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1.
Bioinformatics ; 2020 Feb 05.
Artigo em Inglês | MEDLINE | ID: mdl-32022854

RESUMO

MOTIVATION: Approximate Bayesian computation (ABC) is an important framework within which to infer the structure and parameters of a systems biology model. It is especially suitable for biological systems with stochastic and nonlinear dynamics, for which the likelihood functions are intractable. However, the associated computational cost often limits ABC to models that are relatively quick to simulate in practice. RESULTS: We here present a Julia package, GpABC, that implements parameter inference and model selection for deterministic or stochastic models using i) standard rejection ABC or ABC-SMC, or ii) ABC with Gaussian process emulation. The latter significantly reduces the computational cost. AVAILABILITY AND IMPLEMENTATION: https://github.com/tanhevg/GpABC.jl. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

2.
Chemosphere ; 244: 125556, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32050346

RESUMO

Carbon source and dissolved oxygen are the critical factors which sustain the stable redox environment for the microbes to implement the removal of nitrogen and organics in vertical flow constructed wetlands (VFCWs). The effect mechanisms of the COD/N ratios in intermittently aerated VFCWs are needed to be investigated in order to increase the synchronous removal efficiency of pollutants. In this study, the combined effects of COD/N ratios (3, 6, 12) and intermittent aeration in VFCWs on pollutant removal, microbial communities and related function genes were studied. The results showed the increase of COD/N ratios from 3 to 12 enhanced the removal efficiency of TN, NO3--N and COD. The removals of NH4+-N decreased as the COD/N ratio increased. The optimal removals of TN (87.65%), NH4+-N (93.20%), NO3--N (80.80%) and COD (73.93%) were obtained in VFCW2 (COD/N ratios was 6). Illumina Miseq High-throughput sequencing analysis showed that high COD/N ratios increased the richness and diversity of microbial communities. The absolute abundance of nirK, nosZ, nirS, amoA, nxrA, and anammox bacterial 16S rRNA presented various changes under the different ratios of COD/N. The increase of COD/N ratios enhanced the copy numbers of nirS, nirK and nosZ, which participate in denitrification process. High COD/N ratios (6 and 12) were in favor of Actinobacteria, Firmicutes and Chloroflexi, which mainly play important roles in the process of denitrification. This paper implies that the combination of carbon source and aeration is necessary to sustain high microbial activities during pollutant removal in VFCWs.

3.
Thorac Cancer ; 2020 Jan 23.
Artigo em Inglês | MEDLINE | ID: mdl-31971663

RESUMO

BACKGROUND: To investigate whether human papillomavirus (HPV) infection is associated with primary lung cancer among the Fujian population. METHODS: HPV infection was detected in 140 pairs of lung cancer tissues and matched paracancerous tissues by examining the 21 clinically relevant HPV types using a combination of viral highly conserved L1 region PCR amplification and specific probe reverse hybridization. Paired χ2 test was used to analyze differences in detection rates of HPV between lung cancer and paracancerous tissues. Differences in detection rates of HPV in lung cancer tissues were analyzed using χ2 test or the exact probability method. The rank sum test was used to analyze differences in the distributions of routine indices of blood and pulmonary function in lung cancer tissues between the HPV negative and positive groups. RESULTS: HPV infection was detected in 13 of the 140 tumor specimens and in 16 of the paired normal lung tissues. There was no significant correlation between HPV infection and lung cancer (P > 0.05). The diagnosed HPV infection rates did not differ significantly among lung cancer tissues with different stratification (P > 0.05). However, the platelet count, platelet pressure, residual gas volume, functional residual volume, and residual gas volume/lung total distribution may differ between HPV-negative and HPV-positive lung cancer tissues (0.000625 < P < 0.05). CONCLUSIONS: We concluded that HPV infection may not be associated with the risk of primary lung cancer in the Fujian population. However, HPV infection may affect platelet and residual lung function in primary lung cancer patients.

4.
ACS Appl Mater Interfaces ; 12(4): 4833-4842, 2020 Jan 29.
Artigo em Inglês | MEDLINE | ID: mdl-31914316

RESUMO

Development of low-cost and efficient (electro)catalysts with tunable 2e/4e oxygen reduction reaction (ORR) selectivity toward energy conversion, biomimetic catalysis, and biosensing has attracted growing interest. Herein, we reported that carbon nanohybrids with O- or N-coordinated Cu (Cu-OC or Cu-NC) showed superior activity for 2e and 4e electrocatalytic ORR with selectivities of 84.0% and 97.2%, respectively. Experimental evidence demonstrated that the strong electron-rich O-doped carbon in Cu-OC donated electrons to Cu2+, weakening the binding strength of H2O2 at Cu-O centers and facilitating the 2e ORR pathway for selective production of H2O2. However, the poor electron-donor ability of the N-doped carbon in Cu-NC made Cu-N sites more electron deficient due to the reduced electron transfer from N-doped carbon to Cu2+, promoting 4e ORR by enhancing adsorption of O2 and the ORR intermediates. The high 4e ORR activity of Cu-NC rendered its potential for application in a Zn-air battery and oxidase-mimicking activity for 3,3',5,5'-tetramethylbenzidine (TMB) and ascorbic acid (AA) oxidation. The maximal velocity (Vmax) of TMB and AA oxidation over Cu-NC was higher than some natural oxidases and noble-metal-based artificial enzymes. The lower activation energy for AA oxidation over Cu-NC resulted in a 263-fold higher oxidative rate than TMB, further prompting nonenzymatic sensing of AA by the competitive oxidation strategy.

5.
Biomed Mater ; 2020 Jan 28.
Artigo em Inglês | MEDLINE | ID: mdl-31995534

RESUMO

Good osseointegration and gingival epithelial sealing play a key role in preventing peri-implantitis of dental implants. In addition to antibacterial ability, the transmucosal surface of the implant is beneficial to the growth of fibroblasts and epithelial cells, while its body surface is suitable to the growth of osteoblasts and resistant to epithelial cells and fibroblasts. In this study, both microgrooves mimicking extracellular matrix (ECM) and titanium (Ti) dioxide nanotubes with different parameter settings were produced on the Ti surfaces. The behavior of MG63 osteoblasts, L929 fibroblasts, SCC epithelial cells and P. gingivalis on these decorated Ti surfaces were detected to quantify their performances in osseointegration, biological sealing and antimicrobial ability. Via a scoring method based on these results, we concluded that 100~50~20~10~5µm widths grooves arranged in horizontal direction at 2µm depth (ECM1) were priority for the design of implant transmucosal surface. Changing the depth into 3.6µm and further decorating with 55nm nanotubes, a best surface design for the implant body was acquired. Hierarchical ECM-like micron/nano patterns provide novel designs of dental implants to achieve excellent gingival epithelial sealing and osseointegration, which would facilitate the clinical application of dental implants.

6.
Fitoterapia ; : 104471, 2020 Jan 06.
Artigo em Inglês | MEDLINE | ID: mdl-31917302

RESUMO

Three new thiophene derivatives, ecliprostins A-C (1-3), have been isolated from the aerial parts of a Compositae medicinal plant Eclipta prostrata, and structures of them have been elucidated by comprehensive spectroscopic analyses. Both ecliprostins A (1) and B (2) feature an acetylenic bithiophenyl backbone and also incorporate an isovalerate moiety, while ecliprostin C (3) is a symmetrical dimer of compound 1 and represents the first example bonded via an ether bridge among the very limited natural dimers. All three compounds show antibacterial activity against Staphylococcus aureus.

7.
Food Chem ; 310: 125830, 2020 Apr 25.
Artigo em Inglês | MEDLINE | ID: mdl-31784072

RESUMO

Grape (Vitis vinifera L.) pomace, the residue of red wine production, is a good source material for production of anthocyanins. In this study, an effective and simple method for semi-preparative isolation of anthocyanins from grape pomace was developed. Ultrasonication with acidified MeOH was used to extract anthocyanins, with 56.15 mg total anthocyanins being obtained from 50 g grape pomace. Crude extracts were purified by XAD-7HP column chromatography, followed by isolation of the anthocyanin mixtures using semi-preparative HPLC, and subsequent identification of anthocyanin monomers by HPLC-DAD-MS/MS. Fourteen anthocyanins were isolated with high purities (≥90%), among which were non-acylated and acylated anthocyanins, and their cis and trans isomers. It is believed this is the first time that nearly all primary anthocyanin monomers in grapes have been isolated simultaneously using a single-step semi-HPLC procedure. The findings of this study will contribute to further research on anthocyanin monomers and profitable utilization of grape pomace.

8.
Microb Ecol ; 79(1): 134-147, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31165188

RESUMO

Soil Actinomycetes have been used as biocontrol agents against soil-borne plant diseases, yet little is known about their effects on the structure of the rhizosphere microbiota and the long-term effects on crop yield and disease intensity after the application of Actinomycetes is stopped. Here, we conducted 3-year plot experiments to investigate the roles of two Actinomycetes strains (Streptomyces pactum Act12 and Streptomyces rochei D74) in the biocontrol of soil-borne root diseases and growth promotion of monkhood (Aconitum carmichaelii). We also examined their long-term effects after soil application of a mixed Actinomycetes preparation (spore powder) was completed. High-throughput sequencing was used to analyze shifts in the rhizosphere microbiota. The antifungal activity and root colonization ability of the two Actinomycetes were also tested. Disease severity of southern blight and root rot decreased following application of the Actinomycetes preparation, whereas biomass yield of tubers increased compared with the control group. Significant effects of disease control and plant growth promotion were also observed after application was stopped. The Actinomycetes preparation induced marked increases in the abundance of beneficial microbes and decreases in the abundance of harmful microbes in rhizosphere soil. Adding cell-free culture filtrates of both strains Act12 and D74 inhibited the growth of fungal pathogens capable of causing southern blight (Sclerotium rolfsii) and root rot (Fusarium oxysporum) in A. carmichaelii. A GFP-labeled strain was used to show that D74 can colonize roots of A. carmichaelii. In conclusion, a preparation of two Actinomycetes plays a role in the biocontrol of root diseases and growth promotion of A. carmichaelii by inhibiting pathogen growth and shaping the rhizosphere microbiota.

9.
Microb Biotechnol ; 13(1): 107-117, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-29931737

RESUMO

Sexual mating of compatible sporida is essential for Sporisorium scitamineum to form dikaryotic mycelia and then cause infection on sugarcane. Our previous work identified a Pseudomonas sp. ST4 from a soil sample, which showed a promising biocontrol potential by inhibiting the mating of S. scitamineum sporida and hyphal growth. In this study, we set to isolate the active compounds from Pseudomonas sp. ST4 through solid fermentation. High-performance liquid chromatography (HPLC) separation coupling with bioassay showed that Pseudomonas sp. ST4 produced a range of antimicrobial compounds. Two of the major components were purified following acetate extraction, silica gel and HPLC separation. Nuclear magnetic resonance (NMR) and liquid chromatography-mass spectrometry (LC-MS) analysis identified these active compounds are 4-hydroxybenzaldehyde and indole-3-carbaldehyde respectively. Further analysis showed that the former compound only inhibited the hyphal growth of the fungus at a concentration of 3 mM, while the latter interfered the fungal sexual mating at a concentration of 0.6 mM and affected hyphal growth at a concentration of 2 mM. Treatment of corn plants with 3 mM indole-3-carbaldehyde significantly inhibited corn smut infection, with a control rate up to 94%. Further analysis of the structure and activity relationship revealed that indole has a much stronger inhibitory activity against the fungal sexual mating than indole-3-carbaldehyde. The results from this study provide new agents for control and prevention of the sugarcane smut disease, and the active compounds could also be used to probe the molecular mechanisms of fungal sexual mating.

10.
Biomaterials ; 228: 119569, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31678845

RESUMO

The current conventional photo-therapeutic agents often show low therapy efficacy because of their single treatment model, the limited penetration depth of excitation light and hypoxia in the tumor microenvironment (TME). Herein, a new type of phthalocyanine manganese (MnPcE4) photosensitizer with strong NIR absorption was designed and fabricated for the first time, and was used to modify pure Bi nanomaterials to obtain an intelligent multifunctional Bi/MnPcE4 nanocomposites. The Mn2+ in the Bi/MnPcE4 nanocomposite could catalyze H2O2 to generate O2, thus helping to overcome TME hypoxia and enhancing the photodynamic therapy (PDT) efficacy. Further, the nanocomposites showed excellent T1-weighted MRI performance. Our novel use of a pure metal Bi core, offers lower toxicity, higher CT imaging performance, and a photothermal therapy (PTT) effect triggered by 808 nm near infrared (NIR) laser. Moreover, in vivo fluorescence imaging (in vivo FL) vividly showed that the nanocomposite rapidly accumulates in tumor sites due to the enhanced permeability and retention (EPR) effect and metabolized in the organs. The presence of Bi enables the use of these nanocomposites as a CT contrast agent, and the Mn content enables them to be used in MRI. This triple imaging ability implies that our nanocomposites have a high potential for use in imaging directed tumor therapy.

11.
BMC Complement Altern Med ; 19(1): 358, 2019 Dec 10.
Artigo em Inglês | MEDLINE | ID: mdl-31822288

RESUMO

BACKGROUND: No previous study has investigated the association between oolong tea consumption and esophageal squamous cell carcinoma (ESCC), we aim to elucidate the association between oolong tea consumption and ESCC and its joint effects with a novel composite index. METHODS: In a hospital-based case-control study, 646 cases of ESCC patients and 646 sex and age matched controls were recruited. A composite index was calculated to evaluate the role of demographic characteristics and life exposure factors in ESCC. Unconditional logistic regression was used to calculate the point estimates between oolong tea consumption and risk of ESCC. RESULTS: No statistically significant association was found between oolong tea consumption and ESCC (OR = 1.39, 95% CI: 0.94-2.05). However, drinking hot oolong tea associated with increased risk of ESCC (OR = 1.60, 95% Cl: 1.06-2.41). Furthermore, drinking hot oolong tea increased ESCC risk in the high-risk group (composite index> 0.55) (OR = 3.14, 95% CI: 1.93-5.11), but not in the low-risk group (composite index≤0.55) (OR = 1.16, 95% CI: 0.74-1.83). Drinking warm oolong tea did not influence the risk of ESCC. CONCLUSIONS: No association between oolong tea consumption and risk of ESCC were found, however, drinking hot oolong tea significantly increased the risk of ESCC, especially in high-risk populations.


Assuntos
Dieta/estatística & dados numéricos , Neoplasias Esofágicas/epidemiologia , Carcinoma de Células Escamosas do Esôfago/epidemiologia , Chá , Estudos de Casos e Controles , Feminino , Temperatura Alta , Humanos , Masculino , Pessoa de Meia-Idade , Razão de Chances
12.
Front Genet ; 10: 1091, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31824557

RESUMO

Genomic selection uses single-nucleotide polymorphisms (SNPs) to predict quantitative phenotypes for enhancing traits in breeding populations and has been widely used to increase breeding efficiency for plants and animals. Existing statistical methods rely on a prior distribution assumption of imputed genotype effects, which may not fit experimental datasets. Emerging deep learning technology could serve as a powerful machine learning tool to predict quantitative phenotypes without imputation and also to discover potential associated genotype markers efficiently. We propose a deep-learning framework using convolutional neural networks (CNNs) to predict the quantitative traits from SNPs and also to investigate genotype contributions to the trait using saliency maps. The missing values of SNPs are treated as a new genotype for the input of the deep learning model. We tested our framework on both simulation data and experimental datasets of soybean. The results show that the deep learning model can bypass the imputation of missing values and achieve more accurate results for predicting quantitative phenotypes than currently available other well-known statistical methods. It can also effectively and efficiently identify significant markers of SNPs and SNP combinations associated in genome-wide association study.

13.
J Physiol Biochem ; 75(4): 607-618, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31786730

RESUMO

Previous studies have shown that stromal interaction molecule1 (STIM1)-mediated store-operated Ca2+ entry (SOCE) contributes to intracellular Ca2+ accumulation in H9C2 cells subjected to hypoxia/reoxygenation(H/R) injury. The aim of the present study was to investigate the effect of resveratrol on STIM1-mediated intracellular Ca2+ accumulation and subsequent cell death in the context of myocardial ischemia/reperfusion (I/R) injury. C57 BL/6 mice were fed with either saline or resveratrol (50 mg/kg daily for 2 weeks) and then subjected to myocardial I/R injury. TTC/Evans Blue staining and TUNEL assay were performed to quantify the infarct size and apoptosis index. The cardiac function was evaluated by echocardiography. Neonatal rat ventricular cardiomyocytes (NRVCs) underwent hypoxia/reoxygenation (H/R) to establish the in vitro model. To achieve over-expression, NRVCs were transfected with STIM1-adenovirus vector. Apoptosis was analyzed by TUNEL assay. Cell viability was measured using MTS assay and cell necrosis was determined by LDH release assay. Intracellular Ca2+ concentration was detected by laser scanning confocal microscopy using a Fluo-3AM probe. Resveratrol significantly reduced apoptosis, decreased infarct size, and improved cardiac function in mice subjected to myocardial I/R injury. In NRVCs, resveratrol also downregulated STIM1 expression accompanied by decreased intracellular Ca2+ accumulation elicited by H/R injury. In addition, resveratrol reduced cell apoptosis, upregulated the Bcl-2, decreased Bax, and cleaved caspase-3 expression. Furthermore, the effects of resveratrol on STIM1-mediated intracellular Ca2+ accumulation, apoptotic proteins, and H/R-induced cell injury were exacerbated by STIM1 over-expression and were partly abolished by SOCE inhibitor SKF96365 in NRVCs in vitro. Our findings demonstrate that resveratrol exerts anti-apoptotic activity and improves cardiac functional recovery following myocardial I/R by inhibiting STIM1-induced intracellular Ca2+ accumulation.

14.
Open Biol ; 9(12): 190150, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31795914

RESUMO

An important capacity of genes is the rapid change of expression levels to cope with the environment, known as expression responsiveness or plasticity. Elucidating the genomic mechanisms determining expression plasticity is critical for understanding the molecular basis of phenotypic plasticity, fitness and adaptation. In this study, we systematically quantified gene expression plasticity in four metazoan species by integrating changes of expression levels under a large number of genetic and environmental conditions. From this, we demonstrated that expression plasticity measures a distinct feature of gene expression that is orthogonal to other well-studied features, including gene expression level and tissue specificity/broadness. Expression plasticity is conserved across species with important physiological implications. The magnitude of expression plasticity is highly correlated with gene function and genes with high plasticity are implicated in disease susceptibility. Genome-wide analysis identified many conserved promoter cis-elements, trans-acting factors (such as CTCF), and gene body histone modifications (H3K36me3, H3K79me2 and H4K20me1) that are significantly associated with expression plasticity. Analysis of expression changes in perturbation experiments further validated a causal role of specific transcription factors and histone modifications. Collectively, this work reveals the general properties, physiological implications and multivariable regulation of gene expression plasticity in metazoans, extending the mechanistic understanding of gene regulation.

15.
J Mol Model ; 26(1): 18, 2019 Dec 26.
Artigo em Inglês | MEDLINE | ID: mdl-31879806

RESUMO

A variety of researches on boron oxide clusters have indicated the key role of boronyl (BO) group in the structures and bonding. Based upon global structural searches and electronic structure calculations at the B3LYP and single-point coupled cluster single double (triple) (CCSD(T)) levels, we present the possibility of construction of lithium-doped boron oxide B8O2Li+/0 clusters (1-2). Different from the structures of pure B6+/0/- and B6(BO)20/-, the B8O2Li+/0 which can be formulated as B6(BO)2Li+/0 are not the double-chain structures, they are the crown-like structure, and the Li is like a diamond that links the crown. Detailed AdNDP analyses indicate the π aromaticity of B8O2Li+ (1). The results obtained in this work reveal that the metal could influence the structures and properties of boron oxides significantly.

16.
Chin J Integr Med ; 2019 Dec 27.
Artigo em Inglês | MEDLINE | ID: mdl-31883057

RESUMO

OBJECTIVE: To elevate the effects of Qingxuan Jiangya Decoction (, QXJYD) on hypertension and vascular structural remodeling (VSR) in spontaneously hypertensive rats (SHRs), and investigate the underlying mechanisms. METHODS: SHRs (n=8) were given intra-gastric administration with 60 mg/kg of QXJYD or saline, daily for 8 weeks, while rats in SHR-control (n=8) and WKY (n=8) groups were received equal volumes of saline solution. Systolic blood pressures (SBP), diastolic blood pressures (DBP) and mean blood pressures (MBP) were measured once a week. The levels of angiotensin II (Ang II), endothelin 1 (ET-1) and plasma renin activity (PRA) were tested by enzyme-linked immunosorbent assay (ELISA) and radioimmunoassay, respectively. The effect of QXJYD on VSR was determined by examining the media thickness and the ex vivo contractility of thoracic aortic. The proliferation and fibrosis of vascular smooth muscle cells (VSMCs) were examined via immunohistochemical (IHC) staining for proliferating cell nuclear antigen (PCNA), collagen I and collagen III, respectively. The mRNA and protein expressions of transforming growth factor ß 1 (TGF- ß 1), Smad3 and phosphorylation of Smad3 in thoracic aorta tissues were determined by real-time polymerase chain reaction (PCR) and Western blot assay, respectively. RESULTS: QXJYD treatment led to a significant decrease of the elevation of blood pressure in SHRs and reduced the levels of Ang II, ET-1 and PRA in the serum (P<0.05). In addition, QXJYD treatment remarkably ameliorated VSR and vascular function in SHRs. Moreover, QXJYD inhibited VSMC proliferation and fibrosis by suppressing the expression of PCNA, collagen I and collagen III in thoracic aortic. Furthermore, QXJYD inhibited the expression of TGF- ß 1, Smad3 and the phosphorylation of Smad3, respectively (P<0.05). CONCLUSION: QXJYD reversed VSR by inhibiting VSMC proliferation and collagen deposition via regulation of TGF- ß 1/Smad signaling pathway, which may, in part, illuminate its anti-hypertensive activities.

17.
Wei Sheng Yan Jiu ; 48(6): 925-931, 2019 Nov.
Artigo em Chinês | MEDLINE | ID: mdl-31875817

RESUMO

OBJECTIVE: To evaluate the association of pickled food、fried food and smoked food combined with smoking and alcohol drinking with lung cancer. METHODS: A hospital-based case-control study was conducted. A total of 1902 cases(24-90 years old) diagnosed in the Union Hospital and First Affiliated Hospital of Fujian Medical University and Fuzhou General Hospital of Nanjing Military Region and 2026(23-87 years old) controls matched healthy populaition for age(±3 ages) and gender from January 2006 to December 2013. Unconditional Logistic regression was used to analyze the combined effects and interactions of pickled food, fried food and smoked food with smoking and drinking, and to explore their relationship with the risk of lung cancer. RESULTS: The result of unconditional Logistic regression analysis demonstrated that fried food and smoked food were risk factors of lung cancer. Compare with the people whose fired food intake<3 times/week, the people whose fired food intake ≥3 times/week had a 2. 954-folds increased lung cancer risk(95% CI 2. 065-4. 226). Compare with the people whose smoked food intake<3 times/week, the people whose smoked food intake ≥3 times/week had a 6. 774-folds increased lung cancer risk(95% CI 3. 309-13. 866). The result of combined effect demonstrated that compare with the non-smoking drinker whose food intake score was 0, the smoking drinker whose food intake score was 1 had a 2. 108-folds increased lung cancer risk(95% CI 1. 551-2. 865); compare with the non-smoking drinker whose food intake score was 0, the smoking drinker whose food intake score ≥2 had a 2. 191-folds increased lung cancer risk(95% CI 1. 377-3. 484). The result of interaction analysis demenstrated that intake of two or three kinds of risky food(≥1 time/week) increased the risk of lung cancer(OR = 1. 309, 95% CI 1. 010-1. 696) and it was more dangerous to smokers and drinkers. As for smokers, intake of two or three kinds of risky food was associated with an increased risk of lung cancer in an exposure-response manner(Ptrend<0. 001). CONCLUSION: The intake of fried food and smoked food are independent risk factors of lung cancer. In addition, the pickled food, fried food and smoked food have combined effects on smoking and alcohol drinking, and the risk of lung cancer increases when the risk factors are present. The intake of the three kinds of risky food increases the risk of lung cancer in smokers.


Assuntos
Alimentos , Neoplasias Pulmonares , Adulto , Idoso , Idoso de 80 Anos ou mais , Consumo de Bebidas Alcoólicas , Estudos de Casos e Controles , Alimentos em Conserva , Humanos , Pessoa de Meia-Idade , Fatores de Risco , Fumaça , Adulto Jovem
18.
BMC Genomics ; 20(1): 881, 2019 Nov 21.
Artigo em Inglês | MEDLINE | ID: mdl-31752667

RESUMO

BACKGROUND: Targeted therapy for non-small cell lung cancer is histology dependent. However, histological classification by routine pathological assessment with hematoxylin-eosin staining and immunostaining for poorly differentiated tumors, particularly those from small biopsies, is still challenging. Additionally, the effectiveness of immunomarkers is limited by technical inconsistencies of immunostaining and lack of standardization for staining interpretation. RESULTS: Using gene expression profiles of pathologically-determined lung adenocarcinomas and squamous cell carcinomas, denoted as pADC and pSCC respectively, we developed a qualitative transcriptional signature, based on the within-sample relative gene expression orderings (REOs) of gene pairs, to distinguish ADC from SCC. The signature consists of two genes, KRT5 and AGR2, which has the stable REO pattern of KRT5 > AGR2 in pSCC and KRT5 < AGR2 in pADC. In the two test datasets with relative unambiguous NSCLC types, the apparent accuracy of the signature were 94.44 and 98.41%, respectively. In the other integrated dataset for frozen tissues, the signature reclassified 4.22% of the 805 pADC patients as SCC and 12% of the 125 pSCC patients as ADC. Similar results were observed in the clinical challenging cases, including FFPE specimens, mixed tumors, small biopsy specimens and poorly differentiated specimens. The survival analyses showed that the pADC patients reclassified as SCC had significantly shorter overall survival than the signature-confirmed pADC patients (log-rank p = 0.0123, HR = 1.89), consisting with the knowledge that SCC patients suffer poor prognoses than ADC patients. The proliferative activity, subtype-specific marker genes and consensus clustering analyses also supported the correctness of our signature. CONCLUSIONS: The non-subjective qualitative REOs signature could effectively distinguish ADC from SCC, which would be an auxiliary test for the pathological assessment of the ambiguous cases.

19.
Math Biosci Eng ; 16(6): 6231-6241, 2019 Jul 04.
Artigo em Inglês | MEDLINE | ID: mdl-31698559

RESUMO

RNA modification plays an indispensable role in the regulation of organisms. RNA modification site prediction offers an insight into diverse cellular processing. Regarding different types of RNA modification site prediction, it is difficult to tell the most relevant feature combinations from a variant of RNA properties. Thereby, the performance of traditional machine learning based predictors relied on the skill of feature engineering. As a data-driven approach, deep learning can detect optimal feature patterns to represent input data. In this study, we developed a predictor for multiple types of RNA modifications method called DeepMRMP (Multiple Types RNA Modification Sites Predictor), which is based on the bidirectional Gated Recurrent Unit (BGRU) and transfer learning. DeepMRMP makes full use of multiple RNA site modification data and correlation among them to build predictor for different types of RNA modification sites. Through 10-fold cross-validation of the RNA sequences of H. sapiens, M. musculus and S. cerevisiae, DeepMRMP acted as a reliable computational tool for identifying N1-methyladenosine (m1A), pseudouridine (Ψ), 5-methylcytosine (m5C) modification sites.

20.
ACS Appl Mater Interfaces ; 11(51): 47659-47670, 2019 Dec 26.
Artigo em Inglês | MEDLINE | ID: mdl-31713407

RESUMO

The development of a stimulus-responsive nanosystem provides an effective method for improving the accuracy and efficiency of chemotherapy. Meanwhile, traditional photodynamic therapy (PDT) has been substantially restricted by the low dosage of photosensitizer and limited penetration depth of the ultraviolet (UV) or visible light used for excitation. Here, we designed a smart multifunctional nanoplatform by coating core-shell composite mesoporous silica-encapsulated upconversion nanoparticles and chlorin e6 (Ce6) with degradable calcium phosphate, followed by the loading of doxorubicin (DOX). In our structure, the as-synthesized nanoplatform exhibits high responsiveness to a low pH value and degrades rapidly in the weakly acidic tumor microenvironment, allowing the quick release of loaded DOX in tumor sites. Interestingly, the loaded DOX, whose release depends on the pH value and positively correlates with the calcium-ion concentration, enables drug release to be monitored in real time. Combined with photosensitizer Ce6-induced PDT triggered by an 808 nm near-infrared light, synergistic chemo-photodynamic therapy is achieved, thus leading to a highly efficient anticancer treatment in vitro and in vivo. Importantly, the inherent properties of rare earth ions (Gd3+, Yb3+, and Nd3+) make the nanoplatform possess UCL, MRI, and CT trimode imaging capabilities, thus achieving a multiple imaging modality-guided synergistic therapy.

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