bluuebunny/crossref_metadata_2025_split huggingface dataset:
Different forms of informal coercion in psychiatry – a qualitative study
Authors: Pelto-Piri Veikko , Kjellin Lars , Hylén Ulrika , Valenti Emanuele , Priebe Stefan 
Published: November 2019

Abstract
Objectives The objective of the study was to investigate how mental health professionals describe and reflect upon different forms of informal coercion. Results In a deductive qualitative content analysis of focus group interviews, several examples of persuasion, interpersonal leverage, inducements, and threats were found. Persuasion was sometimes described as being more like a negotiation. Some participants worried about that the use of interpersonal leverage and inducements risked to pass into blackmail in some situations. In a following inductive analysis, three more categories of informal coercion was found: cheating, using a disciplinary style and referring to rules and routines. Participants also described situations of coercion from other stakeholders: relatives and other authorities than psychiatry. The results indicate that informal coercion includes forms that are not obviously arranged in a hierarchy, and that its use is complex with a variety of pathways between different forms before treatment is accepted by the patient or compulsion is imposed.
Photosynthetic performance and photosynthesis-related gene expression coordinated in a shade-tolerant species Panax notoginseng under nitrogen regimes
Authors: Zhang Jin-Yan , Cun Zhu , Chen Jun-Wen 
Published: November 2019

Abstract
Nitrogen (N) is an essential component of photosynthetic apparatus. However, the mechanism that photosynthetic capacity is suppressed by N is not completely understood. Photosynthetic capacity and photosynthesis-related genes were comparatively analyzed in a shade-tolerant species Panax notoginseng grown under the levels of low N (LN), moderate N (MN) and high N (HN). Photosynthetic assimilation was significantly suppressed in the LN- and HN-grown plants. Compared with the MN-grown plants, the HN-grown plants showed thicker anatomic structure and larger chloroplast accompanied with decreased ratio of mesophyll conductance (gm ) to Rubisco content (gm /Rubisco) and lower Rubisco activity. Meanwhile, LN-grown plants displayed smaller chloroplast and accordingly lower internal conductance (gi ). LN- and HN-grown individuals allocated less N to light-harvesting system (NL ) and carboxylation system (NC ), respectively. N surplus negatively affected the expression of genes in Car biosynthesis ( GGPS , DXR , PSY , IPI and DXS ) and non-net carboxylative process (CEF-PSI). The LN individuals outperformed others with respect to non-photochemical quenching. The expression of genes ( FBA, PGK, RAF2, GAPC, CAB, PsbA and PsbH ) encoding enzymes of Calvin cycle and structural protein of light reaction were obviously repressed in the LN individuals, accompanying with a reduction in Rubisco content and activity. Correspondingly, the expression of genes encoding RAF2 , RPI4 , CAB and PetE were repressed in the HN-grown plants. LN-induced depression of photosynthetic capacity might be caused by the deceleration on Calvin cycle and light reaction of photosynthesis, and HN-induced depression of ones might derive from an increase in the form of inactivated Rubisco and the deprivation of photoprotection.
Physiological and proteomic responses to drought stress in leaves of Amygdalus&nbsp;Mira (Koehne) Yü et Lu
Authors: Xu Liping , Jin Guangze , Guan Fachun , Luo Qiuxiang , Meng Fan Juan 
Published: November 2019

Abstract
Background:Plant development is strongly influenced by various stresses, such as drought and salinity. Drought is a serious threat which can reduce agricultural productivity and obstruct plant growth. Although the mechanism of plants adapted to drought stress has been studied extensively, the adaptive strategies of Amygdalus Mira (Koehne) Yü et Lu grown in drought and re-watered habitats remain undefined. In this paper, A. Mira from the Tibetan Plateau have outstanding environmental, economic, nutritional and medicinal values, and can thrive in extreme drought. Results:This paper investigated physiological and proteomic responses in leaves of A. Mira during the period of drought stress and recovery, to understand their strategies mechanism. The changes of plant growth, photosynthesis, enzymes and non-enzymatic antioxidant during drought and re-watering were analyzed in leaves. Compared with controls, A. Mira showed stronger adaptive and resistant characteristics to drought stress. Proteomic technique was also be used to study mechanisms of drought tolerance in A. Mira leaves. Differentially expressed proteins were identified using mass spectrometry. Accordingly, 103 proteins involved in 10 functional categories: Cytoskeleton dynamics, Energy metabolism, Carbohydrate metabolism, Photosynthesis, Transcription and translation, Transport, Stress and defense, Molecular chaperones, Other materials metabolism, and Unknown function were identified. These results showed that increase of stress-defense-related proteins in leaves after drought treatment were contributed to cope with drought stress. Importantly, A. Mira developed adaptive mechanism to scavenge reactive oxygen species (ROS), including enhancement of antioxidant enzymes activities and non-enzymatic low molecular, reduction of energy, and efficiency of adjusting gas exchanges. Conclusions:These results may help improve understanding concerning the adaptation of A. Mira to drought.
Isopentenyl Phosphate Kinases are Ubiquitous and Copy Numbers are Conserved in Plant Genomes
Authors: Hu Ben , Yao Heng , Li Feng , Wang Ran , Xu Yalong , Wang Zhong , jin lifeng 
Published: November 2019

Abstract
Key message: Isopentenyl phosphate kinase (IPK) is a key enzyme in mevalonate pathway in isoprenoid biosynthesis. We analyzed 37 presumptive IPK sequences from 35 plants. An specific evolution model was found in plant IPKs, which can be used as an new target in studying the plant isoprenoids metabilte. Abstract: Isopentenyl phosphate kinase (IPK) is a recently discovered enzyme played key role in mevalonate pathway in isoprenoid biosynthesis. Here, we showed that IPKs are ubiquitously present in plant genomes. All IPKs previously identified had AAK domain. From 35 plant species with genome assembly data available, we extracted all AAK family members. Using OrthoMCL, we identified a group of 37 sequences in which Arabidopsis IPK was included. Further analysis showed that each peptide sequence in this group has a His residue which is a signature of IPK enzyme, indicating that the genes in this group were IPKs. Not like these in other domains of life which showed spotty distribution over the tree of life, virtually all plant genomes we analyzed here had IPK genes. Further, copy numbers of IPKs were very conserved in that no higher than 2 copies remained in each plant genome. Plant IPKs formed a distinctive clade in phylogenetic tree of plant AAK gene family, and had a phylogenetic topology conformed to that of plant species. The IPKs we identified here would provide new molecular targets for characterization of plant mevalonate pathway, and shed light on biochemistry of plant isoprenoids biosynthesis.
Identification and Analysis of the FAD Gene Family in Walnuts (Juglans regia L.) Based on Transcriptome Data
Authors: Liu Kai , Zhao Shugang , Wang Shuang , Wang Hongxia , Zhang Zhihua 
Published: November 2019

Abstract
Background Walnut fatty acids, the main component of walnut kernels, contain a large amount of unsaturated fatty acids, such as linoleic acid and linolenic acid, which are essential fatty acids in humans and have important effects on human growth and health. Fatty acid desaturase (FAD) is widely distributed throughout the biological world. Its main function is to remove hydrogen from carbon chains in the biosynthesis of unsaturated fatty acids to synthesize C=C double bonds.Results In the current research, 25 members of the JrFAD gene family were identified by bioinformatics analysis; the expression of fatty acid synthesis genes in walnut kernels at different developmental stages was analysed by transcriptome sequencing, and the expression of JrFAD3-1 , an enzyme gene for linolenic acid synthesis, was particularly prominent. The results showed that the relative expression level of FAD3-1 changed dramatically with the kernel development stage, and the expression changes showed a "bell shape". There was a significant positive correlation between the expression of JrFAD3-1 from 90-100 days after anthesis and the content of alpha-linolenic acid from 100-130 days after anthesis, with a correlation coefficient of 0.991. JrFAD3-1 can be considered closely related to Betula pendula and Corylus heterophylla .Conclusion 25 walnut kernels FAD genes were identified and comprehensive analyzed for the first time. The function of a walnut kernels FAD3-1 gene was also characterized from its location in the phylogeny. This work lays a theoretical foundation for the regulation of unsaturated fatty acid synthesis and provide techniques and methods for the creation of new germplasm.
Blood Transcriptome Analysis reveals Age-associated changes in Expression Profile of Immune-Related Gene in Golden snub-nosed Monkey(Rhinopithecus roxellana)
Authors: Huanhuan Shao , Jiabo Deng , Linfeng Wu , Xuedan Li , Lili Niu , Jianqiu Yu , Yang Pu , Huijuan Yan , Weigan Chen , Tan Xuemei 
Published: November 2019

Abstract
Background Golden snub-nosed monkeys ( Rhinopithecus roxellana ) are an endangered species in China.In the present study, the blood transcriptomes of nine monkeys were characterized by using RNA-Seq technology.Results 57.31 Gb high-quality sequencing data was obtained. The clean data of each sample was >5 Gb, and 86.17% to 94.48% of the reads of each sample could be compared to reference genome of snub-nosed monkey. After assembly, we obtained 24,992 genes, including 3,917 new genes. Many genes were up-regulated or down-regulated with age. In adult group of R. roxellana roxellana, there were 76 differential genes, including 68 up-regulated and 8 down-regulated genes, compared with the young group. While, compared with the adult group, in the old group there were 58 differential genes, including 25 up-regulated genes and 23 down-regulated genes. In R. roxellana qinlingensis , compared with the young group, 117 differential genes were obtained, including 34 up-regulated and 83 down-regulated genes. Functional enrichment analysis indicated that the up-regulated genes were mainly related to innate immune response and T-cell activity, while the down-regulated genes were mainly involved in B-cell activity, suggesting that immune competence of adult group increased gradually compared to young group. However, the adaptive immune function declined gradually in the old group.Conclusions Our findings will contribute to understand on the molecular mechanisms of age-related changes in immune system, which will provide a foundation for future study in snub-nosed monkey.
A combined microRNA and transcriptome analysis illuminates the resistance response of rice against brown planthopper
Authors: Tan Jiaoyan , Wu Yan , Guo Jianping , Li Huimin , Zhu Lili , Chen Rongzhi , He Guangcun , Du Bo 
Published: November 2019

Abstract
Background: The brown planthopper (BPH, Nilaparvata lugens Stål) is a kind of phloem-feeding pest that adversely affects rice yield. Recently, the BPH-resistance gene, BPH6, was cloned and applied in rice breeding to effectively control BPH. However, the molecular mechanisms underlying BPH6 are poorly understood. Results: Here, an integrated miRNA and mRNA expression profiling analysis was performed on BPH6-transgenic (BPH6G) and Nipponbare (wild type, WT) plants after BPH infestation, and a total of 217 differentially expressed miRNAs (DEMs) and 7,874 differentially expressed mRNAs (DEGs) were identified. 29 miRNAs, including members of miR160, miR166 and miR169 family were opposite expressed during early or late feeding stages between the two varieties, whilst 9 miRNAs were specifically expressed in BPH6G plants, suggesting involvement of these miRNAs in BPH6-mediated resistance to BPH. In the transcriptome analysis, 949 DEGs were opposite expressed during early or late feeding stages of the two genotypes, which were enriched in metabolic processes, cellular development, cell wall organization, cellular component movement and hormone transport, and certain primary and secondary metabolite synthesis. 24 genes were further selected as candidates for BPH resistance. Integrated analysis of the DEMs and DEGs showed that 34 miRNAs corresponding to 42 target genes were candidate miRNA-mRNA pairs for BPH resistance, 18 pairs were verified by qRT-PCR, and two pairs were confirmed by in vivo analysis. Conclusions: For the first time, we reported integrated small RNA and transcriptome sequencing to illustrate resistance mechanisms against BPH in rice. Our results provide a valuable resource to ascertain changes in BPH-induced miRNA and mRNA expression profiles and enables the analysis of the comprehensive plant-insect interactions required for efficient insect control.
Synchronous dissection of chloroplast and mitochondrial genomes remodels the intra- and inter-genus phylogeny for the agriculturally important genus Brassica
Authors: Qiao Jiangwei , Zhang Xiaojun , Chen Biyun , Huang Fei , Xu Kun , Huang Qian , Huang Yi , Hu Qiong , Wu Xiaoming 
Published: November 2019

Abstract
Background : The genus Brassica mainly comprises three diploid and three recently derived allotetraploid species, most of which are highly important vegetable, oil or ornamental crops cultivated worldwide. Despite being extensively studied, the origination of the allotetraploid crops and the overall phylogeny of Brassica genus are still far from completely resolved, which has greatly hindered the development of novel Brassica crops. Here, we target and integrate the chloroplast DNA and mitochondrial DNA to investigate the genetic diversity and relationships in large plant populations centering on Brassica genus. Results : The phylogenetic analyses based on a data set including 72 de novo assembled whole chloroplast genomes, delineated a comprehensive evolutional atlas inside and around Brassica genus. The maternal origin of both B. juncea and B. carinata are monophyletic from cam-type B. rapa and B. nigra , respectively. Nonetheless, the current B. napus contains three major cytoplasmic haplotypes: the cam -type which directly inherited from B. rapa , polima -type which is close to cam -type as a sister, and the predominant nap -type. Intriguingly, nap -type seems phylogenetically integrated with certain sparse C-genome wild species, thus implying that which may have primarily contributed the cytoplasm and the corresponding C subgenome to B. napus . Human breeding creation of the B. napus cytoplasmic male sterile lines (e.g., mori and nsa ) dramatically disturbed the concurrent inheritance between mtDNA and cpDNA. Strong parallel evolution among genera Raphanus , Sinapis, Eruca , Moricandia with Brassica indicates their uncomplete divergence from each other. Conclusions : The overall variation data and elaborated phylogenetic relationships obtained herein can substantially facilitate the development of novel Brassica crops, e.g. the allotetraploid rapeseed with new cytonuclear integrations and the allohexaploid rapeseed.
Fine mapping of the BnUC2 locus related to leaf up-curling and plant semi-dwarfing in Brassica napus
Authors: Huang Chengwei , Yang Mao , Shao Danlei , Wang Yangming , Wan Shubei , He Jianbo , Meng Zuqing , Guan Rongzhan 
Published: November 2019

Abstract
Background Studies of leaf shape development and plant stature have made important contributions to the fields of plant breeding and developmental biology. The optimization of leaf morphology and plant height to improve lodging resistance and photosynthetic efficiency, increase planting density and yield, and facilitate mechanized harvesting is a desirable goal in Brassica napus.Results Here, we investigated a B. napus germplasm resource exhibiting up-curled leaves and a semi-dwarf stature. In progeny populations derived from NJAU5737 and Zhongshuang 11 (ZS11), we found that the up-curled leaf trait was controlled by a dominant locus, BnUC2. We then fine mapped the BnUC2 locus onto an 83.19-kb interval on chromosome A05 using single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers. We further determined that BnUC2 was a major plant height QTL that explained approximately 70% of the phenotypic variation in two BC5F3 family populations derived from NJAU5737 and ZS11. This result implies that BnUC2 was also responsible for the observed semi-dwarf stature. The fine mapping interval of BnUC2 contained five genes, two of which, BnaA05g16700D (BnaA05.IAA2) and BnaA05g16720D, were revealed by comparative sequencing to be mutated in NJAU5737. This result suggests that the candidate gene mutation (BnaA05g16700D) in the conserved Degron motif GWPPV (P63S) was responsible for the BnUC2 locus. In addition, investigation of agronomic traits in a separation population indicated that plant height, main inflorescence length, and branching height were significantly reduced by BnUC2, whereas yield was not significantly altered. Our findings may provide an effective foundation for plant type breeding in B. napus.Conclusions Using SNP and SSR markers, a dominant locus (BnUC2) related to up-curled leaves and semi-dwarf stature in B. napus has been fine mapped onto an 83.19-kb interval of chromosome A05 containing five genes. The BnaA05g16700D (BnaA05.IAA2) is inferred to be candidate gene responsible for the BnUC2 locus.
Bromide impairs the circadian clock and glycolytic homeostasis via disruption of autophagy in rat H9C2 cardiomyocytes
Authors: Jiang Yicheng , Gu Yang , Xu Hai , Tian Xiaoyi , Zhang Xuefeng , Xu Xiaojin , Yan Wenting , Zhang Xiwen 
Published: November 2019

Abstract
Background Trace elements function as essential cofactors that are involved in various biochemical processes in mammals. Autophagy is vital for nutrient supplement, which is an important Zeitegber for the circadian homeostasis in heart. Here, we considered the possibility that autophagy, as well as the cardiomyocyte clock and glycolysis are interlinked. Detrimental effects were observed when cardiac system is exposed to bromine containing drugs. This study investigated the effects and mechanisms of bromide on the circadian clock and glycolytic metabolism of H9C2 cardiomyocytes. Methods H9C2 cardiomyocytes were incubated with sodium bromide at indicated doses for 24 hours, cell viability, mRNA expression of clock genes, glycolytic genes and autophagic genes were examined using various cellular and molecular approaches. Also, circadian oscillation rhythm of these genes was determined by serum shock with sodium bromide or equal amounts of sodium chloride. Results Bromide modestly affects cell viability and apoptosis of H9C2 cardiomyocytes. Bromide dampens the clock and glycolytic ( Hk2 and Pkm2 ) gene expression rhythmicity in a dose-dependent manner. Additionally, bromide inhibits autophagic process in H9C2 cardiomyocytes. In contrast, rapamycin (an autophagy inducer) dramatically restores the inhibitory effect of NaBr on the mRNA expression levels of clock genes ( Bmal1 , Cry1 and Rorα ) and glycolytic genes ( Hk2 and Pkm2 ). Conclusions Our results reveal that bromide represses the clock and glycolytic gene expression patterns, partially through inhibition of autophagy.
Genome wide identification and characterization of cucumber bHLH family genes and the functional characterization of CsbHLH041 in NaCl and ABA tolerance in Arabidopsis and cucumber
Authors: Li Jialin , Wang Ting , Han Jing , Ren Zhonghai 
Published: November 2019

Abstract
Background The basic/helix-loop-helix (bHLH) transcription factor family exists in all three eukaryotic kingdoms as important regulatory components in biological growth and development. To date, there has been relatively little effort to systematically carry out comprehensive genomic and functional analyses of bHLH genes in cucumber ( Cucumis sativus L.).Results Here, a total of 142 bHLH genes were identified in the cucumber genome released recently and further classified into 32 subgroups based on the phylogenetic analysis, conserved motifs and gene structures. Multiple sequence alignment analyses showed that the sequences of CsbHLH proteins were highly conserved. The chromosomal distribution, synteny analysis, gene duplications of these 142 CsbHLHs were further analyzed. A cis-element analysis revealed that there were many elements related to stress responsiveness and plant hormones in the promoter regions of CsbHLH genes. Phylogenetic comparison of the bHLH members between cucumber and Arabidopsis , revealed cucumber bHLH proteins were clustered into the different functional clades of Arabidopsis bHLH members. The transcript abundance analysis of selected CsbHLHs under abiotic stresses (NaCl, ABA and low temperature treatments) identified five CsbHLH genes could simultaneously respond to the three abiotic stresses. Tissue-specific expression profiles of these five genes were also analyzed. In addition, 35S:CsbHLH041 enhanced the tolerance to salt and ABA in transgenic Arabidopsis and in cucumber seedlings, suggesting CsbHLH041 is an important regulator in response to abiotic stresses. Finally, the functional interoperability network among the CsbHLH proteins was analyzed.Conclusion This study provided a good foundation for further research into the functions and regulatory mechanisms of CsbHLH proteins and identified candidate genes for stress resistance in cucumber.
Variations in the delivery of primary diabetes care in Malaysia Lessons to be learnt and potential for improvement
Authors: Mustapha Feisul , Aagaard-Hansen Jens , Lim Shiang Cheng , Nasir Nazrila Hairizan , Aris Tahir , Bjerre-Christensen Ulla 
Published: November 2019

Abstract
Background The paper describes variations in the organisation of clinical services for diabetes patients in ten public primary health clinics in Malaysia with the view to learn from current innovations and improve diabetes service provision. Methods This study combined the use of secondary data and a qualitative multi-case study approach applying observations in ten randomly selected MOH health clinics in Kuala Lumpur and Selangor, and semi-structured interviews of the Family Medicine Specialists from the same clinics. Results Although there are specific Ministry of Health guidelines for diabetes care, some clinics had introduced innovations for diabetes care such as the novel ‘personalised care’, ‘one-stop-centre’ and utilisation of patients’ waiting time for health education. Analysis showed that there was room for improvement in terms of task shifting to free precious time of staff with specialised functions, streamlining appointments for various examinations, increasing continuity of consultations with same doctors and monitoring of performance. Conclusion We contend that there is a potential for increased effectiveness and efficiency of primary diabetes care in Malaysia without increasing the resources – a potential that may be tapped into by systematic learning from on-going innovation.