp Margot , Pellizzone Antonia , Vesterinen Eero J. , Kisand Veljo , Vasemägi Anti 
Published: June 2020

Abstract
BackgroundNext generation sequencing (NGS) technologies are extensively used to dissect the molecular mechanisms of host-parasite interactions in human pathogens. However, ecological studies have yet to fully exploit the power of NGS as a rich source for formulating and testing new hypotheses. MethodsWe studied Eurasian perch (Perca fluviatilis) and its eye parasite (Trematoda, Diplostomidae) communities in fourteen lakes that differed in humic content in order to explore host-parasite-environment interactions. We hypothesised that high humic content along with low pH would decrease the abundance of the intermediate hosts (gastropods), thus limiting the occurrence of diplostomid parasites in humic lakes. This hypothesis was initially invoked by whole eye RNA-seq data analysis and subsequently tested using PCR-based detection and a novel targeted metabarcoding approach.ResultsWhole eye transcriptome results revealed over expression of immune-related genes and the presence of eye parasite sequences in RNA-seq data obtained from perch living in clear-water lakes. Both PCR-based and targeted-metabarcoding approach showed that perch from humic lakes were completely free from diplostomid parasites, while the prevalence of eye flukes in clear-water lakes that contain low amounts of humic substances was close to 100%, with the majority of NGS reads assigned to Tylodelphys clavata. ConclusionsHigh intraspecific diversity of T. clavata indicates that massively parallel sequencing of naturally pooled samples represents an efficient and powerful strategy for shedding light on cryptic diversity of eye parasites. Our results demonstrate that perch populations in clear-water lakes experience contrasting eye parasite pressure compared to those from humic lakes, which is reflected by prevalent differences in the expression of immune-related genes in the eye. This study highlights the utility of NGS to discover novel host-parasite-environment interactions and provide unprecedented power to characterize the molecular diversity of cryptic parasites.
Identification and Functional Enrichment Analysis of Differentially Expressed Genes in Osteoarthritis
Authors: Xu Chen , Meng Ling-bing , Xiao Yu , Qiu Yong , Du Ying-jue , Huang Cibo , Wang Fang 
Published: June 2020

Abstract
Background Osteoarthritis (OA) is a chronic, progressive, inflammatory, degenerative disease, which has become an osteoarthropathy that seriously affects physical health and quality of life of elderly people. However, the etiology and pathogenesis of OA remains unclear. Therefore, the study purposed to utilize bioinformatics technology to perform identification and functional enrichment analysis of differentially expressed genes in osteoarthritis. Method The main methods of this study consist of access to microarray data (GSE82107 and GSE55235), identification of differently expressed genes (DEGs) by GEO2R between OA and normal synovium samples, enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) by Gene Set Enrichment Analysis (GSEA), construction and analysis of protein-protein interaction (PPI) network, significant module and hub genes. Result A total of 300 DEGs were identified, consisting of 64 up-regulated genes and 11 down-regulated genes in OA samples compared to normal synovium tissues. Gene set enrichment analysis of DEGs provided a comprehensive overview of some major pathophysiological mechanisms in OA: cellular response to hydrogen peroxide, P53 signaling pathway and so on. The study also built the PPI network, and a total of 10 key genes were identified: CYR61, PENK, GOLM1, DUSP1, ATF3, STC2, FOSB, PRSS23, TF, and TNC. Conclusion DEGs exists between OA patients and normal cartilage tissue, which may be involved in the related mechanism of OA development, especially cellular response to hydrogen peroxide and CYR61.
Improved Muscle Function After Injury with the Application of a Biological Decellularized Matrix
Authors: Ayadi Amina El , Threlkeld Melody R.S. , Wolf Steven E. , Song Juquan 
Published: June 2020

Abstract
Background: Skeletal muscle injury leads to loss of muscle function that lasts well into recovery and can be permanent. Application of the novel bio-scaffold termed porcine-derived urinary bladder matrix (UBM) has a potential benefit to mitigate injury through tissue regeneration. To date, findings of potential benefit in animal models were limited to short assessment times. The purpose of this study was to investigate whether UBM treatment 14 days after injury sustainably improves the recovery of muscle function in injured mice. Methods: C57BL/6 adult male mice received bilateral laceration injuries on the gastrocnemius (GN) muscle under anesthesia and were then treated with vehicle or 150 µg of UBM nanoparticles. Treatment was applied immediately after injury or 14 days later. Muscle isometric force was measured 60 days after injury. Previous time course analyses have shown that muscle function did not start to improve until after 42 days after injury. Therefore, we designed a second experiment to trace the time course of UBM effects on muscle function recovery by measuring the isometric muscle force at 49 and 90 days after injury. In vitro, we analyzed the effects of UBM on muscle cell proliferation and differentiation. Results: UBM promotes muscle cell proliferation and differentiation. Twitch (Pt), tetanic (Po) force and maximal fatigue were significantly decreased in the injured mice on day 60. Muscle fatigue maximum force significantly recovered when UBM treatment was applied 14 days after injury (p<0.05) but not when UBM was applied immediately after the injury. Time course analysis demonstrated that UBM improvement of Pt and Po was evident by day 49 after injury (p<0.05). However, no further muscle function improvement was observed on day 90. Conclusions: Delayed treatment with the UBM improves muscle function recovery following laceration injury starting 49 days after injury. These effects may be mediated by improvements in muscle cell proliferation and differentiation. This animal model is suitable to test other therapeutic strategies to improve muscle function after injury.