bluuebunny/crossref_metadata_2025_split huggingface dataset:
A transcriptomic profile of topping responsive non-coding RNAs in tobacco roots (Nicotiana tabacum)
Authors: Chen Xi , Sun Shuo , Liu Fangjie , Shen Enhui , Liu Lu , Ye Chuyu , Xiao Bingguang , Timko Michael P. , Zhu Qian-Hao , Fan Longjiang , Cao Peijian 
Published: November 2019

AbstractBackgroundNon-coding RNAs (ncRNAs), including microRNAs (miRNAs), long ncRNAs (lncRNAs) and circular RNAs (circRNAs), accomplish remarkable variety of biological functions. However, the composition of ncRNAs and their interactions with coding RNAs in modulating and controlling of cellular process in plants is largely unknown. Using a diverse group of high-throughput sequencing strategies, the mRNA, miRNA, lncRNA and circRNA compositions of tobacco (Nicotiana tabacum) roots determined and their alteration and potential biological functions in response to topping treatment analyzed.ResultsA total of 688 miRNAs, 7423 non-redundant lncRNAs and 12,414 circRNAs were identified, among which, some selected differentially expressed RNAs were verified by quantitative real-time PCR. Using the differentially expressed RNAs, a co-expression network was established that included all four types of RNAs. The number of circRNAs identified were higher than that of miRNAs and lncRNAs, but only two circRNAs were present in the co-expression network. LncRNAs appear to be the most active ncRNAs based on their numbers presented in the co-expression network, but none of them seems to be an eTM (endogenous Target Mimicry) of miRNAs. Integrated with analyses of sequence interaction, several mRNA-circRNA-miRNA interaction networks with a potential role in the regulation of nicotine biosynthesis were uncovered, including a QS-circQS-miR6024 interaction network. In this network miR6024 was significantly down-regulated, while the expression levels of its two targets, circQS and its host geneQS, were sharply increased following the topping treatment.ConclusionsThese results illustrated the transcriptomic profiles of tobacco roots, the organ responsible for nicotine biosynthesis. mRNAs always play the most important roles, while ncRNAs are also expressed extensively for topping treatment response, especially circRNAs are the most activated in the ncRNA pool. These studies also provided insights on the coordinated regulation module of coding and non-coding RNAs in a single plant biological sample. The findings reported here indicate that ncRNAs appear to form interaction complex for the regulation of stress response forming regulation networks with transcripts involved in nicotine biosynthesis in tobacco.
Transcriptomic analysis of α-synuclein knockdown after T3 spinal cord injury in rats
Authors: Zeng Hong , Yu Bao-fu , Liu Nan , Yang Yan-yan , Xing Hua-yi , Liu Xiao-xie , Zhou Mou-wang 
Published: November 2019

Abstract
Background
Endogenous α-synuclein (α-Syn) is involved in many pathophysiological processes in the secondary injury stage after acute spinal cord injury (SCI), and the mechanism governing these functions has not been thoroughly elucidated to date. This research aims to characterize the effect of α-Syn knockdown on transcriptional levels after SCI and to determine the mechanisms underlying α-Syn activity based on RNA-seq.

Result
The establishment of a rat model of lentiviral vector-mediated knockdown of α-Syn in Sprague-Dawley rats with T3 spinal cord contusion (LV_SCI group). The results of the RNA-seq analysis showed that there were 337 differentially expressed genes (DEGs) between the SCI group and the LV_SCI group, and 153 DEGs specific to LV_SCI between the (SCI vs LV_SCI) and (SCI vs CON) comparisons. The top 20 biological transition terms were identified by Gene ontology (GO) analysis. The Kyoto Gene and Genomic Encyclopedia (KEGG) analysis showed that the LV_SCI group significantly upregulated the cholinergic synaptic & nicotine addiction and the neuroactive ligand receptor interaction signaling pathway. Enriched chord analysis analyzes key genes. Further cluster analysis, gene and protein interaction network analysis and RT-qPCR results showed that Chrm2 and Chrnb2 together significantly in both pathways. The proliferation of muscarinic cholinergic receptor subtype 2 (Chrm2) and nicotinic cholinergic receptor subtype β2 (Chrnb2), and the neurogenesis were elevated in the injury site of LV_SCI group by immunofluorescence. Further by subcellular localization, the LV_SCI group enhanced the expression of Chrnb2 at the cell membrane.

Conclusion
Knockdown of α-Syn after SCI enhance motor function and promote neurogenesis probably through enhancing cholinergic signaling pathways and neuroreceptor interactions. This study not only further clarifies the understanding of the mechanism of knockdown of α-Syn on SCI but also helps to guide the treatment strategy for SCI.
Changes of intestinal bacterial microbiota in coronary heart disease complicated with nonalcoholic fatty liver disease
Authors: Zhang Yiwen , Xu Jun , Wang Xuemei , Ren Xinhua , Liu Yulan 
Published: November 2019

AbstractBackgroundPrevious study reported that patients who suffered coronary heart disease (CHD) complicated with non-alcoholic fatty liver disease (NAFLD) had worse cardiac function and clinical outcomes than patients with CHD only. Notably, the mechanism is still unclear. This study aimed to investigate the changes and roles of intestinal bacterial microbiota in CHD-NAFLD patients.Methods and resultsPeople were recruited and divided into three groups, including CHD patients (without NAFLD), CHD-NAFLD patients and healthy controls (HCs). Each group contained 24 people. Fecal samples and clinical information were carefully collected. The Illumina sequencing of 16S rRNA was applied to profile the overall structure of the fecal bacterial microbiota and the characteristics of the bacterial microbiota based on the Operational Taxonomic Units. In clinical information, the CHD-NAFLD patients showed an increase in BMI, uric acid and triglyceride. There was a significant reduction in the abundance ofParabacteroidesandCollinsellain overall CHD patients (including CHD-NAFLD and CHD patients). The intestinal bacterial microbiota in CHD-NAFLD patients showed an increase in the abundance ofCopococcusandVeillonella, and a reduction in the abundance ofParabacteroides,Bacteroides fragilis,Ruminococcus gnavus, Bacteroides dorei, andBifidobacterium longum subsp infantis. Among them, the abundance ofRuminococcus gnavusandBacteroides doreiwas significantly lower than that in CHD patients. Additionally, BMI positively correlated with the abundance ofCopococcusand negatively correlated with the abundance ofBifidobacterium longum subsp infantis. The abundance ofVeillonellapositively correlated with AST. The abundance ofBacteroides doreinegatively correlated with ALT and AST. It indicates that the abundance of intestinal microbiota was related to the changes in clinical indexes.ConclusionsChanges of intestinal bacterial microbiota in CHD-NAFLD patients may be important factors affecting the degree of metabolic disorder, which may be one of the important reasons for the worse clinical outcome and disease progression in CHD-NAFLD patients than in CHD patients.
Identification and evaluation of reference genes for quantitative real-time PCR analysis in Polygonum cuspidatum based on transcriptome data
Authors: Wang Xiaowei , Wu Zhijun , Bao Wenqi , Hu Hongyan , Chen Mo , Chai Tuanyao , Wang Hong 
Published: November 2019

Abstract
Background
Polygonum cuspidatum of the Polygonaceae family is a traditional medicinal plant with many bioactive compounds that play important roles in human health and stress responses. Research has attempted to identify biosynthesis genes and metabolic pathways in this species, and quantitative real-time PCR (RT-qPCR) has commonly been used to detect gene expression because of its speed, sensitivity, and specificity. However, no P. cuspidatum reference genes have been identified, which hinders gene expression studies. Here, we aimed to identify suitable reference genes for accurate and reliable normalization of P. cuspidatum RT-qPCR data.

Results
Twelve candidate reference genes, including nine common (ACT, TUA, TUB, GAPDH, EF-1γ, UBQ, UBC, 60SrRNA, and eIF6A) and three novel (SKD1, YLS8, and NDUFA13), were analyzed in different tissues (root, stem, and leaf) without treatment and in leaves under abiotic stresses (salt, ultraviolet [UV], cold, heat, and drought) and hormone stimuli (abscisic acid [ABA], ethylene [ETH], gibberellin [GA3], methyl jasmonate [MeJA], and salicylic acid [SA]). Expression stability in 65 samples was calculated using the △CT method, geNorm, NormFinder, BestKeeper, and RefFinder. Two reference genes (NDUFA13 and EF-1γ) were sufficient to normalize gene expression across all sample sets. They were also the two most stable genes for abiotic stresses and different tissues, whereas NDUFA13 and SKD1 were the top two choices for hormone stimuli. Considering individual experimental sets, GAPDH was the top-ranked gene under ABA, ETH, and GA3 treatments, while 60SrRNA showed good stability under MeJA and cold treatments. ACT, UBC, and TUB were suitable genes for drought, UV, and ABA treatments, respectively. TUA was not suitable because of its considerable variation in expression under different conditions. The expression patterns of PcPAL, PcSTS, and PcMYB4 under UV and SA treatments and in different tissues normalized by stable and unstable reference genes demonstrated the suitability of the optimal reference genes.

Conclusions
We propose NDUFA13 and EF-1γ as reference genes to normalize P. cuspidatum expression data. To our knowledge, this is the first systematic study of reference genes in P. cuspidatum which could help advance molecular biology research in P. cuspidatum and allied species.
Genome-wide identification and expression analysis of SWEET gene family in Litchi chinensis reveal the involvement of LcSWEET2a/3b in early seed development
Authors: Xie Hanhan , Wang Dan , Qin Yaqi , Ma Anna , Fu Jiaxin , Qin Yonghua , Hu Guibing , Zhao Jietang 
Published: November 2019

Abstract
Background
SWEETs (Sugar Will Eventually be Exported transporters) function as sugar efflux transporters that perform diverse physiological functions, including phloem loading, nectar secretion, seed filling, and pathogen nutrition. The SWEET gene family has been identified and characterized in a number of plant species, but little is known about in Litchi chinensis, which is an important evergreen fruit crop.

Results
In this study, 16 LcSWEET genes were identified and nominated according to its homologous genes in Arabidopsis and grapevine. Multiple sequence alignment showed that the 7 alpha-helical transmembrane domains (7-TMs) were basically conserved in LcSWEETs. The LcSWEETs were divided into four clades (Clade I to Clade IV) by phylogenetic tree analysis. A total of 8 predicted motifs were detected in the litchi LcSWEET genes. The 16 LcSWEET genes were unevenly distributed in 9 chromosomes and there was one pairs of segmental duplicated events by synteny analysis. The expression patterns of the 16 LcSWEET genes showed higher expression levels in reproductive organs. The temporal and spatial expression patterns of LcSWEET2a and LcSWEET3b indicated they play central roles during early seed development.

Conclusions
The litchi genome contained 16 SWEET genes, and most of the genes were expressed in different tissues. Gene expression suggested that LcSWEETs played important roles in the growth and development of litchi fruits. Genes that regulate early seed development were preliminarily identified. This work provides a comprehensive understanding of the SWEET gene family in litchi, laying a strong foundation for further functional studies of LcSWEET genes and improvement of litchi fruits.
To what extent is multi-morbidity associated with new onset depression in patients attending cardiac rehabilitation?
Authors: Sever Serdar , Doherty Patrick , Harrison Alexander Stephen , Golder Su 
Published: November 2019

Abstract
Background
Depression is associated with increased mortality and poor prognosis in patients with cardiovascular disease (CVD). However, little is known about the patient characteristics associated with new onset post heart event depressive symptoms, specifically medical comorbidities, among cardiac rehabilitation (CR) participants. Therefore, this paper examines the comorbidity profile and characteristics associated with new onset depressive symptoms in patients attending CR.

Methods
An observational study using the routine practice data of British Heart Foundation National Audit of Cardiac Rehabilitation (NACR) from the last six years between April 2012 and March 2018. Patients with new onset post heart event depression and no previous documented history of depression were selected as the study population. An independent samples t-test and chi square tests were used to compare the association between new onset depressive symptoms and patient variables including demographics, clinical measures and comorbidities. A binary logistic regression was conducted to investigate the predictors of new onset depressive symptoms employing log-likelihood ratio statistic.

Results
The analyses included 109,055 CR patients with new onset depression measured by Hospital Anxiety and Depression Scale (HADS). At baseline assessment, comorbidity measures associated with new onset depressive symptoms were increased total number of comorbidities and a range of comorbidities - including diabetes, angina, arthritis, chronic back problems, asthma, stroke, anxiety, rheumatism, claudication, osteoporosis, chronic bronchitis and emphysema. After multivariate adjustments were done, at the start of CR, the significant predictors of new onset depressive symptoms were physical inactivity, high HADS anxiety score measurement, increased weight, total number of comorbidities, diabetes, stroke, chronic back problems, being from areas with higher levels of social deprivation, being single, and male.

Conclusion
The research findings establish new insights into the association between patient demographic and clinical variables across a range of comorbidities in patients with new onset post heart event depressive symptoms. At the start of CR, patients with new onset depressive symptoms need to be assessed skilfully as they tend to have a complex multi-morbid presentation linked to psychosocial risk factors known to hinder CR engagement.
Methods for diagnosing bile acid malabsorption: a systematic review
Authors: Lyutakov Ivan , Ursini Francesco , Penchev Plamen , Caio Giacomo , Carroccio Antonio , Volta Umberto , De Giorgio Roberto 
Published: November 2019

Abstract
Background
Bile acid malabsorption (BAM) and bile acid-related diarrhea represent an under-recognized cause of chronic diarrhea mainly because of limited guidance on appropriate diagnostic and laboratory tests. We aimed to perform a systematic review of the literature in order to identify and compare the diagnostic accuracy of different diagnostic methods for patients with BAM, despite a proven gold standard test is still lacking.

Methods
A PubMed literature review and a manual search were carried out. Relevant full papers, evaluating the diagnostic accuracy of different methods for BAM, were assessed. Available data were analyzed to estimate the sensitivity and specificity of each published test.

Results
Overall, more than one test was considered in published papers on BAM. The search strategy retrieved 574 articles; of these, only 16 were full papers (with a total of 2.332 patients) included in the final review. Specifically, n = 8 studies used 75Selenium-homotaurocholic-acid-test (75SeHCAT) with a < 10% retention threshold; n = 8 studies evaluated fasting serum 7-α-hydroxy-4-cholesten-3-one (C4); n = 3 studies involved total fecal bile acid (BA) excretion over 48 h; n = 4 studies assessed fibroblast growth factor 19 (FGF19). 75SeHCAT showed an average sensitivity and specificity of 87.32 and 93.2%, respectively, followed by serum C4 (85.2 and 71.1%) and total fecal BA (66.6 and 79.3%). Fasting serum FGF19 had the lowest sensitivity and specificity (63.8 and 72.3%). All the extracted data were associated with substantial heterogeneity.

Conclusions
Our systematic review indicates that 75SeHCAT has the highest diagnostic accuracy for BAM, followed by serum C4 assay. The diagnostic yield of fecal BA and FGF19 assays is still under investigation. Our review reinforces the need for novel biomarkers aimed to an objective detection of BAM and therefore improving the management of this condition.
Assessment of prevalence and risk factors of helicobacter pylori infection in an oilfield Community in Hebei, China
Authors: Wang Wenhai , Jiang Wei , Zhu Shengtao , Sun Xiujing , Li Peng , Liu Kejia , Liu Henghui , Gu Junchao , Zhang Shutian 
Published: November 2019

Abstract
Background
Only a paucity of large-scale perspective and cross-sectional studies on H. pylori infection in China have been published. The purpose of this study was to investigate the prevalence and risk factors for H. pylori infection among residents of Jidong community located in Hebei Province of China.

Methods
A perspective, cross-sectional study was conducted in Jidong community. Questionnaires and 13C-urea breath test were performed, and 10-ml blood samples were obtained for laboratory tests.

Results
Four thousand seven hundred ninety-six subjects were enrolled in this study, and 2506 (52.25%) were H. pylori positive. There was no difference in prevalence between both sexes (P = 0.5974). Age (P = 0.004) and education level (P = 0.0128) were significantly associated with H. pylori infection, and there were statistical trends in the prevalence across five age subgroups (χ2 test for trend = 23.5; P < 0.001) and education levels (χ2 test for trend = 19.50; P < 0.001). H. pylori infection was also associated with marital status (P = 0.0243), source of drinking water (P = 0.0433), frequency of eating raw garlic (P = 0.0310), alcohol drinking (P = 0.0207), knowledge about H. pylori transmission route (P = 0.0125) and related diseases (P = 0.0257). Age, alcohol drinking and knowledge about transmission route were found to be independent predictors of H. pylori infection.

Conclusions
More than half of the population was infected with H. pylori in Jidong community. The socio-demographic profiles, socio-economic factors and lifestyle are worthy taking into consideration to prevent diseases associated with H. pylori infection. Understanding the prevalence and risk patterns for H. pylori infection in China will help in prioritizing public health efforts to better manage the H. pylori infection.
Genetic analysis of 62 Chinese families with Duchenne muscular dystrophy and strategies of prenatal diagnosis in a single center
Authors: Zhang Jingjing , Ma Dingyuan , Liu Gang , Wang Yuguo , Liu An , Li Li , Luo Chunyu , Hu Ping , Xu Zhengfeng 
Published: November 2019

Abstract
Background
Duchenne muscular dystrophy (DMD) is a severe X-linked recessive neuromuscular disorder. Patients with DMD usually have severe and fatal symptoms, including progressive irreversible muscle weakness and atrophy complicated with gastrocnemius muscle pseudohypertrophy. DMD is caused by mutations in the dystrophin-encoding DMD gene, including large rearrangements and point mutations. This retrospective study was aimed at supplying information on our 4-year clinical experience of DMD genetic and prenatal diagnosis at the Department of Prenatal Diagnosis in Women’s Hospital of Nanjing Medical University.

Methods
Multiplex ligation-dependent probe amplification (MLPA) was used to detect the exon deletions or duplications. And Ion AmpliSeq™ panel for inherited disease was used as the next-generation sequencing (NGS) method to identify the point mutations in exons of DMD gene, but the introns were not sequenced.

Results
In this study, the large deletions and duplications of DMD gene were detected in 32 (51.6%) of the 62 families, while point mutations were detected in 20 families (32.3%). The remaining 10 families with a negative genetic diagnosis need to be reevaluated for clinical symptoms or be detected by other molecular methods. Notably, six novel mutations were identified, including c.412A > T(p.Lys138*), c.2962delT(p.Ser988Leufs*16), c.6850dupA (p.Ser2284Lysfs*7), c.5139dupA (p.Glu 1714Argfs*5), c.6201_6203delGCCins CCCA(p.Val2069Cysfs*14) and c.10705A > T (p.Lys3569*). In 52 families with positive results, 45 mothers (86.5%) showed positive results during carrier testing and de novo mutations arose in 7 probands. The prenatal diagnosis was offered to 34 fetuses whether the pregnant mother was a carrier or not. As a result, eight male fetuses were affected, three female fetuses were carriers, and the remaining fetuses had no pathogenic mutation.

Conclusions
This study reported that MLPA and NGS could be used for screening the DMD gene mutations. Furthermore, the stepwise procedure of prenatal diagnosis of DMD gene was shown in our study, which is important for assessing the mutation type of fetuses and providing perinatal care in DMD high-risk families.
Delayed administration of suramin attenuates peritoneal fibrosis in rats
Authors: Xiong Chongxiang , Liu Na , Shao Xiaofei , Sharif Sairah , Zou Hequn , Zhuang Shougang 
Published: November 2019

AbstractBackgroundPeritoneal fibrosis is the most common complication of peritoneal dialysis, but there is currently no effective treatment. We previously reported that suramin pretreatment prevents the development of peritoneal fibrosis in a rat model of peritoneal fibrosis induced by chlorhexidine gluconate (CG). Here, we further examined the effectiveness of delayed administration of suramin on peritoneal fibrosis and the mechanism (s) involved in this process.MethodsIn the rat model of peritoneal fibrosis induced by CG, suramin or saline was administered at day 21 and 28. All rats were then sacrificed to collect peritoneal tissues for Western blot analysis and histological staining at day 35.ResultsOur results demonstrated that delayed administration of suramin starting at 21 days following CG injection can ameliorate peritoneal damage, with greater efficacy after two injections. Suramin also reduced the expression of α-smooth muscle actin, Collagen 1, and Fibronectin and suppressed phosphorylation of Smad-3, epidermal growth factor receptor (EGFR), signal transducers, activator of transcription 3 (STAT3) as well as extracellular signal-regulated kinases 1/2 (ERK 1/2) in the peritoneum injured with CG. Moreover, delayed administration of suramin inhibited overproduction of transforming growth factor-β1(TGF-β1) and expression of several pro-inflammatory cytokines, including monocyte chemoattractant protein-1, tumor necrosis factor-α, interleukin-1, and interleukin-6.ConclusionsOur results indicated that suramin can attenuate progression of peritoneal fibrosis by a mechanism involving inhibition of the TGF-β1/Smad3 and EGFR signaling pathways as well as suppression of multiple proinflammatory cytokines. Thus, suramin may have the potential to offer an effective treatment for peritoneal fibrosis.