bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative transcriptomics of stem bark reveals genes associated with bast fiber development in Boehmeria nivea L. Gaud (ramie)
Authors: Xie Jiyong , Li Jiaqi , Jie Yucheng , Xie Deyu , Yang Di , Shi Huazhong , Zhong Yingli 
Published: January 2020

Abstract
Background: Boehmeria nivea L. Gaud (Ramie) produces one of the longest natural fibers in nature. The bark of ramie mainly comprises of the phloem tissue of stem and is the raw material for fiber. Therefore, identifying the molecular regulation of phloem development is important for understanding of bast fiber biosynthesis and improvement of fiber quality in ramie.Results: In this study, we collected top bud (TB), bark from internode elongating region (ER) and bark from internode fully elongated region (FER) from the ramie variety Zhongzhu No. 1. Histological study indicated that these samples contain phloem tissues at different developmental and maturation stages, with a higher degree of maturation of phloem tissue in FER. RNA sequencing (RNA-seq) was performed and de novo transcriptome was assembled. Unigenes and differentially expressed genes (DEGs) in these three samples were identified. The analysis of DEGs by using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed clear differences in gene expression between ER and FER. Some unigenes involved in secondary cell wall biosynthesis were up-regulated in both ER and FER, while unigenes for some cell wall components or cell wall modifications showed differential expression between ER and FER. In addition, the ethylene respond factors (ERFs) in the ethylene signaling pathway were up-regulated in FER, and ent-kaurenoic acid oxidase (KAO) and GA 20-oxidase (GA20ox) for gibberellins biosynthesis were up-regulated while GA 2-oxidase (GA2ox) for gibberellin inactivation was down-regulated in FER.Conclusions: Both morphological study and gene expression analysis supported a burst of phloem and vascular developmental processes during the fiber maturation in the ramie stem, and ethylene and gibberellin are likely to be involved in this process. Our findings provide novel insights into the phloem development and fiber maturation in ramie, which could be useful for fiber improvement in ramie and other fiber crops.
A multicenter randomized trial of personalized acupuncture, fixed acupuncture, letrozole and placebo on live birth for infertility in women with polycystic ovary syndrome
Authors: Huang Shiya , Hu Min , Ng Ernest Hung Yu , Stener-Victorin Elisabet , Zheng Yanhua , Wen Qidan , Wang Cong , Lai Maohua , Li Juan , Gao Xingcheng , Wang Xinhua , Hu Zhenxing , Xia Tian , Hu Rongkui , Liu Jianping , Wen Xiaohui , Li Shuna , Quan Kewei , Liang Xingyan , Shang Hongcai , Ma Hongxia , Qiao Jie 
Published: January 2020

Abstract
BACKGROUND traditional Chinese Medicine (TCM) usually involves syndrome and disease differentiation, and for acupuncture selection of appropriate points and skillful needling techniques. Many clinical trials on acupuncture used fixed acupuncture protocols without accounting for individual differences. We here design a multicenter randomized controlled trial (RCT) to evaluate whether personalized or fixed acupuncture increases the likelihood of live births for infertility in women with polycystic ovary syndrome (PCOS) compared with letrozole or placebo letrozole. We hypothesis that letrozole is more effective than personalized acupuncture, and personalized acupuncture is more effective than fixed acupuncture, which is more effective than placebo letrozole. Moreover, personalized acupuncture is more likely to reduce miscarriage rate and the risk of pregnancy complications than letrozole.METHODS / DESIGN The study is a randomized assessor-blind controlled trial. A total of 1,100 infertile women with PCOS will be recruited from 28 hospitals and randomly allocated into four groups: A) personalized acupuncture, B) fixed acupuncture, C) letrozole, or D) placebo letrozole. They will receive treatment for 16 weeks and the primary outcome is live birth. Secondary outcomes include ovulation rate, conception rate, pregnancy rate, pregnancy loss rate, changes in hormonal and metabolic parameters, and changes in quality-of-life scores. The adverse events (AEs) will be recorded throughout the trial. All statistical analyses will be performed using the SPSS program V.21.0 (SPSS, Chicago, Illinois, USA) and a p value <0.05 will be considered statistically significant.DISCUSSION This study is the first multicentre RCT to compare personalized or fixed acupuncture, letrozole or placebo letrozole on live birth for infertility in women with PCOS. The findings will inform whether personalized acupuncture therapy could be as an alternative treatment method on live birth for infertile women with PCOS.
Bacillus velezensis LG37: Transcriptome profiling and functional verification of GlnK and NmtA in ammonia (NH4+) assimilation
Authors: Liu Guangxin , V Sarath Babu , Dong Yanjun , Li Xinfeng , A Binda Tembeng , Zhao Lijuan , Tu Jiagang , He Jin , lin li 
Published: January 2020

Abstract
Background
In recent years, interest in Bacillus velezensis has increased significantly due to its role in many industrial water bioremediation processes, including probiotics. In this study, we isolated and assessed the transcriptome of Bacillus velezensis LG37 (isolated from aquaculture pond) under different nitrogen sources. Since Bacillus species exhibit heterogeneity, it is worth to investigate the molecular information of LG37 through ammonia nitrogen assimilation, where ammonia’s nitrogen is considered toxic to aquatics.
Results
Here, a total of 812 differentially expressed genes (DEGs) from the transcriptomic sequencing of LG37 grown minimal medium supplemented with ammonia (treatment) or glutamine (control) were obtained, from which 56 had Fold Change ≥ 2. BLAST NCBI and UniProt databases revealed 27 out of the 56 DEGs were potentially involved in NH 4 + assimilation. Among them, 8 DEGs together with the two-component regulatory system glnK/glnL were randomly selected for validation by quantitative real-time RT-PCR, and the relative expression level showed that glnK/glnL were significantly upregulated that were consistent with the RNA-seq data coupled with six other genes. Moreover, the transcriptome and relative expression analysis showed that the transporter ( amtB ) gene of LG37 was not involved in ammonia transport even in the highest ammonia concentrations. Besides, CRISPR-Cas9 knockout and overexpression LG37 mutants of glnK further evidenced the exclusion of amtB regulation, suggesting involvement of alternative transporter. Additionally, in the transcriptomic data, a novel ammonium transporter nmtA was expressed significantly in increased ammonia concentrations. Subsequently, OE nmtA and Δ nmtA LG37 strains showed a unique expression pattern compared to that of wild-LG37 strain.
Conclusion
Based on the transcriptome data, regulation of nitrogen related genes were promptly screened from the newly isolated LG37 strain to analyse the key regulating factors during ammonia assimilation. The novel NmtA transporter of LG37 became apparent in ammonia transport instead of AmtB, which transport ammonium nitrogen in other Bacillus strains, using the genomic editing tools. Collectively, this study defines the heterogeneity of B. velezensis LG37 all alone through comprehensive transcriptome analysis subsequently by genome editing techniques, sheds light on the enigmatic mechanisms under different nitrogen sources also reveal the need for further research.
Comparative genomics analysis of c-di-GMP metabolism and regulation in Microcystis aeruginosa
Authors: Chen Meng , Xu Chun-Yang , Wang Xu , Ren Chong-Yang , Ding Jiao , Li Li 
Published: January 2020

Abstract
Background: Cyanobacteria are of special concern because they proliferate in eutrophic water bodies worldwide and affect water quality. As an ancient photosynthetic microorganism, cyanobacteria can survive in ecologically diverse habitats because of their capacity to rapidly respond to environmental changes through a web of complex signaling networks, including using second messengers to regulate physiology or metabolism. A ubiquitous second messenger, bis-(3′,5′)-cyclic-dimeric-guanosine monophosphate (c-di-GMP), has been found to regulate essential behaviors in a few cyanobacteria but not Microcystis, which are the most dominant species in cyanobacterial blooms. In this study, comparative genomics analysis was performed to explore the genomic basis of c-di-GMP signaling in Microcystis aeruginosa.
Results: Proteins involved in c-di-GMP metabolism and regulation, such as diguanylate cyclases, phosphodiesterases, and PilZ-containing proteins, were encoded in M. aeruginosa genomes. However, the number of identified protein domains involved in c-di-GMP signaling was not proportional to the size of M. aeruginosa genomes (4.99 Mb in average). Pan-genome analysis showed that genes involved in c-di-GMP metabolism and regulation are conservative in M. aeruginosa strains. Phylogenetic analysis showed good overall congruence between the three types of phylogenetic trees based on 31 highly conserved protein-coding genes, sensor domain-coding genes, and pan-genome matrix. Propensity for gene loss analysis revealed that most of genes involved in c-di-GMP signaling are stable in M. aeruginosa strains. Moreover, bioinformatics and structure analysis of c-di-GMP signal-related GGDEF and EAL domains revealed that they all possess essential conserved amino acid residues that bind the substrate. In addition, it was also found that all selected M. aeruginosa genomes encode PilZ domain containing proteins.
Conclusions: Comparative genomics analysis of c-di-GMP metabolism and regulation in M. aeruginosa strains helped elucidating the genetic basis of c-di-GMP signaling pathways in M. aeruginosa. Knowledge of c-di-GMP metabolism and relevant signal regulatory processes in cyanobacteria can enhance our understanding of their adaptability to various environments and bloom-forming mechanism.
Keywords: Microcystis aeruginosa, Comparative genomics, c-di-GMP, Phylogenetic analysis, GGDEF, EAL, HD-GYP, PilZ
Transcriptome-wide map of m6A circRNAs identified in a rat model of hypoxia mediated pulmonary hypertension
Authors: Su Hua , Wang Guowen , Wu Lingfang , Ma Xiuqing , Ying Kejing , Zhang Ruifeng 
Published: January 2020

Abstract
Background: Hypoxia mediated pulmonary hypertension (HPH) is a lethal disease and lacks effective therapy. CircRNAs play significant roles in physiological process. Recently, circRNAs are found to be m 6 A-modified. The abundance of circRNAs was influenced by m 6 A. Furthermore, the significance of m 6 A circRNAs has not been elucidated in HPH yet. Here we aim to investigate the transcriptome-wide map of m 6 A circRNAs in HPH.
Results: Differentially expressed m 6 A abundance was detected in lungs of HPH rats. M 6 A abundance in circRNAs was significantly reduced in hypoxia in vitro . M 6 A circRNAs were mainly from protein-coding genes spanned single exons in control and HPH groups. Moreover, m 6 A influenced the circRNA–miRNA–mRNA co-expression network in hypoxia. M 6 A circXpo6 and m 6 A circTmtc3 were firstly identified to be downregulated in HPH.
Conclusion: Our study firstly identified the transcriptome-wide map of m 6 A circRNAs in HPH. M 6 A can influence circRNA–miRNA–mRNA network. Furthermore, we firstly identified two HPH-associated m 6 A circRNAs: circXpo6 and circTmtc3. However, the clinical significance of m 6 A circRNAs for HPH should be further validated.
Key words: m 6 A circRNAs; hypoxia mediated pulmonary hypertension; m 6 A circXpo6; m 6 A circTmtc3
Genome-wide identification and expression profiling of SET DOMAIN GROUP family in Dendrobium catenatum
Authors: Chen Dong-Hong , Qiu Han-Lin , Huang Yong , Zhang Lei , Si Jin-Ping 
Published: January 2020

Abstract
Background: Dendrobium catenatum used as a precious Chinese herbal medicine is a kind of epiphytic orchid plant which grows on the trunks and cliffs and often faces up to diverse environmental stresses. SET DOMAIN GROUP (SDG) proteins act as histone lysine methyltransferases which are involved in pleiotropic developmental events and stress responses through modifying chromatin structure and regulating gene transcription, but their roles in D. catenatum are unknown.
Results: In this study, we identified 44 SDG proteins from D. catenatum genome. Subsequently, comprehensive analyses related to gene structure, protein domain organization, and phylogenetic relationship were performed to evaluate these D. catenatum SDG (DcSDG) proteins, along with the well-investigated homologs from the model plants Arabidopsis thaliana and Oryza sativa as well as the newly characterized 42 SDG proteins from a closely related orchid plant Phalaenopsis equestris . We showed DcSDG proteins can be grouped into eight distinct classes (I~VII and M), mostly consistent with the previous description. Based on the catalytic substrates of the reported SDG members mainly in Arabidopsis, Class I (E(z)-Like) is predicted to account for the deposition of H3K27me2/3, Class II (Ash-like) for H3K36me, Class III (Trx/ATX-like) for H3K4me2/3, Class M (ATXR3/7) for H3K4me, Class IV (Su(var)-like) for H3K27me1, Class V (Suv-like) for H3K9me, as well as class VI (S-ET) and class VII (RBCMT) for methylation of both histone and non-histone proteins. RNA-seq derived expression profiling showed that DcSDG proteins usually have wide but distinguished expression in different tissues and organs. Finally, environmental stresses examination showed the expression of DcASHR3, DcSUVR3, DcATXR4, DcATXR5b, and DcSDG49 is closely associated with drought-recovery treatment, the expression of DcSUVH5a , DcATXR5a and DcSUVR14a is significantly influenced by low temperature, and even 61% DcSDG genes are in response to heat shock.
Conclusions: This study systematically identifies and classifies SDG genes in orchid plant D. catenatum , indicates their functional divergence during the evolution, and discovers their broad roles in the developmental programs and stress responses. These results provide constructive clues for further functional investigation and epigenetic mechanism dissection of SET-containing proteins in orchid.
Integrated Care Search: Development and validation of a PubMed search filter for retrieving the integrated care research evidence
Authors: Damarell Raechel A. , Lewis Suzanne , Trenerry Camilla , Tieman Jennifer J. 
Published: January 2020

Abstract
Background Integrated care is an increasingly important principle for organising healthcare. Integrated care models show promise in reducing resource wastage and service fragmentation whilst improving the accessibility, patient-centredness and quality of care for patients. Those needing reliable access to the growing research evidence base for integrated care can be frustrated by search challenges reflective of the topic's complexity. The aim of this study is to report the empirical development and validation of two search filters for rapid and effective retrieval of integrated care evidence in PubMed. One filter is optimised for recall and the other for precision.Methods An Expert Advisory Group comprising international integrated care experts guided the study. A gold standard test set of citations was formed from screening Handbook Integrated Care chapter references for relevance. This set was divided into a Term Identification Set (20%) for determining candidate terms using frequency analysis; a Filter Development Set (40%) for testing performance of term combinations; and a Filter Validation Set (40%) reserved for confirming final filter performance. In developing the high recall filter, recall was steadily increased while maintaining precision at ≥ 50%. Similarly, the high precision filter sought to maximise precision while keeping recall ≥ 50%. For each term combination tested, an approximation of precision was obtained by reviewing the first 100 citations retrieved in Medline for relevance.Results The gold standard set comprised 534 citations. The search filter optimised for recall ('Broad Integrated Care Search') achieved 86.0%-88.3% recall with corresponding low precision (47%-53%). The search filter optimised for precise searching ('Narrow Integrated Care Search') demonstrated precision of 73%-95% with recall reduced to between 55.9% and 59.8%. These filters are now available as one-click URL hyperlinks in the website of International Foundation for Integrated Care.Conclusions The Broad and Narrow Integrated Care Search filters provide potential users, such as policy makers and researchers, seamless, reliable and ongoing access to integrated care evidence for decision making. These filters were developed according to a rigorous and transparent methodology designed to circumvent the challenges of information retrieval posed by this complex, multifaceted topic.
HIV/AIDS treatment failure and associated factors in Ethiopia: Meta-analysis
Authors: Endalamaw Aklilu , Mekonnen Mengistu , Geremw Demeke , Ambaw Fekadu , Tesera Hiwot , Habtewold Tesfa Dejenie 
Published: January 2020

Abstract
Background: The national burden of human immunodeficiency virus treatment failure and associated factors in the Ethiopian context is required to provide evidence towards a renewed ambitious future goal.
Methods: We accessed Ethiopian Universities’ online repository library, Google Scholar, PubMed, Web of Science, and Scopus to get the research articles. We run I-squared statistics to see heterogeneity. Publication bias was checked by using Egger’s regression test. The pooled prevalence was estimated using the DerSimonian-Laird random-effects model. We employed the sensitivity analysis to see the presence of outlier result in the included studies.
Results: The overall human immunodeficiency treatment failure was 15.9% (95% confidence interval: 11.6%-20.1%). Using immunological, virological, and clinical definition, human immunodeficiency treatment failure was 10.2% (95% confidence interval: 6.9%-13.6%), 5.6% (95% confidence interval: 2.9%-8.3%), and 6.3% (95% confidence interval: 4.6%-8.0%), respectively. The pooled effects of World Health Organization clinical stage III/IV (Adjusted Odd Ratio=1.9; 95% CI: 1.3-2.6), presence of opportunistic infections (Adjusted Odd Ratio= 1.8; 95% CI: 1.2-2.4), and poor adherence to highly active antiretroviral therapy (Adjusted Odd Ratio= 8.1; 95% CI: 4.3-11.8) on HIV treatment failure were estimated.
Conclusions: Human immunodeficiency virus treatment failure in Ethiopia found to be high. Being on advanced clinical stage, presence of opportunistic infections, and poor adherence to highly active antiretroviral therapy were the contributing factors of human immunodeficiency virus treatment failure. Human immunodeficiency virus intervention programs need to address the specified contributing factors of human immunodeficiency virus treatment failure. Behavioral intervention to prevent treatment interruption is required to sustain human immunodeficiency virus treatment adherence.
Protocol Registration: It has been registered in the PROSPERO database with a registration number of CRD42018100254.
SERT and BDNF polymorphisms interplay on neuroticism in borderline personality disorder
Authors: Salinas Valeria , Villarroel Juana , Silva Hernán , Herrera Luisa , Jerez Sonia , Zazueta Alejandra , Montes Cristian , Nieto Rodrigo , Bustamante M. Leonor 
Published: January 2020

Abstract
Objective Genetic factors underlying different personality traits are not entirely understood, particularly how genes interact to modulate their effect. We studied 76 patients diagnosed with borderline personality disorder (BPD), characterized by extreme levels of personality traits, especially neuroticism (N), in which we genotyped two polymorphisms, the 5HTTLPR of the Serotonin transporter (SERT) gene, and the Val66Met of the Brain-derived neurotrophic factor (BDNF) gene.Results We found an association with SERT, where S-allele carriers had significantly higher levels of N than L-homozygous. Furthermore, we found that the protective effect of L-homozygosity is only evident on A-allele carriers of the BDNF Val66Met polymorphism. Genetic constitution in SERT and BDNF seems to be important in neuroticism, the most relevant personality trait on BPD.
Reference values of fat mass index and fat-free mass index in healthy Spanish adolescents.
Authors: Durá-Travé Teodoro , Gallinas-Victoriano Fidel , Chueca-Guindulain María , Berrade-Zubiri Sara , Malumbres-Chacón María , Moreno-González Paula 
Published: January 2020

Abstract
Background . Body mass index (BMI) does not allow to discriminate the composition of the different body compartments. The aim of this study is to elaborate reference values ​of the fat mass index (FMI) and fat-free mass index (FFMI) in healthy adolescents using anthropometric techniques in order to be available as reference standards in daily clinical practice.
Whole genome characterization of autochthonous Bos taurus brachyceros and introduced Bos indicus indicus cattle breeds in Cameroon regarding their adaptive phenotypic traits and pathogen resistance
Authors: paguem Archile Eric , Abanda Babette , Achukwi Mbunkah Daniel , Baskaran Praveen , Czemmel Stefan , Renz Alfons , Eisenbarth Albert 
Published: January 2020

AbstractBackgroundWest African indigenous taurine cattle display unique adaptive traits shaped by husbandry management, regional climate and exposure to endemic pathogens. They are less productive with respect to milk and meat production which has been associated with a number of factors, amongst others small size, traditional beliefs and husbandry practices. This resulted in the severe dwindling of their populations size rendering them vulnerable to extinction. The Namchi (Doayo) taurine cattle breed has documented resistance traits against trypanosome infection and exposure to tick infestation. Nonetheless, the historically later introduced Zebu cattle are the main cattle breeds in Africa today, even though they suffer more from locally prevailing pathogens. By using a reference-based whole genome sequencing approach, we sequenced for the first time the genomes of five cattle breeds from Cameroon: the Namchi (Doayo), an endangered trypanotolerant taurine breed, the Kapsiki, an indigenous trypanosusceptible taurine breed, and three Zebu (Bos indicus indicus) breeds: Ngaoundere Gudali, White Fulani and Red Fulani.ResultsApproximately 167 Giga bases of raw sequencing data were generated and mapped to the cattle reference genome UMD3.1. The coverage was 22 to 30-fold. The single nucleotide polymorphisms (SNPs) were compared with reference genomes of EuropeanBos taurusHolstein and of AsianBos indicusBrahman and the African trypanotolerant N’Dama breeds.Of a total of 50 million SNPs identified, 3.43 million were breed-specific ranging from 0.37 to 0.47 million SNPs in the domestic Cameroonian breeds and approximately 0.58 million constituted of small insertions and deletions. We identified breed specific-non-synonymous variants as genetic traits that could explain certain cattle-breed specific phenotypes such as increased tolerance against trypanosome parasites in the Namchi (Doayo) breed, heat tolerance in the Kapsiki breed, and growth, metabolism and meat quality in the Gudali breeds. Phylogenetic comparison grouped Namchi (Doayo) to the African Zebu clade indicating a hybrid status of the selected animal with a Zebu breed, albeit it showed the Namchi breed’s phenotype.ConclusionsThe findings provide the first comprehensive set of full genome variant data of the most important Cameroonian cattle breeds. The genomic data shall constitute a foundation for breed amelioration whilst exploiting the heritable traits and support conservation efforts for the endangered local cattle breeds.