bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-Wide Association Study of Rice Rooting Ability at the Seedling Stage
Authors: Xu Xin , Ye Junhua , Yang Yingying , Zhang Mengchen , Xu Qun , Feng Yue , Yuan Xiaoping , Yu Hanyong , Wang Yiping , Yang Yaolong , Wei Xinghua 
Published: August 2020

Abstract
Background
Rice rooting ability is a complex agronomical trait that displays heterosis and plays an important role in rice growth and production. Only a few quantitative trait loci (QTLs) have been identified by bi-parental population. More genes or QTLs are required to dissect the genetic architecture of rice rooting ability.

Results
To characterize the genetic basis for rice rooting ability, we used a natural rice population, genotyped by a 90 K single nucleotide polymorphism (SNP) array, to identify the loci associated with rooting-related traits through the genome-wide association study (GWAS). Population structure analysis divided the natural population into two subgroups: indica and japonica. We measured four traits for evaluating rice rooting ability, namely root growth ability (RGA), maximum root length (MRL), root length (RL), and root number (RN). Using the association study in three panels consisting of one for the full population, one for indica, and one for japonica, 24 SNPs associated with rooting ability-related traits were identified. Through comparison of the relative expression levels and DNA sequences between germplasm with extreme phenotypes, results showed that LOC_Os05g11810 had non-synonymous variations at the coding region, which may cause differences in root number, and that the expression levels of LOC_Os04g09900 and LOC_Os04g10060 are closely associated with root length variation.

Conclusions
Through evaluation of the rice rooting ability-related traits and the association mapping, we provided useful information for understanding the genetic basis of rice rooting ability and also identified some candidate genes and molecular markers for rice root breeding.
Systematic analysis of the Capsicum ERF transcription factor family: identification of regulatory factors involved in the regulation of species-specific metabolites
Authors: Song Jiali , Chen Changming , Zhang Shuanglin , Wang Juntao , Huang Zhubing , Chen Muxi , Cao Bihao , Zhu Zhangsheng , Lei Jianjun 
Published: August 2020

Abstract
Background
ERF transcription factors (TFs) belong to the Apetala2/Ethylene responsive Factor (AP2/ERF) TF family and play a vital role in plant growth and development processes. Capsorubin and capsaicinoids have relatively high economic and nutritional value, and they are specifically found in Capsicum. However, there is little understanding of how ERFs participate in the regulatory networks of capsorubin and capsaicinoids biosynthesis.

Results
In this study, a total of 142 ERFs were identified in the Capsicum annuum genome. Subsequent phylogenetic analysis allowed us to divide ERFs into DREB (dehydration responsive element binding proteins) and ERF subfamilies, and further classify them into 11 groups with several subgroups. Expression analysis of biosynthetic pathway genes and CaERFs facilitated the identification of candidate genes related to the regulation of capsorubin and capsaicinoids biosynthesis; the candidates were focused in cluster C9 and cluster C10, as well as cluster L3 and cluster L4, respectively. The expression patterns of CaERF82, CaERF97, CaERF66, CaERF107 and CaERF101, which were found in cluster C9 and cluster C10, were consistent with those of accumulating of carotenoids (β-carotene, zeaxanthin and capsorubin) in the pericarp. In cluster L3 and cluster L4, the expression patterns of CaERF102, CaERF53, CaERF111 and CaERF92 were similar to those of the accumulating capsaicinoids. Furthermore, CaERF92, CaERF102 and CaERF111 were found to be potentially involved in temperature-mediated capsaicinoids biosynthesis.

Conclusion
This study will provide an extremely useful foundation for the study of candidate ERFs in the regulation of carotenoids and capsaicinoids biosynthesis in peppers.
Functional characterization and regulatory mechanism of wheat CPK34 kinase in response to drought stress
Authors: Li Ge-Zi , Li Han-Xiao , Xu Meng-Jun , Wang Peng-Fei , Xiao Xiang-Hong , Kang Guo-Zhang 
Published: August 2020

Abstract
Background
Drought is one of the most adverse environmental factors limiting crop productions and it is important to identify key genetic determinants for food safety. Calcium-dependent protein kinases (CPKs) are known to be involved in plant growth, development, and environmental stresses. However, biological functions and regulatory mechanisms of many plant CPKs have not been explored. In our previous study, abundance of the wheat CPK34 (TaCPK34) protein was remarkably upregulated in wheat plants suffering from drought stress, inferring that it could be involved in this stress. Therefore, here we further detected its function and mechanism in response to drought stress.

Results
Transcripts of the TaCPK34 gene were significantly induced after PEG-stimulated water deficiency (20% PEG6000) or 100 μM abscisic acid (ABA) treatments. The TaCPK34 gene was transiently silenced in wheat genome by using barley stripe mosaic virus-induced silencing (BSMV-VIGS) method. After 14 days of drought stress, the transiently TaCPK34-silenced wheat seedlings showed more sensitivity compared with control, and the plant biomasses and relative water contents significantly decreased, whereas soluble sugar and MDA contents increased. The iTRAQ-based quantitative proteomics was employed to measure the protein expression profiles in leaves of the transiently TaCPK34-silenced wheat plants after drought stress. There were 6103 proteins identified, of these, 51 proteins exhibited significantly altered abundance, they were involved in diverse function. And sequence analysis on the promoters of genes, which encoded the above identified proteins, indicated that some promoters harbored some ABA-responsive elements. We determined the interactions between TaCPK34 and three identified proteins by using bimolecular fluorescent complementation (BiFC) method and our data indicated that TaCPK34directly interacted with the glutathione S-transferase 1 and prx113, respectively.

Conclusions
Our study suggested that the TaCPK34 gene played positive roles in wheat response to drought stress through directly or indirectly regulating the expression of ABA-dependent manner genes, which were encoding identified proteins from iTRAQ-based quantitative proteomics. And it could be used as one potential gene to develop crop cultivars with improved drought tolerance.
Sequencing of five poultry strains elucidates phylogenetic relationships and divergence in virulence genes in Morganella morganii
Authors: Palmieri Nicola , Hess Claudia , Hess Michael , Alispahic Merima 
Published: August 2020

Abstract
Background
M. morganii is a bacterium frequently associated with urinary infections in humans. While many human strains are sequenced, only the genomes of few poultry strains are available. Here, we performed a detailed characterization of five highly resistant Morganella morganii strains isolated in association with Escherichia coli from diseased domestic Austrian poultry flocks, namely geese, turkeys and chicken layers. Additionally, we sequenced the genomes of these strains by NGS and analyzed phylogenetic clustering, resistance and virulence genes in the context of host-specificity.

Results
Two strains were identified to be Extended Spectrum Beta Lactamase (ESBL) and one as AmpC beta-lactamases (AMP-C) phenotype, while two were ESBL negative. By integrating the genome sequences of these five poultry strains with all the available M. morganii genomes, we constructed a phylogenetic tree that clearly separates the Morganella genus into two clusters (M1 and M2), which approximately reflect the proposed subspecies classification (morganii and sibonii). Additionally, we found no association between phylogenetic structure and host, suggesting interspecies transmission. All five poultry strains contained genes for resistance to aminocoumarins, beta-lactams, colistin, elfamycins, fluoroquinolones, phenicol, rifampin and tetracycline. A comparative genomics analysis of virulence genes showed acquisition of novel virulence genes involved in secretion system and adherence in cluster M2. We showed that some of these genes were acquired by horizontal gene transfer from closely related Morganellaceae species and propose that novel virulence genes could be responsible for expansion of tissue tropism in M. morganii. Finally, we detected variability in copy number and high sequence divergence in toxin genes and provided evidence for positive selection in insecticidal toxins genes, likely reflecting host-related adaptations.

Conclusions
In summary, this study describes i) the first isolation and characterization of M. morganii from goose and turkey, ii) a large-scale genetic analysis of M. morganii and an attempt to generate a global picture of the M. morganii intraspecific phylogenetic structure.
Establishment and application of a multiple cross displacement amplification combined with nanoparticles-based biosensor method for the detection of Bordetella pertussis
Authors: Li Shijun , Liu Chunting , Liu Ying , Ma Qing , Wang Yue , Wang Yi 
Published: August 2020

Abstract
Background
Bordetella pertussis is the causative agent of pertussis, a respiratory tract infectious disease.
Efficient techniques for detection of B. pertussis isolates are important for clinical diagnosis.
Multiple cross displacement amplification (MCDA), a novel isothermal amplification based molecular detection method, has been developed to overcome the technical drawback of the current methods in recent years. This aim of this study is to develop a MCDA with Nanoparticles-based Lateral Flow Biosensor (MCDA-LFB) for the detection of B. pertussis.

Results
A set of 10 primers based on the pertussis toxin (PT) promoter region sequence of B. pertussis was designed. The B. pertussis-MCDA-LFB assay was successfully established and optimized at 64 °C for reaction of 40 min. The detection limit was determined as 10 fg/reaction of pure DNA, and no cross-reactions to non-B. pertussis strains were observed, based on the specificity validation. The whole operation, ranging from template preparation to result reporting, could be completed within 70 min without requirement of costly equipment. The B. pertussis-MCDA-LFB in clinic sample detection yielded identical positive rates with traditional culture and showed higher sensitivity than conventional PCR. The results of MCDA-LFB are easier to read due to the usage of LFB.

Conclusions
The isothermal amplification based MCDA-LFB established in the present study is a specific, sensitive, rapid and economical technique for the detection of B. pertussis.
Metabolome and transcriptome analyses reveal chlorophyll and anthocyanin metabolism pathway associated with cucumber fruit skin color
Authors: Wang Min , Chen Lin , Liang Zhaojun , He Xiaoming , Liu Wenrui , Jiang Biao , Yan Jinqiang , Sun Piaoyun , Cao Zhenqiang , Peng Qingwu , Lin Yu’e 
Published: August 2020

Abstract
Background
Fruit skin color play important role in commercial value of cucumber, which is mainly determined by the content and composition of chlorophyll and anthocyanins. Therefore, understanding the related genes and metabolomics involved in composition of fruit skin color is essential for cucumber quality and commodity value.

Results
The results showed that chlorophyll a, chlorophyll b and carotenoid content in fruit skin were higher in Lv (dark green skin) than Bai (light green skin) on fruit skin. Cytological observation showed more chloroplast existed in fruit skin cells of Lv. A total of 162 significantly different metabolites were found between the fruit skin of the two genotypes by metabolome analysis, including 40 flavones, 9 flavanones, 8 flavonols, 6 anthocyanins, and other compounds. Crucial anthocyanins and flavonols for fruit skin color, were detected significantly decreased in fruit skin of Bai compared with Lv. By RNA-seq assay, 4516 differentially expressed genes (DEGs) were identified between two cultivars. Further analyses suggested that low expression level of chlorophyll biosynthetic genes, such as chlM, por and NOL caused less chlorophylls or chloroplast in fruit skin of Bai. Meanwhile, a predicted regulatory network of anthocyanin biosynthesis was established to illustrate involving many DEGs, especially 4CL, CHS and UFGT.

Conclusions
This study uncovered significant differences between two cucumber genotypes with different fruit color using metabolome and RNA-seq analysis. We lay a foundation to understand molecular regulation mechanism on formation of cucumber skin color, by exploring valuable genes, which is helpful for cucumber breeding and improvement on fruit skin color.
Loneliness as a risk factor for frailty transition among older Chinese people
Authors: Sha Sha , Xu Yuebin , Chen Lin 
Published: August 2020

Abstract
Background
Previous literature has reported that loneliness is a strong predictor of frailty risk. However, less is known about the role of loneliness in frailty transition types. This study aimed to examine whether and how loneliness are related to frailty transition among older Chinese people.

Methods
Our study used participants (aged ≥60 years) from 2008/2009, 2011/2012 and 2014 waves of the Chinese Longitudinal Healthy Longevity Survey (CLHLS). Loneliness was assessed by a single question asking how often the respondent feels lonely. The FRAIL Scale was created to measure physical frailty for our study, and frailty was also assessed by a broader definition of the frailty index. Frailty transition as an outcome variable has been designed as two types according to the measurement of frailty.

Results
Greater loneliness at baseline reduced the possibility of remaining in a robust or prefrail physical frailty state after 3 years (OR = 0.78, 95%CI: 0.68–0.91, p < 0.01). Greater loneliness was associated with an increased risk of worsening physical frailty over time: compared with those who had never felt lonely, the odds ratios for people who often felt lonely were 1.19 (95%CI: 1.01–1.41, p < 0.05) after 3 years and 1.34 (95%CI: 1.08–1.66, p < 0.01) after 6 years. The association between loneliness and change in the frailty index differed in the survey periods: loneliness at baseline was found to increase the possibility of participants remaining in frailty (seldom loneliness: OR = 1.78, 95%CI: 1.25–2.55, p < 0.01; often loneliness: OR = 1.74, 95%CI: 1.21–2.50, p < 0.01) after 6 years, but no significance was shown in the 3-year follow up. Additionally, loneliness at baselines was significantly associated with frailty transition at follow up among the male participants. However, a similar association was not observed among the female participants.

Conclusion
Older people with a high level of loneliness tend to be frail in the future, and greater loneliness is related to an increased risk of worsening frailty and remaining frail. Male elderly with a high level of loneliness were more likely to have a worse frailty transition than female elderly in China.
Complications rate of and risk factors for the unplanned reoperation of degenerative lumbar spondylolisthesis in elderly patients: a retrospective single-Centre cohort study of 33 patients
Authors: Zhong Weiyang , Liang Xinjie , Luo Xiaoji , Huang Tianji , Quan Zhengxue 
Published: August 2020

Abstract
Background
The study was to investigate the complications rate of and risk factors for unplanned reoperation among elderly patients who underwent posterior lumbar fusion (PLF) for degenerative lumbar spondylolisthesis (DLS).

Methods
A total of 1100 DLS patients who were older than 60 years were reviewed from January 2006 to December 2016. 33 patients underwent unplanned reoperations and were analysed and divided into two groups (group A: posterolateral fusion, 650 patients; group B: intervertebral fusion, 450 patients). Sex, body mass index (BMI), radiographic data and clinical outcome data were analysed to evaluate the complications rate of and the risk factors for unplanned reoperations.

Results
A total of 33 patients underwent unplanned reoperations (3%). The patients were followed up for an average of 4.20 ± 2.25 years (group A) and 4.32 ± 2.54 years (group B) without a significant difference. Significant differences were found in mean age, levels of involvement, hospital stay, surgery time, and blood loss between the groups. The causes of unplanned operation were wound infection, screw misplacement, neurological deficit, nonunion, and screw fracture, which were significant except for wound infection between the groups. Higher BMI (obesity), diabetes mellitus (DM), more bleeding and sex (female) were risk factors for complications. Cases of screw misplacement, neurological deficit, nonunion and screw fracture in group A were more significant than those in group B.

Conclusion
Patients with higher BMI, DM, older age, posterolateral fusion, and female sex predicted a higher incidence of unplanned reoperations. Spine surgeons may need to pay more attention to their preoperative training and to improving surgical techniques that could reduce the reoperation rate.
The effects of family, society and national policy support on treatment adherence among newly diagnosed tuberculosis patients: a cross-sectional study
Authors: Chen Xu , Du Liang , Wu Ruiheng , Xu Jia , Ji Haoqiang , Zhang Yu , Zhu Xuexue , Zhou Ling 
Published: August 2020

Abstract
Background
Non-adherence to tuberculosis (TB) treatment is the most important cause of poor TB outcomes, and improving support for TB patients is a primary priority for governments, but there has been little research on the effects of family, social and national policy support factors on TB treatment adherence. The current study evaluated treatment adherence among newly diagnosed TB patients in Dalian, north-eastern China, and determined the effects of family, society, and national policy support factors on treatment adherence.

Methods
A cross-sectional survey was conducted among newly diagnosed TB patients treated at the outpatient department of Dalian Tuberculosis Hospital from September 2019 to January 2020. Data were collected using a questionnaire that measured medication adherence, family support, social support, and national policy support and so on. Differences between groups were assessed using Chi-square tests and Fisher’s exact tests. Ordinal logistic regression analysis was used to determine the predictors of adherence.

Results
A total of 481 newly diagnosed TB patients were recruited, of whom 45.7% had good adherence, and 27.4 and 26.8% had moderate and low adherence, respectively. Patients who had family members who frequently supervised medication (OR:0.34, 95% CI:0.16–0.70), family members who often provided spiritual encouragement (OR:0.13, 95% CI:0.02–0.72), a good doctor-patient relationship (OR:0.61, 95% CI:0.40–0.93), more TB-related knowledge (OR:0.49, 95% CI:0.33–0.72) and a high need for TB treatment policy support (OR:0.38, 95% CI:0.22–0.66) had satisfactory medication adherence. However, patients who had a college degree or higher (OR:1.69, 95% CI:1.04–2.74) and who suffered adverse drug reactions (OR:1.45, 95% CI:1.00–2.11) were more likely to have lower adherence.

Conclusions
Our findings suggested that non-adherence was high in newly diagnosed TB patients. Patients who had family members who frequently supervised medication and provided spiritual encouragement and a good doctor-patient relationship and TB-related knowledge and a high need for policy support contributed to high adherence. It is recommended to strengthen medical staff training and patient and family health education and to increase financial support for improving adherence.
Whole-exome sequencing identifies a novel mutation in spermine synthase gene (SMS) associated with Snyder-Robinson Syndrome
Authors: Qazi Talal J. , Wu Qiao , Aierken Ailikemu , Lu Daru , Bukhari Ihtisham , Hussain Hafiz M. J. , Yang Jingmin , Mir Asif , Qing Hong 
Published: August 2020

Abstract
Background
Loss of function mutations in the spermine synthase gene (SMS) have been reported to cause a rare X-linked intellectual disability known as Snyder-Robinson Syndrome (SRS). Besides intellectual disability, SRS is also characterized by reduced bone density, osteoporosis and facial dysmorphism. SRS phenotypes evolve with age from childhood to adulthood.

Methods
Whole exome sequencing was performed to know the causative gene/pathogenic variant. Later we confirmed the pathogenic variant through Sanger sequencing. Furthermore, we also performed the mutational analysis through HOPE SERVER and SWISS-MODEL. Also, radiographs were also obtained for affected individual to confirm the disease features.

Results
In this article, we report the first Pakistani family consisting of three patients with SRS and a novel missense pathogenic variant in the SMS gene (c.905 C > T p.(Ser302Leu)). In addition to the typical phenotypes, one patient presented with early-onset seizures. Clinical features, genetic and in-silico analysis linked the affected patients of the family with Snyder-Robinson and suggest that this novel mutation affects the spermine synthase activity.

Conclusion
A novel missense variant in the SMS, c.905C > T p. (Ser302Leu), causing Snyder- Robinson Syndrome (SRS) is reported in three members of Pakistani Family.
Whole exome sequencing revealed a novel homozygous variant in the DGKE catalytic domain: a case report of familial hemolytic uremic syndrome
Authors: Gholizad-kolveiri Soraya , Hooman Nakysa , Alizadeh Rasoul , Hoseini Rozita , Otukesh Hasan , Talebi Saeed , Akouchekian Mansoureh 
Published: August 2020

Abstract
Background
Atypical hemolytic uremic syndrome (aHUS) is a rare disease characterized by microangiopathic hemolytic anemia caused by small vessel thrombosis, thrombocytopenia, and renal failure. The common cause of aHUS is a dysregulation in the alternative complement pathway. Mutations in none complement genes such as diacylglycerol kinase epsilon (DGKE) can also result in this syndrome.

Case presentation
Here, we report on a 19-year-old female with the clinical diagnosis of aHUS, who has unaffected consanguineous parents and an older sibling who was deceased from aHUS when she was seven months old.
We performed whole exome sequencing (WES) followed by evaluation of detected variants for functional significance, using several online prediction tools. Next, in order to confirm the detected pathogenic variant in proband and segregation analysis in her family, Sanger sequencing was done. The novel variant was analyzed in terms of its impact on the protein 3-dimensional structure by computational structural modeling.
The results revealed that the proband carried a novel homozygous missense variant in DGKE located in exon 6 of the gene (NM_003647.3, c.942C > G [p.Asn314Lys]), and in silico analysis anticipated it as damaging. Protein computational study confirmed the influence of potential pathogenic variant on structural stability and protein function.

Conclusion
We suggest that some variations in the catalytic domain of DGKE like p.Asn314Lys which can cause alterations in secondary and 3-D structure of protein, might lead to aHUS.