bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of an Autophagy-Related Gene Signature that Can Improve Prognosis of Hepatocellular Carcinoma Patients
Authors: Huo Xingxing , Qi Jian , Huang Kaiquan , Bu Su , Yao Wei , Chen Ying , Nie Jinfu 
Published: August 2020

Abstract
Background: Autophagy is a programmed cell degradation mechanism that has been associated with several physiological and pathophysiological processes, including malignancy. Improper induction of autophagy has been proposed to play a pivotal role in the progression of hepatocellular carcinoma (HCC).Methods: Univariate Cox regression analysis of overall survival (OS) was performed to identify risk-associated autophagy-related genes (ARGs) in HCC data set from The Cancer Genome Atlas (TCGA). Multivariate cox regression was then performed to develop a risk prediction model for the prognosis of 370 HCC patients. The multi-target receiver operating characteristic (ROC) curve was used to determine the model’s accuracy. Besides, the relationship between drug sensitivity and ARGs expression was also examined.Results: A total of 62 differentially expressed ARGs were identified in HCC patients. Univariate and multivariate regression identified five risk-associated ARGs (HDAC1, RHEB, ATIC, SPNS1 and SQSTM1) that were correlated with OS in HCC patients. Of importance, the risk-associated ARGs were independent risk factors in the multivariate risk model including clinical parameters such as malignant stage (HR=1.433, 95% CI=1.293-1.589, P<0.001). In addition, the area under curve for the prognostic risk model was 0.747, which indicates the high accuracy of the model in prediction of HCC outcomes. Interestingly, the risk-associated ARGs were also correlated with drug sensitivity in HCC cell lines.Conclusion: We developed a novel prognostic risk model by integrating the molecular signature and clinical parameters of HCC, which can effectively predict the outcomes of HCC patients.
Effects of Biofilm Transfer and Electron Mediators Transfer on Klebsiella quasipneumoniae&nbsp;sp.203 Electricity Generation Performance in MFCs
Authors: Guo Yating , Wang Guozhen , Zhang Hao , Wen Hongyu , Li Wen 
Published: August 2020

Abstract
Background: Extracellular electron transfer ( EET ) is essential in improving the power generation performance of electrochemically active bacteria ( EAB ) in microbial fuel cells ( MFCs ) . Currently, the EET mechanisms of dissimilatory metal-reducing ( DMR ) model bacteria Shewanella oneidensis and Geobacter sulfurreducens have been thoroughly studied. Klebsiella has also been proved to be an EAB capable of EET, but the EET mechanism has not been perfected. This study investigated the effects of biofilm transfer and electron mediators transfer on Klebsiella quasipneumoniae sp. 203 electricity generation performance in MFCs.Results: Herein, we covered the anode of MFC with a layer of microfiltration membrane to block the effect of the biofilm mechanism, and then explore the EET of the electron mediator mechanism of K.quasipneumoniae sp. 203 and electricity generation performance. In the absence of short-range electron transfer, we found that K.quasipneumoniae sp. 203 can still produce a certain power generation performance, and coated-MFC reached 40.26 mW / m 2 at a current density of 770.9 mA / m 2 whereas the uncoated-MFC reached 90.69 mW / m 2 at a current density of 1224.49 mA / m 2 . The difference in the electricity generation performance between coated-MFC and uncoated-MFC was probably due to the microfiltration membrane covered in anode, which inhibited the growth of EAB on the anode. Therefore, we speculated that K.quasipneumoniae sp. 203 can also perform EET through the biofilm mechanism. The protein content, the integrity of biofilm and the biofilm activity all proved that the difference in the electricity generation performance between coated-MFC and uncoated-MFC was due to the extremely little biomass of the anode biofilm. To further verify the effect of electron mediators on electricity generation performance of MFCs, 10µM 2,6-DTBBQ, 2,6-DTBHQ and DHNA were added to coated-MFC and uncoated-MFC. Combining the time-voltage curve and CV curve, we found that 2,6-DTBBQ and 2,6-DTBHQ had high electrocatalytic activity toward the redox reaction of K.quasipneumoniae sp.203-inoculated MFCs. It was also speculated that K. quasipneumoniae sp. 203 produced 2,6-DTBHQ and 2,6-DTBBQ.Conclusions: To the best of our knowledge, the three modes of EET did not exist separately. K.quasipneumoniae sp.203 will adopt the corresponding electron transfer mode or multiple ways to realize EET according to the living environment to improve electricity generation performance.
Cost-effectiveness analysis of ceritinib vs. crizotinib in previously untreated anaplastic lymphoma kinase (ALK)-positive non-small cell lung cancer (NSCLC) in Hong Kong
Authors: Loong Herbert , Wong Carlos K H , Leung Linda K S , Chan Catherine P K , Chang Andrea , Zhou Zheng-yi , Xie Jipan , Gibbs Meaghan 
Published: August 2020

Abstract
Introduction: Lower-dose ceritinib (450mg) once-daily with food was approved in 2018 in Hong Kong (HK) for first-line treatment of patients with anaplastic lymphoma kinase-positive (ALK+) advanced non-small cell lung cancer (NSCLC). This study examined the cost-effectiveness of ceritinib vs. crizotinib in the first-line treatment of ALK+ NSCLC from a HK healthcare service provider's or government's perspective. Methods: Costs and effectiveness of first-line ceritinib vs. crizotinib over a 20-year time horizon was evaluated using a partitioned survival model with three health states (stable disease, progressed disease, and death). The efficacy data for ceritinib were obtained from a phase 3 trial comparing ceritinib with chemotherapy for advanced non-small cell lung cancer (ASCEND-4) and extrapolated using parametric survival models. Long-term survival associated with crizotinib were estimated using hazard ratio of crizotinib vs. ceritinib obtained from matching-adjusted indirect comparison based on ASCEND-4 and PROFILE 1014 trials. Drug acquisition, administration, adverse events costs, and medical costs associated with each health state were obtained from public sources and converted to 2018 US Dollars. Incremental costs per quality-adjusted-life-year (QALY) and life-year (LY) gained were estimated for ceritinib vs. crizotinib. Results: The base case results showed that ceritinib was associated with 3.22 QALYs, 4.51 LYs, and total costs of $157,581 over 20 years. Patients receiving crizotinib had 2.68 QALYs, 3.85 LYs, and $150,424 total costs over the same time horizon. The incremental cost per QALY gained for ceritinib vs crizotinib was $13,343. Results were robust to deterministic sensitivity analyses in most scenarios. Conclusion: Ceritinib offers a cost-effective option compared to crizotinib for previously untreated ALK+ advanced NCSLC in HK.
Arabidopsis paralogous genes RPL23aA&nbsp;and RPL23aB&nbsp;encode functionally equivalent proteins
Authors: Xiong Wei , Chen Xiangze , Zhu Chengxin , Zhang Jiancong , Lan Ting , Liu Lin , Mo Beixin , Chen Xuemei 
Published: August 2020

Abstract
Background: In plants, each ribosomal protein (RP) is encoded by a small gene family but it is largely unknown whether the family members are functionally diversified. There are two RPL23a paralogues genes ( RPL23aA and RPL23aB ) found in Arabidopsis thaliana. Knock-down of RPL23aA using RNAi impeded growth and led to morphological abnormalities, whereas knock-out of RPL23aB had no observable phenotype, thus these two RPL23a paralogous proteins have been used as examples of ribosomal protein paralogues with functional divergence in many published papers. Results: In this study, we characterized T-DNA insertion mutants of RPL23aA and RPL23aB . A rare non-allelic non-complementation phenomenon was found in the F1 progeny of the rpl23aa X rpl23ab cross, which revealed a dosage effect of these two genes. Both of RPL23aA and RPL23aB were found to be expressed almost in all examined tissues as revealed by GUS reporter analysis. Expression of RPL23aB driven by the RPL23aA promoter can rescue the phenotype of rpl23aa , indicating these two proteins are actually equivalent in function. Interestingly, based on the publicly available RNA-seq data, we found that these two RPL23a paralogues were expressed in a concerted manner and the expression level of RPL23aA was much higher than that of RPL23aB at different developmental stages and in different tissues. Conclusions: Our findings suggest that RPL23aA and RPL23aB proteins actually have equal function and presence of paralogous genes for the RPL23a protein in plants might be necessary to maintain its adequate dosage.
Current status of periodontitis and its association with tobacco use among adult population of Sunsari district, Nepal
Authors: Goel Khushboo , Sharma Shivalal , Baral Dharnidhar , Agrawal Santosh 
Published: August 2020

Abstract
Background: Tobacco products are considered significant but preventable factors related to initiation and progression of periodontal diseases. We assessed the prevalence of periodontitis and evaluated its association with tobacco use and other factors among the adult population of eastern Nepal.Methods: A community-based cross-sectional study was conducted in the rural municipalities in the province one of eastern Nepal. A total of 440 individuals were interviewed with a set of a standardized pre-tested semi-structured questionnaire. Data on social demographics, adverse oral habits followed by periodontal clinical examination were recorded. Prevalence of periodontitis was assessed by a case definition given by CDC-AAP. Univariate and multivariate logistic regression analysis was used to measure the association between tobacco use and other factors with periodontitis.Results: The overall prevalence of periodontitis was found to be 71.6%. Majority (85.4%) of tobacco users had periodontitis and they were significantly associated with the disease and its severity. The study identified age groups, 45 – 65 years (AOR=7.58, 95% CI, 3.93-14.61), plaque index (AOR=1.01, 95% CI, 1.00-1.02), smoking (AOR=3.14, 95% CI, 1.36-7.27), khaini users (smokeless tobacco, AOR=2.27, 95% CI, 1.12-4.61) and teeth loss (AOR=2.02, 95% CI, 1.21-3.38) as the significant factors associated with periodontitis.Conclusion: The prevalence of periodontitis is high in the surveyed rural adult population. Along with age, plaque, teeth loss and smoking, smokeless tobacco in the form of khaini are identified as significant factors contributing to periodontitis.
New Findings on Submerged Patch Reefs and Reefal Carbonate Rocks at Water Depths of 70-100 meters on the Insular Shelf off Miyako-jima, Southern Ryukyus, Japan
Authors: Inoue Takahiko , Arai Kohsaku 
Published: August 2020

Abstract
Sub-bottom profiling (SBP) surveys and bathymetric mapping conducted off the shore of Miyako-jima, which belongs to the southern Ryukyus in the Ryukyu Island Arc, have revealed the presence of mound-shaped structures 3-8 m high and 50-120 m wide at depths of 70-100 m. The SBP surveys showed that the mounds possess strong distinct, convex upward reflector shapes at the top, which we interpret as submerged reefs and reefal sediments. Additionally, modern stratified sediment layers that cover these mound-shaped structures indicate that those reefs began forming and advancing shoreward in a back-stepping fashion as a result of sea-level rise. An analysis of the mound distribution shown by SBP and multibeam echo sounding (MBES) surveys suggest that they might have been formed during the lowstand stage of sea-level change, which includes the Last Glacial Period, because the distribution of these mounds is limited to water depths of 70 m to 100 m, deeper than where present-day reefs grow. The SBP images hint that such high-resolution seismic profiles, accompanied by detailed bathymetric mapping off the reefal area, have the potential to provide effective indicators of not only coral reef paleoenvironment development, but also the tectonic setting of this offshore area.
A nationwide survey of intraoperative management for one-lung ventilation in Taiwan: time to accountable for diversity in protective lung ventilation
Authors: Kuo Chuan-Yi , Liu Ying-Tung , Chen Tzu-Shan , Lam Chen-Fuh , Wu Ming-Cheng 
Published: August 2020

Abstract
Background: There is a major paradigm shift for intraoperative mechanical ventilator support by the introduction of lung protective ventilation strategies to reduce postoperative pulmonary complications and improve overall clinical outcomes in non-thoracic surgeries. However, there is currently a lack of standardized practice guideline for lung protection during thoracic surgeries that require one-lung ventilation (OLV). This study aimed to collect the expert opinions of the thoracic anesthesiologists in perioperative care for OLV surgery in Taiwan.

Methods: This prospective cross-sectional study was undertaken in 16 tertiary hospitals in Taiwan from January to February 2019. A structured survey form was distributed across the participating hospitals and the thoracic anesthesiologists were invited to complete the form voluntarily. The survey form consisted of three parts, including the basic information of the institutional anesthesia care standards, ventilatory settings for a proposed patient receiving OLV surgery and expert opinions on OLV.

Results: A total of 71 thoracic anesthesiologists responded to the survey. Double-lumen tubes are the most commonly used (93.8%) airway devices for OLV. The most commonly recommended ventilator setting during OLV is a tidal volume of 6-7 ml/kg PBW (67.6%) and a PEEP level of 4-6 cmH2O (73.5%). Dual controlled ventilator modes are used by 44.1% of the anesthesiologists. During OLV, high oxygen fraction (FiO2 >0.8) is more commonly supplemented to achieve an oxygen saturation higher than 94%. The consensus of anesthesiologists on the indices for lung protection in thoracic surgery is considerably low. Large majority of the anesthesiologists (91.5%) highly recommend that an international clinical practice guideline on the protective lung ventilation strategy for thoracic anesthesia should be established.

Conclusions: This study found that the thoracic anesthesiologists in Taiwan share certain common practices in ventilator support during OLV. However, they are concerned about the lack of fundamental clinical evidences to support the beneficial outcomes of the current lung protective strategies applicable to OLV. Large-scale trials are needed to form an evidence-based clinical practice guideline for thoracic anesthesia.
Survival prediction models since liver transplantation - comparisons between Cox models and machine learning techniques
Authors: Kantidakis Georgios , Putter Hein , Lancia Carlo , de Boer Jacob , Braat Andries E , Fiocco Marta 
Published: August 2020

Abstract
Background: Predicting survival of recipients after liver transplantation is regarded as one of the most important challenges in contemporary medicine. Hence, improving on current prediction models is of great interest. Nowadays, there is a strong discussion in the medical field about machine learning (ML) and whether it has greater potential than traditional regression models when dealing with complex data. Criticism to ML is related to unsuitable performance measures and lack of interpretability which is important for clinicians. Methods: In this paper, ML techniques such as random forests and neural networks are applied to large data of 62294 patients from the United States with 97 predictors selected on clinical/statistical grounds, over more than 600, to predict survival from transplantation. Of particular interest is also the identification of potential risk factors. A comparison is performed between 3 different Cox models (with all variables, backward selection and LASSO) and 3 machine learning techniques: a random survival forest and 2 partial logistic artificial neural networks (PLANNs). For PLANNs, novel extensions to their original specification are tested. Emphasis is given on the advantages and pitfalls of each method and on the interpretability of the ML techniques. Results: Well-established predictive measures are employed from the survival field (C-index, Brier score and Integrated Brier Score) and the strongest prognostic factors are identified for each model. Clinical endpoint is overall graft-survival defined as the time between transplantation and the date of graft-failure or death. The random survival forest shows slightly better predictive performance than Cox models based on the C-index. Neural networks show better performance than both Cox models and random survival forest based on the Integrated Brier Score at 10 years. Conclusion: In this work, it is shown that machine learning techniques can be a useful tool for both prediction and interpretation in the survival context. From the ML techniques examined here, PLANN with 1 hidden layer predicts survival probabilities the most accurately, being as calibrated as the Cox model with all variables.
Rubidium chloride modulated the fecal microbiota community in mice
Authors: Chen Qian , He Zhiguo , Zhuo Yuting , Li Shuzhen , Yang Wenjing , Hu Liang , Zhong Hui 
Published: August 2020

Abstract
Background: The microbiota plays an important role in host health. Although rubidium (Rb) has been used to study for depression and cancers, the interaction between microbial commensals and Rb is still unexplored. To gain the knowledge of the relationship between Rb and microbes, 51 mice receiving RbCl-based treatment and 13 untreated mice were evaluated of their characteristics and bacterial microbiome changes.Results: The 16S ribosomal RNA gene sequencing of feces showed RbCl generally maintained fecal microbial community diversity, while the shifts in fecal microbial composition were apparent after RbCl exposure for the first time. RbCl significantly enhanced the abundances of Rikenellaceae, Alistipes, Clostridium XlVa and sulfate-reducing bacteria including Deltaproteobacteria, Desulfovibrionales, Desulfovibrionaceae and Desulfovibrio. While, RbCl significantly inhibited the abundances of Tenericutes, Mollicutes, Anaeroplasmatales, Anaeroplasmataceae and Anaeroplasma lineages. Besides, with regarding to the composition of archaea, RbCl significantly enhanced the abundances of Crenarchaeota, Thermoprotei, Sulfolobales, Sulfolobaceae and Sulfolobus lineages. Conclusions: These results revealed that enrichments of Clostridium XlVa and Alistipes could affect the levels of serotonin, a critical signaling molecule of brain-gut-microbiota axis. Therefore, anticancer and anti-depressant effects of RbCl might be partly mediated by modifying brain-gut-microbiota axis.
Characterizing glycosyltransferases by a combination of sequencing platforms applied to the leaf tissues of Stevia rebaudiana
Authors: Zhang Shaoshan , Liu Qiong , Lyu Chengcheng , Chen Jinsong , Xiao Renfeng , Chen Jingtian , Yang Yunshu , Zhang Huihui , Hou Kai , Wu Wei 
Published: August 2020

Abstract
Background: Stevia rebaudiana (Bertoni) is considered one of the most valuable plants because of the steviol glycosides (SGs) that can be extracted from its leaves. Glycosyltransferases (GTs), which can transfer sugar moieties from activated sugar donors onto saccharide and nonsaccharide acceptors, are widely distributed in the genome of S. rebaudiana and play important roles in the synthesis of steviol glycosides.Results: Six stevia genotypes with significantly different concentrations of SGs were obtained by induction through various mutagenic methods, and the contents of seven glycosides (stevioboside, Reb B, ST, Reb A, Reb F, Reb D and Reb M) in their leaves were considerably different. Then, NGS and single-molecule real-time (SMRT) sequencing were combined to analyse leaf tissue from these six different genotypes to generate a more complete and correct full-length transcriptome of S. rebaudiana . Two phylogenetic trees of glycosyltransferases (SrUGTs) were constructed by the neighbour-joining method and successfully predicted the functions of SrUGTs involved in SG biosynthesis. With further insight into glycosyltransferases (SrUGTs) involved in SG biosynthesis, the weighted gene co-expression network analysis (WGCNA) method was used to characterize the relationships between SrUGTs and SGs, and forty-four potential SrUGTs were finally obtained, including SrUGT85C2 , SrUGT74G1 , SrUGT76G1 and one SrUGT91D2, which have already been reported to be involved in the glucosylation of steviol glycosides, illustrating the reliability of our results.Conclusion: Combined with the results obtained by previous studies and those of this work, we systematically characterized glycosyltransferases in S. rebaudiana and forty-four candidate SrUGTs involved in the glycosylation of steviol glucosides were obtained. Moreover, the complete and correct full-length transcriptome obtained in this study will provide valuable support for further research investigating S. rebaudiana .
Leaf Open Time Sinogram (LOTS): A novel approach for Patient specific quality assurance of Total marrow irradiation
Authors: Thiyagarajan Rajesh , Sharma Dayananda Shamurailatpam , Kaushik Suryakant , Sawant Mayur , Krishnan Ganapathy , Nambiraj Arunai , CHILUKURI SRINIVAS , Sundar Sham , Patro Kartikeswar , Arjunan Manikandan , MP Noufal , Sivaraman Rangasamy , Easoee Jose , Jalali Rakesh 
Published: August 2020

Abstract
There is no ideal detector-phantom combination to perform patient specific quality assurance (PSQA) for total marrow (TMI) and Lymphoid (TMLI) irradiation plan. In this study, 3D dose reconstruction using mega voltage computed tomography detectors measured leaf open time sinogram (LOTS) was investigated for PSQA of TMI/TMLI patients in helical tomotherapy. The feasibility of this method was first validated for ten non-TMI/TMLI patients, by comparing reconstructed dose with a) ion-chamber (IC) and helical detector array (ArcCheck) measurement and b) planned dose distribution using 3Dγ analysis for 3%@3mm and dose to 98%(D98%) and 2%(D2%) of PTVs. Same comparison was extended for ten treatment plans from five TMI/TMLI patients. In all non-TMI/TMLI patients, reconstructed absolute dose was within ±1.8% of planned and IC measurement. The planned dose distribution agrees with reconstructed and ArcCheck measured dose with mean(SD) 3Dγ of 98.7%(1.57%) and 2Dγ of 99.48%(0.81%). The deviation in D98% and D2% were within 1.71% and 4.1% respectively. In all 25 measurement locations from TMI/TMLI patients, planned and IC measured absolute dose agrees within ±1.2%. Although sectorial fluence verification using ArcCHECK measurement for PTVs chest from five upper body TMI/TMLI plans showed mean±SD 2Dγ of 97.82%±1.27%, the reconstruction method resulted poor mean(SD) 3Dγ of 92.00%(±5.83%), 64.80%(±28.28%), 69.20%(±30.46%), 60.80%(±19.37%) and 73.2% (±20.36%) for PTVs brain, chest, torso, limb and upper body respectively. The corresponding deviation in median D98% and D2% of all PTVs were <3.8% and 9.5%. Re-optimization of all upper body TMI/TMLI plans with new pitch and modulation factor of 0.3 and 3 leads significant improvement with 3Dγ of 100% for all PTVs and median D98% and D2% <1.6%. LOTS based PSQA for TMI/TMLI is accurate, robust and efficient. A field width, pitch and modulation factor of 5cm, 0.3 and 3 for upper body TMI/TMLI plan is suggested for better dosimetric outcome and PSQA results.