266 research outputs found

    Integrating Overlapping Structures and Background Information of Words Significantly Improves Biological Sequence Comparison

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    Word-based models have achieved promising results in sequence comparison. However, as the important statistical properties of words in biological sequence, how to use the overlapping structures and background information of the words to improve sequence comparison is still a problem. This paper proposed a new statistical method that integrates the overlapping structures and the background information of the words in biological sequences. To assess the effectiveness of this integration for sequence comparison, two sets of evaluation experiments were taken to test the proposed model. The first one, performed via receiver operating curve analysis, is the application of proposed method in discrimination between functionally related regulatory sequences and unrelated sequences, intron and exon. The second experiment is to evaluate the performance of the proposed method with f-measure for clustering Hepatitis E virus genotypes. It was demonstrated that the proposed method integrating the overlapping structures and the background information of words significantly improves biological sequence comparison and outperforms the existing models

    The Application Value of the Central Lymph Node Metastasis Risk Assessment Model in Papillary Thyroid Microcarcinoma of Stage cN0: A Study of 828 Patients

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    BackgroundThe aim of this study is to build a risk assessment system for central lymph node metastasis (CLNM) in papillary thyroid microcarcinoma (PTMC) of stage cN0 and to explore its application value in clinical practice.MethodsA total of 500 patients with PTMC who underwent thyroid operation from 2013 to 2015 in Ningbo First Hospital were selected as the model group. Independent risk factors related to CLNM in PTMC were analyzed and determined, and a risk assessment system for CLNM was preliminarily established. Furthermore, the clinicopathological data from 328 PTMC patients with the same conditions as the model group from 2016 to 2017 were further collected as the validation group to verify the diagnostic value of the risk assessment system.ResultsThe risk assessment system was based on the score rating (score ≤ 5 was classified as low risk, 6–8 was classified as medium risk, and ≥9 was classified as high-risk). The area under the receiver operating characteristic curve (ROC) was 0.687 (95% CI: 0.635–0.783). According to the risk assessment system, 328 PTMC patients in the validation group were scored. Among the low-risk group, the moderate-risk group, and the high-group, 96.8%, 58.1%, and 43.2% were the CLNM (-) patients, and 3.1%, 41.9%, and 65.8% were CLNM (+) patients, respectively. The area under ROC was 0.837 (95% CI: 0.778–0.869).ConclusionsThe risk assessment system in this study is of diagnostic value and can provide a theoretical foundation for intraoperative decision-making of prophylactic central neck dissection (pCND)

    Clinical and Biological Implications of Mutational Spectrum in Acute Myeloid Leukemia of FAB Subtypes M0 and M1

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    Background/Aims: Acute myeloid leukemia (AML) of French-American-British (FAB) subtypes M0 and M1 are both poorly differentiated AML, but their mutational spectrum and molecular characteristics remain unknown. This study aimed to explore the mutational spectrum and prognostic factors of AML-M0 and M1. Methods: Sixty-five AML patients derived from The Cancer Genome Atlas (TCGA) database were enrolled in this study. Whole-genome sequencing was performed to depict the mutational spectrum of each patient. Clinical characteristics at diagnosis, including peripheral blood (PB) white blood cell counts (WBC), blast percentages in PB and bone marrow (BM), FAB subtypes and the frequencies of known recurrent genetic mutations were described. Survival was estimated using the Kaplan-Meier methods and log-rank test. Univariate and multivariate Cox proportional hazard models were constructed procedure. Results: Forty-six patients had more than five recurrent genetic mutations. FLT3 had the highest mutation frequency (n=20, 31%), followed by NPM1 (n=18, 28%), DNMT3A (n=16, 25%), IDH1 (n=14, 22%), IDH2 (n=12, 18%), RUNX1 (n=11, 17%) and TET2 (n=7, 11%). Univariate analysis showed that age >= 60 years and TP53 mutations had adverse effect on EFS (P=0.015, P=0.036, respectively) and OS (P=0.003, P=0.004, respectively), WBC count >= 50x10(9)/L and FLT3-ITD negatively affected EFS (P=0.003, P=0.034, respectively), whereas NPM1 mutations had favorable effect on OS (P=0.035) and allogeneic hematopoietic stem cell transplantation (allo-HSCT) on EFS and OS (all P= 50x10(9)/L was an independent risk factor for EFS (P=0.002) and TP53 mutations for OS (P=0.043). Conclusions: Our study provided new insights into the mutational spectrum and molecular signatures of AML-M0 and M1. We proposed that FLT3-ITD, NPM1 and TP53 be identified as markers for risk stratification of AML-M0 and M1. Patients with AML-M0 and M1 would likely benefit from allo-HSCT. (C) 2018 The Author(s) Published by S. Karger AG, Base

    Activation of M3 Muscarinic Acetylcholine Receptors Delayed Cardiac Aging by Inhibiting the Caspase-1/IL-1β Signaling Pathway

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    Background/Aims: Because the prevalence of age-related cardiac impairment increases as the human lifespan increases, it is important to combat the effects of aging. Recently, the cardiac M3 muscarinic acetylcholine receptor (M3-mAChR) has been demonstrated to play important roles in cardiac development and in the pathogenesis of cardiac diseases. However, the role of M3-mAChR in aging remains largely unknown. Therefore, the aim of this study was to investigate the involvement of M3-mAChR in the progression of cardiac aging. Methods: We established a cardiac aging model in mice through subcutaneous injection with D-galactose at a dose of 100 mg/kg/day for 6 weeks. D-galactose was also used to induce aging in primary cultured neonatal mouse cardiomyocytes. The myocardium from mice was stained with hematoxylin and eosin for histological analysis. The protein expression levels of p53 and p21 were determined using western blotting. The mRNA and protein expression levels of M3-mAChR, caspase-1, and interleukin (IL)-1β were determined using real-time PCR, immunohistochemical staining, and western blotting. Results: The expression of M3-mAChR was down-regulated in the myocardium from aged mice and D-galactose-treated mice, while the expression levels of caspase-1 and its downstream molecule IL-1β were significantly increased. The M3-mAChR agonist choline reduced the increase in caspase-1 in cardiomyocytes induced by D-galactose, which was reversed by the M3-mAChR antagonist 4-DAMP. Moreover, 4-DAMP promoted D-galactose-induced cardiomyocyte aging, which was attenuated by a caspase-1 inhibitor. Conclusion: Activation of M3-mAChR delayed cardiac aging by inhibiting the caspase-1/IL-1β signaling pathway

    Preparation and Application of Starch/Polyvinyl Alcohol/Citric Acid Ternary Blend Antimicrobial Functional Food Packaging Films

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    Ternary blend films were prepared with different ratios of starch/polyvinyl alcohol (PVA)/citric acid. The films were characterized by field emission scanning electron microscopy (FE-SEM), thermogravimetric analysis, as well as Fourier transform infrared (FTIR) analysis. The influence of different ratios of starch/polyvinyl alcohol (PVA)/citric acid and different drying times on the performance properties, transparency, tensile strength (TS), water vapor permeability (WVP), water solubility (WS), color difference (ΔE), and antimicrobial activity of the ternary blends films were investigated. The starch/polyvinyl alcohol/citric acid (S/P/C1:1:0, S/P/C3:1:0.08, and S/P/C3:3:0.08) films were all highly transparent. The S/P/C3:3:0.08 had a 54.31 times water-holding capacity of its own weight and its mechanical tensile strength was 46.45 MPa. In addition, its surface had good uniformity and compactness. The S/P/C3:1:0.08 and S/P/C3:3:0.08 showed strong antimicrobial activity to Listeria monocytogenes and Escherichia coli, which were the food-borne pathogenic bacteria used. The freshness test results of fresh figs showed that all of the blends prevented the formation of condensed water on the surface of the film, and the S/P/C3:1:0.08 and S/P/C3:3:0.08 prevented the deterioration of figs during storage. The films can be used as an active food packaging system due to their strong antibacterial effect
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