bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome regulation of carotenoids in five flesh-colored watermelon (Citrullus lanatus)
Authors: Yuan Pingli , Umer Muhammad Jawad , He Nan , Zhao Shengjie , Lu Xuqiang , Zhu Hongju , Gong Chengsheng , Diao Weinan , Gebremeskel Haileslassie , Kuang Hanhui , wenge liu 
Published: January 2021

Abstract
Background: Fruit flesh color in watermelon (Citrullus lanatus) is a great index for evaluation of the appearance quality and a key contributor influencing consumers' preferences, but the molecular mechanism of this intricate trait remain largely unknown. Here, the carotenoids and transcriptome dynamics during the fruit development of cultivated watermelon with five different flesh colors were analyzed.Results: A total of 13 carotenoids and 16781 differentially expressed genes (DEGs) including 1295 transcription factors (TFs) were detected in five watermelon genotypes during the fruit development. The comprehensive accumulation patterns of carotenoids were closely related to flesh color. A number of potential structural genes and transcription factors were found to be associated with the carotenoid biosynthesis pathway using comparative transcriptome analysis. The differentially expressed genes were divided into six subclusters and distributed in different GO terms and metabolic pathways. Furthermore, we performed weighted gene co-expression network analysis and predicted hub genes in six main modules determining carotenoid contents. Cla018406 (a chaperone protein dnaJ-like protein) may be a candidate gene for β-carotene accumulation and highly expressed in orange flesh-colored fruit. Cla007686 (a zinc finger CCCH domain-containing protein) was highly expressed in the red flesh-colored watermelon, maybe a key regulator of lycopene accumulation. Cla003760 (membrane protein) and Cla021635 (photosystem I reaction center subunit II) were predicted to be hub genes and may play an essential role in yellow flesh formation.Conclusions: The composition and contents of carotenoid in five watermelon genotypes vary greatly. A series of candidate genes were revealed through combined analysis of metabolites and transcriptome. These results provide an important data resource for dissecting the candidate genes and molecular basis governing flesh color formation in watermelon fruit.
Identification of lncRNAs associated with the pathogenesis of ankylosing spondylitis
Authors: Huang Dan , Liu Jian , Wan Lei , Fang Yanyan , Long Yan , Zhang Ying , Bao Bingxi 
Published: January 2021

Abstract
Background: Ankylosing spondylitis (AS) is a chronic autoimmune disease affecting the sacroiliac joint. To date, few studies have examined the association between long non-coding RNAs (lncRNAs) and AS pathogenesis. As such, we herein sought to characterize patterns of AS-related lncRNA expression and to evaluate the potential role played by these lncRNAs in this complex autoimmune context. Methods: We conducted a RNA-seq analysis of peripheral blood mononuclear cell (PBMC) samples isolated from five AS patients and corresponding controls. These data were then leveraged to characterize AS-related lncRNA expression patterns. We further conducted GO and KEGG enrichment analyses of the parental genes encoding these lncRNAs, and we confirmed the validity of our RNA-seq data by assessing the expression of six lncRNAs via qRT-PCR in 15 AS and control patient samples. Pearson correlation analyses were additionally employed to examine the associations between the expression levels of these six lncRNAs and patient clinical index values. Results: We detected 56575 total lncRNAs in AS and control patient samples during our initial RNA-seq analysis, of which 200 and 70 were found to be up- and down-regulated (FC > 2 or < 0.05; P<0.05), respectively, in AS samples relative to controls. In qRT-PCR validation assays, we confirmed the significant upregulation of NONHSAT118801.2, ENST00000444046, and NONHSAT183847.1 and the significant downregulation of NONHSAT205110.1, NONHSAT105444.2, and NONHSAT051856.2 in AS patient samples. We further found the expression of NONHSAT118801.2 and NONHSAT183847.1 to be positively correlated with disease severity. Conclusion: Overall, our findings highlight several lncRNAs that are specifically expressed in PBMCs of AS patients, indicating that they may play key functions in the pathogenesis of this autoimmune disease. Specifically, we determined that NONHSAT118801.2 and NONHSAT183847.1 may influence the occurrence and development of AS.
Reliability of genomic variants across different next-generation sequencing platforms and bioinformatic processing pipelines
Authors: Weißbach Stephan , Sys Stanislav Jur`Evic , Hewel Charlotte , Todorov Hristo , Schweiger Susann , Winter Jennifer , Pfenninger Markus , Torkamani Ali , Evans Doug , Burger Joachim , Everschor-Sitte Karin , May-Simera Helen , Gerber Susanne 
Published: January 2021

Abstract
BackgroundNext Generation Sequencing (NGS) is the fundament of various studies, providing insights into questions from biology and medicine. Nevertheless, integrating data from different experimental backgrounds can introduce strong biases. In order to methodically investigate the magnitude of systematic errors in single nucleotide variant calls, we performed a cross-sectional observational study on a genomic cohort of 99 subjects each sequenced via (i) Illumina HiSeq X, (ii) Illumina HiSeq, and (iii) Complete Genomics and processed with the respective bioinformatic pipeline. We also repeated variant calling for the Illumina cohorts with GATK, which allowed us to investigate the effect of the bioinformatics analysis strategy separately from the sequencing platform's impact. Results The number of detected variants/variant classes per individual was highly dependent on the experimental setup. We observed a statistically significant overrepresentation of variants uniquely called by a single setup, indicating potential systematic biases. Insertion/deletion polymorphisms (indels) were associated with decreased concordance compared to single nucleotide polymorphisms (SNPs). The discrepancies in indel absolute numbers were particularly prominent in introns, Alu elements, simple repeats, and regions with medium GC content. Notably, reprocessing sequencing data following the best practice recommendations of GATK considerably improved concordance between the respective setups.ConclusionWe provide empirical evidence of systematic heterogeneity in variant calls between alternative experimental and data analysis setups. Furthermore, our results demonstrate the benefit of reprocessing genomic data with harmonized pipelines when integrating data from different studies.
Assessment of necessity of neuronavigation in localization of clavarial extra-axial lesions in the setting of limited resources.
Authors: Soffar Hussein , Alsawy Mohamed F. 
Published: January 2021

Abstract
BACKGROUND: Neuronavigation is a very beneficial tool in modern neurosurgicalpractice. However, the neuronavigation is not available in most of the hospitals in our country raising the question about its importance in localizing the clavarial extra-axial lesions and to what extent it is safe to operate without it.METHODS: We studied twenty patients with clavarial extra-axial lesions who underwent surgical interventions. All lesions were preoperatively located with both neuronavigation and the usual linear measurements. Both methods were compared regarding the time consumed to localize the tumor and the accuracy of each method to anticipate the actual center of the tumor.RESULTS: The mean error of distance between the planned center of the tumor and the actual was 6.50±1.762 mm in conventional method, whereas the error was 3.85±1.309 mm in IGS method. Much more time was consumed during the Neuronavigation method including booting,registration, positioning. A statistically significant difference was found between the mean time passed in the conventional method and IGS method (2.05±0.826, 24.90±1.334, respectively), P-value<0.001.CONCLUSION: in the setting of limited resources, the linear measurement localization method seems to have an accepted accuracy in localization of clavarial extra-axial lesions and it saves more time than neuronavigation method.
Institutional outbreak involving multiple clades of IMP-producing Enterobacter cloacae complex sequence type 78 at a cancer center in Tokyo, Japan
Authors: Harada Sohei , Aoki Kotaro , Ohkushi Daisuke , Okamoto Koh , Takehana Kazumi , Akatsuchi Tomomi , Ida Keito , Shoji Daigo , Ishii Yoshikazu , Doi Yohei , Moriya Kyoji , Hayama Brian 
Published: January 2021

Abstract
Background: Information about the clinical and microbiological characteristics of IMP-producing Enterobacterales has been limited. Here, we describe an institutional outbreak of IMP-producing Enterobacter cloacae complex (ECC) involving multiple clades of ECC sequence type (ST) 78 strains.Methods: Antimicrobial susceptibility testing, whole-genome sequencing, and conjugation experiments of 18 IMP-producing ECC strains isolated during four-year study period were performed. Species and subspecies were determined by average nucleotide identity analysis and clonal relatedness of the isolates was analyzed with multilocus sequence typing and core-genome single nucleotide polymorphism (SNP) analysis. Relevant clinical information was extracted from medical records.Results: Fourteen of 18 IMP-producing ECC isolates were determined as Enterobacter hormaechei ST78. Sixteen isolates, including 13 isolates belonging to ST78, carried blaIMP-1 in In316-like class 1 integron and also carried IncHI2 plasmids. Conjugation experiments were successful for 12 isolates carrying blaIMP-1 on IncHI2 plasmids and for an isolate carrying blaIMP-11 on an IncL/M plasmid. Although isolation of ST78 strains was clustered in a 14-months period suggesting nosocomial transmission, these strains were subdivided into three clades by SNP analysis: clade A (n = 10), clade B (n = 1), clade C (n = 3). A part of clonal relatedness was unexpected by the epidemiological information at the time of isolation of the strains. Most of the IMP-producing ECC strains were susceptible to non-b-lactam antibiotics and had relatively low minimum inhibitory concentrations to carbapenems (£4 mg/mL). Four of five infections caused by IMP-producing ECC were treated successfully.Conclusions: Whole-genome sequencing analysis revealed the outbreak was caused by three different clades of ST78 strains, where patients had favorable treatment outcome of the infections compared with that caused by Enterobacterales producing other carbapenemases, possibly due to their non-multidrug-resistant phenotype.
Network pharmacology based research into the effect and mechanism of Yinchenhao Decoction against Cholangiocarcinoma
Authors: Chen Zhiqiang , Lin Tong , Liao Xiaozhong , Li Zeyun , Lin Ruiting , Qi Xiangjun , Chen Guoming , Sun Lingling , Lin Lizhu 
Published: January 2021

Abstract
Background: Cholangiocarcinoma refers to an epithelial cell malignancy with poor prognosis. Yinchenhao decoction (YCHD) showed positive effects on cancers, and associations between YCHD and cholangiocarcinoma remain unclear. This study aimed to screen out the effective active components of Yinchenhao decoction (YCHD) using network pharmacology, estimate their potential targets, screen out the pathways, as well as delve into the potential mechanisms on treating cholangiocarcinoma. Methods: By the traditional Chinese medicine system pharmacology database and analysis platform (TCMSP) as well as literature review, the major active components and their corresponding targets were estimated and screened out. Using the software Cytoscape 3.6.0, a visual network was established using the active components of YCHD and the targets of cholangiocarcinoma. Based on STRING online database, the protein interaction network of vital targets was built and analyzed. With the Database for Annotation, Visualization, and Integrated Discovery (DAVID) server, the gene ontology (GO) biological processes and the Kyoto encyclopedia of genes and genomes (KEGG) signaling pathways of the targets enrichment were performed. The AutoDock Vina was used to perform molecular docking and calculate the binding affinity. The PyMOL software was utilized to visualize the docking results of active compounds and protein targets. In vivo experiment, the IC50 values and apoptosis rate in PI-A cells were detected using CCK-8 kit and Cell Cycle Detection Kit. The predicted targets were verified by the real-time PCR and western blot methods. Results: 32 effective active components with anti-tumor effects of YCHD were sifted in total, covering 209 targets, 96 of which were associated with cancer. Quercetin, kaempferol, beta-sitosterol, isorhamnetin, and stigmasterol were identified as the vital active compounds, and AKT1, IL6, MAPK1, TP53 as well as VEGFA were considered as the major targets. The molecular docking revealed that these active compounds and targets showed good binding interactions. These 96 putative targets exerted therapeutic effects on cancer by regulating signaling pathways (e.g., hepatitis B, the MAPK signaling pathway, the PI3K-Akt signaling pathway, and MicroRNAs in cancer). Our in vivo experimental results confirmed that YCHD showed therapeutic effects on cholangiocarcinoma by decreasing IC50 values, down-regulating apoptosis rate of cholangiocarcinoma cells, and lowering protein expressions. Conclusion:As predicted by network pharmacology strategy and validated by the experimental results, YCHD exerts anti-tumor effectsthrough multiple components, targets, and pathways, thereby providing novel ideas and clues for the development of preparations and the treatment of cholangiocarcinoma.
Development of Space Environment Customized Risk Estimation for Satellites (SECURES)
Authors: Nagatsuma Tsutomu , Nakamizo Aoi , Kubota Yasubumi , Nakamura Masao , Koga Kiyokazu , Miyoshi Yoshizumi , Matsumoto Haruhisa 
Published: January 2021

Abstract
Plasma variations in the geospace environment driven by solar wind–magnetosphere interactions are one of the major causes of satellite anomaly. To mitigate the effect of satellite anomaly, the risk of space weather disturbances predicted by space weather forecasting needs to be known in advance. However, the risk of satellite anomaly owing to space weather disturbances is not the same for all satellites, because the risk depends not only on the space environment itself but also on the design and materials of individual satellites. From the viewpoint of satellite operators, it is difficult to apply a general alert level of the space environment to the risk of individual satellites. To provide tailored space weather information, we have developed SECURES (Space Environment Customized Risk Estimation for Satellites) by combining models of the space environment and those of spacecraft charging. In SECURES, we focus on the risk of spacecraft charging (surface/internal) for geosynchronous satellites. For the risk estimation of surface charging, we have combined the global magnetosphere magnetohydrodynamics (MHD) model with the satellite surface charging models. For the risk estimation of internal charging, we have combined the radiation belt models with the satellite internal charging models. We have developed prototype products for both types of charging/electrostatic discharge (ESD). The development of SECURES and our achievements are introduced in this paper.
The Analysis of Fertility Quality of Life and the Influencing Factors of Patients with Repeated Implantation Failure
Authors: Ni Ying , Tong Chenye , Huang Limin , Zhou Wenjie , Zhang Aijun 
Published: January 2021

Abstract
Background: The objective of this study was to investigate the current status of fertility quality of life (QoL) and explore the influencing factors for infertile women with repeated implantation failure (RIF).Methods: The sample consisted of 137 infertile women with RIF who were under treatment from January 2019 to December 2019 in the Reproductive Medical Center of Ruijin Hospital, affiliated with Shanghai Jiaotong University School of Medicine in China. A general information questionnaire, FertiQoL scale, perceived social support scale (PSSS), self-rating anxiety scale (SAS), and self-rating depression scale (SDS) were used to analyse the fertility QoL and related factors of RIF patients.Results: The total fertility QoL score of RIF patients was 60.44 ± 11.60. The results of multivariate regression analysis showed that residence, financial difficulties, male infertility, BMI index, depression, and family social support were the main factors that influenced the fertility QoL of RIF patients (adjusted R2 = 0.762).Conclusion: Based on the results of this study, RIF patients’ psychological status must be addressed. Corresponding interventions such as building a sound family and social support system, creating a good medical environment and offering diverse health education should be provided to improve the fertility QoL of RIF patients.
Clinicopathological features and risk factors analysis of lymph node metastasis and long-term prognosis in patients with synchronous multiple gastric cancer
Authors: Chen Liang , Yue Chao , Li Gang , Ming Xuezhi , Gu Rongmin , Wen Xu , Zhou Bin , Peng Rui , Wei Wei , Chen Huanqiu 
Published: January 2021

Abstract
Background As a common malignancy, gastric cancer (GC) remains an important threat to human’s health. The incidence of synchronous multiple gastric cancer (SMGC) has increased obviously with technical advances of endoscopic and pathological examinations. Several studies have investigated the relationship between SMGC and solitary gastric cancer (SGC). However, little is known about the relationship between early and advanced SMGCs, and the independent risk factors of lymph node metastasis and prognosis in SMGC patients remain unclear.Methods We retrospectively collected 57 patients diagnosed as SMGC and underwent radical gastrectomies from December 2011 to September 2019. Epidemiological data and clinicopathological characteristics of all patients were recorded. Postoperative follow-up was performed by telephone or outpatient service. Chi-square test or Fisher’s exact test was adopted in analysis of categorical data. Continuous data were analyzed by using unpaired t-test. Univariate and multivariate analyses were performed to investigate the independent risk factors of lymph node metastasis and tumor recurrence of SMGC.Results There were 45 males and 12 females. The average age was 62.1-year-old. There were 20 patients with early SMGC and 37 patients with advanced SMGC. Most of patients (91.2%) had two malignant lesions. Tumor recurrence occurred in 8 patients, among which 7 patients died from recurrence. The rates of total gastrectomy, tumor size ≥2 cm, poorly-differentiated type, lymph node metastasis, ulcer and nerve invasion and preoperative CEA level were significantly higher in advanced SMGC patients compared to those with early SMGC. Lymphovascular cancer plug and preoperative CA125 were the independent risk factors of lymph node metastasis in patients with SMGC. Lymph node metastasis, nerve invasion and preoperative AFP might be the risk factors of tumor recurrence of SMGC, but need further validation.Conclusions In patients with SMGC, the presence of tumor size ≥2 cm, poorly-differentiated type, lymph node metastasis, ulcer, nerve invasion and relatively high preoperative CEA level might indicate the advanced SMGC. More attention should be paid to lymph node metastasis in SMGC patients with lymphovascular cancer plug and high preoperative CA125. Lymph node metastasis, nerve invasion and preoperative AFP might be associated with recurrence of SMGC, needing further validation.
A Bifunctional Cytochrome P450 Enzyme Involved in the O-Dealkylation and N-Dealkoxymethylation toward Chloroacetanilide Herbicides in Rhodococcus sp. B2
Authors: liu hongming , Yuan Meng , Liu Aimin , Zhu Guo-ping , Sun Li-na 
Published: January 2021

Abstract
Background: The chloroacetamide herbicides pretilachlor is an emerging pollutant. Due to the large amount of use, its presence in the environment threatens human health. However, the molecular mechanism of pretilachlor degradation remains unknown. Results: Now, Rhodococcus sp. B2 was isolated from rice field and shown to degrade pretilachlor. The maximum pretilachlor degradation efficiency (86.1%) was observed at a culture time of 5 d, an initial substrate concentration 50 mg/L, pH 6.98, and 30.1°C. One novel metabolite N-hydroxyethyl-2-chloro-N-(2, 6-diethyl-phenyl)-acetamide was identified by gas chromatography-mass spectrometry (GC-MS). Draft genome comparison demonstrated that a 32,147-bp DNA fragment, harboring gene cluster (EthRABCDB2), was absent from the mutant strain TB2 which could not degrade pretilachlor. The Eth gene cluster, encodes an AraC/XylS family transcriptional regulator (EthRB2), a ferredoxin reductase (EthAB2), a cytochrome P450 monooxygenase (EthBB2), a ferredoxin (EthCB2) and a 10-kDa protein of unknown function (EthDB2). Complementation with EthABCDB2 and EthABDB2, but not EthABCB2 in strain TB2 restored its ability to degrade chloroacetamide herbicides. Subsequently, codon optimization of EthABCDB2 was performed, after which the optimized components were separately expressed in Escherichia coli, and purified using Ni-affinity chromatography. A mixture of EthABCDB2 or EthABDB2 but not EthABCB2 catalyzed the N-dealkoxymethylation of alachlor, acetochlor, butachlor, and propisochlor and O-dealkylation of pretilachlor, revealing that EthD acted as a ferredoxin in strain B2. EthABDB2 displayed maximal activity at 30 °C and pH 7.5. Conclusions: This is the first report of a P450 family oxygenase catalyzing the O-dealkylation and N-dealkoxymethylation of pretilachlor and propisochlor, respectively. And the results of the present study provide a microbial resource for the remediation of chloroacetamide herbicides-contaminated sites.