bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strict bladder filling and rectal emptying during prostate SBRT - does it make a dosimetric or clinical difference?
Authors: Byun David Jaihun , Gorovets Daniel J. , Jacobs Lauren M. , Happersett Laura , Zhang Pengpeng , Pei Xin , Burleson Sarah , Zhang Zhigang , Hunt Margie , McBride Sean , Kollmeier Marisa A. , Zelefsky Michael J. 
Published: July 2020

Abstract
Background: To evaluate inter-fractional variations in bladder and rectum during prostate stereotactic body radiation therapy (SBRT) and determine dosimetric and clinical consequences. Methods: Eighty-five patients with 510 computed tomography (CT) images were analyzed. Median prescription dose was 40 Gy in 5 fractions. Patients were instructed to maintain a full bladder and empty rectum prior to simulation and each treatment. A single reviewer delineated organs at risk (OARs) on the simulation (Sim-CT) and Cone Beam CTs (CBCT) for analyses. Results: Bladder and rectum volume reductions were observed throughout the course of SBRT, with largest mean reductions of 86.9 mL (19.0%) for bladder and 6.4 mL (8.7%) for rectum noted at fraction #5 compared to Sim-CT (P<0.01). Higher initial Sim-CT bladder volumes were predictive for greater reduction in absolute bladder volume during treatment (ρ=-0.69; P<0.01). Over the course of SBRT, there was a small but significant increase in bladder mean dose (+4.5±12.8%; P<0.01) but no significant change in the D2cc (+0.8±4.0%; P=0.28). The mean bladder trigone displacement was in the anterior direction (+4.02±6.59 mm) with a corresponding decrease in mean trigone dose (-3.6±9.6%; P<0.01) and D2cc (-6.2±15.6%; P<0.01). There was a small but significant increase in mean rectal dose (+7.0±12.9%, P<0.01) but a decrease in rectal D2cc (-2.2±10.1%; P=0.04). No significant correlations were found between relative bladder volume changes, bladder trigone displacements, or rectum volume changes with rates of genitourinary or rectal toxicities. Conclusions: Despite smaller than expected bladder and rectal volumes at the time of treatment compared to the planning scans, dosimetric impact was minimal and not predictive of detrimental clinical outcomes. These results cast doubt on the need for excessively strict bladder filling and rectal emptying protocols in the context of image guided prostate SBRT and prospective studies are needed to determine its necessity.
Extracellular vesicles from human mesenchymal stem cells expedite chondrogenesis in 3D human degenerative disc cell cultures
Authors: Hingert Daphne , Ekström Karin , Aldridge Jonathan , Crescitelli Rosella , Brisby Helena 
Published: July 2020

Abstract
Background: Extracellular vesicles (EVs) from human mesenchymal stem cells (hMSCs) are known to be mediators of intercellular communication and has been suggested as possible therapeutic agents in many diseases. Their potential use in intervertebral disc (IVD) degeneration associated with low back pain (LBP) is yet to be explored. Since LBP affects more than 85% of the western population resulting in high socioeconomic consequences there is a demand for exploring new and possibly mini-invasive treatment alternatives. In this study, the effect of hMSCs derived small EVs (sEVs) on degenerated disc cells (DCs) isolated from patients with degenerative discs and chronic LBP was investigated in a 3D in vitro model. Methods: hMSCs were isolated from bone marrow aspirate and EVs were isolated from conditioned media of the hMSCs by differential centrifugation and filtration. 3D pellet cultures of DCs were stimulated with the EVs at 5x1010 vesicles/mL concentration for 28 days and compared to control. The pellets were harvested at day 7, 14, and 28 and evaluated for cell proliferation, viability, ECM production, apoptotic activity, chondrogenesis and cytokine secretions.Results: The findings demonstrated that treatment with sEVs from hMSCs resulted in more than 50% increase in cell proliferation and decrease in cellular apoptosis in degenerated DCs from this patient group. ECM production was also observed as early as in day 7 and was more than three times higher in the sEVs treated DC pellets compared to control cultures. Further, sEVs treatment suppressed secretion of MMP-1 in the DCs. Conclusion: hMSC derived sEVs improved cell viability and expedited chondrogenesis in DCs from degenerated IVDs. These findings open up for new tissue regeneration treatment strategies to be developed for degenerative disorders of the spine.
Circ_0002232 Acts as a Potential Biomarker for AML and Reveals a Potential ceRNA Network of Circ_0002232/miR-92a-3p/PTEN
Authors: Deng zhaoqun , Su Xiao-yu , Zhu Xin , Zhao Qian , Ke Jin-ming , Wu De-long , Yi Yun-yun , Yi Jing , Lin Jiang , Qian Jun , Deng Zhao-qun 
Published: July 2020

Abstract
Background: PTEN, known as a classical tumor suppressor, has been reported to be down-expressed in acute myeloid leukemia (AML) and affected the progression of AML patients. CircRNAs, an emerging type of non-coding RNAs, could act as competing endogenous RNAs (ceRNAs) and has been reported to regulate the expression of PTEN through sponging miRNA in many solid tumors. But there are rarely studies focused on the role of circ-PTEN in AML. Our research was aimed to investigate the expression level of circ_0002232, one of circular RNAs of PTEN, reveal the clinical significance and potential ceRNA interaction network in AML of it.Methods: Circ_0002232 expression in 117 AML patients and 48 controls was detected by using Real-time quantitative PCR. The diagnostic value of circ_0002232 expression was evaluated by receiver operating characteristic curve. Kaplan-Meier curves were used to analyse the impact of circ_0002232 for overall survival. CeRNA network of circ_0002232 was predicted by using interaction prediction websites.Results: Compared with controls, circ_0002232 was notably low-expressed in AML (P<0.001). According to the result of receiver operating characteristic curve, circ_0002232 expression could distinguish AML patients from controls (P<0.001). There were significant differences in patients’ age (P=0.002), FAB classifications (P=0.025), white blood cell count (P=0.034) and platelet count (P=0.047) between low-expressed circ_0002232 group and high-expressed circ_00022332 group. Moreover, there was a positive correlation between circ_0002232 expression and patients’ age (Pearson r=0.256, P=0.0053). Interestingly, we found that patients in low-expressed circ_0002232 group had better overall survival both in whole AML (P=0.019) and non-APL AML (P=0.044). Remarkably, the expression of circ_0002232 was positively correlated with PTEN (Pearson r=0.769, P<0.001). Furthermore, there was a negative correlation in AML between circ_0002232 and miR-92a-3p (Pearson r=-0.262, P=0.032), miR-92a-3p and PTEN (Pearson r=-0.358, P=0.019). Interaction prediction websites revealed that circ_0002232 might regulate the expression of PTEN through sponging miR-92a-3p and affect the process of AML.Conclusions: Circ_0002232, one of circRNAs of PTEN, was remarkably down-regulated in AML and could act as a promising biomarker for the diagnosis of AML. In addition, there might be a potential ceRNA interaction network of circ_0002232/miR-92a-3p/PTEN in AML.
The correlation of intraoperative hypotension and postoperative cognitive impairment: a meta-analysis of randomized controlled trials
Authors: Feng Xiaojin , Hu Jialing , Hua Fuzhou , Zhang Jing , Zhang Lieliang , Xu Guohai 
Published: July 2020

Abstract
Background: There is no consensus on whether intraoperative hypotension is associated with postoperative cognitive impairment. Hence, we performed a meta-analysis to evaluate the correlation of intraoperative hypotension and the incidence of postoperative delirium (POD) or postoperative cognitive dysfunction (POCD).Methods: We searched PubMed, Embase, and Cochrane Library databases to find randomized controlled trials (RCTs) in which reported the relationship between intraoperative hypotension and POD or POCD. The retrieval time is up to January 2020, without language restrictions. Quality assessment of the eligible studies was conducted by two researchers independently with the Cochrane evaluation system.Results: We analyzed five eligible RCTs. Based on the relative mean arterial pressure (MAP), participants were divided into low-target and high-target groups. For the incidence of POD, there were two studies with 99 participants in the low-target group and 94 participants in the high-target pressure group. For the incidence of POCD, there were four studies involved 360 participants in the low-target group and 341 participants in the high-target group, with a study assessed both POD and POCD. No significant difference between the low-target and the high-target group was observed in the incidence of POD (RR = 3.30, 95% CI 0.80 to 13.54, P = 0.10), or POCD (RR = 1.26, 95% CI 0.76 to 2.08, P = 0.37). Furthermore, it also demonstrates that intraoperative hypotension prolonged the length of ICU stay, but did not increased the mortality, the length of hospital stay, and mechanical ventilation (MV) time.Conclusions: There is no significant correlation between intraoperative hypotension and the incidence of POD or POCD. Keywords: Intraoperative hypotension, Postoperative delirium, Postoperative cognitive dysfunction, Meta-analysis
The protective effect of 3% diquafosol on meibomian gland morphology in glaucoma patients treated with prostaglandin analogs: a 12-month follow-up study
Authors: Guo Yue , Ha Jun Young , Piao Helong , Sung Mi Sun , Park Sang Woo 
Published: July 2020

Abstract
Background: To determine if 3% diquafosol (DQS) can preserve the meibomian gland morphology in glaucoma patients treated with prostaglandin analogs (PGA) for a 12-month follow-up period.Methods: This study included 84 eyes of 46 normal tension glaucoma (NTG) patients who were treated with either preservative-containing PGA (PC-PGA; 16 patients, 28 eyes), preservative-free PGA (PF-PGA; 21 patients, 39 eyes), or a combination of PC-PGA and 3% DQS (PC-PGA+DQS; 9 patients, 17 eyes). The meibography of the upper eyelid was acquired using Keratograph® 5M at baseline and at each follow-up (1, 3, 6, 9, and 12 months). Meibomian gland loss (MGL) was quantitatively analyzed by using ImageJ software. Results: In the PC-PGA group, MGL increased significantly from baseline to month 9 and month 12, whereas no significant changes were observed in the PF-PGA and PC-PGA+DQS groups during the entire 12 months. All groups showed similar MGL at each follow-up time from baseline to six months. However, MGL in the PC-PGA group was significantly higher than those in the PF-PGA and PC-PGA+DQS groups at the 9 and 12 months.Conclusions: Combining 3% DQS with PC-PGA was as effective as PF-PGA in preserving the meibomian gland morphology for at least 12 months. Our results suggest that 3% DQS may be a promising strategy for managing glaucoma patients with a high risk of developing meibomian gland dysfunction due to preservative-containing topical medications.
SARS-CoV-2 Origins and Evolution: Insights from Coronaviruses Recombination and Phylogenetic Analysis
Authors: Murahwa Alltalents Tutsirayi , Onywera Harris , Nindo Fredrick 
Published: July 2020

Abstract
Background: It is imperative in the midst of a global epidemic to investigate the origins of the infectious agent especially when it has reached parts of the world with either ailing economies or pre-existing political turmoil consistent with non-functional health systems. Methods: To explore the possibility of cross species infection, genomic recombination and the emergence of novel coronaviruses in the near future we carried out recombination and phylogenetic analysis to determine the spatio-temporal evolution and origins of the current SARS-CoV-2 virus. Results: Our findings prove using two robust recombination tools, RDPv4.100 and SimPlot3.5.1 analysis that SARS-CoV-2 is a recombinant of pangolin and bat RaTG13 sequences as been previously shown elsewhere. We also report one novel recombination event between two SARS-CoV-2 sequences (SARS-CoV-2 sequence, MT188341, SARS-CoV-2 sequence, MT293183). Bearing in mind that the prerequisite for recombination is the occurrence two viral sequences in the same reservoir, biological niche or host at the same time we postulate either co-infection with the two viral sequences, or superinfection, both scenarios have not been reported elsewhere. Conclusion: The possibility of recombination between the SARS-CoV-2 sequences poses the likelihood of the emergence of new and maybe more or less virulent “strains” of the virus. We believe that the future of science lies in our ability to be able to use computational based methods to predict the genetic sequences of infectious agents of the next epidemics. The addition of more SARS-CoV-2 sequences has a bearing on the understanding of the origin, evolution and clinical outcome prediction of given viral genomes. More SARS-CoV-2 sequences are needed to elucidate our understanding of this family of viruses.
Integrated bioinformatics analysis and screening hub genes in papillary thyroid cancer
Authors: Fan Rong , Dong Lijin , Li Ping , Wang Xiaoming , Chen Xuewei 
Published: July 2020

Abstract
Background

With the increasing incidence, papillary thyroid cancer (PTC) is receiving more and more attention, but the pathogenesis of which is still not completely elucidated. The purpose of this study was to explore key biomarkers and new therapeutic targets in PTC.
Methods

GEO2R and Venn online software were used for differential gene screening analysis. Hub genes were screened via STRING and Cytoscape, following Gene Ontology and KEGG enrichment analysis. Finally, survival analysis and expression validation were performed via UALCAN online software and immunohistochemistry.
Results

We screened 334 consistently differentially expressed genes (DEGs), composed of 136 upregulated genes and 198 downregulated genes. Gene ontology enrichment analysis suggested that DEGs mainly enriched in the cancer-related pathways and functions. PPI network visualization was performed to select 17 upregulated and 13 downregulated DEGs. Finally, the expression verification and overall survival analysis conducted in the Gene Expression Profiling Interactive Analysis Tool (GEPIA) and UALCAN showed that LPAR5, TFPI and ENTPD1 were related to the development of PTC and the prognosis of PTC patients, and the expression of LPAR5 was verified by tissue chip.
Conclusions

In summary, the hub genes and pathways identified in the present study not only provided new biomarkers for PTC, but also will be useful for elucidating the pathogenesis of PTC.
QT interval monitoring with handheld heart rhythm ECG device in COVID-19 patients.
Authors: Minguito-Carazo Carlos , Echarte-Morales Julio , Benito-González Tomás , Castillo-García Samuel Del , Rodríguez-Santamarta Miguel , Sánchez-Muñoz Enrique , González-Maniega Clea , Bergel-García Ruben , Menéndez-Suárez Paula , Prieto-González Silvia , Palacios-Echavarren Carmen , Borrego-Rodríguez Javier , Flores-Vergara Guisela , Iglesias-Garriz Ignacio , Fernández-Vázquez Felipe 
Published: July 2020

Abstract
Objectives: To evaluate the feasibility of QTc monitoring with a smart device in COVID-19 patients receiving QTc-interfering therapies.Background: QTc prolongation is an adverse effect of COVID-19 therapies. The use of a handheld device in this scenario has not been addressed.Methods: Prospective study of consecutive COVID-19 patients treated with hydroxychloroquine ± azithromycin ± lopinavir-ritonavir. ECG monitoring was performed with 12-lead ECG or with KardiaMobile-6L. Both registries were also sequentially obtained in a cohort of healthy patients. We evaluated differences in QTc in COVID-19 patients between 3 different monitoring strategies: 12-lead ECG at baseline and follow-up (A), 12-lead ECG at baseline and follow-up with the smart device (B), and fully monitored with handheld 6-lead ECG (group C). Time needed to obtain an ECG registry was also documented.Results: 182 COVID-19 patients were included (A: 119(65.4%); B: 50(27.5%); C: 13(7.1%). QTc peak during hospitalization did significantly increase in all groups. No differences were observed between the 3 monitoring strategies in QTc prolongation (p=0.864). In the control group, all but one ECG registry with the smart device allowed QTc measurement and mean QTc did not differ between both techniques (p=0.612), displaying a moderate reliability (ICC 0.56 [0.19-0.76]). Time of ECG registry was significantly longer for the 12-lead ECG than for handheld device in both cohorts (p<0.001).Conclusion: QTc monitoring with KardiaMobile-6L in COVID-19 patients was feasible. Time of ECG registration was significantly lower with the smart device, which may offer an important advantage for prevention of virus dissemination among healthcare providers.
T-S Fuzzy Systems Optimization Identification Based on FCM and PSO
Authors: Ren Yaxue , Liu Fucai , Lv Jingfeng , Meng Aiwen , Wen Yintang 
Published: July 2020

Abstract
The division of fuzzy space is very important in the identification of premise parameters and the Gaussian membership function is applied to the premise fuzzy set. However, the two parameters of Gaussian membership function, center and width, are not easy to be determined. In this paper, a novel T-S fuzzy model optimal identification method of optimizing two parameters of Gaussian function based on Fuzzy c-means (FCM) and particle swarm optimization (PSO) algorithm is presented. Firstly, we use FCM algorithm to determine the Gaussian center for rough adjustment. Then, under the condition that the center of Gaussian function is fixed, the PSO algorithm is used to optimize another adjustable parameter, the width of the Gaussian membership function, to achieve fine tuning, so as to complete the identification of prerequisite parameters of fuzzy model. In addition, the recursive least squares (RLS) algorithm is used to identify the conclusion parameters. Finally, the effectiveness of this method for T-S fuzzy model identification is verified by simulation examples, and the higher identification accuracy can be obtained by using the novel identification method described compared with other identification methods.
Development of a karyotype associated with the genome map and its applications in identification and characterization of chromosomes in peanut
Authors: Fu Liuyang , Wang Qian , Li Lina , Lang Tao , Guo Junjia , Wang Siyu , Sun Ziqi , Han Suoyi , Huang Bingyan , Dong Wenzhao , Zhang Xinyou , Du Pei 
Published: July 2020

Abstract
Background
Chromosomal structural variants are important materials for crop breeding and genetic research. Oligo fluorescence in situ hybridization (oligo FISH) is a useful tool for the identification of chromosomal structural variants.
Results
We developed 114 new repetitive oligos based on genome-wide tandem repeats (TRs) using genomic reference sequences of the cultivar Tifrunner and the diploid species Arachis ipaensis by bioinformatics and FISH. These oligo probes were positioned and classified into 28 types. Signals produced by representative probes from eight types were in the secondary constriction, middle arm, and terminal regions; signals of four probe types were on the B subgenome; and one probe being able to produce signals on only one pair of chromosomes could be used to recognize a special genome or chromosomes of peanut. Based on new and previous oligo probes, we developed a cocktail Multiplex #3 including FAM modified TIF-439, TIF-185-1, TIF-134-3, TIF-165-3, and TAMRA modified Ipa-1162, Ipa-1137, DP-1, and DP-5, which combined with the total genomic DNA of A. duranensis and A. ipaensis probes, and 45S rDNA and 5S rDNA probes to establish a karyotype associated with the genome map of peanut and identify 14 chromosomal structural variants.
Conclusions
The new oligo probes are useful and convenient for distinguishing peanut chromosomes or specific segments of peanut chromosomes. Comparisons of oligo sites in the karyotype and chromosome plots of electronic location revealed the characteristics of repeated sequences, and showed that the assembly of repeated sequence in peanut genomic reference sequence was incomplete. We therefor demonstrated the great potentials of the new oligo probes in facilitating chromosome identification and characterization, and provided novel materials for further study and genetic improvement of peanut.
A comprehensive study on chloroplast RNA editing by performing a broad-spectrum RNA-seq analysis
Authors: zhang aidi , fang jing , jiang xiaohan , wang tengfei , zhang xiujun 
Published: July 2020

Abstract
Background

RNA editing is a post-transcriptional modification that complement variation at the DNA level. Until now, different RNA editing systems were found in the major eukaryotic lineages. However, the evolution trajectory in plant chloroplast remains unclear. To gain a better understanding of RNA editing in plant chloroplast, in this study, based on publicly available RNA-seq data across three clades (fern, gymnosperm, and angiosperm), we provided a detailed analysis of RNA editing events in plant chloroplasts and discussed the evolution of RNA editing in land plants.
Results

There were a total of 5,389 editing sites located in leaf chloroplast identified across 21 plants after rigorous screening. We found that the cluster of RNA editing sites across 21 plants complied with the phylogenetic tree based on linked protein sequences approximately, there is a common phenomenon that more editing sites occurred in ancient plants for all the three clades. Statistics results revealed that majority (~ 95%) of the editing events resulted in non-synonymous codon changes, RNA editing occurred in second codon position was mainly the largest, and RNA editing caused an overall increase in hydrophobicity of the resulting proteins. The analyses also revealed that there was an uneven distribution of editing sites among species, genes, and codon positions, the average RNA editing extent varied among different plants as well as genes, a lowest RNA editing extent (0.43) was detected in Selaginella moellendorffii. Finally, we found that the loss of editing sites along angiosperm evolution is mainly occurring by reduce of cytosines content, where fern plants has the highest cytosine content.
Conclusions

Many of the RNA sites identified in our study have not been previously reported and provide a valuable data set for future research community. Our findings also provide valuable information for evolution of RNA editing in plants.