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1.
PLoS One ; 15(6): e0234469, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32579588

RESUMO

Online forums in Chinese universities play an important role in understanding collective behavior of college students. Of particular interest are community and popularity. We address these two issues by examining data from Bulletin Board Systems (BBSs) of four Chinese universities. To characterize users' behavior, we introduce a hypothesis test to infer individual preferred boards, which yields a polarization of users. We also perform a multilevel algorithm to detect communities of each BBS network. We measure the similarity between the board-preferred polarization and the algorithmically identified community structure by quantitative and visual tools. The resulting discrepancy indicates that board labels are inadequate to represent underlying communities. To reveal online popularity, we employ latent Dirichlet allocation to mine topics from threads to compare popularity in different universities. Based on which, we implement the Cox-Stuart test to explore the change in popularity over time and reproduce significantly ascending and descending topics around a decade. Finally, we devise a two-step model based on users' preference and interests to reproduce the observed connectivity patterns.

2.
Sci Rep ; 10(1): 456, 2020 01 16.
Artigo em Inglês | MEDLINE | ID: mdl-31949173

RESUMO

We study opinion dynamics on complex social networks where each individual holding a binary opinion on a certain subject may change her/his mind to match the opinion of the majority. Two rules of interactions between individuals, termed as classic majority and influence majority rules, respectively, are imposed on the social networks. The former rule allows each individual to adopt an opinion following a simple majority of her/his immediate neighbors, while the latter one lets each individual calculate the influence of each opinion and choose to follow the more influential one. In this calculation, the influences of different opinions are counted as the sum of the influences of their respective opinion holders in neighborhood area, where the influence of each individual is conveniently estimated as the number of social connections s/he has. Our study reveals that in densely-connected social networks, all individuals tend to converge to having a single global consensus. In sparsely-connected networks, however, the systems may exhibit rich properties where coexistence of different opinions, and more interestingly, multiple steady states of coexistence can be observed. Further studies reveal that low-degree and high-degree nodes may play different roles in formulating the final steady state, including multi-steady states, of the systems under different opinion evolution rules. Such observations would help understand the complex dynamics of opinion evolution and coexistence in social systems.

3.
World J Urol ; 2019 Dec 07.
Artigo em Inglês | MEDLINE | ID: mdl-31813027

RESUMO

OBJECTIVE: To investigate whether prostatic arterial embolization (PAE) could be recommended as a routine therapy for benign prostatic hyperplasia (BPH), we conducted an updated meta-analysis to assess the efficacy and safety of PAE compared with transurethral resection of the prostate (TURP). METHODS: Systematic literature retrieval by searching data from Web of science, Pubmed, Embase, Cochrane Library, ClinicalTrial.gov, CNKI, Wanfang and VIP databases was carried out to identify all related trials from the inception dates to June 2019. We also conducted subgroup analyses depending on the kind of study design, kind of PAE and kind of TURP. RESULTS: Nine studies comparing PAE with TURP involving a total of 860 BPH patients were selected. Postoperative reduced IPSS score (MD 2.50; 95% CI 0.78-4.21; P = 0.004), postoperative reduced QOL score (MD 0.40; 95% CI 0.09-0.71; P = 0.01), postoperative reduced PV (MD 8.59; 95% CI 4.74-12.44; P < 0.00001) and postoperative increased Qmax (MD 2.54; 95% CI 1.02-4.05; P = 0.001) were better in TURP than in PAE; however, PAE was associated with lower sexual dysfunction rate (OR 0.24; 95% CI 0.15-0.39; P < 0.00001) compared with TURP. Meanwhile, no significant difference in postoperative reduced PVR (MD 0.46; 95% CI - 2.08 to 3.00; P = 0.72) and complication (OR 0.57; 95% CI 0.21-1.55; P = 0.27) between PAE and TURP group was demonstrated. CONCLUSION: PAE was inferior to TURP in the improvement of postoperative IPSS, QOL, PV, Qmax and TURP still remained the gold standard. However, PAE may be a valuable alternative to TURP in the treatment of BPH patients who refuse surgery or with surgery contraindication.

4.
PeerJ ; 7: e7836, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31660264

RESUMO

Background: Bladder cancer is one of the most common cancers, and its histopathological type is mainly bladder urothelial carcinoma, accounting for about 90%. The prognostic biomarkers of bladder cancer are classified into clinical features biomarkers and molecular biomarkers. Nevertheless, due to the existence of individual specificity, patients with similar pathological characteristics still have great differences in the risk of disease recurrence. Therefore, it is often inaccurate to predict the survival status of patients based on clinical characteristic biomarkers, and a prognostic molecular biomarker that can grade the risk of bladder cancer patients is needed. Methods: A total of three bladder urothelial carcinoma datasets were used in this study from the Cancer Genome Atlas database and Gene Expression Omnibus database. In order to avoid overfitting, all samples were randomly divided into one training set and three validation sets, which were used to construct and test the prognostic biomarker model of bladder urothelial carcinoma. Univariate and multivariate Cox regression were used to screen candidate mRNAs and construct prognostic biomarkers model. Kaplan-Meier survival analysis and the receiver operating characteristic (ROC) curve were used to evaluate the predictive performance of the model. Results: A prognostic biomarker model of bladder urothelial carcinoma combining with eight mRNA was constructed. Kaplan-Meier analyses indicated that a significant difference in the survival time of patients between the high-risk and the low-risk group. The area under the ROC curve were 0.632 (95% confidence interval (CI) [0.541-0.723]), 0.693 (95% CI [0.601-0.784]) and 0.686 (95% CI [0.540-0.831]) when the model was used to predict the patient's survival time in three validation datasets. The model showed high accuracy and applicability.

5.
Oncol Lett ; 16(5): 5631-5638, 2018 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-30344718

RESUMO

The aim of the present study was to evaluate the association between xeroderma pigmentosum group C (XPC) polymorphisms and pancreatic cancer (PC) risk. A total of 7 XPC tagging SNPs (tag-SNPs) were selected from the International HapMap Project Databases (rs2228001A/C, rs2470353G/C, rs2228000C/T, rs3731114C/G, rs3729587G/C, rs2607775C/G and rs3731055G/A) and were genotyped in 205 patients with PC and 230 non-cancer control subjects using a SNaPshot assay. The C allelic gene frequency of rs2470353 was higher in patients with PC compared with that in the control group (P=0.003). Compared with the GG gene type, PC risk was increased in subjects with GC and GC+CC gene types (P=0.012 and P=0.006, respectively). PC risk increased 3.505-fold for the subjects who were heavy smokers (tobacco, ≥25 packets/year) with the GC+CC gene type (P=0.008). The G allelic gene frequency of rs2607775 was higher in PC patients compared with that in the control group (P=0.003). Compared with the CC gene type, PC risk increased in subjects with CG and CG+GG gene types (P=0.013 and P=0.005, respectively). Furthermore, PC risk increased 3.950-fold in subjects who were heavy smokers (tobacco, ≥25 packets/year) with the CG+GG gene type (P=0.001). Haplotype analysis further revealed that the CCC haplotype of rs2228000, rs3731114 and rs3729587 increased PC risk (odds ratio, 1.610; 95% confidence interval, 1.035-2.481; P=0.034). The present study revealed that XPC gene polymorphisms could increase the risk of PC in the study population, particularly among heavy smokers.

6.
Sci Rep ; 8(1): 4814, 2018 03 19.
Artigo em Inglês | MEDLINE | ID: mdl-29556044

RESUMO

The threshold model has been widely adopted for modelling contagion processes on social networks, where individuals are assumed to be in one of two states: inactive or active. This paper studies the model on directed networks where nodal inand out-degrees may be correlated. To understand how directionality and correlation affect the breakdown of the system, a theoretical framework based on generating function technology is developed. First, the effects of degree and threshold heterogeneities are identified. It is found that both heterogeneities always decrease systematic robustness. Then, the impact of the correlation between nodal in- and out-degrees is investigated. It turns out that the positive correlation increases the systematic robustness in a wide range of the average in-degree, while the negative correlation has an opposite effect. Finally, a comparison between undirected and directed networks shows that the presence of directionality and correlation always make the system more vulnerable.

8.
Genet. mol. biol ; 41(1): 18-26, Jan.-Mar. 2018. tab, graf
Artigo em Inglês | LILACS-Express | ID: biblio-892468

RESUMO

Abstract This study aimed to determine the association between the polymorphisms and haplotypes in the xeroderma pigmentosum group D (XPD) gene and the risk of pancreatic cancer in the Chinese Han population. SNaPshot was used for genotyping six SNP sites of the XPD gene. Comparisons of the correlations between different genotypes in combination with smoking and the susceptibility to pancreatic cancer were performed. Individual pancreatic cancer risk in patients who carry mutant C alleles (AC, CC, and AC+CC) at rs13181 increased (p < 0.05). Taking non-smoking individuals who carry the AA genotype as a reference, and non-smoking individuals who carry mutant allele C (AC+CC), the risk of pancreatic cancer increased by 3.343 times in individuals who smoked ≥ 20 cigarettes daily, 3.309 times in individuals who smoked ≥ 14 packs per year, 5.011 times in individuals who smoked ≥ 24 packs per year, and 4.013 times in the individuals who smoked ≥ 37 packs per year (P < 0.05). In addition, haplotype analysis revealed that haplotype AGG, which comprised rs13181, rs3916874 and rs238415, was associated with a 1.401-fold increase in pancreatic cancer risk (p < 0.05). We conclude that the polymorphism of XPD Lys751Gln (rs13181) in combination with smoking contributes to increased risk of pancreatic cancer in the Chinese Han population. Haplotype AGG might be a susceptibility haplotype for pancreatic cancer.

9.
Genet Mol Biol ; 41(1): 18-26, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29260835

RESUMO

This study aimed to determine the association between the polymorphisms and haplotypes in the xeroderma pigmentosum group D (XPD) gene and the risk of pancreatic cancer in the Chinese Han population. SNaPshot was used for genotyping six SNP sites of the XPD gene. Comparisons of the correlations between different genotypes in combination with smoking and the susceptibility to pancreatic cancer were performed. Individual pancreatic cancer risk in patients who carry mutant C alleles (AC, CC, and AC+CC) at rs13181 increased (p < 0.05). Taking non-smoking individuals who carry the AA genotype as a reference, and non-smoking individuals who carry mutant allele C (AC+CC), the risk of pancreatic cancer increased by 3.343 times in individuals who smoked ≥ 20 cigarettes daily, 3.309 times in individuals who smoked ≥ 14 packs per year, 5.011 times in individuals who smoked ≥ 24 packs per year, and 4.013 times in the individuals who smoked ≥ 37 packs per year (P < 0.05). In addition, haplotype analysis revealed that haplotype AGG, which comprised rs13181, rs3916874 and rs238415, was associated with a 1.401-fold increase in pancreatic cancer risk (p < 0.05). We conclude that the polymorphism of XPD Lys751Gln (rs13181) in combination with smoking contributes to increased risk of pancreatic cancer in the Chinese Han population. Haplotype AGG might be a susceptibility haplotype for pancreatic cancer.

10.
Chronic Dis Transl Med ; 3(1): 60-66, 2017 Mar 25.
Artigo em Inglês | MEDLINE | ID: mdl-29063057

RESUMO

OBJECTIVE: To analyze the clinical epidemiological characteristics of patients with gallbladder carcinoma recruited from 17 hospitals in five northwestern provinces of China (Shaanxi Province, Gansu Province, Qinghai Province, Ningxia Hui Autonomous Region, and Xinjiang Uygur Autonomous Region) from 2009 to 2013, and to summarize the clinical diagnosis and treatment data of gallbladder carcinoma. METHODS: Clinical information of 2379 patients with gallbladder carcinoma from 17 hospitals in five northwestern provinces of China was retrospectively collected and analyzed using the "Questionnaire for Gallbladder Carcinoma Patients in Northwestern Area of China." All information was verified with EpiData software and analyzed with SPSS 13.0 software. RESULTS: (1) Gallbladder carcinoma accounted for 2.7% (2379/86,609) of all biliary tract diseases during the study period, which was significantly higher than that from 1986 to 1998 (P < 0.001). (2) Gallbladder carcinoma was more prone to occur in elderly women. The male:female incidence ratio was 1.0:2.1, the average age of onset of disease was 63.7 ± 11.3 years, and the incidence was higher in farmers than in other occupational groups. (3) A total of 57.2% (1360/2379) of patients with gallbladder carcinoma also had gallstones. (4) Abdominal pain (1796/2379, 75.5%) and jaundice (727/2379, 30.6%) were the most common clinical manifestations, 81.2% (1527/1881) were positive in those receiving B ultrasound examinations and 90.7% (1567/1727) were positive in those undergoing computed tomography, and 64.5% (1124/1742) of patients with gallbladder carcinoma were positive for carbohydrate antigen (CA) 19-9. (5) The pathological type of gallbladder carcinoma was mainly moderately and poorly differentiated adenocarcinoma with a high degree of malignancy. At admission, 55.1% (1091/1981) of patients had stage IV cancer among patients with TNM staging information; 55.9% (1331/2379) had lymphatic metastasis, 29.7% (706/2379) had bile duct metastasis, and 53.1% (1263/2379) had liver metastasis. (6) A total of 283 patients (283/2379, 11.9%) had incidentally detected gallbladder carcinoma. (7) The rate of radical surgical resection was 30.4% (723/2379). CONCLUSION: The proportion of gallbladder carcinoma in biliary tract diseases in the northwestern area of China was significantly higher from 2009 to 2013 than from 1986 to 1998. Gallbladder carcinoma was common in older women and mainly diagnosed at an advanced stage. Compared with other surveys in different regions, the rate of metastasis in this survey was high, leading to a low resection rate. Populations at high risk should undergo B-ultrasound examinations at regular follow-up intervals to increase the rate of early diagnosis of gallbladder carcinoma.

11.
PLoS One ; 12(1): e0169771, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28072847

RESUMO

Individual decision to accept a new idea or product is often driven by both self-adoption and others' persuasion, which has been simulated using a double threshold model [Huang et al., Scientific Reports 6, 23766 (2016)]. We extend the study to consider the case with limited persuasion. That is, a set of individuals is chosen from the population to be equipped with persuasion capabilities, who may succeed in persuading their friends to take the new entity when certain conditions are satisfied. Network node centrality is adopted to characterize each node's influence, based on which three heuristic strategies are applied to pick out persuaders. We compare these strategies for persuader selection on both homogeneous and heterogeneous networks. Two regimes of the underline networks are identified in which the system exhibits distinct behaviors: when networks are sufficiently sparse, selecting persuader nodes in descending order of node centrality achieves the best performance; when networks are sufficiently dense, however, selecting nodes with medium centralities to serve as the persuaders performs the best. Under respective optimal strategies for different types of networks, we further probe which centrality measure is most suitable for persuader selection. It turns out that for the first regime, degree centrality offers the best measure for picking out persuaders from homogeneous networks; while in heterogeneous networks, betweenness centrality takes its place. In the second regime, there is no significant difference caused by centrality measures in persuader selection for homogeneous network; while for heterogeneous networks, closeness centrality offers the best measure.


Assuntos
Heurística , Modelos Psicológicos , Comunicação Persuasiva , Humanos
12.
J Dermatol Sci ; 85(3): 226-234, 2017 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-27955882

RESUMO

BACKGROUND: Various studies have demonstrated that the Breslow thickness, tumor ulceration and mitotic index could serve as prognostic markers in patients with cutaneous melanoma. Recently, however, as these clinicopathological biomarkers lack efficient interpretation of endogenous mechanism of melanoma, the emphasis on the prognosis of melanoma has transformed to molecular tumor markers. OBJECTIVE: This study was designed to identify survival-related long non-coding RNAs (lncRNAs), and based on the different expressions of these lncRNAs, clinical risk-specific diagnosis and adjuvant therapy could be employed on melanoma patients, especially patients in the early course of disease or patients with a Breslow thickness no more than 2mm. METHODS: The clinical information and corresponding RNA expression data were obtained from The Cancer Genome Atlas dataset and Gene Expression Omnibus dataset (GSE65904). All samples were categorized into one training dataset and two validation datasets. Cox proportional hazard regression analysis was then used to identify survival-related lncRNAs and risk assessment signature was constructed in training dataset. Kaplan-Meier method was used to estimate the utility of this signature in predicting the duration of survival of patients both in the training dataset and two validation datasets. Meanwhile receiver operating characteristic analyses were used to evaluate the predictive effectiveness of this signature in two validation datasets. RESULTS: It was found that the signature was effective while used for risk stratification, and Kaplan-Meier analyses indicated that the duration of survival of patients in high-risk groups were significantly shorter than that of low-risk groups. Moreover, areas under the receiver operating characteristic curve were 0.711 (95% confidence interval: 0.618-0.804) and 0.698 (95% confidence interval: 0.614-0.782) when this signature was used to predict the patients' duration of survival in two validation datasets respectively, indicating the superior specificity and sensitivity of this signature. CONCLUSION: We identified a four-lncRNA prognostic signature with the ability of risk stratification for melanoma patients. Risk score acquired from this signature, combining with differential diagnosis and differential adjuvant therapy, could potentially improve the prognosis quality of life for patients, especially patients in the early course of disease or patients with a Breslow thickness no more than 2mm.


Assuntos
Biomarcadores Tumorais/metabolismo , Melanoma/diagnóstico , Melanoma/mortalidade , RNA Longo não Codificante/metabolismo , Neoplasias Cutâneas/diagnóstico , Neoplasias Cutâneas/mortalidade , Transcriptoma , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Antineoplásicos/uso terapêutico , Biomarcadores Tumorais/análise , Quimioterapia Adjuvante , Conjuntos de Dados como Assunto , Feminino , Humanos , Interferons/uso terapêutico , Estimativa de Kaplan-Meier , Masculino , Melanoma/patologia , Melanoma/terapia , Pessoa de Meia-Idade , Valor Preditivo dos Testes , Prognóstico , Qualidade de Vida , RNA Longo não Codificante/análise , Curva ROC , Medição de Risco , Biópsia de Linfonodo Sentinela , Neoplasias Cutâneas/patologia , Neoplasias Cutâneas/terapia , Adulto Jovem
13.
Sci Rep ; 6: 27931, 2016 06 24.
Artigo em Inglês | MEDLINE | ID: mdl-27338266

RESUMO

Long noncoding RNAs (lncRNAs) play a crucial role in tumorigenesis. The aim of this study is to identify lncRNA signature that can predict breast cancer patient survival. RNA expression data from 1064 patients were downloaded from The Cancer Genome Atlas project. Cox regression, Kaplan-Meier, and receiver operating characteristic (ROC) analyses were performed to construct a model for predicting the overall survival (OS) of patients and evaluate it. A model consisting of three lncRNA genes (CAT104, LINC01234, and STXBP5-AS1) was identified. The Kaplan-Meier analysis and ROC curves proved that the model could predict the prognostic survival with good sensitivity and specificity in both the validation set (AUC = 0.752, 95% confidence intervals (CI): 0.651-0.854) and the microarray dataset (AUC = 0.714, 95%CI: 0.615-0.814). Further study showed the three-lncRNA signature was not only pervasive in different breast cancer stages, subtypes and age groups, but also provides more accurate prognostic information than some widely known biomarkers. The results suggested that RNA-seq transcriptome profiling provides that the three-lncRNA signature is an independent prognostic biomarker, and have clinical significance. In addition, lncRNA, miRNA, and mRNA interaction network indicated lncRNAs may intervene in breast cancer pathogenesis by binding to miR-190b, acting as competing endogenous RNAs.


Assuntos
Biomarcadores Tumorais/genética , Neoplasias da Mama/genética , Neoplasias da Mama/mortalidade , RNA Longo não Codificante/genética , Transcriptoma/genética , Adulto , Idoso , Idoso de 80 Anos ou mais , Sequência de Bases , Feminino , Perfilação da Expressão Gênica , Humanos , Masculino , MicroRNAs/genética , Pessoa de Meia-Idade , Modelos Teóricos , Prognóstico , Análise de Sequência de RNA
14.
J Math Biol ; 73(6-7): 1561-1594, 2016 12.
Artigo em Inglês | MEDLINE | ID: mdl-27084186

RESUMO

In the face of serious infectious diseases, governments endeavour to implement containment measures such as public vaccination at a macroscopic level. Meanwhile, individuals tend to protect themselves by avoiding contacts with infections at a microscopic level. However, a comprehensive understanding of how such combined strategy influences epidemic dynamics is still lacking. We study a susceptible-infected-susceptible epidemic model with imperfect vaccination on dynamic contact networks, where the macroscopic intervention is represented by random vaccination of the population and the microscopic protection is characterised by susceptible individuals rewiring contacts from infective neighbours. In particular, the model is formulated both in populations without and then with demographic effects (births, deaths, and migration). Using the pairwise approximation and the probability generating function approach, we investigate both dynamics of the epidemic and the underlying network. For populations without demography, the emerging degree correlations, bistable states, and oscillations demonstrate the combined effects of the public vaccination program and individual protective behavior. Compared to either strategy in isolation, the combination of public vaccination and individual protection is more effective in preventing and controlling the spread of infectious diseases by increasing both the invasion threshold and the persistence threshold. For populations with additional demographic factors, we investigate temporal evolution of infected individuals and infectious contacts, as well as degree distributions of nodes in each class. It is found that the disease spreads faster but is more restricted in scale-free networks than in the Erdös-Rényi ones. The integration between vaccination intervention and individual rewiring may promote epidemic spreading due to the birth effect. Moreover, the degree distributions of both networks in the steady state is closely related to the degree distribution of newborns, which leads to uncorrelated connectivity. All the results demonstrate the importance of both local protection and global intervention, as well as the demographic effects. Our work thus offers a more comprehensive description of disease containment.


Assuntos
Controle de Doenças Transmissíveis/métodos , Epidemias/prevenção & controle , Modelos Biológicos , Saúde Pública/métodos , Vacinação , Humanos
15.
Sci Rep ; 6: 23766, 2016 Mar 31.
Artigo em Inglês | MEDLINE | ID: mdl-27029498

RESUMO

The threshold model has been widely adopted as a classic model for studying contagion processes on social networks. We consider asymmetric individual interactions in social networks and introduce a persuasion mechanism into the threshold model. Specifically, we study a combination of adoption and persuasion in cascading processes on complex networks. It is found that with the introduction of the persuasion mechanism, the system may become more vulnerable to global cascades, and the effects of persuasion tend to be more significant in heterogeneous networks than those in homogeneous networks: a comparison between heterogeneous and homogeneous networks shows that under weak persuasion, heterogeneous networks tend to be more robust against random shocks than homogeneous networks; whereas under strong persuasion, homogeneous networks are more stable. Finally, we study the effects of adoption and persuasion threshold heterogeneity on systemic stability. Though both heterogeneities give rise to global cascades, the adoption heterogeneity has an overwhelmingly stronger impact than the persuasion heterogeneity when the network connectivity is sufficiently dense.


Assuntos
Modelos Psicológicos , Comunicação Persuasiva , Rede Social , Redes Comunitárias/estatística & dados numéricos , Humanos , Conformidade Social
16.
Plant Physiol ; 170(2): 618-26, 2016 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-26620522

RESUMO

Maize (Zea mays) is one of the most important crops worldwide. To understand the biological processes underlying various traits of the crop (e.g. yield and response to stress), a detailed protein-protein interaction (PPI) network is highly demanded. Unfortunately, there are very few such PPIs available in the literature. Therefore, in this work, we present the Protein-Protein Interaction Database for Maize (PPIM), which covers 2,762,560 interactions among 14,000 proteins. The PPIM contains not only accurately predicted PPIs but also those molecular interactions collected from the literature. The database is freely available at http://comp-sysbio.org/ppim with a user-friendly powerful interface. We believe that the PPIM resource can help biologists better understand the maize crop.


Assuntos
Bases de Dados de Proteínas , Genoma de Planta/genética , Proteínas de Plantas/metabolismo , Mapas de Interação de Proteínas , Zea mays/metabolismo , Internet , Fenótipo , Proteínas de Plantas/genética , Interface Usuário-Computador , Zea mays/genética
17.
Comput Math Methods Med ; 2015: 842784, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26539246

RESUMO

Kidney renal clear cell carcinoma (KIRC) is one of the most common cancers with high mortality all over the world. Many studies have proposed that genes could be used to predict prognosis in KIRC. In this study, RNA expression data from next-generation sequencing and clinical information of 523 patients downloaded from The Cancer Genome Atlas (TCGA) dataset were analyzed in order to identify the relationship between gene expression level and the prognosis of KIRC patients. A set of five genes that significantly associated with overall survival time was identified and a model containing these five genes was constructed by Cox regression analysis. By Kaplan-Meier and Receiver Operating Characteristic (ROC) analysis, we confirmed that the model had good sensitivity and specificity. In summary, expression of the five-gene model is associated with the prognosis outcomes of KIRC patients, and it may have an important clinical significance.


Assuntos
Biomarcadores Tumorais/genética , Carcinoma de Células Renais/genética , Neoplasias Renais/genética , Adulto , Idoso , Idoso de 80 Anos ou mais , Carcinoma de Células Renais/mortalidade , Proteínas de Transporte de Cátions/genética , Biologia Computacional , Feminino , Perfilação da Expressão Gênica , Humanos , Estimativa de Kaplan-Meier , Neoplasias Renais/mortalidade , Masculino , Manosidases/genética , Proteínas de Membrana/genética , Pessoa de Meia-Idade , Modelos Genéticos , Nucleotidiltransferases/genética , Prognóstico , Modelos de Riscos Proporcionais , Curva ROC
18.
Biomed Res Int ; 2015: 841956, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26064958

RESUMO

In clinic, oral leukoplakia (OLK) may develop into oral cancer. However, the mechanism underlying this transformation is still unclear. In this work, we present a new pipeline to identify oral cancer related genes and microRNAs (miRNAs) by integrating both gene and miRNA expression profiles. In particular, we find some network modules as well as their miRNA regulators that play important roles in the development of OLK to oral cancer. Among these network modules, 91.67% of genes and 37.5% of miRNAs have been previously reported to be related to oral cancer in literature. The promising results demonstrate the effectiveness and efficiency of our proposed approach.


Assuntos
Leucoplasia Oral/genética , MicroRNAs/biossíntese , Neoplasias Bucais/genética , Proteínas de Neoplasias/biossíntese , Regulação Neoplásica da Expressão Gênica , Redes Reguladoras de Genes , Humanos , Leucoplasia Oral/complicações , Leucoplasia Oral/patologia , MicroRNAs/genética , Neoplasias Bucais/etiologia , Neoplasias Bucais/patologia , Proteínas de Neoplasias/genética , Mapas de Interação de Proteínas/genética
19.
Mol Med Rep ; 10(3): 1335-42, 2014 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-25017645

RESUMO

Octamer­binding transcription factor 4 (OCT4) is one of the factors associated with self­renewal and differentiation in cancer stem cells, and is crucial for the progression of various types of human malignancy. However, the expression and function of OCT4 in human pancreatic cancer has not been fully elucidated. The purpose of the present study was to investigate the function and molecular mechanisms of OCT4 in pancreatic cancer cells. The clinical significance of OCT4 expression was assessed by an immunohistochemical assay using a tissue microarray procedure in pancreatic cancer tissues and cells with different degrees of differentiation. A loss­of­function approach was used to examine the effects of a lentivirus­mediated OCT4 small hairpin RNA vector on biological behaviors, including cell proliferative activity and invasive potential. The results demonstrated that the expression levels of OCT4 protein in cancer tissues were significantly elevated compared with those in adjacent non­cancerous tissues (65.0 vs. 42.5%; P=0.005), which was correlated with tumor differentiation (P=0.008). The knockdown of OCT4 inhibited the proliferation and invasion of pancreatic cancer cells (Panc­1) expressing high levels of OCT4, accompanied with decreased expression of AKT, proliferating cell nuclear antigen (PCNA) and matrix metalloproteinase­2 (MMP­2). In conclusion, the present study reveals that the increased expression of OCT4 is correlated with the differentiation of pancreatic cancer, while knockdown of OCT4 suppresses the growth and invasion of pancreatic cancer cells through inhibition of AKT pathway­mediated PCNA and MMP­2 expression, suggesting that OCT4 might serve as a potential therapeutic target for the treatment of pancreatic cancer.


Assuntos
Fator 3 de Transcrição de Octâmero/genética , Neoplasias Pancreáticas/genética , Neoplasias Pancreáticas/terapia , Proteínas Proto-Oncogênicas c-akt/metabolismo , Diferenciação Celular , Linhagem Celular Tumoral , Proliferação de Células , Feminino , Regulação Neoplásica da Expressão Gênica , Técnicas de Silenciamento de Genes , Terapia Genética , Humanos , Masculino , Metaloproteinase 2 da Matriz/genética , Metaloproteinase 2 da Matriz/metabolismo , Pessoa de Meia-Idade , Invasividade Neoplásica/genética , Fator 3 de Transcrição de Octâmero/metabolismo , Neoplasias Pancreáticas/patologia , Antígeno Nuclear de Célula em Proliferação/genética , Antígeno Nuclear de Célula em Proliferação/metabolismo , Proteínas Proto-Oncogênicas c-akt/genética , RNA Interferente Pequeno/genética , RNA Interferente Pequeno/metabolismo , Transdução de Sinais
20.
Biomed Res Int ; 2014: 750961, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24516854

RESUMO

Sophora japonica Linn (Chinese Scholar Tree) is a shrub species belonging to the subfamily Faboideae of the pea family Fabaceae. In this study, RNA sequencing of S. japonica transcriptome was performed to produce large expression datasets for functional genomic analysis. Approximate 86.1 million high-quality clean reads were generated and assembled de novo into 143010 unique transcripts and 57614 unigenes. The average length of unigenes was 901 bps with an N50 of 545 bps. Four public databases, including the NCBI nonredundant protein (NR), Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), and the Cluster of Orthologous Groups (COG), were used to annotate unigenes through NCBI BLAST procedure. A total of 27541 of 57614 unigenes (47.8%) were annotated for gene descriptions, conserved protein domains, or gene ontology. Moreover, an interaction network of unigenes in S. japonica was predicted based on known protein-protein interactions of putative orthologs of well-studied plant genomes. The transcriptome data of S. japonica reported here represents first genome-scale investigation of gene expressions in Faboideae plants. We expect that our study will provide a useful resource for further studies on gene expression, genomics, functional genomics, and protein-protein interaction in S. japonica.


Assuntos
Perfilação da Expressão Gênica/métodos , Análise de Sequência de RNA/métodos , Sophora/genética , Sophora/metabolismo , Transcriptoma/genética , Bases de Dados Genéticas
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