bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discrimination between human populations using a small number of differentially methylated CpG sites: A preliminary study using lymphoblastoid cell lines and peripheral blood samples of Caucasian and Chinese origin.
Authors: Daca-Roszak Patrycja , Jaksik Roman , Paczkowska Julia , Witt Michal , Zietkiewicz Ewa 
Published: April 2020

Abstract
Background Epigenetics is one of the factors shaping natural variability observed among human populations. A small proportion of heritable inter-population differences are observed in the context of both the genome-wide methylation level and the methylation status of individual CpG sites. It has been demonstrated that a limited number of carefully selected differentially methylated sites may allow discrimination between main human populations. However, most of the few published results have been performed exclusively on B-lymphocyte cell lines. Results The goal of our study was to identify a set of CpG sites sufficient to discriminate between Caucasian and Chinese populations based on the difference in the DNA methylation profile not only in cell lines but also in primary cell samples. The preliminary selection of CpG sites differentially methylated in these two populations (pop-diff-met CpGs) was based on the analysis of two groups of commercially available ethnically-specific B-lymphocyte cell lines, performed using Illumina Infinium Human Methylation 450 BeadChip Array. A subset of ten pop-diff-met CpGs characterized by the best differentiating criteria (|Mdiff|>1, q<0.05; lack of the confounding genomic features), and ten additional CpGs in their immediate vicinity, were further tested using pyrosequencing technology in both B-lymphocyte cell lines and in the primary samples of the peripheral blood representing two analyzed populations. To assess the population-discriminating potential of the selected set of CpGs (further referred to as “composite pop(CEU-CHB)-diff-met CpG marker”), three classification methods were applied. The predictive ability of the composite 8-site pop(CEU-CHB)-diff-met CpG marker was assessed using 10-fold cross-validation method on two independent sets of samples. Concussions Our results showed that less than 10 pop-diff-met CpG sites may distinguish Caucasian and Chinese populations; importantly, this small composite pop-diff-met CpG marker performs well in both lymphoblastoid cell lines and in non-homogenous blood samples.
Comparison of Conventional Fenestration Discectomy Versus Percutaneous Transforaminal Endoscopic Discectomy for Treating Lumbar Disc Herniation
Authors: Li Quanyi , zhou yongchun 
Published: April 2020

Abstract
Purpose: To compare the efficacy of conventional interlaminar fenestration discectomy (IFD) versus percutaneous transforaminal endoscopic discectomy (PTED) for treating lumbar disc herniation (LDH). Methods: The clinical data of 1,100 patients who had been diagnosed with LDH from January 2012 to December 2017 were retrospectively analysed. IFD was performed on the 605 patients in Group A, while PTED was performed on the 505 patients in Group B. The Oswestry Disability Index (ODI), Visual Analogue Scale (VAS) for pain, and modified Macnab criteria were adopted to evaluate the outcomes. Moreover, the surgery durations, intraoperative blood loss, postoperative off-bed activities, and postoperative lengths of hospital stay for the two groups were observed. Results: The follow-up period ranged from 24 months to 60 months, with an average duration of 43 months. As the excellent and good outcome rate was 93.5% in Group A and 92.6% in Group B, there were no significant differences in efficacy between the two groups (P > 0.05). However, Group B had significantly less intraoperative blood loss and shorter bed rest durations and postoperative lengths of hospital stay than did Group A (P < 0.05). There were two cases of postoperative recurrence in Group A and three in Group B. Conclusions: Although conventional IFD and PTED had similar levels of efficacy in treating LDH, transforaminal endoscopic discectomy exhibited several advantages, such as less trauma, less bleeding, and a shorter length of hospital stay, and it can be considered an ideal surgical option for treating LDH.Save and Continue
The pattern of serum lithium test requesting across three UK regions: a service evaluation of adherence to monitoring guidelines.
Authors: Fryer Anthony , Parfitt Ceri , Duff Christopher J , Scargill Jonathan , Green Lewis , Holland David , Heald Adrian H 
Published: April 2020

Abstract
Background Bipolar disorder is the fourth most common mental health condition, affecting ~1% of UK adults. Lithium is an effective treatment for prevention of relapse and hospital admission, and is widely recommended as a first-line treatment. We previously showed in other areas that laboratory testing patterns are variable with sub-optimal conformity to guidance. We therefore examined lithium results and requesting patterns relative to monitoring recommendations. Methods Data on lithium levels and intervals between requests were extracted from Clinical Biochemistry laboratory information systems at the University Hospitals of North Midlands, Salford Royal Foundation Trust and Pennine Acute Hospitals from 2012-2018 (46,555 requests; 3,371 individuals). Data were examined with respect to region/source of request, age and sex. Results Lithium levels on many requests were outside the recommended UK therapeutic range (0.4-0.99 mmol/L); 19.2% below the range and 6.1% above the range (median [Li]: 0.60 mmol/L). A small percentage were found at the extremes (3.2% at <0.1mmol/L, 1.0% at >1.4mmol/L). These findings were comparable across all sites. Most requests were from general practice (56.3%) or mental health units (34.4%), though those in the toxic range (≥1.4 mmol/L) were more likely to be from acute care or other secondary care units (63.9%). For requesting interval, there was a distinct peak at 12 weeks, consistent with guidance for those stabilised on lithium therapy. There was no peak evident at 6 months, as recommended for those aged <65 years on unchanging therapy. There was a peak at 0-7 days, reflecting those requiring closer monitoring (e.g. treatment initiation or for toxicity). However, for those with initial lithium concentrations within the BNF range (0.4-0.99 mmol/L), 69.4% of tests were requested outside expected testing frequencies. Conclusions Our data showed: (a) lithium levels are often maintained at the lower end of the recommended therapeutic range, (b) patterns of lithium results and testing frequency were comparable across three UK sites with differing models of care and, (c) re-test intervals demonstrate a noticeable peak at the recommended 3-monthly, but not at 6-monthly intervals. Many tests were repeated outside expected frequencies, indicating the need for additional work to minimise inappropriate testing.
Prediction and identification of immune genes related to the prognosis of patients with colon adenocarcinoma and its mechanisms
Authors: Chen Sihan , GD Cao , Wei Wu , Yida LU , Xiaobo He , Lei Yang , Ke Chen , Chen Bo , Xiong MM 
Published: April 2020

Abstract
Background: Colon adenocarcinoma(COAD) is a type of gastrointestinal tumor with a high degree of malignancy, and its immunotherapy method has been stagnant. Recently, with the development of network databases and the development of bioinformatics tools, we can analyze the data in the current database to find out which genes may be the target of immunotherapy for COAD.Methods: We use various codes and packages of R language to analyze the downloaded data, construct a riskScore model of immune genes and clinical data, and use Cox regression analysis to explore the clinical relationship between riskScore and COAD.Results: We found that seven immune genes associated with the survival prognosis of COAD were related to the construction of a riskScore model. And Cox regression analysis found that there was clinical significance and statistical significance between the riskScore model and clinical data of COAD. Some traditional immune microenvironment cells also increase their cell content with the increase of riskScore.Conclusions: We found 7 immune genes (SLC10A2, CXCL3, IGHV5-51, INHBA, STC1, UCN and OXTR) that affect the clinical prognosis of COAD patients and can construct a riskScore model. It may be a target for future COAD immunotherapy.
Learning Outcomes of a Flipped Classroom Teaching Approach in an Adult-health Nursing Course: A Quasi-Experimental Study
Authors: Fan Jun-Yu , Tseng Ying-Jung , Chao Li-Fen , Chen Shiah-Lian , Jane Sui-Whi 
Published: April 2020

Abstract
Background: New teaching strategies must be developed not only to enhance nurse’s competence but also to allow nurses to respond to the complex health care needs of today’s society. The purpose of this study was to explore the learning outcomes of a flipped classroom teaching approach in an adult-health nursing course for students in a two-year Bachelor of Science in Nursing program.Methods: The study had a quasi-experimental design. An 18-week flipped classroom teaching approach was applied in an adult-health nursing course. In total, 485 nursing students enrolled in the study, with 287 in the experimental group and 198 in the control group. The Self-Evaluated Core Competencies Scale, Metacognitive Inventory for Nursing Students, Self-Directed Learning Readiness Scale, and self-designed learning satisfaction questionnaire were used to evaluate the students’ learning outcomes.Results: The experimental group showed a statistically significant increase in the overall scores for self-evaluated core competencies, the “self-modification” subscale of the Metacognitive Inventory for Nursing Students, and in overall self-directed learning readiness; further, they also showed high levels of course satisfaction.Conclusions: A flipped classroom teaching approach had a positive impact on student’s learning motivation and contributed to better learning outcomes in an adult-health nursing course. The flipped classroom combined with hybrid teaching methods is a suitable and effective learning strategy for a registered nurse (RN) to Bachelor of Science in nursing (BSN) program to tackle today’s complex revolution in nursing curricula, and may enhance nursing students’ abilities to address numerous challenges.
CILP2 overexpression predicts poor prognosis in colorectal cancer
Authors: Huang Feng , Peng Yuanfei , Ye Qing , Chen Jinhu , Li Yangming , Liu Shengyuan , Xu Yangmei , Huang Lijie 
Published: April 2020

Abstract
Background: Cartilage Intermediate Layer Protein 2 (CILP2), a glycoprotein with mutations associated with abnormal blood lipid concentrations in normal and cardiovascular diseases patients, was barely reported with clinical features of tumors. We evaluated the role of CILP2 among all stages and histology in colorectal cancer (CRC) in the Cancer Genome Altas (TCGA), and furtherly verified using immunohistochemistry assay within human CRC tissues.
Materials and methods : Clinical information and RNA-seq data were derived from TCGA colorectal carcinoma cohort. CILP2 expression at mRNA level was estimated by bioinformatical analysis of TCGA cases. Tissue microarray (TMA) was constructed containing paraffin-embedded 64 pairs of CRC and matched adjacent normal tissues. The expression at protein level was detected in 64 pairs of CRC and matched adjacent normal tissues by immunohistochemical analysis. CILP2 expression level and its clinical value were estimated by bioinformatical analysis with linear and logistic regression. Survival analysis was performed between high and low groups of CILP2 expression by Cox regression analysis, and P value was calculated by log-rank test. Kaplan-Meier curves were tested by log-rank test.
Results : CILP2 was significantly higher expressed in the colorectal cancer tissues when compared with paired adjacent normal tissues in TCGA cohort ( P <0.001) and in TMA cohort ( P =0.001). In addition, CILP2 high-expression was strongly correlated with T3/4 stage ( P =0.001), N1/2/3 stage ( P =0.005), M1 stage ( P =0.048), and higher clinical stage (UICC 2010 stage) ( P <0.001) in TCGA cohort, and also positively associated with T3/4 stage ( P =0.022) and higher clinical stage (UICC 2010 stage) ( P =0.03) in TMA cohort. Furthermore, CILP2 overexpression predicted poor prognosis and could be as an independent prognostic factor ( P =0.003).
Conclusion : We revealed that CILP2 is associated with advanced stages and could play a role as an independent predictor of poor survival in colorectal cancer.
Key words: CILP2; Colorectal cancer; TCGA; Immunohistochemistry; Prognosis
Invasive pulmonary aspergillosis in immunocompetent patients hospitalised with influenza A-related pneumonia: a multicenter retrospective study
Authors: Chen Liang , Han Xiudi , Li YanLi , Zhang Chunxiao , Xing Xiqian 
Published: April 2020

Abstract
Background Increasing cases of pulmonary aspergillosis (IPA) in immunocompetent patients with severe influenza have been reported. Howevere, the risk factors for occurence and death are largely unknown.Methods Data of hospitalised patients with influenza A-related pneumonia (FluA-p) obtained from five teaching hospitals from 2031 to 2018, were reviewed. Univariate and multivariate logistical regression analyses were performed to determine the risk factors involved in the acquisition and 60-day mortality in IPA patients. Results Of the 693 FluA-p patients included in the study, 3.0% (21/693) were IPA patients with a 60-day mortality of 42.9% (9/21). Adjusted for confounders, a Cox proportional hazard model showed that IPA was associated with increased risk for 60-day mortality [hazard ratio ( HR) 4.336, 95% confidence interval (CI) 1.191-15.784, p = 0.026] in FluA-p patients. A multivariate logistic regression model confirmed that age (odd ratio ( OR) 1.147, 95% CI 1.048-1.225, p = 0.003), systemic corticosteroids use before IPA diagnosis ( OR 33.773, 95% CI 5.681-76.764, p < 0.001), leukocytes > 10×10 9 /L ( OR 1.988, 95% CI 1.028-6.454, p = 0.029) and lymphocytes < 0.8×10 9 /L on admission ( OR 34.813, 95% CI 1.676-73.006, p = 0.022), were related with the acquisition of IPA. Early neuraminidase inhibitor use ( OR 0.290, 95% CI 0.002-0.584, p = 0.021) was associated with a decreased risk for a 60-day mortality in IPA patients. Conclusions Our results showed that IPA worsen the clinical outcomes of FluA-p patients. The risk factors for the acquisition and death were helpful for the clinicians in preventing and treating IPA.
Recurrence and retreatment of anterior communicating artery aneurysm after endovascular treatment
Authors: Jang Chang Ki , Chung Joonho , Lee Jae Whan , Huh Seung Kon , Son Nak-Hoon , Park Keun Young 
Published: April 2020

Abstract
Background

To describe our experiences with endovascular treatment (EVT) of anterior communicating artery (Acom) aneurysms (AcomAs), and to evaluate the incidence of recurrence and risk factors for recurrence and retreatment

Methods

The study comprised 260 patients who were treated at a single center between January 2010 and December 2018. Patients who had EVT, including stent-assisted coiling of AcomA, were included. All medical records were retrospectively reviewed. The incidence of recurrence and risk factors for recurrence and retreatment were evaluated. Univariate analysis and multivariate logistic regression analysis were conducted.

Results

Recurrence of AcomA occurred in 38 (14.6%) patients. Mean follow-up duration was 27 months. Multivariate logistic regression analysis indicated that ruptured aneurysm (odds ratio [OR] 3.55, P=0.001), dome direction (anterior) (OR 3.86, P=0.002), maximal diameter (OR 1.19, P=0.02), and mean age (OR 0.96, P=0.02) were independent risk factors for aneurysm recurrence. Among cases of recurrence, 10 (3.8%) patients had major recurrence. Ruptured aneurysm (OR 14.7, P=0.004), maximal diameter (OR 1.56, P=0.02), inflow angle (OR 1.04, P=0.03), and Raymond-Roy classes II and III (incompletely occluded status of coiling) (OR 6.19, P=0.03) showed significant relation to retreatment in multivariate logistic regression analysis.

Conclusions

In our study, recurrence rate of AcomA after EVT was 14.6%. Rupture, anterior dome direction, maximal diameter, and mean age were significantly associated with recurrence. Retreatment rate of recurrent AcomA cases after EVT was 3.8%. Patients with AcomA with large inflow, rupture, large size, or incomplete occlusion may be at a high risk of retreatment of recurring aneurysm.
How plant production in the Mongolian grasslands is affected by wind-eroded coarse-textured topsoil
Authors: Kong Kaman , Nandintsetseg Banzragch , Shinoda Masato 
Published: April 2020

Abstract
While it is known that soil erosion by wind in drylands results in soil loss and redistribution and changes the texture of topsoil, there is little information about how these changes in the topsoil might affect the productivity of vegetation and if they result in degradation of the grasslands in wind-eroded regions such as Mongolian grasslands. In this study, we compared two different scenarios of vegetation growth, namely a wind-eroded scenario and an actual field condition, on two different grasslands in Mongolia (steppe and desert steppe) using an ecosystem model. The simulations of the wind-eroded scenario were based on a topsoil (0–0.1 m depth) with 1% clay and 99% sand, designed to represent an extremely wind-eroded soil surface that had permanently lost the fine clay particles and had gained sand particles. The effects of temperature, nutrient and water stresses on plant production were quantitively estimated. The model gave reasonably good simulations of the vegetation and soil water dynamics during the growing seasons (April–September) from 2002–2011. The simulation results showed that water had more effect on plant production than nitrogen and temperature at the two sites, and stresses because of a lack of water and nutrients generally affected plant production in the wind-eroded coarse-textured topsoil. Plant production was 20.2% lower in the wind-eroded scenario than in the actual field condition in the desert steppe under water-stressed conditions but plant production was slightly higher (5.0%) in the wind-eroded scenario on the steppe that received more rainfall, because of a reverse texture effect, where water continues to infiltrate from the coarse topsoil (0–0.1 m depth) to the deeper root-zone (0.1–0.3 m depth) because of lower evapotranspiration from soil, and facilitates growth. When this happens, there is enough soil moisture in the root-zone, and plant growth is mostly affected by the nitrogen supply.
Integrated Genomic and Transcriptomic Analysis Revealed Mutation Patterns of De-differentiated Liposarcoma and Leiomyosarcoma
Authors: Liu Wenshuai , Tong Hanxing , Zhang Chenlu , Zhuang Rongyuan , Guo He , Chentao Lv , Yang Hua , Lin Qiaowei , Guo Xi , Wang Zhiming , Wang Yan , Shen Feng , Wang Shengzhou , Wang Guan , Dai Chun , Lu Weiqi , Zhang Yong , Zhou Yuhong 
Published: April 2020

Abstract
Background Treating patients with advanced sarcomas is challenging due to great histologic diversity among different subtypes. Leiomyosarcoma (LMS) and liposarcoma (LPS) are the most common histologic types of soft tissue sarcoma (STS). Although both LMS and de-differentiated LPS (DDLPS) are relatively aggressive and have a high rate of recurrence, they have significant differences in histology, biology, and clinical behaviors. Methods 32 STS (20 LMS and 12 DDLPS) samples and matched peripheral blood were collected from Zhongshan Hospital, Fudan University with patient consents. WES was conducted on all the tumor/blood pairs. Somatic single nucleotide variations (SNV) and indel were identified using Genome Analysis Toolkits (GATK). Recurrent somatic copy-number alterations (SCNA) were called using GISTIC2.0. RNA-Seq was further conducted, then their chromosome rearrangement was revealed using STAR-Fusion. Next, differential gene expression analysis and pathway enrichment analysis were performed using DeSeq2 and NetwokAnalyst. Stromal and immunological landscape profiling was conducted using MCP-counter. Results WES identified different genetic variation patterns in LMS and DDLPS. Amplification of oncogenes is prominent in DDLPS, while loss of function mutation and deletion of tumor suppressors mostly occur in LMS. A focal amplification affecting chromosome 12q13–15 region which encodes MDM2, CDK4 and HMGA2, is notable in DDLPS. Mutations in tumor suppressors such as TP53, ATRX, PTEN, and RB1 are identified in LMS. RNA-seq confirmed overexpression of MDM2, CDK4 and HMGA2 in DDLPS and down-regulation of TP53 and RB1 in LMS. It also revealed different fusion patterns between LMS and DDLPS. The rate of gene fusion is significantly higher in DDLPS than in LMS (p=0.007) and fusion transcripts involving chromosome 12 can only be found in DDLPS. Stromal and immunological profiling indicate that microenvironmental signatures are highly correlated with histologic types, and DDLPS have more endothelial cell and fibroblast content than LMS. Conclusions Our analysis revealed recurrent genetic variation in LMS and DDLPS. DDLPS harbor frequent fusion events and may produce neoepitopes, which can be targeted to produce safer CAR-T (Chimeric Antigen Receptor T) cells for immunotherapy. Additionally, our study suggested the tumor microenvironment of sarcoma can potentially be correlated to patients' clinical outcomes and used to guide personalized treatment.
Bronchiolar Adenoma with ERBB2 exon 20 insertion: report of four cases and review of the literature
Authors: Wu Qian , Li Lin , Zheng Ke , Tang Yuan , Jiang Lili 
Published: April 2020

Abstract
Objectives: Ciliated muconodular papillary tumor (CMPT) is a rare peripheral lung tumor and is considered to be a subtype of Bronchial Adenoma (BA). Although recent studies have suggested that BA belongs to a neoplastic disease, the complete histogenesis of BA is not fully understood and molecular data is limited. Methods: We demonstrated clinicopathologic features of four cases of BA and performed immunohistochemical and next generation sequencing to characterize its molecular features. Besides, a review of previous literature was done to comprehensively conclude the molecular characteristic of this disease.Results: We found ERBB2, EGFR, BRAF and AKT1 mutations in BAs. It’s the first time that ERBB2 exon 20 insertion has been reported in BA. Conclusion: BA is a rare pulmonary disease mainly affected elderly Asian patients. More and more abnormal molecular changes were observed, which confirmed the neoplastic nature of BA. However, it also raise the debate about BA’s biological behavior.