bluuebunny/crossref_metadata_2025_split huggingface dataset:
ATANN3 is involved in extracellular ATP-regulated auxin transport and distribution in Arabidopsis thaliana seedlings
Authors: Han Lijuan , Xia Shuyan , Xu Jiawei , Zhu Ruojia , Shang Zhonglin , Kang Erfang 
Published: August 2021

Abstract
Background
Extracellular ATP (eATP) exists in the apoplast of plants and plays multiple roles in growth, development, and stress responses. It has been reported that eATP stimulation suppresses growth rate and alters growth orientation of root and hypocotyls of Arabidopsis thaliana seedlings by affecting auxin accumulation and transport in these organs. However, the mechanism of eATP-stimulated vegetative organ growth remains unclear. Annexins are involved in multiple aspects of plant cellular metabolism, while the role of annexins in response to apoplast signal remains unclear. Here, by using loss-of-function mutants, we investigated the role of several annexins in eATP-regulated root and hypocotyl growth. Since mutant of AtANN3 did not respond to eATP sensitively, the role of AtANN3 in eATP regulated auxin transport was intensively investigated.
Results
First, the inhibitory effect of eATP on root or hypocotyl elongation was weakened or impaired in AtANN3 null mutants (atann3). Meanwhile, single-, double- or triple-null mutant of AtANN1, AtANN2 or AtANN4 responded to eATP stimulation in same manner and degree with Col-0. The abundance and distribution of Dr5-GUS and Dr5-GFP indicated that eATP-induced accumulation and asymmetric distribution of auxin in root tip or hypocotyl cells, which appeared in wild type controls, were lacking in atann3 seedlings. Further, eATP-induced accumulation and asymmetric distribution of PIN2-GFP in root tip cells or PIN3-GFP in hypocotyl cells were reduced in atann3 seedlings.
Conclusions
AtANN3 may be involved in eATP-regulated seedling growth through regulating auxin transport and accumulation in vegetative organs.
Comparative Assessment and Novel Strategy on Methods for Imputing Proteomics Data
Authors: Shen Minjie , Chang Yi-Tan , Wu Chiung-Ting , Parker Sarah J. , Saylor Georgia , Wang Yizhi , Yu Guoqiang , Eyk Jennifer E. Van , Clarke Robert , Herrington David M. , Wang Yue 
Published: August 2021

Abstract
Missing values are a major issue in quantitative proteomics analysis. While many methods have been developed for imputing missing values in high-throughput proteomics data, a comparative assessment of imputation accuracy remains inconclusive, mainly because mechanisms contributing to true missing values are complex and existing evaluation methodologies are imperfect. Moreover, few studies have provided an outlook of future methodological development. We first re-evaluate the performance of eight representative methods targeting three typical missing mechanisms. These methods are compared on both simulated and masked missing values embedded within real proteomics datasets, and performance is evaluated using three quantitative measures. We then introduce fused regularization matrix factorization, a low-rank global matrix factorization framework, capable of integrating local similarity derived from additional data types. We also explore a biologically-inspired latent variable modeling strategy - convex analysis of mixtures - for missing value imputation and present preliminary experimental results. While some winners emerged from our comparative assessment, the evaluation is intrinsically imperfect because performance is evaluated indirectly on artificial missing or masked values not authentic missing values. Nevertheless, we show that our fused regularization matrix factorization provides a novel incorporation of external and local information, and the exploratory implementation of convex analysis of mixtures presents a biologically plausible new approach.
ebv-circRPMS1 Promotes the Progression of EBV-Associated Gastric Carcinoma via Sam68 Complex Dependent Activation of METTL3
Authors: Zhang Jing-yue , Du Yu , Gong Li-ping , Shao Yi-ting , Pan Li-jie , Feng Zhi-ying , Pan Yu-hang , Huang Jun-ting , Wen Jing-yun , Sun Li-ping , Chen Gao-feng , Chen Jian-ning , Shao Chun-Kui 
Published: August 2021

Abstract
Background: Emerging studies have showed that circular RNAs (circRNAs) are important regulators for tumorigenesis by modulating malignant behaviors of tumor cells. However, the functions of EBV-encoded circRNAs in EBV-associated gastric carcinoma (EBVaGC) remain poorly understood. Methods: The expression of ebv-circRPMS1 in EBVaGC tissues, xenografts and cell lines were analyzed by BaseScope, qRT-PCR and in situ hybridization (ISH). The effects of ebv-circRPMS1 on gastric carcinoma (GC) cell proliferation, apoptosis, migration and invasion were measured by CCK8, EdU, immunofluorescence (IF), FACS and Transwell assays. qRT-PCR, Western blotting, ChIP, RNA fluorescence in situ hybridization (RNA-FISH), luciferase reporter assays, mass spectrum, RNA immunoprecipitation (RIP), and pulldown assays were used to investigate the molecular mechanisms. Xenograft mouse model was also used to analyze the effect of ebv-circRPMS1 on GC growth and metastasis in vivo.Results: We demonstrated that ebv-circRPMS1 promoted the proliferation, migration, invasion and anti-apoptosis of EBVaGC cells. Mechanistically, ebv-circRPMS1 recruited the Sam68 complex to the promoter of METTL3 and enhanced its transcription. Moreover, overexpression of METTL3 induced transcriptional activation of downstream genes (such as SNAI1, ZMYM1 and SOCS2) via m6A modifications on their mRNAs, which were associated with tumor progression. Besides, RNA binding proteins (RBPs) such as QKI, DHX9 and ILF3, might involve in ebv-circRPMS1 biogenesis. In clinical EBVaGC samples, ebv-circRPMS1 was associated with distant metastasis and poor prognosis. Conclusion: These findings indicated that ebv-circRPMS1 contributed to EBVaGC progression through recruiting the Sam68 complex to activate METTL3 expression and its downstream targets. Ebv-circRPMS1, Sam68 and METTL3 may serve as therapeutic targets for EBVaGC.
WITHDRAWN: Synthesis of CoFe 2 O 4 /BiOI Nanocomposite: Effects on Staphylococcus aureus, Escherichia coli, Pseudomonas Aeruginosa and Bacillus Cereus
Authors: Gheidari Davood , Mehrdad Morteza , Maleki Saloomeh , Hosseini Samanesadat 
Published: August 2021

Abstract
With the increase of general knowledge and the advancement of science and technology, antibacterial substances were used more than antibiotics. In our current study, the antibacterial virtues of CFO/BiOI nanocomposite were investigated due to its high importance on Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa and Bacillus cereus. MIC, MBC , Disk Diffusion and IC50 tests Cefalotin (CF), Amoxicillin (AMX), Gentamicin (GM), Trimethoprim-sulphamethoxazole (SXT) and Ceftriaxone (CRO) antibiotics in concentration 30W, 10i, 10t , 25h and 30 were used to find the antibacterial properties of the synthesized nanocomposite, respectively. For the synthesis of nanocomposites polyethylene glycol (PEG) and sulfonic acid was used as a solvent. It is noteworthy that the synthesis was performed by heat dissolution method without the presence of surfactant. Also, various techniques such as X-Ray Diffraction(XRD), Scanning Electron Microscope (SEM), High resolution mapping and Energy Dispersive X-ray spectroscopy (EDAX) have been used to determine the properties of produced nanocomposites. SEM test results showed that the formed nanoparticles were globular and their size was limited area of 22 to 34 nm. The results showed CFO / BiOI nanocomposite exhibits strong significant biological activity against Bacillus cereus. The results of MBC (Minimum Bactericidal Concentration) and MIC (Minimum Inhibition Concentration) tests for CFO/BiOI nanocomposites on bacteria were examined in the range of 0.12-0.48 mg/ml and 0.06 to 0.24 mg/ml respectively. According to the results, the minimum IC50 value was determined at a concentration of 0.061 mg/ml. On the other hand, the most resisting and susceptible bacteria in this method were Pseudomonas aeruginosa and Bacillus cereus, respectively. These findings are identical to those of a prior study on CoFe2O4 nanoparticles antibacterial properties. MBC of the nanocomposites, 50 µl from all the tubes that showed no obvious bacterial growth were distributed on BHI agar plates and incubated for 24 h at 37 ◦C. The MBC endpoint is defined as the lowest concentration which killed 98% of the bacterial population.
Posterior-only Debridement, Internal Fixation, and Interbody Fusion Using Titanium Mesh in the Surgical Treatment of Thoracolumbar Tuberculosis With Spinal Epidural Abscess: A Minimum 5-year Follow-up
Authors: Gao Qile , Han Chaofei , Romani Manini Daudi , Guo Chaofeng , Tang Mingxing , Wang Yuxiang , Deng Ang , Liu Shaohua , Zhang Hongqi 
Published: August 2021

Abstract
Objective: To investigate the clinical efficacy and feasibility of posterior-only debridement, internal fixation, and interbody fusion using titanium mesh in the surgical treatment of thoracolumbar tuberculosis (TB) with spinal epidural abscess.Methods: From January 2008 to January 2014, a total of 45 patients (27 male and 18 female) were reviewed. The patients were diagnosed with thoracolumbar TB with spinal epidural abscess. The patients underwent posterior-only debridement, internal fixation, and interbody fusion using titanium mesh. Hence, we assessed the intraoperative and postoperative complications, disease recurrences, kyphosis deformity correction, and neurological improvement following the American Spinal Injury Association (ASIA). We used SPSS 22.0 for the statistical analyses. An independent Student’s t-test was used for the analysis of preoperative and postoperative continuous variables. The value of P (P<0.05) was considered statistically significant.Results: The mean age of patients was 37.76 ±10.94 years (17–59 years). The mean follow-up time was 82.76 ±12.56 months (60–128 months). The mean kyphosis Cobb angle preoperative was 29.36 ±13.29° (5–55°) and postoperative was 3.58 ±5.44° (–6–13°), given the value of P (P<0.001). According to the neurological score by the ASIA scale, there were 3 cases of grade B, 11 cases of grade C, 16 cases of grade D, and 15 cases of grade E preoperatively. The neurological score improved by 1~2 grades. All patients achieved pain relief and the VAS score significantly reduced at the last follow-up (P＜0.05). While 1 patient had cerebrospinal fluid leakage, 1 had a neurological complication, 1 had delayed surgical wound healing, and 1 had a disease recurrence. No pseudoarthrosis or implant failure occurred in our patients. All patients achieved solid bone graft fusion.Conclusion: For thoracolumbar TB patients with spinal epidural abscess, posterior-only debridement, internal fixation, and interbody fusion using titanium mesh are safe and effective surgical treatments.*As a note, Qile Gao and Chaofei Han are Co-First authors.
Identification of a Novel Prognosis-Associated ceRNA Network in Lung Adenocarcinoma via Bioinformatics analysis
Authors: Li Yumiao , Yu Xiaoxue , Zhang Yuhao , Wang Xiaofang , Zhao Linshan , Liu Dan , Zhao Guofa , Gao Xiangpeng , Fu Jiejun , Zang Aimin , Jia Youchao 
Published: August 2021

Abstract
Backgroud: Long noncoding RNAs (lncRNAs) play an important role in the occurrence and development of lung adenocarcinoma (LUAD). The purpose of this study was to identify novel abnormally regulated lncRNA-microRNA (miRNA)-messenger RNA (mRNA) competing endogenous RNA (ceRNA) networks related to LUAD prognosis.Methods: We programmed an Agilent Microarray Scanner to screen for differentially expressed (DE) lncRNAs and mRNAs in 4 paired LUAD samples. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to annotate the DE lncRNAs and mRNAs. R bioinformatics packages, The Cancer Genome Atlas (TCGA) LUAD database and a Kaplan-Meier (KM) survival analysis tools were used to validate the microarray data and construct the lncRNA-miRNA-mRNA ceRNA regulatory network. Then, quantitative real-time PCR was used to validate the DE lncRNAs in 7 LUAD cell lines.Results: A total of 2819 DE lncRNAs and 2396 DE mRNAs (P-value < 0.05 and fold change ≥2 or ≤0.5) were identified in 4 paired LUAD tissue samples. In total, 255 of these DE lncRNAs were also identified in TCGA. The GO and KEGG analysis results suggested that the DE genes were most enriched in angiogenesis and cell proliferation and closely related to human cancers. Moreover, the differential expression of ENST00000609697, ENST00000602992, and NR_024321 was consistent with the microarray data, as determined by quantitative real-time PCR validation in 7 LUAD cell lines, but only ENST00000609697 was associated with the overall survival of LUAD patients (log-rank P=0.029). Finally, through analysis of ENST00000609697 target genes, we identified the ENST00000609697–hsa-miR-6791-5p–RASL12 ceRNA network, which may play a tumor-suppressive role in LUAD.Conclusion: ENST00000609697 was abnormally expressed in LUAD. Furthermore, downregulation of ENST00000609697 and its target gene RASL12 were associated with poor prognosis in LUAD. The ENST00000609697–hsa-miR-6791-5p–RASL12 axis may play a tumor-suppressive role. These results may suggest new prognostic and therapeutic biomarkers for LUAD.
Methylprednisolone, Venous Thromboembolism, and Association with Heparin to 30 Days in Hospital Survival in Severe COVID-19 Pneumonia
Authors: Go Ronaldo C. , Nyirenda Themba , Bojarian Maryam , Hosseini Davood , Rahim Mehek , Kim Kevin , Rose Keith M. 
Published: August 2021

Abstract
BACKGROUNDMortality in severe COVID-19 pneumonia is associated with thrombo-inflammation. Corticosteroids are given to attenuate the inflammation, but they are associated with thrombosis. The aims of this study were to determine the risk of venous thromboembolism between no methylprednisolone and methylprednisolone (dose versus duration) and to evaluate the synergistic dose-dependent association of heparin and methylprednisolone to 30 days in hospital survival. METHODSThis was a secondary analysis of a retrospective cohort. Patients included in this study were older than 18 years of age and admitted for severe COVID-19 pneumonia between March to June 2020 in 13 hospitals in New Jersey, United States. A propensity score analysis between administration of methylprednisolone and no methylprednisolone was fitted for 11 variables and Youden Index Method was used to determine cut-off between low dose and high dose methylprednisolone. Multivariate cox regression was performed to assess risk.RESULTSIn 759 patients, the incidence of venous thromboembolism was 9% of patients who received methylprednisolone and 3% of patients who did not receive methylprednisolone with a [RR =2.92 (95% CI 1.54, 5.55 P< 0.0001)]. The was a higher incidence of mechanical ventilation in the methylprednisolone group. The median d-dimer between patients with venous thromboembolism was higher compared to those without (P<0.0003). However, the d-dimer was not statistically significant between those who had venous thromboembolism between methylprednisolone and no methylprednisolone groups. (P 0.40). There was no higher risk in high dose versus low dose[RR=0.524 (95% CI 0.26, 1.06 P 0.4)]; however, the risk for DVT/PE between methylprednisolone for > 7 days and < 7 days was statistically significant. (RR=5.46 95% CI 2.87, 10.34 P < 0.0001). Patients who received low dose and therapeutic heparin had a trend towards higher risk of mortality compared to prophylactic heparin (HR=1.81 95% CI 0.994 to 3.294) (P=0.0522). There was no difference in 30 days in hospital survival between high dose with prophylactic or therapeutic heparin (HR=0.827 95% CI 0.514 to 1.33) (P=0.4335). CONCLUSIONSMethylprednisolone for > 7 days had a higher association of venous thromboembolism. There was no added benefit of therapeutic heparin to methylprednisolone on mechanically ventilated patients.
Cytoplasmic eIF6 Promotes OSCC Malignant Behavior Through AKT Pathway
Authors: Zhao Zechen , Chu Weming , Zheng Yang , Wang Chao , Yang Yuemei , Xu Teng , Yang Xueming , Zhang Wei , Ding Xu , Li Gang , Zhang Hongchuang , Zhou Junbo , Ye Jinhai , Wu Heming , Song Xiaomeng , Wu Yunong 
Published: August 2021

Abstract
Background: Eukaryotic translation initiation factor 6 (eIF6), also known as integrin β4 binding protein, is involved in the formation and translation of ribosomes and acts as an anti-association factor. It is also essential for the growth and reproduction of cells, including tumor cells. Yet, its role in oral squamous cell carcinoma (OSCC) remains unclear. Methods: The expression characteristics of eIF6 in 233 samples were comprehensively analyzed by immumohistochemical staining (IHC). Effects of eIF6 over-expression and knockdown on cell proliferation, migration and invasion were determined by CCK-8, wound healing and Transwell assays. Western blot, immunofluorescence (IF) and co-immunoprecipitation (co-IP) were performed for mechanism verification.Results: We found that cytoplasmic eIF6 was abnormally highly expressed in OSCC tissues, and its expression was associated with tumor size and the clinical grade. Amplification of eIF6 promoted the growth, migration, and invasion capabilities of OSCC cell lines in vitro and tumor growth in vivo. Through Western blot analysis, we further discovered that eIF6 significantly promotes epithelial-mesenchymal transformation (EMT) in OSCC cells, while depletion of eIF6 can reverse this process. Mechanistically, eIF6 promotes tumor progression by activating the AKT signaling pathway. By performing co-immunoprecipitation, we discovered a direct interaction between endogenous eIF6 and AKT protein in the cytoplasm. Conclusions: This was the first report on the role and mechanism of eIF6 in OSCC. These results demonstrated that eIF6 could be a new therapeutic target in OSCC, thus providing a new basis for the prognosis of OSCC patients in the future.
LC-MS Peak Assignment Based on Unanimous Selection by Six Machine Learning Algorithms
Authors: Ito Hiroaki , Matsui Takashi , Konno Ryo , Itakura Makoto , Kodera Yoshio 
Published: August 2021

Abstract
Recent Mass spectrometry (MS)-based techniques enable deep proteome coverage with relative quantitative analysis, resulting in increased identification of very weak signals accompanied by increased data size of liquid chromatography (LC)–MS/MS spectra. However, the identification of weak signals using an assignment strategy with poorer performance resulted in imperfect quantification with misidentification of peaks and ratio distortions. Manually annotating a large number of signals within a very large dataset is not a realistic approach. In this study, therefore, we utilized machine learning algorithms to successfully extract a higher number of peptide peaks with high accuracy and precision. Our strategy evaluated each peak identified using six different algorithms; peptide peaks identified by all six algorithms (i.e., unanimously selected) were subsequently assigned as true peaks, which resulted in a reduction in the false-positive rate. Hence, exact and highly quantitative peptide peaks were obtained, providing better performance than obtained applying the conventional criteria or using a single machine learning algorithm.
Discrete Element Simulation Analysis of Damage and Failure of Hydrate-Bearing Sediments
Authors: Zhao Mingxin , Liu Huaishan , Ma Qing , Xing Lei , Xia Qiuping , Yang Xilei , Li Fenglin , Li Xuefeng 
Published: August 2021

Abstract
It is of great significance to study the damage and failure law of hydrate-bearing sediments for for exploration and development, as well as for warning secondary disasters such as tsunami and earthquake. The discrete element modeling and simulation method has the advantages of low cost, strong repeatability and accurate response to the microstructure of samples, therefore , the discrete element method is used to simulate and analyze the damage and failure law of hydrate-bearing sediments in this paper. First, a triaxial undrained shear teat model of hydrate-bearing sediments is established. by discrete element simulation software; Then, the effects of different influencing factors on the fracture characteristics of hydrate hydrate-bearing sediments is studied; Finally, the effects of different factors on the initiation stress and damage stress of hydrate sediments are analyzed, and the damage law of hydrate-bearing sediments is obtained. The results show that: (1) The cementation of hydrate particles is greater than its bearing effect, thus the lithology of sediments changes from loose sand body to brittle rock with the increase of hydrate saturation, resulting in the corresponding change of fracture characteristics from loose sand body failure to brittle rock failure. (2) With the increase of hydrate saturation, the initiation stress of sediment shows a step-by-step increase law, and the damage stress is positively correlated with the shear modulus. (3) The heterogeneity of hydrate distribution is closely related to the failure mode of sediments. With the increase of hydrate distribution heterogeneity, the initiation stress displays an increase-decrease-increase pattern while the damage stress shows a law of increasing and then decreasing, which has the high sensitivity to heterogeneity of hydrate distribution. The research results have certain theoretical reference significance for the exploitation practice of natural gas hydrate.
Case Report: A World Trade Center (WTC) responder presenting with moderate stage dementia by age 57, suggesting an extended severity of WTC-associated illness'
Authors: Gandy Sam , Bender H Allison , Luccini Roberto , Ashleigh Theophania , Ciardullo Julie , Clouston Sean A. P. , Bromet Evelyn J , Luft Benjamin , Sano Mary 
Published: August 2021

Abstract

Recent evidence indicates that World Trade Center Responders (WTCRs) are apparently at increased risk for a clinical syndrome that includes PTSD (posttraumatic stress disorder) and MCI (mild cognitive impairment). The association of these behavioral and cognitive symptoms was first described by Bromet, Luft, Clouston, and colleagues. No autopsy characterization of the syndrome has yet emerged, though biofluid and neuroimaging biomarker data support features of (1) progressive behavioral and cognitive dysfunction, (2) proteinopathy involving the appearance of neurodegeneration-related molecules in the peripheral circulation, and (3) a substantial regional loss of brain volume. Inciting factors such as inhalation of neurotoxins and/or psychological stressors (or a combination of both) have been proposed as contributory to the pathogenesis, but no definitive etiologic agent has been identified. In general, the subpopulation of WTCRs who developed PTSD and MCI were those with documentable extended exposure to the central feature of “Ground Zero” known as “the pile”, and those who developed MCI were primarily a subgroup of those who had developed PTSD. Multiomic studies are underway to determine whether this subgroup might be enriched for genetic, genomic, and/or proteomic features that might have predisposed them to pathological responses to stress, environmental toxins, or both. In 2017, we had occasion to evaluate “E.T.”; at that time, a 57-year-old bilingual (English and Spanish speaking) right-handed WTCR was referred to an urban medical center dementia specialty clinic for assessment of his cognitive and behavioral functioning. While early-onset dementia can occur sporadically, the proximity of E.T. to “the pile” at “Ground Zero”, and the course of E.T.’s illness raise the possibility that WTC-related cognitive-behavioral syndromes may progress well beyond the stage of MCI to that of moderate dementia (and beyond) and that this progression may occur in the absence of full-blown PTSD.