bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide identification of the peptide transporter family in rice and analysis of the PTR expression modulation in two near-isogenic lines with different nitrogen use efficiency
Authors: Yang Xinghai , Xia Xiuzhong , Zeng Yu , Nong Baoxuan , Zhang Zongqiong , Wu Yanyan , Tian Qinglan , Zeng Weiying , Gao Ju , Zhou Weiyong , Liang Haifu , Li Danting , Deng Guofu 
Published: February 2020

Abstract
Background: Nitrogen (N) is a major nutrient element for crop yield improvement, but it also causes environmental problems. Therefore, N use efficiency (NUE) enhancement is an important strategy to solve this problem. In plants, the members of the peptide transporter (PTR) gene family are involved in nitrate uptake and transport. In this study, we performed a genome-wide analysis on PTR genes in Nipponbare, R498, and Oryza glaberrima, and identified 96, 85, and 78 PTR genes respectively. Results: Phylogenetic tree showed that the 96 PTR genes could be classified into 8 groups, and the distributions of PTR genes in Asian cultivated riceand African cultivated rice were consistent. The number of PTR gene was higher in peanuts and soybeans, which were 125 and 127, respectively. The 521 PTR genes in rice, maize, sorghum, peanut, soybean and Arabidopsis could be classified into 4 groups, and the PTR gene distribution was different between monocots and dicots. In Nipponbare genome, the 25 PTR genes were distributed in 5 segmental duplication regions on chromosome 1, 2, 3, 4, 5, 7, 8, 9, and 10. Rice PTR genes have 0-11 introns and 1-12 exons , and 16 PTR genes have the NPF (NRT1/PTR family ) domain. The results of RNA-Seq showed that the number of differentially expressed genes (DEGs) between NIL15 and NIL19 were 928, 1467, and 1586 at three stages, respectively. Under low N conditions, the number of differentially expressed PTR genes increased significantly. The RNA-Seq data was analyzed using WGCNA to predict the potential interaction between genes. We classified the genes with similar expression pattern into one group, and obtained 25 target modules. Among these modules, three modules may be involved in rice nitrogen uptake and utilization, especially the brown module, in which hub genes were annotated as protein kinase that may regulate rice N metabolism. Conclusions: In this study, we comprehensively analyzed the PTR gene family in rice. Ninety-six PTR genes were identified in Nippobare genome and twenty-five genes locates on five large segmental duplication regions. The Ka/Ks ratio indicated that many PTR genes had nudergone positive selection. The RNA-seq results showed that many PTR genes were involved in rice UNE. Protein kinases may play an important role in regulating NUE in rice. These results will provide a fundamental basis for molecular breeding of NUE in rice.
Response of phytohormone mediated plant homeodomain (PHD) family to abiotic stress in upland cotton (Gossypium hirsutum spp.)
Authors: Wu Huanhuan , Zheng Lei , Qanmber Ghulam , Guo Mengzhen , Wang Zhi , Yang Zuoren 
Published: February 2020

Abstract
Background The sequencing and annotations of cotton genomes provide strong theoretical support to reveal more physiological phenomena and functions. Plant homeodomain (PHD) protein family have been reported to be involved in regulating diverse biological processes in plants. However, their functions have not yet been carried out in cotton. Results In this study, we performed a genome-wide analysis of the PHD genes in cotton, including the chromosomal location, phylogenetic relationship, gene structure, and conserved domains. Using a phylogenetic analysis, we divided the 297 PHD genes into five subgroups. The GhPHDs were unevenly distributed across all 26 chromosomes in upland cotton, and whole genome duplication events analyses showed that purifying selection might contributed greatly to the maintenance of function in the GhPHD family. Expression pattern analysis based on RNA-seq data and qRT-PCR results showed that the most of GhPHD genes have significant tissue-specific spatial and temporal expression patterns, indicating GhPHD have multiple functions in growth and development. We further summarized the cis -acting elements in response to abiotic stresses and plant hormones, and treated cotton seedlings with abiotic stresses and plant hormones, respectively. Then, GhPHD gene expression level were detected by qRT-PCR, which indicated that GhPHD could response to stresses and plant hormones. Co-expression network analysis also indicated that GhPHDs were essential for plant growth and development, and phytohormone mediate GhPHD response to abiotic stress can improve plant tolerance to adverse environment. Conclusion This study provides useful information to facilitate the further study of the function of the GhPHD family.
Proteomic and metabolic profile analysis of low-temperature storage responses in Ipomoea batata Lam. tuberous roots
Authors: Cui Peng , Li Yongxin , Cui Chenke , Huo Yanrong , Lu Guoquan , Yang Huqing 
Published: February 2020

Abstract
Background: Sweetpotato ( Ipomoea batatas L.) is one of the seven major food crops grown worldwide, with 70-75% of production in China.Cold stress often can cause protein expression pattern and substance contents variations for tuberous roots of sweetpotato during low-temperature storage. Recently, we developed proteometabolic profiles of the fresh sweetpotatoes (cv. Xinxiang) in an attempt to discern the cold stress-responsive mechanism of tuberous root crops during post-harvest storage. Results: For roots stored under 4℃ condition, the activities of SOD, CAT, APX, O 2 .- producing rate, proline and especially soluble sugar contents were significantly increased as compared to sweetpotatoes exposed to room temperature (13℃). Most of the differentially expressed proteins (DEPs) were implicated in pathways related to metabolic pathway (~22%), especially phenylpropanoids (~10%) and followed by starch and sucrose metabolism (~3%). α-amylase, sucrose synthase and fructokinase were significantly up-regulated in starch and sucrose metabolism, while β-glucosidase, glucose-1-phosphate adenylyl-transferase and starch synthase were opposite. Furthermore, metabolome profiling revealed that glucosinolate biosynthesis, tropane, piperidine and pyridine alkaloid biosynthesis as well as protein digestion and absorption played a leading role in metabolic pathways of sweetpotato roots. More importantly, leucine, tryptophan, tyrosine, isoleucine and valine were all significantly up-regulated in glucosinolate biosynthesis. Conclusions: Our proteomic and metabolic profile analysis of sweetpotato roots stored at low temperature reveal that the antioxidant enzymes activities, proline and especially soluble sugar content were significantly increased. Most of the DEPs were implicated in phenylpropanoids and followed by starch and sucrose metabolism. Glucosinolate biosynthesis played a leading role in metabolic pathways of sweetpotao roots. More importantly, leucine, tryptophan, tyrosine, isoleucine and valine were all significantly up-regulated in glucosinolate biosynthesis.
Developing Public-Private Partnership Framework for Managing Adverse Health Effects of Environmental Disaster (A case study of Lake Urmia -Iran)
Authors: Gharaee Hojatolah , Rezapour Ramin , Derakhshani Naser , Ghojazadeh Morteza , Azami-Aghdash Saber 
Published: February 2020

Abstract
Background Due to the limited resources of the public sector, the presence of the private sector as an auxiliary to the health sector, to mitigate adverse health effects (AHEs) caused by environmental disasters, seems necessary. Therefore, the present study aimed to develop a Public-Private Partnership (PPP) framework for managing AHE of environmental disasters (case study of Lake Urmia-Iran). Methods This is a qualitative study with grounded theory approach, conducted in 2019. Required data were collected through semi-structured interviews with 20 experts selected through purposive sampling, and analyzed using Content-Analysis. To formulate the initial framework, an experts’ panel, composed of 12 experts, was formed. Delphi method was used to determine the validity of the framework. Results Most participants found the private sector participation in this field, essential and useful. The most important infrastructure for the private sector participation was designing a legal framework and providing adequate resources and facilities. Pollutant assessment and education of families for disease prevention are among the most important areas that the private sector can participate. To evaluate the performance of the private sector, periodic and short-term reports together with documentation should be used, and the evaluation tool should be the checklists agreed by two sectors. Payments to the private sector should be for periodic objectives, based on performance, and after performance confirmation, in the form of combination of fee for services, per capita and performance-based system. Preventing waste of resources, improving service coverage, greater efficiency and attracting public participation were the most important benefits of the private sector participation. Conclusions PPP can be considered by policy makers as an effective policy for reducing the AHE of environmental disasters (especially drying lakes). To this end, the framework presented in this study can be used as an action guide by national and local authorities and policymakers.
The Burden of Laboratory-confirmed Influenza Infection in Lebanon Between 2008 and 2016: A single tertiary care center experience
Authors: Assaf-Casals Aia , Saleh Zeina , Khafaja Sarah , Fayad Danielle , Ezzeddine Hady , Saleh Mohammad , Chamseddine Sarah , Sayegh Rouba , Sharara Sima , Chmaisse Ahmad , Kanj Souha , Kanafani Zeina , Hanna-Wakim Rima , Araj George , Mahfouz Rami , Saito Reiko , Suzuki Hiroshi , Zaraket Hassan , Dbaibo Ghassan 
Published: February 2020

Abstract
BACKGROUND: Influenza is a major cause of morbidity and mortality worldwide. Following the 2009 pandemic, there was widened interest in studying influenza burden in all regions. However, data from the World Health Organization (WHO) Middle East and North Africa (MENA) region remain limited particularly from Lebanon. METHODS: A retrospective chart review extending over a period of 8 seasons from Jan 1st, 2008 till June 30 th , 2016 at a tertiary care center in Beirut was performed. All laboratory-confirmed cases of influenza were included for analysis. Data on epidemiology, clinical presentation, complications, antiviral use and mortality were collected for analysis. RESULTS: A total number of 1829 cases of laboratory-confirmed influenza were identified. Average annual positivity rate was 14%. Both influenza A and B co-circulated in each season with predominance of influenza A. Influenza virus started circulating in December and peaked in January and February. The age group of 19-50 years accounted for the largest proportion of cases (22.5%) followed by the age group of 5-19 years (18%). Pneumonia was the most common complication reported in 33% of cases. Mortality reached 3.8%. The two extremes of age (<2 years and ≥ 65years) were associated with a more severe course of disease, hospitalization, intensive care unit (ICU) admission, complications, and mortality rate. Of all the identified cases, 26% were hospitalized. Moderate-to-severe disease was more likely in influenza B cases but no difference in mortality was reported between the two types. Antivirals were prescribed in 68.8% and antibiotics in 41% of cases. There seemed to be an increasing trend in the number of diagnosed and hospitalized cases over the years of the study. CONCLUSION: Influenza causes a substantial hospitalization burden annually in Lebanon with significant morbidity across all age groups. A population based prospective surveillance study is needed to better estimate the burden of Influenza in Lebanon that would help formulate a policy on influenza control.
Evaluating the prevalence of plasmid- mediated quinolone resistant and ESBL- production in Uropathogenic Escherichia coli and the commensal gut microbiota in pregnant women: A comparative analysis
Authors: Mohebi Samane , Kholdi Soudeh , Hadadi Mahtab , hashemizadeh zahra 
Published: February 2020

Abstract
Background: ß-lactam and ﬂuoroquinolone antibiotics are frequently prescribed for urinary tract infections (UTIs). This study aimed to determine the prevalence of plasmid-mediated quinolone resistance (PMQR) and extended spectrum β-lactamases (ESBLs) in E. coli from UTIs in comparison with the E. coli isolates from gut microbiota (fecal flora).Methods: A total of 54 E. coli urine isolates and 54 E. coli fecal flora isolates were collected from pregnant women (same host) from April to September 2018. Antimicrobial susceptibility testing was determined by disk diffusion method. ESBLs were detected via double-disk test (DDST). ESBL and PMQR-encoding genes were identified, using PCR.Results: The highest resistance rate was found against nalidixic acid (42 isolates in urinary and 41 in fecal flora isolates) and the lowest resistance rate belonged to levofloxacin (23 isolates) and ofloxacin (25 isolates) in urinary and fecal flora isolates. The most prevalent PMQR genes were qnrS (29 isolates in urinary and 34 in fecal flora isolates) followed by qnrB, aac (6′)- Ib-cr and qnrA in urinary and fecal flora isolates. There was a significant association between qnrS gene and blaTEM in urinary and fecal flora isolates.Conclusions: Resistance to quinolones antibiotics was highest among fecal flora isolates, especially qnrS among other determinants of the qnr gene. In addition, it seems that high load of PMQR genes in commensal flora has a potential to spread to pathogenic organisms.
WITHDRAWN: Quercetin-conjugated superparamagnetic iron oxide nanoparticles enhances Nrf2 expression through miR-27a intervention to prevent memory dysfunction in diabetic rats
Authors: Ebrahimpour Shiva , Shahidi Seyedeh Bahar , Aabbasi Mahnoosh , Tavakoli Zahra , Esmaeili Abolghasem 
Published: February 2020

Abstract
Background: Oxidative stress is involved in the development of diabetes-induced cognitive impairment. Nrf2 as a redox-sensing gene can be regulated by some microRNAs. This study aimed to evaluate the effects of quercetin (QC) and quercetin-conjugated superparamagnetic iron oxide nanoparticles (QCSPIONs) on Nrf2-controlled antioxidant genes via the miR-27a. Streptozotocin was applied to produce type 1 diabetes in male Wistar rats. Animals (five groups of 8 rats) were treated for 35 days. Real-time polymerase chain reaction method was applied to assess the expression levels of miR-27a, Nrf2, SOD1, GPX1, and CAT. Moreover, total antioxidant capacity (TAC) and histological alterations were investigated. Results: A significant up-regulation in the expression level of miR-27a was observed in diabetic rats in comparison to control (p<0.01). The mRNA expression levels of Nrf2, SOD1, GPX1 and CAT were significantly down-regulated under diabetic condition (p<0.0001, p<0.01, p<0.0001 and p<0.0001, respectively). Interestingly, QCSPIONs decreased expression level of miR-27a (p<0.01) and subsequently enhanced the expression levels of the Nrf2 (P<0.5), SOD1 (P<0.0204) and CAT (P<0.01) to the control level. Significant difference was not recognized in the expression level of GPX1 under QCSPIONs treatment. In addition, QC in pure and especially conjugated form was able to normalize TAC (p<0.01) and regenerate pathological lesions in STZ-diabetic rats. Conclusions: Result demonstrates that QCSPIONs as an effective combined therapy can reduce the miR-27a expression, that in turn increases the mRNA Nrf2 expression and its responsive antioxidant genes, resulting in the prevention of diabetic complications.
Detection of Human Cytomegalovirus in Patients with Epithelial Ovarian Cancer and its Impacts on Survival
Authors: Yin Min , Chen Aiping , Zhao Fei , Ji Xuechao , Li Chuan , Wang Guangning 
Published: February 2020

Abstract
Background: The cause of epithelial ovarian cancer(EOC) is not elucidated. It has been proved that infectious agents could contribute to ovarian carcinogenesis. Human cytomegalovirus (HCMV) has been detected in several types of tumors. Objective: To investigate the potential role of HCMV infection in EOC, we evaluated the prevalence of HCMV proteins in EOC tissue sections and its impacts on patients’ survival. Methods: Formalin-fixed, paraffin-embedded tissues from 66 patients with EOC and 30 patients with benign ovarian cystadenoma were studied. Specimens were detected for expression of HCMV immediate-early protein (IE) and HCMV tegument protein (pp65) by immunohistochemistry. Results: HCMV-IE protein expression was detected in 82% of EOC and 36% of benign tumors; pp65 was detected in 97% of EOC and 63% of benign tumors. Extensive expression of HCMV-IE protein was associated with higher stage of EOC. Reactivation of latent HCMV within the tumor at interval debulking surery may be induced by neoadjuvant chemotherapy before surgery. Extensive HCMV-IE expression was associated with shorter median overall survival than focal or negative expression (39 versus 41 months, P = 0.03). Conclusions: This study demonstrate a high prevalence of HCMV proteins in tissue sections from patients with EOC. HCMV infections can be potential risks for EOC development. The relationship between HCMV and clinical outcomes highlight the need for further researches on the oncomodulatory role of HCMV in ovarian cancer.
Clinicopathological signature and prognostic value of RNA:m5C methyltransferases in gliomas
Authors: Wang Peng , Huang Kai , Wu Miaojing , Hu Qing , Tao Chuming , Li Kuangxun , Zhu Xingen 
Published: February 2020

Abstract
Background: Glioma is the most common primary intracranial tumor, accounting for the vast majority of intracranial malignant tumors. Aberrant expression of RNA:5-methylcytosine(m5C) methyltransferases has recently been the focus of research relating to the occurrence and progression of tumors. However, the prognostic value of RNA:m5C methyltransferases in glioma remains unclear. This study investigated RNA: m5C methyltransferase expression and defined its clinicopathological signature and prognostic value in gliomas.
Methods: We systematically studied the RNA-sequence data of RNA:m5C methyltransferases underlying gliomas in the Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA) datasets and identified different subtypes using Consensus clustering analysis. Gene Ontology (GO) and Gene Set Enrichment analysis (GSEA) was used to annotate the function of these genes. Univariate Cox regression and the least absolute shrinkage and selection operator (LASSO) Cox regression algorithm analyses were performed to construct the risk score model. Kaplan-Meier method and Receiver operating characteristic (ROC) curves were used to assess the overall survival of glioma patients. Additionally, Cox proportional regression model analysis was developed to address the connections between the risk scores and clinical factors.
Results: Consensus clustering of RNA:m5C methyltransferases identified three clusters of gliomas with different prognostic and clinicopathological features. Meanwhile, Functional annotations demonstrated that RNA:m5C methyltransferases were significantly associated with the malignant progression of gliomas. Thereafter, five RNA:m5C methyltransferase genes were screened to construct a risk score model which can be used to predict not only overall survival but also clinicopathological features in gliomas. ROC curves revealed the significant prognostic ability of this signature. In addition, Multivariate Cox regression analyses indicated that the risk score was an independent prognostic factor for glioma outcome.
Conclusion: We demonstrated the role of RNA:m5C methyltransferases in the initiation and progression of glioma. We have expanded on the understanding of the molecular mechanism involved, and provided a unique approach to predictive biomarkers and targeted therapy.
M 6A-related genes characterization in hepatocellular cancer identifies prognostic relevant gene signatures
Authors: zhu peng , Ren Qianqian , He Nan , Zhou Cheng , Gong Zhao , Jin Qianna 
Published: February 2020

Abstract
Background Hepatocellular carcinoma (HCC) is among the most common types of cancers that threat the public health worldwide. N6-methyladenosine (m6A) RNA methylation, associated with cancer initiation and progression, is dynamically regulated by m6A RNA methylation associated genes. However, little is known about the expression status and the prognostic value of m6A associated genes in HCC. This study aimed to identify the expression profiling pattern and clinical significance of m6A-related genes in HCC. Methods The Cancer Genome Atlas (TCGA-LIHC), the Gene Expression Omnibus (GSE14520) and the Human Protein Atlas (HPA) databases were gathered for this study. Consensus clustering analysis was performed to identify the clusters of HCC with different clinical outcome. A prognostic signature built by the least absolute shrinkage and selection operator (LASSO) Cox regression model was utilized to discover subtypes correlated with different clinical outcomes of HCC patients and the differences between subgroups were characterized in terms of epigenetic dysregulation and somatic mutation frequencies. Results Most of the m6A-related genes were upregulated and involved with the prognosis and malignancy of HCC. A four-gene prognostic signature revealed two HCC subtypes (namely, risk-high group and risk-low group) that correlated with different clinical outcomes. Patients in risk-high group were accompanied with much more epigenetic silencing and significant mutation at TP53 and FLG, while ALB were mutated frequently for risk-low group. Conclusion Our characterization tightly links the expression of m6A genes with clinical outcomes of HCC, providing valuable molecular-level information that points to decoding heterogeneity, guiding personalized management and treatment of HCC patients.
Development of a Forceps Force Limiter Using Leaf Spring Buckling
Authors: Noda Satsuya 
Published: February 2020

Abstract
To prevent accidents in minimally invasive surgeries, force limiters have been developed for forceps grippers.
When a force limiter is in use, if the absolute value of its spring constant is reduced, the risk of damage to the organs decreases.
This paper proposes the use of a leaf spring buckling mechanism as a force limiter for forceps.
The results obtained indicate that the spring constant of a buckled leaf spring is lower than that of a normal coil spring.
Furthermore, the use of a leaf spring allows the independent adjustment of its thickness and width, based on the stress and force values.
This enables an easy calibration of the threshold value.
In the experiments, the spring constant of the buckled leaf spring was 0.15 N/mm, which is half of that of a normal coil spring.
After calibrating the gripping force, it was confirmed that the force limiter reduced the extent of damage to the dummy organs in the ex vivo experiments.