bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patient and Public Involvement in doctoral research: Reflections and experiences of the PPI contributors and researcher
Authors: Dawson Shoba , Ruddock Angela , Parmar Veena , Morris Rebecca , Cheraghi-sohi Sudeh , Giles Sally , Campbell Stephen 
Published: April 2020

Abstract

Background:Patient and Public Involvement (PPI) has received considerable attention in the last two decades and working in partnership and co-design have now become a prerequisite in health services research in the UK. However, there is a lack of evidence and consistency in recording PPI and related activities. Researchers and PPI contributors are encouraged to record and reflect on the impact of PPI on research. There is significant variation in the way PPI contributors are involved, and it is often limited to some stages of the research cycle than others, without any reflections on the decision-making process for such involvement or any transferable learning. This has resulted in failure to provide a narrative of the research journey including researchers’ and PPI contributors’ personal reflections of involvement. Therefore, this paper provides an exemplar of what PPI in a doctoral research context should look like by providing a detailed account of how PPI was embedded in a doctoral research project, the PPI contributors and researcher’s reflections and key recommendations for involving people specifically in doctoral research.Methods:A reflective approach was taken using data from PPI contributor and researcher notes, e-mail correspondence, meeting notes. Data is presented narratively to reflect on the experiences of involvement throughout the research cycle.Results:Undertaking PPI enhanced the quality and relevance of the doctoral research, contributed to the recruitment of study participants, data analysis and dissemination. Building trust and relationships with PPI contributors was key to continued involvement throughout the life of the project and beyond. There is a need to adopt flexible approaches rather than a one-size-fits-all model when working with PPI contributors. Reflections by PPI contributors and the researcher emphasises that involvement was a rewarding experience. Conclusions: This paper contributes to the wider literature by providing an exemplar of how PPI can be embedded in doctoral research and demonstrates the value of PPI to the research process and the individuals involved. We also present recommendations on how PPI can be incorporated by doctoral and postdoctoral researchers when planning PPI in their research project.
A Novel Signature Based On Mtorc1 Pathway In Hepatocellular Carcinoma
Authors: Mo Zhuomao , Zhang Shuqiao , Zhang Shijun 
Published: April 2020

Abstract
BackgroundmTORC1 signal pathway play a role in the initiation and progression of hepatocellular carcinoma (HCC), but no relevant gene signature was developed. This research aimed to explore the potential correlation between mTORC1 signal pathway and HCC and establish the related genes signature.MethodsHCC cases were retrieved from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO) databases. The genes to be included in mTORC1-assiociated signature were selected by performing univariate, multivariate Cox regression analysis and lasso regression analysis. Then, the signature was verified by survival analysis and multiple receiver operating characteristic (ROC) curve. Moreover, the correlation between signature and immune cells infiltration was investigated. Furthermore, a nomogram was established and evaluated by C-index and calibration plot.ResultsThe signature was established with the six genes (ETF1, GSR, SKAP2, HSPD1, CACYBP and PNP). Under the grouping from signature, patients in the high- risk group showed worse survival than those in the low-risk group in both three datasets. The signature was found significantly associated with the infiltration of B cells, CD4+T-cells, CD8+T-cells, dendritic cells, macrophages and neutrophils. The univariate and multivariate Cox regression analysis indicated that mTORC1 related signature can be the potential independent prognostic factor in HCC. Finally, the nomogram involved age, gender, stage and signature have been established.ConclusionThe mTORC1 associated gene signature established and validated in our research could be used as a potential prognostic factor in HCC. *These authors contributed equally.
Genomic circular RNA expression profile analysis indicated hsa_circRNA_000780 as a diagnostic marker for gastric cancer
Authors: Song Jian , Yu Shuyong , Zhong Dunjing , Yang Weizhong , Jia Zhen , Yuan Guihong , Li Ping , Zhang Ronglin , Li Yini , Zhong Guobing , Chen Zhaowei 
Published: April 2020

Abstract
Background: This study aimed to find the specific circular RNA (circRNA) for gastric cancer (GC) and lay the foundation for the early diagnosis of GC.Methods: Four patients with GC were selected for this study. The total RNA of their cancer tissues and adjacent tissues was extracted, and the circRNA was screened. The top eight upregulated and downregulated circRNAs with statistical significance between GC and paired adjacent nontumorous tissues were identified using real-time fluorescent quantitative polymerase chain reaction (PCR). The expression level of circRNA was identified by quantitative reverse transcription PCR in 78 cases of GC and its adjacent tissues, and in the gastric juice of 30 patients with chronic nonatrophic gastritis, 30 with chronic atrophic gastritis, 21 with early GC, and 57 with advanced GC.Results: A total of 445 circRNAs, including 69 upregulated and 376 downregulated circRNAs, were found to be significantly aberrantly expressed in GC tissues. Most of the differentially expressed circRNAs originated from chr1, chr3, chr4, chr6, and chr11. Hsa_circRNA_000780 was significantly downregulated in 80.77% of GC tissues. Its level in GC tissues correlated with the tumor size, tumor stage, T stage, venous invasion, carcinoembryonic antigen, and carbohydrate antigen 19-9 expression. More importantly, hsa_circRNA_000780 was found in the gastric juice of early and advanced GC.Conclusions: This study uncovered the new hsa_circRNA expression profile in human GC. Among them, hsa_circRNA_000780 was significantly downregulated in GC tissues and gastric juice. It had the potential to be used as a novel biomarker for the screening of early GC.
The effect of two surgical approach Lordosis correction in degenerative lumbar diseases: minimally invasive oblique lumbar interbody fusion (OLIF) versus transforminal lumbar interbody fusion (TLIF)
Authors: Li Renjie , Shao Xiaofeng , Jiang Weimin 
Published: April 2020

Abstract
Background: The present study aimed to compare clinical outcomes and radiographic results of oblique lumbar interbody fusion (OLIF) with transforaminal lumbar interbody fusion (TLIF) in patients with lumbar spondylolisthesis.Methods: We retrospectively reviewed and compared 28 patients who underwent OLIF (OLIF group) and 35 who underwent TLIF (TLIF group). The operation time, intraoperative hemorrhage, bed rest duration, and length of hospital stay were compared between the 2 groups. Clinical results were evaluated with the ODI and VAS for back and leg pain. Radiological results were evaluated with disc height (DH), foraminal height (FH), fused segment lordosis (FSL) and lumbar lordosis (LL).Results: The OLIF group had less intraoperative blood loss, shorter operative time, bed rest time, and hospital stay than TLIF group (P<0.05). The OLIF group had lower VAS scores for back pain and lower VAS scores for leg pain after surgery compared with before surgery (P<0.05), The OLIF group had lower ODI after surgery compared with before surgery (P<0.05). The was no significant difference in decrease value in VAS and ODI after surgery between the two groups (P>0.05). No significant differences were found in DH, FH and LL between the 2 groups preoperatively (P>0.05). The OLIF group showed higher DH and FH than the TLIF group at all time points (P<0.05). No significant differences were found in FSH between the 2 groups at any time point.Conclusions: OLIF has similar good long-term clinical outcomes of TLIF with the additional benefits of less initial postoperative pain, early rehabilitation, shorter hospitalization, and fewer complications.
DeephageTP: A Convolutional Neural Network Framework for Identifying Phage-specific Proteins from metagenomic sequencing data
Authors: Chu Yunmeng , Guo Shun , Cui Dachao , Zhang Haoran , Fu xiongfei , Ma Yingfei 
Published: April 2020

Abstract
Background: Bacteriophage (phage) is the most abundant and diverse biological entity on the Earth. This makes it a challenge to identify and annotate phage genomes efficiently on a large scale. Portal (portal protein), TerL (large terminase subunit protein) and TerS (small terminase subunit protein) are the three specific proteins of the tailed phage. Here, we develop a CNN (convolutional neural network)-based framework, DeephageTP, to identify these three proteins from metagenome data. The framework takes one-hot encoding data of the original protein sequences as the input and extracts the predictive features in the process of modeling. The cutoff loss value for each protein category was determined by exploiting the distributions of the loss values of the sequences within the same category. Finally, we tested the efficacy of the framework using three real metagenomic datasets. Result: The proposed multiclass classification CNN-based model was trained by the training datasets and shows relatively high prediction performance ( A ccuracy : Portal, 98.8%; TerL, 98.6%; TerS, 97.8%) for the three protein categories, respectively. The experiments using the independent mimic dataset demonstrate that the performance of the model could become worse along with the increase of the data size. To address this issue, we determined and set the cutoff loss values (i.e., TerL: -5.2, Portal: -4.2, TerS: -2.9) for each of the three categories, respectively. With these values, the model obtains high performance in terms of Precision in identifying the TerL and Portal sequences (i.e, ~ 94% and ~ 90%, respectively) from the mimic dataset that is 20 times larger than the training dataset. More interestingly, the framework identified from the three real metagenomic datasets many novel phage sequences that are not detectable by the two alignment-based methods (i.e., DIAMOND and HMMER). Conclusion: Compared to the conventional alignment-based methods, our proposed framework shows high performance in identifying phage-specific protein sequences with a particular advantage in identifying the novel protein sequences with remote homology to their known counterparts in public databases. Indeed, our method could also be applied for identifying the other protein sequences with the characteristic of high complexity and low conservation. The DeephageTP is available at https://github.com/chuym726/DeephageTP .
Variability of the Bacillus anthracis tryptophan operon
Authors: Eremenko Eugene Ivan , Bobrysheva Olga , Pisarenko Sergey , Ryazanova Alla , Semenova Olga , Aksenova Lyudmila , Kovalev Dmitry , Pechkovskii Grigorii , Evchenko Anna , Kulichenko Alexander 
Published: April 2020

Abstract
BackgroundBacillus anthracis is a causal agent of a zoonotic disease relevant for many countries, and is an agent of bioterrorism. Meanwhile, the reasons for the dependence on tryptophan of some strains with altered virulence have not been established with an almost complete absence of information on the tryptophan operon of this pathogen. In this study, we report gene variability and the structure of the tryptophan operon in B. anthracis strains of the three main lineages.ResultsFor in silico analysis we used 112 B. anthracis genomes, including 68 of those available at the GenBank database and 44 sequenced at our institute. The B. anthracis tryptophan operon has an ancestral structure with a complete set of seven partially overlapping genes. The results show that the variability of all seven tryptophan operon genes is determined by the presence of single nucleotide polymorphisms and InDels. The trpA genes of strains of the main lineage B and trpG genes of strains of the C lineage are pseudogenes and the proteomes lack the corresponding enzymes of the biosynthetic pathway, which may explain the dependence of the strains of line B on tryptophan. ConclusionIn this study, the differences in tryptophan operon genes for B. anthracis strains belonging to different main lineages were demonstrated for the first time. Mutation in the gene of the tryptophan synthase subunit alpha can explain the dysfunction of this enzyme and the dependence on tryptophan in strains of the main lineage B. Identified features suggest a further study of the dependence on tryptophan in B. anthracis strains of the main lineage B and may be of interest from the point of view of intraspecific evolution of the anthrax pathogen.
Ileal bile acid transporter inhibitor improves hepatic steatosis by changing the gut microbiota dysbiosis in NAFLD model mice
Authors: Matsui Masahiro , Fukunishi Shinya , Nakano Takashi , Ueno Takaaki , Higuchi Kazuhide , Asai Akira 
Published: April 2020

Abstract
Background & Aim:

Non-alcoholic fatty liver disease (NAFLD) which is characterized by excessive fat deposition in the liver that is not attributable to consumption of alcohol, highly prevalent in all countries. However, therapeutic agents approved for the treatment of NAFLD are lacking. An ileal bile acid transporter inhibitor (IBATi) which represents a new mode of treatment of chronic idiopathic constipation, leads to increased delivery of bile acids to the colon. We investigated the effect of IBATi for NAFLD through modification of the gut microbiota in mice.
Results

When HFD mice were treated with IBATi, their body weight gain and serum LDL levels were significantly suppressed and NAFLD activity score was significantly decreased. Treatment with IBATi ameliorated the increase of ileal Fgf15 mRNA and the decrease hepatic Cyp7a1 mRNA in HFD mice. The microbial compositions of the feces from these mice were analyzed using 16S rRNA sequencing. The decrease of α-diversity in gut microbiota induced by HFD was recovered by the IBATi treatment. To establish a cause-effect of the improvement efficacy of IBATi for NAFLD, we recolonized antibiotic solution-treated mice reared in SPF conditions by fecal microbiome transplantation (FMT) using stool from the HFD or HFD + IBATi mice. From FMT, the gut microbiota from HFD + IBATi mice prevented hepatic steatosis caused by HFD.
Conclusions

IBATi improves hepatic steatosis by changing the gut microbiota dysbiosis in NAFLD model mice.
Eucommia Ulmoides Flavones as Antibiotic Alternatives in a Low-protein Diet Improve Growth Performance and Intestinal Health in Weaning Piglets
Authors: Yuan Daixiu , Wang Jing , Xiao Dingfu , Li Jiefeng , Liu Yanhong , Tan Bie 
Published: April 2020

Abstract

Background
Eucommia ulmoides flavones (EUF), have been demonstrated to attenuate the inflammation and oxidative stress of piglets. This study was designed to test whether EUF could be as an antibiotic alternative to support growth performance and maintain intestinal health in weanling-piglets. Weaned-piglets (n = 480) were assigned into 3 groups and fed with a low-protein basal diet (NC), or supplementation with antibiotics (PC) or 0.1‰ EUF (EUF). Blood, intestinal contents and intestine were collected on d-15 and d-35, respectively.
Results
The results showed that the body weight on d-35, average daily gain and gain : feed from d 15 to d 35 and d 0 to d 35 in piglets of PC and EUF treatments were higher than (p < 0.05) these in NC treatment, whereas PC and EUF treatments decreased (p < 0.05) the diarrhea index of weanling piglets. Dietary supplementation of EUF significantly enhanced (p < 0.05) the serum concentrations of total protein, alanine transaminase and the immunoglobulin G on d-15 of piglets compared to piglets in NC treatment. EUF supplementation increased (p < 0.05) the jejunal and ileal villus height and the population of ileal lactic acid bacteria on d-15 but remarkable decreased (p < 0.05) the population of ileal coliform bacteria on d-15 and d-35.
Conclusion
These findings indicated the antibiotic alternative capacity of EUF in piglets exhibiting by improving growth performance and intestinal morphology, decreasing colonization of coliform bacteria and diarrhea index in weanling piglets.
Adropin and Apelin -12, two better predictors of metabolic syndrome in obese children
Authors: xiao yanfeng , zhang hong ai , zhang mei zhen , yin chunyan 
Published: April 2020

Abstract
Background: Metabolic syndrome (MetS) is the most extensively described condition associated with childhood and adolescent obesity and is a challenging public health issue. Studies regarding the specificity and sensitivity of serum levels of adropin and apelin -12 as predictors of MetS are limited. The aim was to evaluate the prospective association between adropin and apelin -12 concentrations and MetS and sensitivity as predictors of MetS in the obese children.Methods:: This study involved 138 children. The study group included obese subjects with MetS and the two control groups included obese without MetS and normal weight subjects. Anthropometric parameters and clinical data were collected. Plasma levels of apelin -12, adropin, leptin, adiponectin and TNF-α were measured. Results: Obese children with MetS had significantly higher levels of apelin -12 and significantly lower levels of adropin compared to those without MetS. In logistic regressions, we identified that apelin -12 was risk factor for metabolic syndrome and adropin was the protecting factors of having MetS after adjustment for age, sex and puberty. Furthermore, adropin and apelin -12 are two more sensitive predictors of metabolic syndrome than leptin and adiponect using ROC method. Conclusion: Serum adropin and apelin -12 levels can be useful biomarkers for evaluation of the risk of MetS in obese children. This may provide a novel approach for treatment or prevention of MetS development.
Bioinformatics analysis reveals different gene expression patterns in chondrocytes from knee and finger joints: implications for the effect of mechanical stress in the osteoarthritic development
Authors: Mei Wei , Yin Songjiang , Shi Xiaoqing , Li Xiaochen , Zhang Li , Xing Runlin , Zhang Nongshan , Wang Peimin , Huang Guicheng 
Published: April 2020

Abstract
Background

Mechanical stress has been well known to be a significant risk factor for the onset and progression of osteoarthritis (OA). The objective of this study is to clarify the key genes and the signaling pathways which is associated with the effect of mechanical stress on OA development.
Results

A total of 213 Differentially expressed genes (DEGs) were identified in cultured chondrocytes from knee and finger joints, including 101 up- and 112 down-regulated genes, which brought an enrichment in positive or negative regulation of cell proliferation, positive regulation of cell division, positive regulation of apoptotic process and embryonic limb morphogenesis. Two comparison cohorts shared 122 overlapping genes including 49 up- and 73 down-regulated genes, which enriched in DNA replication, cell division, calcium ion binding and positive regulation of apoptotic process. Twelve hub overlapped genes including Cyclin dependent kinase 1 (CDK1), Kinesin family member 11 (KIF11), Mitotic checkpoint serine/threonine kinase (BUB1) and Mitotic arrest deficient 2 like 1 (MAD2L1) were defined and predicted miRNAs of the genes mainly enriched in Transforming growth factor beta (TGF-β) signaling pathway, Wnt signaling pathway and Mitogen activated kinase-like protein (MAPK) signaling pathway.
Conclusions

Mechanical stress shown multiple influences on chondrocytes, physiologically necessary for maintaining chondrocyte homeostasis and promoting cartilage development, pathologically help for cartilage destruction and OA development via boosting chondrocyte differentiation and hypertrophy and accelerating cell apoptosis.
Impact of nonsteroidal anti-inflammatory drug administration for 12 months on renal function
Authors: Hayashi Kazuhiro , Miki Kenji , Kajiyama Hiroshi , Ikemoto Tatsunori 
Published: April 2020

Abstract
Background: The use of nonsteroidal anti-inflammatory drugs (NSAIDs) is associated with an increased risk of renal complications. Resolution of renal side effects following NSAID administration has been observed following short-term use. Thus, the aim of the present study was to investigate whether switching from long-term NSAID administration to tramadol hydrochloride/acetaminophen (TA) combination tablets results in reversal of renal side effects.Methods: This was a longitudinal retrospective study of 99 patients with chronic musculoskeletal pain. The patients were administrated NSAIDs daily during the first 12 months followed by daily TA combination tablets for 12 months. Estimated glomerular filtration rate (eGFR) and serum levels of aspartate aminotransferase and alanine transaminase were measured at baseline, after NSAIDs administration, and after TA administration.Results: eGFR was significantly reduced following 12-month NSAIDs administration (median, from 84.0 mL/min/1.73 m2 to 72.8 mL/min/1.73 m2), and further reduction was prevented following the subsequent 12-month TA administration. Reduction in eGFR was less in patients who received celecoxib (median, -1.8 mL/min/1.73 m2) during the first 12 months. There was no significant difference in aspartate aminotransferase and alanine transaminase in each period.Conclusions: Thus, patients receiving NSAIDs for 12 months displayed both reversible and irreversible reduction of eGFR upon cessation of NSAIDs and switching to TA. Our data highlights the potential safety benefit of utilizing multimodal analgesic therapies to minimize the chronic administration of NSAIDs.
Predictors of macular pigment and contrast threshold in normolipemic subjects aged 45-65
Authors: Olmedilla-Alonso Begoña , Rodríguez-Rodríguez Elena , Beltrán-de-Miguel Beatriz , Estévez-Santiago Rocío , Sánchez-Prieto Milagros 
Published: April 2020

Abstract
Objective: The dietary carotenoids lutein and zeaxanthin are transported in the bloodstream by lipoproteins and selectively captured in the retina where they constitute macular pigment. There are no lutein and zeaxanthin dietary intake recommendations nor desired blood/tissue concentrations for the general population. The aim of this study was to determine the lutein and zeaxanthin dietary intake, their serum concentrations, lipid profile, macular pigment optical density (MPOD) and the contrast sensitivity (CT), as visual outcome in normolipemic subjects age 45-65 (n=101). Methods: MPOD, L and Z in serum and dietary intake were determined using heterochromatic flicker photometry, high-performance liquid chromatography and 3-day food records. CT was measured with the CGT-1000 Contrast Glaretester at six stimulus sizes, with and without glare. Results: Lutein and zeaxanthin serum concentrations (median): 0.361 and 0.078 µmol/L. Lutein+zeaxanthin intake: 1.1 mg/d (median). MPOD: 0.34 du. Lutein+zeaxanthin intake correlates with their serum concentrations (ρ=0.333, p =0.001), which in turn correlates with MPOD (ρ=0.229, p =0.000) and with the fruit and vegetable consumption (ρ=0.202, p =0.001), but not with the lutein+zeaxanthin dietary intake. HDL-cholesterol correlated with lutein+zeaxanthin serum (ρ=0.253, p =0.000) and with CT under glare conditions (ρ range: 0.016–0.160). MPOD predictors: serum lutein+zeaxanthin, lutein+zeaxanthin/HDL-cholesterol and HDL-cholesterol (R 2 =15.9%). CT predictors: MPOD and sex (β coefficients ranges: -0.950,-0.392; -0.134,-0.393, respectively). Conclusion: There were correlations at all points in time in this sequence between lutein+zeaxanthin intake and the visual outcome and, HDL-cholesterol played a relevant role.