bluuebunny/crossref_metadata_2025_split huggingface dataset:
A four-step strategy for handling missing outcome data in randomised trials affected by a pandemic
Authors: Cro Suzie , Morris Tim P , Kahan Brennan C , Cornelius Victoria R , Carpenter James R 
Published: June 2020

Abstract
Background
The coronavirus pandemic (Covid-19) presents a variety of challenges for ongoing clinical trials, including an inevitably higher rate of missing outcome data, with new and non-standard reasons for missingness. International drug trial guidelines recommend trialists review plans for handling missing data in the conduct and statistical analysis, but clear recommendations are lacking.
Methods
We present a four-step strategy for handling missing outcome data in the analysis of randomised trials that are ongoing during a pandemic. We consider handling missing data arising due to (i) participant infection, (ii) treatment disruptions and (iii) loss to follow-up. We consider both settings where treatment effects for a ‘pandemic-free world’ and ‘world including a pandemic’ are of interest.
Results
In any trial, investigators should; (1) Clarify the treatment estimand of interest; (2) Establish what data are missing for the estimand at hand; (3) Perform primary analysis under the most plausible missing data assumptions followed by; (4) Sensitivity analysis under alternative plausible assumptions. To obtain an estimate of the treatment effect in a ‘pandemic-free world’, data from participants clinically affected by the pandemic (directly via infection or indirectly via treatment disruptions) are not relevant and can be set to missing. For primary analysis, a missing-at-random assumption that conditions on all observed data that are expected to be associated with both the outcome and missingness may be most plausible. For the treatment effect in the ‘world including a pandemic’, all participant data is relevant and should be included in the analysis. For primary analysis, a missing-at-random assumption – potentially incorporating a pandemic time-period indicator and participant infection status – or a missing-not-at-random assumption with a poorer response may be most relevant, depending on the setting. In all scenarios, sensitivity analysis under credible missing-not-at-random assumptions should be used to evaluate the robustness of results. We highlight controlled multiple imputation as an accessible tool for conducting sensitivity analyses.
Conclusions
Missing data problems will be exacerbated for trials active during the Covid-19 pandemic. This four-step strategy will facilitate clear thinking about the appropriate analysis for relevant questions of interest.
Media representations of COVID-19 public health policies: assessing the portrayal of essential health services in Canadian print media
Authors: Ogbogu Ubaka , Hardcastle Lorian 
Published: June 2020

Abstract
Aims: The study assessed how the Canadian print media represented essential healthcare services during the COVID-19 pandemic, including the controversial decision to include liquor and cannabis stores in essential services lists.Methods: Quantitative content analysis of sixty-seven articles published in major Canadian English language newspapers between March 23 and April 1, 2020. Articles were analyzed and coded by two raters. Ratings were analyzed in SPSS.Results and Discussion: Few articles in the sample discussed essential healthcare services and the inclusion of liquor and cannabis stores in essential services lists. Majority of the articles that discussed both topics framed the discussion positively and consistently with current knowledge and evidence.Conclusion: Canadian print media representations of essential healthcare services and associated public debate are largely descriptive and, therefore, fail to engage critically with or advance public understanding of an important health policy issue.
Comparative Parameters Evaluation of Internal Combustion Engines Naturally Aspired and Supercharged With Hybrid Turbocharger
Authors: Rares Chiriac , Chiru Anghel 
Published: June 2020

Abstract
Internal combustion engines have an operating efficiency that can be exploited to increase their performance. Some of the waste gases can be recovered through technical solutions such as turbocharging. The turbocharging solution is one of the most popular technical solutions for increasing the energy performance of internal combustion engines. This requires an analysis of the energy balance of the internal combustion engine. This shows that there is a significant reserve of energy in the exhaust gases, which can be used to increase the engine efficiency. One solution is to use this energy to drive a turbine coupled with an electric generator. This article aims to present the result of the experimental research of the hybrid turbocharger, simulating and validating the new solutions for increasing the energy performance of internal combustion engines through hybrid turbochargers using a coupled electric generator. The simulations will be performed using AMESim software developed by Siemens to demonstrate through calculations the efficiency of new solutions, such as a hybrid turbocharger. The tests will be performed using an diesel internal combustion engine with a cylinder capacity of 1.9 liters which is also simulated with AMESim software. The residual exhaust gases of the internal combustion engine will drive the hybrid turbocharger turbine and generate electricity. Electricity can then be used for storage in the car battery or for consumption by the car's electrical system. The article also includes a comparative study between the power and torque of the naturally aspirated internal combustion engine equipped with a hybrid turbocharger.
Construction and Analysis of a circRNA-Mediated ceRNA Network in Lung Adenocarcinoma
Authors: Wang Zhaojun , Li Haifeng , Wei Li , Zhang Junhang 
Published: June 2020

Abstract
Background: Circular RNAs (circRNAs), a new class of regulatory noncoding RNAs, are involved in gene regulation and may play a role in cancer development. This study aimed to identify circRNAs involved in lung adenocarcinoma (LUAD) using bioinformatics analysis.Methods: CircRNA (GSE101684, GSE101586), miRNA (GSE135918), and mRNA (GSE130779) microarray datasets were downloaded from the Gene Expression Omnibus (GEO) database to identify differentially expressed circRNAs (DECs), miRNAs (DEMs), and mRNAs (DEGs) in LUAD. Circinteractome and StarBase were used to predict miRNAs and mRNAs, respectively. A circRNA-miRNA-mRNA-ceRNA network was constructed. Patient survival was analyzed using UALCAN, and a sub-network was established.Results: Hsa_circ_0072088 was identified as a differentially expressed (upregulated) circRNA in the two datasets. Intersection analysis identified hsa-miR-532-3p and hsa-miR-942 as the two miRNAs with the highest potential for binding to hsa_circ_0072088. Differential expression analysis and target gene prediction were performed to build a ceRNA network of hsa_circ_0072088 using Circinteractome/StarBase 3.0. Intersection analysis showed that TMEM52, IL24, POF1B, KIF1A, NHS, LBH, HIST2H2BE, ABCC3, PYCR1, CD79A, IGF2BP3, ANKRD17, GTSE1, MKI67, CLSPN, PLAU, LUC7L, MAGIX, GPATCH4, and ABAT were potential downstream mRNAs. The association between the expression level of 20 DEGs and LUAD patient survival was analyzed using UALCAN, which showed that IGF2BP3, MKI67, CD79A, and ABAT were related to patient survival.Conclusion: The circRNA hsa_circ_0072088, the miRNAs hsa-miR-532-3p and hsa-miR-942-5p, and the genes IGF2BP3, MKI67, CD79A, and ABAT may serve as prognostic markers in LUAD.
Proximally displaced medial humeral epicondyle fracture in pediatric patients: A clinical case series
Authors: Xu Lujie , Ye Wensong , Li Haibing , Xu Jingfang , Zhu Weiwei , Yang Yi 
Published: June 2020

Abstract
Background

Medial epicondyle fracture comprises a considerable proportion of pediatric elbow injury. The fracture fragment is typically pulled distally by the muscle and the ligament. This study aims to suggest proper recognition of a subset of the fracture that differs from its usual presentation.
Methods

A retrospective case study was conducted during 2011–2016. Of those cases, a subset was identified as proximally displaced (atypical) ones. Distinctive radiologic images, as well as the injury causes, demographic data, clinical signs, treatment ways, and final follow-ups regarding these atypical ones, were presented and discussed. The fracture mechanism was carefully inferred from former theories and the operative findings, and a tentative management strategy was suggested.
Results

Seven out of 112 cases were distinguished as the atypical, which represents 6.25% of the whole sample. Injury causes were all direct or combined direct/indirect force injuries instead of indirect force mostly seen in the typical. Five were operated while two nonoperatively treated. Operated cases revealed stripping of medial epicondyle from its surrounding periosteum/muscle origin or even cartilage. The fracture fragment was either pulled by proximal periosteum or even proximally dissociated. The outcomes of those atypical were mostly acceptable despite some minor defects.
Conclusion

The proximally displaced cases do constitute a portion of medial humeral epicondyle fracture in children. As well as its skeletal manifestation, awareness of its injury mechanism and soft tissue damage is required. Precise restoration of its anatomical structure might be vital for its treatment. Further scientific work is needed regarding its mechanism and management.
Level of evidence:
Level 4.
Employment Changes among Chinese Family Caregivers of Long-Term Cancer Survivors
Authors: Liu Siqi , Su Mingzhu , Yao Nengliang , Zhang Nan , Wang Jialin , Anderson Roger. T. , Sun Xiaojie 
Published: June 2020

Abstract
Background To describe the effect that providing cancer care to long-term cancer survivors has on the employment status of family caregivers (FCGs), and identify cancer-related characteristics that influence FCGs’ employment status in the post-treatment phase in China. Methods We surveyed 1155 cancer survivors (>1 year since completing treatment) from the cross‐sectional study “China Survey of Experiences with Cancer”. Participants reported changes in employment status of their FCGs. Descriptive statistics characterized the sample of survivors and FCGs’ employment status. Separate multivariable logistic regression models were conducted to examine the association between participant cancer characteristics and changes in FCGs’ employment status. Results In the primary treatment phase, 45.6% of all FCGs reduced their working hours and 17.4% stopped working altogether. In the post-treatment phase, 25.2% of FCGs reduced working hours and 6.6% stopped working. A higher probability of change in employment status among FCGs was associated with the following cancer-related characteristics: late-stage diagnosis, chemotherapy treatment, comorbidity, and limited ability to perform physical and mental tasks. Conclusions Cancer treatment and post-treatment demands may have a great number of impacts on the employment and economic productivity of Chinese FCGs. Interventions to assist them in maintaining employment are warranted across the whole survivorship trajectory.
New mutation in PTEN identified in patient with rare bilateral choroidal ganglioneuroma
Authors: Jiang Zhaoxin , Zhang Ting , Chen Chonglin , Sun Limei , Li Songshan , Ding Xiaoyan 
Published: June 2020

Abstract
Background
Choroidal ganglioneuroma is an extremely rare tumor, with little known regarding its pathogenesis. The present study aimed to investigate the phenotype and genetic alterations in one sporadic patient with rare bilateral choroidal ganglioneuroma.
Methods
A 6-year-old boy with histological diagnosis of bilateral ganglioneuroma was recruited in this study. Comprehensive ophthalmic examinations were performed in the patient. Genomic DNA was extracted from peripheral blood collected from the patient, the patient's unaffected family members, and from 200 unrelated control subjects from the same population. Whole exome sequencing was carried out and raw reads were aligned to the human genome reference (hg19) using the Burrows Wheeler Aligner. All available family members were subjected to Sanger sequencing for segregation analysis.
Results
Bilateral and extensive retinal detachments were observed in OCT. The diffuse thickening of choroid was identified in B scan and MRI. Genetic analysis revealed the presence of a novel heterozygous PTEN frameshift mutation, c.498delA (p.Thr167LeufsTer16), in exon 6. It was identified in the affected individual, but not in any of the unaffected family members. Genetic analysis showed that there was no mutant in neurofibromatosis-related genes. There were no obvious abnormalities in other organs in comprehensive systemic examinations.
Conclusions
A novel de novo PTEN mutation was identified in a bilateral choroidal ganglioneuroma case. Although PTEN mutation has been considered to induces multiple abnormalities, choroidal ganglioneuroma can be the first manifestation without abnormalities in other organs. Further studies are needed to confirm this new association between choroidal ganglioneuroma and the PTEN mutation.
The effects of gasification technology on IGFC system efficiency
Authors: Li Pingping , Jin Xianlin , Guo Zhongshan , You Xiaobin , Li Hu , Yao Jinsong , Jiang Lilong , Li Chufu 
Published: June 2020

Abstract
As one of the significant part of IGFC (integrated gasification fuel cell) system, coal gasification technology has an important effect on system efficiency as well as technological process. To figure out what kind of gasifier technology could benefit IGFC system most, we select two representative gasifiers for comparison, which are E-Gas gasifier and Shell gasifier. In this study MW-level E-gas IGFC system and Shell IGFC system models are developed respectively, moreover, the energy analysis of two systems are carried out simultaneously. The results show that SOFC DC Power efficiency and system net plant efficiency of E-gas IGFC system are 52.82% and 50.89% , both higher than Shell IGFC system, which are 49.24% and 49.74%; under the same design conditions, gasifier with high content of CH 4 would be easier to obtain higher SOFC power efficiency as well as system net efficiency. The present work is helpful to provide gasifier selection suggestions for large-scale IGFC system.
Long Non-Coding RNA BCYRN1 Exerts an Oncogenic Rrole in Colorectal Cancer through Regulating miR-204-3p/KRAS Axis
Authors: Yang Liu , Zhang Yinan , Bao Jun , Feng Ji-Feng 
Published: June 2020

Abstract
Background: It has been well documented that long non-coding RNAs (lncRNAs) regulate numerous characteristics of cancer, including proliferation, migration, metastasis, apoptosis, even metabolism. LncRNA BCYRN1 (BCYRN1) is a newly identified brain cytoplasmic lncRNA with 200-nucleotide, which was discovered highly expressed in tumor tissues of cancer, including hepatocellular carcinoma, gastric cancer and lung cancer. However, the roles of BCYRN1 in colorectal cancer (CRC) remain obscure. This study was designed to reveal the acts of BCYRN1 in the occurrence and progression of CRC. Methods: RT-PCR was used to detect the expression level of BCYRN1 in tumor tissues and CRC cell lines. Knock down BCYRN1 in CRC cells, evaluate cell proliferation changes by CCK-8 test, EdU test, and Ki-67 and PCNA expression; evaluate cell migration and invasion changes by wound healing assay, Transwell assay and invasion-related protein expression . Through flow cytometry analysis to assess whether BCYRN1 regulates apoptosis of CRC cells. The dual luciferase reporter gene detects the competitive binding of BCYRN1 to miR-204-3p. In vivo experiments to evaluate the effect of BCYRN1 on tumor development. TargetScan analysis and dual luciferase reporter gene detect the target gene of miR-204-3p. Rescue experiments verified the effect of BCYRN1 on CRC by regulating the effect of miR-204-3p on KRAS.Results: We found that compared with normal tissues and human intestinal epithelial cells (HIECs), BCYRN1 levels were significantly increased in tumor tissues and cell lines of CRC. We further determined that knockdown of BCYRN1 inhibited proliferation, migration, invasion, and promoted apoptosis of CRC cells. In addition, bioinformatics analysis and dual luciferase reporter assay showed that BCYRN1 served as a competitive endogenous RNA (ceRNA) to regulate the development of CRC through competitively binding to miR-204-3p. Further studies proved that overexpression of miR-204-3p reversed the effects of BCYRN1 on CRC. Next, TargetScan analysis and dual luciferase reporter assay indicated that KRAS was a target gene of miR-204-3p and negatively regulated by miR-204-3p. A series of rescue experiments showed that BCYRN1 affected the occurrence and development of CRC by regulating the effects of miR-204-3p on KRAS. In addition, tumorigenic experiments in CRC model mice confirmed that down-regulated BCYRN1 effectively inhibited tumor growth. Conclusions: Our findings suggested that BCYRN1 plays a carcinogenic role in CRC by regulating the miR-204-3p/KRAS axis.
Hill-based Dissimilarity Indices and Null Models for Analysis of Microbial Community Assembly
Authors: Modin Oskar , Liebana Raquel , Saheb-Alam Soroush , Wilén Britt-Marie , Suarez Carolina , Hermansson Malte , Persson Frank 
Published: June 2020

Abstract
Background: High-throughput amplicon sequencing of marker genes, such as the 16S rRNA gene in Bacteria and Archaea, provides a wealth of information about the composition of microbial communities. To quantify differences between samples and draw conclusions about factors affecting community assembly, dissimilarity indices are typically used. However, results are subject to several biases and data interpretation can be challenging. The Jaccard and Bray-Curtis indices, which are often used to quantify taxonomic dissimilarity, are not necessarily the most logical choices. Instead, we argue that Hill-based indices, which make it possible to systematically investigate the impact of relative abundance on dissimilarity, should be used for robust analysis of data. In combination with a null model, mechanisms of microbial community assembly can be analyzed. Here, we also introduce a new software, qdiv, which enables rapid calculations of Hill-based dissimilarity indices in combination with null models.Results: Using amplicon sequencing data from two experimental systems, aerobic granular sludge (AGS) reactors and microbial fuel cells (MFC), we show that the choice of dissimilarity index can have considerable impact on results and conclusions. High dissimilarity between replicates because of random sampling effects make incidence-based indices less suited for identifying differences between groups of samples. Determining a consensus table based on count tables generated with different bioinformatic pipelines reduced the number of low-abundant, potentially spurious amplicon sequence variants (ASVs) in the data sets, which led to lower dissimilarity between replicates. Analysis with a combination of Hill-based indices and a null model allowed us to show that different ecological mechanisms acted on different fractions of the microbial communities in the experimental systems.Conclusions: Hill-based indices provide a rational framework for analysis of dissimilarity between microbial community samples. In combination with a null model, the effects of deterministic and stochastic community assembly factors on taxa of different relative abundances can be systematically investigated. Calculations of Hill-based dissimilarity indices in combination with a null model can be done in qdiv, which is freely available as a Python package (https://github.com/omvatten/qdiv). In qdiv, a consensus table can also be determined from several count tables generated with different bioinformatic pipelines.
Multiple Alu exonizations in 3’UTR of a primate specific isoform of CYP20A1 creates a potential miRNA sponge
Authors: Bhattacharya Aniket , Jha Vineet , Singhal Khushboo , Fatima Mahar , Singh Dayanidhi , Chaturvedi Gaura , Dholakia Dhwani , Kutum Rintu , Pandey Rajesh , Bakken Trygve E. , Seth Pankaj , Pillai Beena , Mukerji Mitali 
Published: June 2020

Abstract
Background: Alu repeats contribute to phylogenetic novelties in conserved regulatory networks in primates. Exaptation of Alus in transcript isoforms could nucleate large-scale mRNA-miRNA interactions and modulate cellular outcomes. Result: Using a functional genomics approach, we report a transcript isoform of an orphan gene, CYP20A1 (CYP20A1_Alu-LT) that arise through exonization of 23 Alus in 3’UTR and is expressed in higher primates. CYP20A1_Alu-LT, confirmed by 3’RACE, is an outlier in length (9kb) and is expressed in multiple cell lines. Using publicly available datasets, we demonstrate its presence in single nucleus RNA-seq of 15928 human cortical neurons (including rosehip neurons). miRanda predicts ~4700 miRNA recognition elements (MREs; with threshold< -25kcal/mol) for ~1000 miRNAs, which have primarily originated within the 3’UTR-Alus post exonization. CYP20A1_Alu-LT could be a potential multi-miRNA sponge as it harbours ≥10 MREs for 140 miRNAs and has cytosolic localization. In order to test this further, we explored whether expression of CYP20A1_Alu-LT correlates with genome wide mRNAs harboring similar MRE targets. We carried out RNAseq with conjoint miRNA-seq analysis in primary human neurons as we observed CYP20A1_Alu-LT to be downregulated during heat shock response and upregulated in HIV1-Tat treatment. CYP20A1_Alu-LT expression was positively correlated with 380 genes that were significantly downregulated in heat shock and upregulated in Tat and harboured MREs for a set of nine expressed miRNAs that were also enriched in CYP20A1_Alu-LT. The enrichment of MREs in the 380 genes were significant compared to random sets of expressed (p=4.716e-12) as well as differentially expressed genes (p=8.134e-12). Gene ontology suggested involvement of these genes in neuronal development and hemostasis pathways. Conclusion: Our study suggests a potential role for CYP20A1_Alu-LT as miRNA sponge due to significant enrichment of MREs within Alus in a transcript isoform specific manner. This highlights a novel component of Alu-miRNA mediated transcriptional modulation that could govern specific physiological outcomes in higher primates.