bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic significance of MYCN related genes in pediatric neuroblastoma: a study based on TARGET and GEO datasets
Authors: Wang Haiwei , Wang Xinrui , Xu Liangpu , Zhang Ji , Cao Hua 
Published: June 2020

Abstract
Background: Neuroblastoma patients with MYCN amplification are associated with poor prognosis. However, the prognostic relevance of MYCN associated genes in neuroblastoma is unclear. Methods: The expression profiles of MYCN associated genes were identified from Therapeutically Applicable Research to Generate Effective Treatments (TARGET) and Gene Expression Omnibus (GEO) datasets. Enriched transcription factors and signaling pathways were determined using gene set enrichment analysis (GSEA). Kaplan-Meier plotter was used to identify the prognostic relevance of MYCN associated genes. Multivariate cox regression and Spearman’s correlation were used to determine the correlation coefficients of MYCN associated genes.Results: In TARGET and GSE85047 datasets, neuroblastoma patients with MYCN amplification were associated with worse prognosis. Transcription factor MYC was positively associated with MYCN amplification in GSEA assay. We identified 13 MYC target genes which were increased in neuroblastoma patients with MYCN amplification in TARGET, GSE19274 and GSE85047 datasets. Moreover, six out of the 13 MYC target genes ARMC6, DCTPP1, EIF4G1, ELOVL6, FBL and PRMT1 were associated with adverse prognosis in TARGET and GSE85047 datasets. Transcription factor E2F1 was up-regulated by MYCN amplification and associated with the poor prognosis of neuroblastoma. Furthermore, RPS19 in ribosome signaling pathway was also associated with MYCN amplification and correlated with the poor prognosis of neuroblastoma. At last, we showed that most of MYCN target genes were correlated with each other. However, EIF4G1 was an independent prognostic marker. And the prognostic effects of the combination of MYCN amplification and EIF4G1 expression were more significant than MYCN or EIF4G1 alone.Conclusions: MYCN target genes ARMC6, DCTPP1, EIF4G1, ELOVL6, FBL, PRMT1, E2F1 and RPS19 had significant prognostic effects in pediatric neuroblastoma. And neuroblastoma patients without MYCN amplification and low EIF4G1 expression had best prognosis.
“Oil-soluble” Reversed Lipid Nanoparticles for Oral Insulin Delivery
Authors: Wang Tao , Shen Liao , Zhang Yadan , Li Haiyan , Wang Yongan , Quan Dongqin 
Published: June 2020

Abstract
Background: In this study, we aimed to design a novel oral insulin delivery system, named “oil-soluble” reversed lipid nanoparticles (ORLN), in which a hydrophilic insulin molecule is encapsulated by a phospholipid (PC) shell and dissolved in oil to prevent the enzymatic degradation of insulin. ORLN was characterized by transmission electron microscopy and dynamic light scattering. Results: In vitro enzymatic stability studies showed higher concentrations of insulin in cells incubated with ORLN-encapsulated insulin than in those incubated with free insulin solution in artificial intestinal fluid (pH 6.5). The protective effect of ORLN was attributed to its special release behavior and the formulation of the PC shell and oil barrier. Furthermore, an in vivo oral efficacy study confirmed that blood glucose levels were markedly decreased after ORLN administration in both healthy and diabetic mice. In vivo pharmacokinetic results showed that the bioavailability of ORLN-conjugated insulin was approximately 28.7% relative to that of the group subcutaneously administered with an aqueous solution of insulin, indicating enhanced oral absorption.Conclusions: In summary, the ORLN system developed here shows promise as a nanocarrier for improving the oral absorption of insulin.
Transcriptome analysis reveals underlying immune response mechanism of fungal disease in Gastrodia elata Bl. f. glauca S. Chow
Authors: Wang Yanhua , Gao Yugang , Zang Pu , Xu Yue 
Published: June 2020

Abstract
Background
Gastrodia elata Bl. f. glauca S. Chow is a rare medicinal plant. G. elata f. glauca is unavoidably infected by pathogens in their growth process, for they are usually grown in a semi-wild state. If it happens, that will seriously affect the yield and quality of their tubers. In previous work, we have successfully isolated and identified the pathogenic fungus from infected tubers in G. elata f. glauca. In this study, healthy and fungal diseased mature tubers of G. elata f. glauca from Changbai Mountain area were used as experimental materials.
Results
A total of 7540 differentially expressed Unigenes (DEGs) were identified (FDR < 0.01, log2FC > 2). Further analysis revealed that transcription factors (TFs) in plant hormone signal transduction pathway and plant pathogen interaction pathway, like WRKY22, GH3, TIFY/JAZ, ERF1, WRKY33, TGA, played vital role in fungal disease response. They mainly involved signal transduction, environmental adaptation, biosynthesis/metabolism of secondary metabolites. In addition, we found jasmonic acid/ethylene is the noteworthy signaling pathway in response to fungal disease in G. elata f. glauca.
Conclusions
The results reveal an underlying immune response mechanism of fungal disease in G. elata f. glauca and provide a novel insight into the breeding of disease resistant varieties of G. elata f. glauca.
Defining treatment strategy for uncomplicated appendicitis based on patient satisfaction feedback: A cross-sectional study
Authors: Tatsuta Kyota , Miyazaki Shinichiro , Ogiku Masahito , Harada Takashi , Yoshiro Nishiwaki 
Published: June 2020

Abstract
Background
Two surgical strategies are available for appendicitis: emergency laparoscopic appendectomy and interval laparoscopic appendectomy. However, timing of surgical intervention remains debatable. This study aimed to compare the surgical outcomes of emergency laparoscopic appendectomy (ELA) and interval laparoscopic appendectomy (ILA) and conduct a questionnaire survey to investigate the use of ELA and patient satisfaction with regard to treatment.
Methods
We included 162 patients who underwent laparoscopic appendectomy at our hospital. Outcomes were assessed by operation time, blood loss, postoperative fasting time, length of hospital stay, and complication rate. Patient satisfaction was measured by questionnaire addressing degree of satisfaction, pre-surgery anxiety, and length of hospital stay. Continuous variables were compared by Student’s t-test, and discrete variables, expressed as percentages, were analyzed via chi-squared test.
Results
Of 162 patients, 74 (46%) and 88 (54%) received emergency and ILA, respectively. No significant difference was observed in the operation time, blood loss, length of hospital stay, or complication rate. Among 66 patients who responded to the questionnaire (28 emergency, 38 interval), a significant difference was observed only in the degree of satisfaction regarding the timing of the surgical intervention (p = 0.04).
Conclusions
Surgical outcomes of emergency and interval appendectomy were equivalent; however, patient satisfaction favored emergency appendectomy, suggesting it is a preferable approach for the treatment of uncomplicated appendicitis.
Trial registration:
NA
Most colitis associated carcinomas lack expression of LGR5: implications for unique pathways of carcinogenesis compared to sporadic colorectal carcinoma
Authors: Iwaya Mai , Ota Hiroyoshi , Nakajima Tomoyuki , Uehara Takeshi , Riddell Robert , Conner James 
Published: June 2020

Abstract
BackgroundLeucine-rich repeat-containing G-protein-coupled receptor 5 (LGR5), a component of the Wnt receptor complex, is thought to lineage label gastric and intestinal stem cells. LGR5 expression is increased in colorectal carcinoma (CRC) compared to normal tissue. Colitis associated colorectal adenocarcinoma (CAC) often shows distinct morphologic and molecular phenotypes compared to sporadic cases. However, the expression profile of LGR5, and by extension the potential role of an intestinal stem cell phenotype, has not been well described in a series of human CAC. MethodRNA in situ hybridization (ISH) for LGR5 expression on 30 CACs (12 cases with conventional morphology and 18 cases with non-conventional type morphology) from 29 inflammatory bowel disease (IBD) patients was performed and compared the expression profile to a control group of 10 sporadic CRCs. ResultLGR5 was positive in 30% (9/30) of CAC cases and 90% (9/10) of sporadic CRCs (p=0.002). A large majority (89%) of LGR5 positive CACs were of the conventional histologic type, and conventional type CAC showed a significantly higher LGR5 score (median 3.0; interquartile range 1.75-3.25) than non-conventional type CAC (median 1.5; interquartile range 1.00-2.00) (p = 0.034). CAC with conventional morphology did have a lower level of LGR5 expression than sporadic CRC. Sporadic CRCs showed a significantly higher LGR5 level score than non-conventional type CACs (p <0.001). ConclusionThese findings suggest that the wider spectrum of tumor morphology in CAC may be associated with absence of a LGR5-expressing intestinal stem cell phenotype.
Analysis for interaction between interleukin-35 gene polymorphisms and risk factors on susceptibility to coronary heart disease in the Chinese Han population
Authors: LI Hu , LIU Ying-Xue , Huang Jin-Yan , Zhu Yu- Feng , Wang Kui 
Published: June 2020

Abstract
Objective
To explore the effect of single nucleotide polymorphisms (SNPs) of interleukin-35 (IL-35) gene and its relationship with environment on the risk of coronary heart disease (CHD).
Methods
Prior to the analysis, we performed hardy Weinberg equilibrium test on the control group. The relationship between the four SNPs of IL-35 gene and the risk of coronary heart disease was studied by multivariate logistic regression. The best interaction was identified with generalized multifactor dimensionality reduction (GMDR). Logistic regression was used for investigation on association between four SNPs and CHD risk.
Results
Logistic regression analysis showed that the C allele of rs428253 and the G allele of rs2243115 were independently correlated with increased risk of CHD, and adjusted ORs (95%CI) were 1.91 (1.28–2.64) and 1.80 (1.30–2.23), respectively. However, there was no significant association between CHD and rs4740 or rs568408. GMDR model, indicated the best model for CHD risk consisted of rs428253 and current smoking, which scored 10/10 for both the sign test and cross-validation consistency (P = 0.010). Therefore, this overall multi-dimensional model had the highest cross-validation consistency, regardless of how the data were divided. This provided an evidence of gene-environment interaction effects. We also found that current smokers with rs428253 - GC/ CC genotype have the highest CHD risk, compared to subjects with never smokers with rs428253 - GG genotype, OR (95%CI) = 3.04 (1.71–4.41), after adjustment for age, gender, hypertension, T2DM and alcohol consumption status.
Conclusions
In this study, the C allele of rs428253 and the G allele of rs2243115, and the interaction rs428253 and current smoking were correlated with increased risk of CHD.
Restless abdomen: a spectrum or a phenotype variant of restless legs syndrome?
Authors: Wang Xi-Xi , Zhu Xiao-Ying , Wang Zan , Dong Jian-Wei , Ondo William G. , Wu Yun-Cheng 
Published: June 2020

Abstract
Background
With the growing awareness of restless legs syndrome(RLS), sensory disorders similar to RLS initially confined to the arms, abdomen, and perineum are more and more being recognized. One of them is restless abdomen, which refers to a restless sensation in abdomen. Our study is designed to evaluate the clinical phenotype of restless abdomen and investigate its relationship with RLS.
Methods
We enrolled 10 patients with restless abdomen according to the RLS diagnostic criteria. Laboratory examinations were performed to exclude mimics and notable comorbidities.
Results
All 10 patients had RLS like symptoms in the abdomen and otherwise satisfied all other RLS diagnostic criteria, and responded to dopaminergic therapy.
Conclusions
Neurologists should be aware of the RLS-related restlessness that can occur in extra-leg anatomy in the absence of episodes of worsening or augmentation of restlessness.
The Effect of The Body Composition to Prognosis in Young Breast Cancer Patients
Authors: Beypinar Ismail , Kaya Furkan , Demir Hacer 
Published: June 2020

Abstract
Background In cancer patients, the effect of the body composition on prognosis is a new clinical area of interest. In patients with class 2 or 3 obesity (BMI > 35), survival found to be worse control groups in a pooled analysis. BMI category is not truly representing body composition and hard to use to determine the true muscle and fat quantity. Computed tomography (CT) is a frequent method to determine body composition precisely.Methods Axial CT images, including all abdominal muscles (psoas, erector spinae, quadratus lumborum) external and internal oblique and rectus abdominis) total skeletal muscle area (SMA), was calculated. Besides, axial CT images of the body fat subcutaneous adipose and visceral adipose tissue distribution (VAT, SAT) areas were calculated in cm2 using threshold values ​​of -30 to -190 for adipose tissue.Results Eighty-four women included in the study. Most of the patients were normal or over-weighted. Invasive ductal carcinoma was the dominant histological subtypes, with 94% of the study population. The count of the sarcopenic and non-sarcopenic patients was 11 and 68 respectively. Although the median OS cannot be reached at the end of the follow-up period for both sarcopenic and non-sarcopenic patients, the difference between groups statistically insignificant. The median OS was not reached for both groups, the difference between low and high VAT groups was statistically significant.Conclusion In this study, we demonstrate sarcopenia may be seen in patients with breast cancer under 40 years old, and it may not have a prognostic effect.
Exploration of the role of tumor mutation burden in clinical significance, immunotherapy response predictor and immune cell infiltration in colon cancer
Authors: Xu Zhengshui , Qu Chao , Guo Jing , Li Xiaopeng , Wu Yunhua , Wang Kai , Zheng Jianbao , Sun Xuejun , Yu Junhui 
Published: June 2020

Abstract
Backgroud:Tumor mutation burden has become a powerful bio-marker to predict prognosis and immunotherapy responsiveness to patients in various cancers, but the role of TMB in colon cancer is still unclear.Methods:The transcriptome profiling data of colon patients and the simple nucleotide variation data of colon cases were downloaded from the Cancer Genome Atlas (TCGA) database. The groups were divided into high TMB and low TMB group according to the median of TMB. Then we explored the relationship between immune checkpoints, immune cells and TMB, respectively. Results: ﻿Mutation profiles of 399 colon cancer samples were analyzed in TCGA database. The senior (age＞65) had a strong relationship with higher-TMB level(p=0.001). Low-TMB group correlated with advanced N stage (P＜0.001), M stage (P＜0.001), and pathologic stage(P＜0.001). High-TMB group had significantly higher mRNA level of PD-L1, TIGIT, HAVCR2, and LAG3 than low-TMB group, which indicated high-TMB referred to better immunotherapy responsiveness in colon cancer. And high-TMB level correlated with higher fractions of CD8T cells (p=0.021), higher CD4 memory T cells(p=0.039), follicular helper T cells (p=0.002)and M1 macrophages (p＜0.001), while the low-TMB groups correlated with higher regulator T cells (p=0.002). So high-TMB correlated with stronger immune cell infiltrationConclusions:The high TMB referred to better clinical pathologic features, better immunotherapy responsiveness and stronger immune cells infiltration in colon cancer. Hence TMB may be a very promising bio-marker to predict prognosis and immunotherapy responsiveness to patients in colon cancer.
Poor Physical Capacity in Bronchiectasis Patients Is Correlated with Poor Quality of Life
Authors: Mäntylä Jarkko , Mazur Witold , Törölä Tanja , Bergman Paula , Kauppi Paula 
Published: June 2020

Abstract
Background: Bronchiectasis (BE) is an increasing burden on healthcare systems, and there is an urgent need for improved treatments, better clinical care and for clinical and translational research on this condition. Reducing the number of exacerbations is one of the key goals in BE management. Patients who suffer from frequent exacerbations are likely to experience more exacerbations, which have negative effects on quality of life (QoL), healthcare utilisation and mortality. Thus, we aimed to investigate the risk factors associated with quality of life (QoL) in a cohort of Finnish non-cystic fibrosis BE patients.Methods: A cross-sectional study is part of the EMBARC. Recruitment occurred between August 2016 and March 2018 from three clinics in Helsinki University Central Hospital, Finland. The study included 95 adult patients (mean age was 69 (SD± 13) years). Seventy nine percent were women. A disease-specific quality of life-bronchiectasis (QoL-B) questionnaire was applied, and scores in the lowest quarter (24%) indicate poor QoL. The bronchiectasis severity index (BSI) and FACED score were used. The severity of dyspnoea was examined using the modified Medical Research Council (mMRC) dyspnoea scale. Results: Almost all (82%) presented with chronic sputum production and exacerbation, with a median rate of 1.7 (SD ±1.6). Exacerbations (OR 1.7), frequent exacerbations (OR 4.9, p < 0.01), high BSI score (OR 1.3, p < 0.01) and extensive disease (OR 3.7, p = 0.05) were predictive of poor QoL. Frequent exacerbations were associated with bronchial bacterial colonisation, low forced expiratory volume in one second (FEV1) and radiological disease severity. Based on the BSI, 34.1% of our cohort had severe disease, whereas 11.6% were classified as severe according to the FACED score. The mMRC dyspnoea score (r = -0.57) and BSI (r = -0.60) were negatively correlated with physical domain in QoL-B questionnaire. Conclusion: Frequent exacerbations, radiological disease severity and high BSI score were predictive of poor QoL. Reduced physical capacity was correlated with dyspnoea and severity of disease. Interventions to reduce bacterial colonisation and to maintain physical functioning should be used to minimize exacerbations and to improve QoL.Study registration: University of Helsinki, faculty of medicine; 148/16.08.2017; Registered 16 August 2017; https://researchportal.helsinki.fi/
Impact of short-read sequencing on the misassembly of a plant genome
Authors: Wang Peipei , Meng Fanrui , Moore Bethany M. , Shiu Shin-Han 
Published: June 2020

Abstract
Background
Availability of plant genome sequences has led to significant advances. However, with few exceptions, the great majority of existing genome assemblies are derived from short read sequencing technologies with highly uneven read coverages indicative of sequencing and assembly issues that could significantly impact any downstream analysis of plant genomes. In tomato for example, 0.6% (5.1 Mb) and 9.7% (79.6 Mb) of short-read based assembly had significantly higher and lower coverage compared to background, respectively.
Results
To understand what the causes may be for such uneven coverage, we first established machine learning models capable of predicting genomic regions with variable coverages and found that high coverage regions tend to have higher simple sequence repeat and tandem gene densities compared to background regions. To determine if the high coverage regions were misassembled, we examined a recently available tomato long-read based assembly and found that 27.8% (1.41 Mb) of high coverage regions were potentially misassembled of duplicate sequences, compared to 1.4% in background regions. In addition, using a predictive model that can distinguish correctly and incorrectly assembled high coverage regions, we found that misassembled, high coverage regions tend to be flanked by simple sequence repeats, pseudogenes, and transposon elements.
Conclusions
Our study provides insights on the causes of variable coverage regions and a quantitative assessment of factors contributing to plant genome misassembly when using short reads.
Strengthening Retina Eye Care Services in Nepal: Retina Eye Care of Nepal project
Authors: Shrestha Arjun , Shrestha Chunu , Karki Pratap , Gurung Hara Maya , Naito Takeshi 
Published: June 2020

Abstract
BackgroundRetinal diseases are very difficult to treat. So, early diagnoses and preventions are very important. But, few eye doctors can treat patients with retinal diseases in Nepal.PurposeTo strengthen retina eye care services in NepalMethodsRetina Eye Care of Nepal (RECON) project was implemented from May 2016 to February 2019 in Nepal. Four Master Eye Doctors (MED) received Training of Trainers (TOT) from Tokushima University, Japan. MEDs developed training materials for different cadres of ophthalmic human resources, enhanced retina eye care facilities, and conducted retina-screening camp in Nepal.ResultTwenty ophthalmologists, 16 optometrists, 48 ophthalmic assistants and 17 ophthalmic nurses, 76 physicians and 28 health workers were trained in retina care. Eight outreach retina camps were conducted.ConclusionThe project was a novel approach to strengthen retina services in Nepal. The aim of the project was accomplished with the ultimate benefits to the needy retina patients who otherwise were going to miss the retina services.
Genome-Wide Association Studies and Whole-Genome Prediction Reveal the Genetic Architecture of KRN in Maize
Authors: An Yixin , Chen Lin , Li Yongxiang , Li Chunhui , Shi Yunsu , Zhang Dengfeng , Li Yu , Wang Tianyu 
Published: June 2020

Abstract
Background: Kernel row number (KRN) is an important trait for the domestication and improvement of maize. To explore the genetic basis of KRN has great research significance and can provide the valuable information for molecular assisted selection.Results: In this study, one single-locus method (MLM) and six multi-locus methods (mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, pKWmEB and ISIS EM-BLASSO) of genome-wide association studies (GWASs) were used to identify significant quantitative trait nucleotides (QTNs) for KRN in an association panel including 639 maize inbred lines that were genotyped by the MaizeSNP50 BeadChip. In three phenotyping environments and with best linear unbiased prediction (BLUP) values, seven GWAS methods revealed different numbers of KRN-associated QTNs, ranging from 11 to 177. Based on these results, seven important regions for KRN located on chromosomes 1, 2, 3, 5, 9, and 10 were identified by at least three methods and in at least two environments. Moreover, 49 genes from the seven regions were expressed in different maize tissues. Among the 49 genes, ARF29 (Zm00001d026540, encoding auxin response factor 29) and CKO4 (Zm00001d043293, encoding cytokinin oxidase protein) were significantly related to KRN based on expression analysis and candidate gene association mapping. Whole-genome prediction (WGP) for KRN was also performed, and we found that the KRN-associated tagSNPs achieved a high prediction accuracy. The best strategy was to integrate the total KRN-associated tagSNPs identified by all GWAS models.Conclusions: These results aid in our understanding of the genetic architecture of KRN and provide useful information for genomic selection for KRN in maize breeding.