bluuebunny/crossref_metadata_2025_split huggingface dataset:
­ Comprehensive analysis of key genes associated with ceRNA networks in nasopharyngeal carcinoma based on bioinformatics analysis
Authors: Xu Yuanji , Huang Xinyi , Ye Wangzhong , Zhang Yangfan , Li Changkun , Bai Penggang , Lin Zhizhong , Chen Chuanben 
Published: July 2020

Abstract
Background. Nasopharyngeal carcinoma (NPC) is an epithelial malignancy with high morbidity rates in the east and southeast Asia. The molecular mechanisms of NPC remain largely unknown. We explored the pathogenesis, potential biomarkers, and prognostic indicators of NPC.Methods. We analyzed mRNAs, long non-coding RNAs (lncRNAs), and microRNAs (miRNAs) in the whole transcriptome sequencing dataset of our hospital (five normal tissues vs. five NPC tissues) and six microarray datasets (62 normal tissues vs. 334 NPC tissues) downloaded from the Gene Expression Omnibus (GSE12452, GSE13597, GSE95166, GSE126683, and GSE70970, GSE43039). Differential expression analyses, gene ontology (GO) enrichment, kyoto encyclopedia of genes and genomes (KEGG) analysis, and gene set enrichment analysis (GSEA) were conducted. The lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) networks were constructed using the miRanda and TargetScan database, and a protein-protein interaction (PPI) network of differentially expressed genes (DEGs) was built using Search Tool for the Retrieval of Interacting Genes (STRING) software. Hub genes were identified using Molecular Complex Detection (MCODE), NetworkAnalyzer, and CytoHubba.Results. We identified 61 mRNAs, 14miRNAs, and 10 lncRNAs as shared DEGs related to NPC in seven datasets. Changes in NPC were enriched in the chromosomal region, sister chromatid segregation, and nuclear chromosome segregation. GSEA indicated that the mitogen-activated protein kinase (MAPK) pathway, phosphatidylinositol-3 OH kinase/protein kinase B (PI3K-Akt) pathway, apoptotic pathway, and tumor necrosis factor (TNF) were involved in the initiation and development of NPC. Finally, 20 hub genes were screened out via the PPI network.Conclusions. Several DEGs and their biological processes, pathways, and interrelations were found in our current study by bioinformatics analyses. Our findings may offer insights into the biological mechanisms underlying NPC and identify potential therapeutic targets, biomarkers and prognostic indicators for NPC.
Antiviral effect of baicalin on Marek’s disease virus in CEF cells
Authors: Yang Fan , Feng Chun , Yao Yongxiu , Qin Aijian , Shao Hongxia , Qian Kun 
Published: July 2020

Abstract
Background: Baicalin, the main metabolic component of S.baicalensis Georgi, has various pharmacological properties including anti-inflammatory, anti-oxidant, anti-apoptotic, anti-bactericidal and anti-viral. The purpose of this study was to investigate the anti-Marek’s disease virus (MDV) activities of baicalin in CEF cells.Results: Here, we showed that baicalin could inhibit viral mRNA, protein levels and overall plaque formation in a time-dependent manner. We also found that baicalin could consistently inhibit MDV replication and directly affect the virus infectivity. Moreover, baicalin treatment has no effect on expression level of antiviral cytokine and inflammatory cytokines in virus infected CEFs.Conclusions: These results demonstrate that baicalin could be a potential drug against MDV infection.
Integrating GWAS , linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.)
Authors: wang tengyue , Wei Lijuan , wang Jia , Xie Ling , Li Yangyang , Ran Shuyao , Ren Lanyang , Lu Kun , Li Jiana , Timko Michael P. , Liu Liezhao 
Published: July 2020

Abstract
Background: Brassica napus is one of the most important oilseed crops, and also an important biofuel plant due to its low air pollution and renewability. Growth period are important traits that affect yield and are crucial for its adaptation to different environments in B. napus . Results: To elucidate the genetic basis of growth period traits, genome-wide association analysis (GWAS) and linkage mapping were employed to detect the quantitative trait loci (QTL) for days to initial flowering (DIF), days to final flowering (DFF), days from initial flowering to final flowering (FP), days from final flowering to maturity (MT), and whole growth period (GP). A total of 146 SNPs were identified by association mapping, and 83 QTLs were identified by linkage mapping using the RIL population. Among these QTLs, 19 were pleiotropic SNPs related to multiple traits, and six (q18DFF.A03-2, q18MT.A03-2, q17DFF.A05-1, q18FP.C04, q17DIF.C05 and q17GP.C09) were consistently detected using both mapping methods. Additionally, we performed RNA sequencing to analyze the differential expression of gene (DEG) transcripts between early- and late-flowering lines selected from the RIL population, and the DEGs were integrated with association mapping and linkage analysis to confirm their roles in the growth period. Consequently, twelve candidate genes associated with growth period traits were identified in B. napus . Among these genes, seven have polymorphic sites in the coding sequence and the upstream 2-kb sequence based on the resequencing data. The haplotype BnaSOC1.A05-Haplb and BnaLNK2.C06-Hapla showed more favorable phenotypic traits. Conclusions: The candidate genes identified in this study will contribute to our genetic understanding of growth period traits and can be used as targets for target mutations or marker assisted breeding for rapeseed adapted to different environments.
Impact on Decision Making Framework for Medicine Appraisal in Chinese Public Hospital Decision-making: Determining the Value of Five DPP-4 inhibitors
Authors: Bao Yun , Gao Bei , Meng Min , Ge Bin , Yang Yan , Ding Chunchun , Shi Bingyin , Tian Limin 
Published: July 2020

Abstract
Background: Decision making for medicine optimization in Chinese public hospitals is decided by a hospital Pharmacy Management Committee (PMC) and is complex, subjective and requires efficient methods to ensure transparency and consistency for the factors being considered. This study aimed to evaluate the EVIDEM framework in medicine optimization for Chinese public hospitals. In this study DPP-4 inhibitors were appraised.Methods: Following EVIDEM methodology, we convened an appraisal group and asked each individual to express their perspectives by assigning weights to each criteria. The estimated value of the five DPP-4 inhibitors was obtained by Multi-Criteria Decision Analysis (MCDA) which combined individual weighting (between 1 and 5) of each criterion with individual scoring for each intervention in each criterion. Results: A systematic literature search was completed and the committee assigned weights for each criterion. The overall value orders for each DPP-4 inhibitor included Sitagliptin (0.45), Linagliptin (0.44), Vildagliptin (0.43), Alogliptin (0.42) and Saxagliptin (0.40). Conclusions: This study was the first pilot using the EVIDEM framework and MCDA for medicine optimization in a Chinese public hospital. We aimed to improve the transparency and consistency of decision-making by using multi-criteria decision analysis while also discussing its limitations.
Giant Nonlinear Optical Activity in Two-Dimensional
Palladium Diselenide
Authors: YU Juan , KUANG Xiaofei , Li Junzi , Zhong Jiahong , Zeng Cheng , Cao Lingkai , Liu Zongwen , Zeng Zhouxiaosong , Luo Ziyu , He Tingchao , Pan Anlian , LIU Yanping 
Published: July 2020

Abstract
Nonlinear optical (NLO) effects in layered atomically thin two-dimensional (2D) materials provide a promising prospect for multifarious optoelectronic applications. The NLO characteristics of transition metal chalcogenides (TMDCs) are attracting growing attention and have been extensively explored recently. However, these materials possess sizable bandgaps ranging from visible to ultraviolet regions, so the investigation of narrow-bandgap materials remains deficient. Here, we report our comprehensive study on the NLO processes in palladium diselenide (PdSe2) flakes that have a near-infrared bandgap. Interestingly, this material exhibits a unique thickness-dependent second harmonic generation (SHG) feature, embodied in the strong (negligible) SHG signals in even (odd) layers, in contrast with that of other TMDCs. Furthermore, the two-photon absorption (TPA) coefficients (β ~4.5×105, 2.83×105, 1.7×105, and 1.85×104 cm/GW) of 1-3 L and bulk PdSe2 are larger by two and three orders of magnitude, compared with that of the conventional 2D materials. Significantly, at the excitation wavelength of 600 nm, a robust saturable absorption with giant modulation depths (αs ~47%, 30%, and 41%) was observed in 1-3 L PdSe2, which has yet been obtained in other 2D materials. Such unique NLO characteristics enable PdSe2 to be a potential candidate for technological innovations in nonlinear optoelectronic devices.
The Transcriptomic Responses of Atlantic Salmon (Salmo salar) to High Temperature Stress Alone, and in Combination with Moderate Hypoxia
Authors: Beemelmanns Anne , Zanuzzo Fábio Sabbadin , Xue Xi , Sandrelli Rebeccah M. , Rise Matthew L. , Gamperl Anthony Kurt 
Published: July 2020

Abstract
Background: Increases in seawater temperatures and in the frequency and severity of hypoxic events are expected with climate change, and may become a challenge for cultured Atlantic salmon and negatively affect their growth, immunology and welfare. Thus, we examined how an incremental temperature increase alone (Warm & Normoxic-WN: 12→20°C; 1°C week-1), and in combination with moderate hypoxia (Warm & Hypoxic-WH: ~70% air saturation), impacted salmon’s hepatic transcriptome expression compared to control fish (CT: 12°C, normoxic) using 44K microarrays and qPCR. Results: Overall, we identified 2,894 differentially expressed probes (DEPs, FDR < 5%), that included 1,111 shared DEPs, while 789 and 994 DEPs were specific to WN and WH fish, respectively. Pathway analysis suggested that the cellular mechanisms affected by the two experimental conditions were quite similar, with up-regulated genes functionally associated with heat shock response, ER-stress, apoptosis and immune defence, while genes connected with general metabolic processes, proteolysis and oxidation-reduction were largely suppressed. The qPCR assessment of 41 microarray-identified genes validated that the heat shock response (hsp90aa1, serpinh1), apoptosis (casp8, jund, jak2) and immune responses (apod, c1ql2, epx) were up-regulated in WN and WH fish, while oxidative stress and hypoxia sensitive genes were down-regulated (cirbp, cyp1a1, egln2, gstt1, hif1α, prdx6, rraga, ucp2). However, the additional challenge of hypoxia resulted in more pronounced effects on heat shock and immune-related processes, including a stronger influence on the expression of 14 immune-related genes. Finally, robust correlations between the transcription of 19 genes and several phenotypic traits in WH fish suggest that changes in gene expression were related to an impaired physiological and growth performance. Conclusion: Increasing temperature to 20°C alone, and in combination with hypoxia, resulted in the up- and down-regulation of genes involved in similar important pathways in Atlantic salmon. However, the heat shock and immune responses of fish exposed to 20°C and hypoxia were more affected, and their transcriptional dysregulation was related to reduced performance. This study provides valuable information on how these two environmental challenges affect the expression of stress-, metabolic- and immune-related genes and pathways and identifies potential biomarker genes for improving our understanding of fish health and welfare.
Integrated Transcriptome and Proteome Analysis Reveals Potential Mechanisms for Differential Abdominal Fat Deposition Between Divergently Selected Chicken Lines
Authors: Wang Lijian , Leng Li , Ding Ran , Gong Pengfei , Liu Chang , Wang Ning , Li Hui , Du Zhi-Qiang , Cheng Bohan 
Published: July 2020

Abstract
Background: Genetic selection for meat production performance of broilers concomitantly causes excessive abdominal fat deposition, accompanied by several adverse effects, such as the reduction of feed conversion efficiency and reproduction performance. Our previous studies have identified important genes regulating chicken fat deposition, using the Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF) as an animal model. However, the molecular mechanism underlying fat deposition differences between fat and lean broilers remains largely unknown. Results: Here, we integrated the transcriptome (RNA-Seq) and quantitative proteome (isobaric tags for relative and absolute quantitation, iTRAQ) profiling analyses on abdominal fat tissues from NEAUHLF chicken lines. Differentially expressed genes (466 DEGs) and proteins (231 DEPs) were identified, and enriched in pathways related to fatty acid metabolism, fatty acid biosynthesis, glycerophospholipid metabolism, and PPAR signaling, and in pathways mainly involved in protein processing, endocytosis and lipid metabolism, respectively. Moreover, several key DEGs and DEPs involved in long-chain fatty acid uptake, in situ lipogenesis (fatty acid and cholesterol synthesis), and lipid droplets accumulation were discovered, and most of them were up-regulated in the fat line, after integrated transcriptome and proteome analysis. Conclusions: Together, our findings provided a novel insight into abdominal fat content discrepancy between the fat and lean chicken lines.
Jordanian National Study of Nurses’ Barriers to Participating in Research
Authors: Hammad Sawsan Abu , Alzoubi Karem , Khabour Omar , Mukattash Tareq 
Published: July 2020

Abstract
Background: The nurses are the healthcare providers and researchers in critical institutions that provided health care for all people, and society needs to invest in them. The purpose of this study was to survey nurses regarding barriers to participate in research studies.Methods: A cross-sectional descriptive study. A total of 447 nurses agreed to participate in the study. Barriers were measured using Barriers of Research Utilization Scale (BRU). Results: More than half (53.3%) of the sample perceived the barriers to be high, whereas 8.9% perceived it as low. Barriers related to the organization scored the highest (P<0.01) compared to the other domains (nurse, innovation and communication).Regression analysis model showed that age, working experience, and nationality were associated with barriers to participate in research.Conclusion: More than half of the nurses in Jordan perceived the barriers of participation in research to be high. The barriers associated with the organization had more influence. A comprehensive approach should be developed to boost participation in research by significantly improving managerial support since it may be the most productive facilitator.
Fine structure of the silk spinning system in the caddisworm, Hydatophylax nigrovittatus (Trichoptera: Limnephilidae)
Authors: KIM Hyo-Jeong , SUN Yan , Moon Myung-Jin 
Published: July 2020

Abstract
Silk is produced by a variety of insects, but only silk made by terrestrial arthropods has been examined in detail. To fill the gap, this study was designed to understand the silk spinning system of aquatic insect. The larvae of caddis flies, Hydatophylax nigrovittatus produce silk through a pair of labial silk glands and use raw silk to protect themselves in the aquatic environment. The result of this study clearly shows that although silk fibers are made under aquatic conditions, the cellular silk production system is quite similar to that of terrestrial arthropods. Typically, silk production in caddisworm has been achieved by two independent processes in the silk glands. This includes the synthesis of silk fibroin in the posterior region, the production of adhesive glycoproteins in the anterior region, which are ultimately accumulated into functional silk dope and converted to a silk ribbon coated with gluey substances. At the cellular level, each substance of fibroin and glycoprotein is specifically synthesized at different locations, and then transported from the rough ER to the Golgi apparatus as transport vesicles, respectively. Thereafter, the secretory vesicles gradually increase in size by vesicular fusion, forming larger secretory granules containing specific proteins. It was found that these granules eventually migrate to the apical membrane and are exocytosed into the lumen by a mechanism of merocrine secretion.
Factors Affecting Infection Control Measures Performed by Dental Workers
Authors: Cheng Hsin-Chung , Yen Yu-Chun , Yen Amy Ming-Fang , Chen Sam Li-Sheng 
Published: July 2020

Abstract

Background We aimed to investigate factors associated with personal self-protection in infection control among dental care workers. Methods A cross-sectional survey with self-report questionnaire was conducted between Jan and Dec, 2018. 275 dentists and 298 dental assistants were enrolled from randomly selected dental care settings.Results Compliance with wearing hair caps, facial masks, and hand washing is not as high as oral masks and gloves (over 90%). For dentists, the level of clinical setting (aOR=3.1, P<0.001) and the correct use of disinfectants for impression materials (aOR=2.0, P<0.05) were associated with hair cap wearing. Gender (aOR=0.15, P<0.05) and correct use of indicator during sterilization (aOR=2.9, P<0.05) were associated with facial mask wearing. The correct use of indicator during sterilization (aOR=2.4, P<0.05) and disinfection for impression materials (aOR=2.2, P<0.05) were associated with hand washing. For dental assistants, longer work experience (aOR=1.05, P<0.05), working days (aOR=1.82, P<0.05), the correct use of disinfectants for impression materials (aOR=2.4, P<0.001), and the frequent use of gloves (aOR=8.0, P<0.05) were associated with facial mask wearing. The surface disinfection of working tables (aOR=2.8, P<0.001) and the frequent changing of gloves (aOR=5.96, P<0.05) were associated with hand washing. Conclusions Gender, the length of work practice, and correct techniques for sterilization use were identified as major factors associated with compliance with self-protection in infection control among dental care workers.
Dimensional Stability and Surface Details Reproduction of Two Extended-Pour Alginate Materials: A Function of Chemical Disinfection and Storage Time. An In- Vitro Study
Authors: Sharif Rania A. , Abdelaziz Khalid M. , Alshahrani Najla Manis Zafer , Almutairi Fatimah Salem , Alaseri Mohrah Awadh Saeed , Abouzeid Hoda Lotfy , Elagib Mohamed Fadul A. 
Published: July 2020

Abstract
Background: Many new extended-pour irreversible hydrocolloid impression materials have been marketed with claims that they demonstrate enhanced surface details accuracy and dimensional stability for up to 120 hours of storage. However, no data in the literature about the effect of storage time on surface details and dimensional stability of extended-pour impression materials upon disinfection. In this study we aimed to evaluate the effect of two chemical disinfection methods and three storage times on dimensional stability and surface details reproduction of 2 extended-pour alginates in comparison with a conventional one.Methods: A total of 243 alginate impressions were recorded from a custom metal die using Tropicalgin (conventional), Hydrogum5 and Chroma print (extended-pour) alginates. Impressions were categorized into 9 groups according to disinfection method (non-disinfected, sprayed or immersed) and storage time (0, 72, 120 hours). After storage in sealed plastic bag with a damp cotton roll, all impressions were poured with type IV dental stone. The stone models were then examined for surface details and dimensions using a magnifier (×10) and digital caliper to assess whether a 25 µm-line on the metal die was completely reproduced over the full 25 mm length and its dimensions compared to the original die. Data were analyzed using one-way (ANOVA) and Tuckey’s post-hoc test, and KrusKal Wallis test and Mann-Whitney's test.Results: With immediate pouring all alginates showed accurate surface details regardless of the disinfection condition, except for immersed Tropicalgin (P<0.05). The extended storage affected surface details of all materials. After 72h, only non-disinfected extended-pour alginates showed dimensional stability. However, after 120h of storage all materials regained dimensional stability except sprayed Tropicalgin.ConclusionsExtended-pour alginates hardly proved to be more advantageous than traditional alginate in terms of surface details accuracy. Disinfection methods had some adverse effects on surface details and dimensional accuracy of both extended-pour and conventional alginate. Extended-pour alginate proved dimensional stability after 120h. It is recommended to immediately pour all alginates whether conventional or extended-pour. Further studies are needed to evaluate impression materials directly to control the confounding variable like gypsum expansion and storage environment in terms of humidity and temperature.
Molecular Epidemiology of Plasmodium Falciparum by Multiplexed Amplicon Deep Sequencing in Senegal
Authors: NDIAYE Tolla , Sy Mouhamad , Gaye Amy , Siddle Katherine J. , Park Daniel J. , Bei Amy K. , Deme Awa B. , Mbaye Aminata , Dieye Baba , Ndiaye Yaye Die , Ndiaye Ibrahima Mbaye , Diallo Mamadou Alpha , Diongue Khadim , Volkman Sarah K. , Badiane Aida Sadikh , Ndiaye Daouda 
Published: July 2020

Abstract
Background
Molecular epidemiology can provide important information regarding the genetic diversity and transmission of Plasmodium falciparum, which can assist in designing and monitoring elimination efforts. However, malaria molecular epidemiology including understanding the genetic diversity of the parasite and performing molecular surveillance of transmission has been poorly documented in Senegal. Next Generation Sequencing (NGS) offers a practical, fast and high-throughput approach to understand malaria population genetics. This study aims to unravel the population structure of P. falciparum and to estimate the allelic diversity, multiplicity of infection (MOI), and evolutionary patterns of the malaria parasite using the NGS platform.
Methods
Multiplex amplicon deep sequencing of merozoite surface protein 1 (PfMSP1) and merozoite surface protein 2 (PfMSP2) genes in fifty-three P. falciparum isolates from two epidemiologically different areas in the South and North of Senegal, was carried out.
Results
A total of 76 Pfmsp1 and 116 Pfmsp2 clones were identified and 135 different alleles were found, 56 and 79 belonged to the pfmsp1 and pfmsp2 genes, respectively. K1 and IC3D7 allelic families were most predominant in both sites. The local haplotype diversity (Hd) and nucleotide diversity (π) were higher in the South than in the North for both genes. For pfmsp1, a high positive Tajima’s D (TD) value was observed in the South (D = 2.0453) while negative TD value was recorded in the North (D=-1.46045) and F-Statistic (Fst) was 0.19505. For pfmsp2, non-directional selection was found with a highly positive TD test in both areas and Fst was 0.02111. The mean MOI for both genes was 3.07 and 1.76 for the South and the North, respectively, with a statistically significant difference between areas (p = 0.001).
Conclusion
This study revealed a high genetic diversity of pfmsp1 and pfmsp2 genes and low genetic differentiation in P. falciparum population in Senegal. The MOI means were significantly different between the Southern and Northern areas. Findings also showed that multiplexed amplicon deep sequencing is a useful technique to investigate genetic diversity and molecular epidemiology of P. falciparum infections.