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Find video protocols related to scientific articles indexed in Pubmed.
Advanced Hepatic Fibrosis and Steatosis Are Associated with Persistently Alanine Aminotransferase Elevation in Chronic Hepatitis C Patients Negative for HCV RNA During Pegylated Interferon Plus Ribavirin Therapy.
J. Infect. Dis.
PUBLISHED: 11-13-2014
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?Clinical implications of persistently alanine aminotransferase (ALT) elevation and associated factors in chronic hepatitis C (CHC) patients who achieved undetectable hepatitis C virus (HCV) RNA during pegylated interferon (PEG-IFN) plus ribavirin (RBV) therapy remain unknown.
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Dendritic cells respond to nasopharygeal carcinoma cells through annexin A2-recognizing DC-SIGN.
Oncotarget
PUBLISHED: 11-06-2014
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Dendritic cells (DCs) play an essential role in immunity and are used in cancer immunotherapy. However, these cells can be tuned by tumors with immunosuppressive responses. DC-specific intercellular adhesion molecule 3-Grabbing Nonintegrin (DC-SIGN), a C-type lectin expressed on DCs, recognizes certain carbohydrate structures which can be found on cancer cells. Nasopharyngeal carcinoma (NPC) is an epithelial cell-derived malignant tumor, in which immune response remains unclear. This research is to reveal the molecular link on NPC cells that induces the immunosuppressive responses in DCs. In this article, we report identification of annexin A2 (ANXA2) on NPC cells as a ligand for DC-SIGN on DCs. N-linked mannose-rich glycan on ANXA2 may mediate the interaction. ANXA2 was abundantly expressed in NPC, and knockdown of ANXA2 suppressed NPC xenograft in mice, suggesting a crucial role of ANXA2 in NPC growth. Interaction with NPC cells caused DC-SIGN activation in DCs. Consequently DC maturation and the proinflammatory interleukin (IL)-12 production were inhibited, and the immunosuppressive IL-10 production was promoted. Blockage of either DC-SIGN or ANXA2 eliminated the production of IL-10 from DCs. This report suggests that suppression of ANXA2 at its expression or glycosylation on NPC may improve DC-mediated immunotherapy for the tumor.
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Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 11-02-2014
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Neurospora crassa has been for decades a principal model for filamentous fungal genetics and physiology as well as for understanding the mechanism of circadian clocks. Eukaryotic fungal and animal clocks comprise transcription-translation-based feedback loops that control rhythmic transcription of a substantial fraction of these transcriptomes, yielding the changes in protein abundance that mediate circadian regulation of physiology and metabolism: Understanding circadian control of gene expression is key to understanding eukaryotic, including fungal, physiology. Indeed, the isolation of clock-controlled genes (ccgs) was pioneered in Neurospora where circadian output begins with binding of the core circadian transcription factor WCC to a subset of ccg promoters, including those of many transcription factors. High temporal resolution (2-h) sampling over 48 h using RNA sequencing (RNA-Seq) identified circadianly expressed genes in Neurospora, revealing that from ?10% to as much 40% of the transcriptome can be expressed under circadian control. Functional classifications of these genes revealed strong enrichment in pathways involving metabolism, protein synthesis, and stress responses; in broad terms, daytime metabolic potential favors catabolism, energy production, and precursor assembly, whereas night activities favor biosynthesis of cellular components and growth. Discriminative regular expression motif elicitation (DREME) identified key promoter motifs highly correlated with the temporal regulation of ccgs. Correlations between ccg abundance from RNA-Seq, the degree of ccg-promoter activation as reported by ccg-promoter-luciferase fusions, and binding of WCC as measured by ChIP-Seq, are not strong. Therefore, although circadian activation is critical to ccg rhythmicity, posttranscriptional regulation plays a major role in determining rhythmicity at the mRNA level.
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ChIP-seq and In Vivo Transcriptome Analyses of the Aspergillus fumigatus SREBP SrbA Reveals a New Regulator of the Fungal Hypoxia Response and Virulence.
PLoS Pathog.
PUBLISHED: 11-01-2014
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The Aspergillus fumigatus sterol regulatory element binding protein (SREBP) SrbA belongs to the basic Helix-Loop-Helix (bHLH) family of transcription factors and is crucial for antifungal drug resistance and virulence. The latter phenotype is especially striking, as loss of SrbA results in complete loss of virulence in murine models of invasive pulmonary aspergillosis (IPA). How fungal SREBPs mediate fungal virulence is unknown, though it has been suggested that lack of growth in hypoxic conditions accounts for the attenuated virulence. To further understand the role of SrbA in fungal infection site pathobiology, chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) was used to identify genes under direct SrbA transcriptional regulation in hypoxia. These results confirmed the direct regulation of ergosterol biosynthesis and iron uptake by SrbA in hypoxia and revealed new roles for SrbA in nitrate assimilation and heme biosynthesis. Moreover, functional characterization of an SrbA target gene with sequence similarity to SrbA identified a new transcriptional regulator of the fungal hypoxia response and virulence, SrbB. SrbB co-regulates genes involved in heme biosynthesis and demethylation of C4-sterols with SrbA in hypoxic conditions. However, SrbB also has regulatory functions independent of SrbA including regulation of carbohydrate metabolism. Loss of SrbB markedly attenuates A. fumigatus virulence, and loss of both SREBPs further reduces in vivo fungal growth. These data suggest that both A. fumigatus SREBPs are critical for hypoxia adaptation and virulence and reveal new insights into SREBPs' complex role in infection site adaptation and fungal virulence.
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[Association between gene polymorphism of CD40 gene and coronary artery lesion in Kawasaki disease].
Zhongguo Dang Dai Er Ke Za Zhi
PUBLISHED: 10-26-2014
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To study the association between two single nucleotide polymorphisms (rs4810485 and rs1535045 in CD40 gene) and Kawasaki disease (KD) in Han Chinese children.
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Serum Biomarkers Predictive of Significant Fibrosis and Cirrhosis in Chronic Hepatitis B.
J. Clin. Gastroenterol.
PUBLISHED: 10-17-2014
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Aspartate aminotransferase to platelet ratio index (APRI) and FIB-4 index are noninvasive biomarkers to evaluate hepatic fibrosis. However, their usefulness in chronic hepatitis B (CHB) patients remains unclear.
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Increasing Biopsy Number and Sampling from Gastric Body Improve the Sensitivity of Rapid Urease Test in Patients with Peptic Ulcer Bleeding.
Dig. Dis. Sci.
PUBLISHED: 09-01-2014
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Previous studies demonstrated that the sensitivity of rapid urease test (RUT) for diagnosis of Helicobacter pylori infection decreased during peptic ulcer bleeding.
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Nanopost-guided self-organization of dendritic inorganic salt structures.
Langmuir
PUBLISHED: 08-29-2014
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The formation of hierarchical architectures is of fundamental importance and yet a relatively elusive problem concerning many natural and industrial processes. In this paper, a nanopost array platform, or a nanopost substrate, has been developed to address this issue through a model study of the drying structures of phosphate buffered saline (PBS) solution. Unlike on a plain surface, highly ramified salt structures are formed by simply allowing the nanopost substrate wetted with the salt solution to dry, a process that completes within minutes at room temperature. The branches of salt structures have similar shapes repeating at different length scales, ranging from ?200 nm up to a few centimeters in length, covering a 2 × 2 cm(2) area patterned with nanoposts fabricated in photoresist via laser interference lithography (LIL). Scanning electromicrograph (SEM) images show that salt structures are formed around nanoposts, and characteristic features of these salt structures can be modulated and predicted based on the surface properties and geometrical arrangements of nanoposts, suggesting that nanoposts can be used to guide the organization and crystallization of salts. This nanopost-guided crystallization approach is robust, rapid, versatile, and amenable to real-time observation and mass production, providing a great opportunity for the study and creation of large-scale hierarchical structures.
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Metabolic syndrome factors and risk of postoperative depression in high-grade glioma patients in a 1.5-year prospective study.
Med. Oncol.
PUBLISHED: 08-21-2014
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To date, the relationship between metabolic syndrome factors and the risk of glioma-related depression is still unclear, and no study investigates this relationship. Our aim was to investigate the relationship between metabolic syndrome factors and the risk of postoperative depression in high-grade patients. A total of 386 high-grade glioma patients participated in blood sample collection for metabolic syndrome factors analysis and the hospital anxiety and depression scale testing. The association between metabolic syndrome factors and the risk of postoperative depression was assessed using Cox regression proportional hazards models, and Student's t tests were used to evaluate the differences in demographic variables and clinical characteristics in subgroups. The incidence of postoperative depression in our 1.5-year follow-up was 30.5%. We found the risk of postoperative depression was elevated with increased blood glucose level [hazard ratios (HR) 2.277, 95% confidence interval (CI) 1.201-4.320, top vs. bottom quartile]. The hazard ratio was increased for z-scores of blood glucose (HR 1.672 per unit standard deviation, 95% CI 1.311-2.133] and of the combined metabolic syndrome score (HR 1.080, 95% CI 1.000-1.167). In addition, risk of postoperative depression risk was increased in high-grade glioma patients with high blood glucose levels (?6.0 mmol/l) (HR 2.084, 95% CI 1.235-3.515). However, we did not find significant associations between postoperative depression and other metabolic syndrome factors, including body mass index, systolic blood pressure, diastolic blood pressure, cholesterol, and triglycerides. Depression is prevalent among patients with high-grade glioma after operation. Blood glucose level is positively associated with the risk of postoperative depression, and might be involved in the etiology of postoperative depression, and may predict its development in high-grade glioma patients.
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Relating gene expression evolution with CpG content changes.
BMC Genomics
PUBLISHED: 08-20-2014
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Previous studies have shown that CpG dinucleotides are enriched in a subset of promoters and the CpG content of promoters is positively correlated with gene expression levels. But the relationship between divergence of CpG content and gene expression evolution has not been investigated. Here we calculate the normalized CpG (nCpG) content in DNA regions around transcription start site (TSS) and transcription terminal site (TTS) of genes in nine organisms, and relate them with expression levels measured by RNA-seq.
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Quercetin induces mitochondrial-derived apoptosis via reactive oxygen species-mediated ERK activation in HL-60 leukemia cells and xenograft.
Arch. Toxicol.
PUBLISHED: 08-20-2014
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Quercetin is a plant-derived bioflavonoid that was recently shown to have multiple anticancer activities in various solid tumors. Here, novel molecular mechanisms through which quercetin exerts its anticancer effects in acute myeloid leukemia (AML) cells were investigated. Results from Western blot and flow cytometric assays revealed that quercetin significantly induced caspase-8, caspase-9, and caspase-3 activation, poly ADP-ribose polymerase (PARP) cleavage, and mitochondrial membrane depolarization in HL-60 AML cells. The induction of PARP cleavage by quercetin was also observed in other AML cell lines: THP-1, MV4-11, and U937. Moreover, treatment of HL-60 cells with quercetin induced sustained activation of extracellular signal-regulated kinase (ERK), and inhibition of ERK by an ERK inhibitor significantly abolished quercetin-induced cell apoptosis. MitoSOX red and 2',7'-dichlorofluorescin fluorescence, respectively, showed that mitochondrial superoxide and intracellular peroxide levels were higher in quercetin-treated HL-60 cells compared with the control group. Moreover, both N-acetylcysteine and the superoxide dismutase mimetic, MnTBAP, reversed quercetin-induced intracellular reactive oxygen species production, ERK activation, and subsequent cell death. The in vivo xenograft mice experiments revealed that quercetin significantly reduced tumor growth through inducing intratumoral oxidative stress while activating the ERK pathway and subsequent cell apoptosis in mice with HL-60 tumor xenografts. In conclusions, our results indicated that quercetin induced cell death of HL-60 cells in vitro and in vivo through induction of intracellular oxidative stress following activation of an ERK-mediated apoptosis pathway.
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Applications of bioinformatics to non-coding RNAs in the era of next-generation sequencing.
Pac Symp Biocomput
PUBLISHED: 08-15-2014
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The human genome encodes a large number of non-coding RNAs, which employ a new and crucial layer of biological regulation in addition to proteins. Technical advancement in recent years, particularly, the wide application of next generation sequencing analysis, provide an unprecedented opportunity to identify new non-coding RNAs and investigate their functions and regulatory mechanisms. The aim of this workshop is to bring together experimental and computational biologist to exchange ideas on non-coding RNA studies.
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Construction the model on the breast cancer survival analysis use support vector machine, logistic regression and decision tree.
J Med Syst
PUBLISHED: 08-14-2014
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The aim of the paper is to use data mining technology to establish a classification of breast cancer survival patterns, and offers a treatment decision-making reference for the survival ability of women diagnosed with breast cancer in Taiwan. We studied patients with breast cancer in a specific hospital in Central Taiwan to obtain 1,340 data sets. We employed a support vector machine, logistic regression, and a C5.0 decision tree to construct a classification model of breast cancer patients' survival rates, and used a 10-fold cross-validation approach to identify the model. The results show that the establishment of classification tools for the classification of the models yielded an average accuracy rate of more than 90% for both; the SVM provided the best method for constructing the three categories of the classification system for the survival mode. The results of the experiment show that the three methods used to create the classification system, established a high accuracy rate, predicted a more accurate survival ability of women diagnosed with breast cancer, and could be used as a reference when creating a medical decision-making frame.
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Volume changes in remnant thyroid tissue after thyroidectomy in Graves disease.
J. Formos. Med. Assoc.
PUBLISHED: 08-09-2014
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Surgery is one of the treatment choices for Graves disease. The residual thyroid tissue may shrink or become larger. The object of this study was trying to find out what factors affect the residual thyroid gland volume change after thyroidectomy in Graves disease.
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SAHA-based novel HDAC inhibitor design by core hopping method.
J. Mol. Graph. Model.
PUBLISHED: 08-08-2014
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The catalytic activity of the histone deacetylase (HDAC) is directly relevant to the pathogenesis of cancer, and HDAC inhibitors represented a promising strategy for cancer therapy. SAHA (suberoanilide hydroxamic acid), an effective HDAC inhibitor, is an anti-cancer agent against T-cell lymphoma. However, SAHA has adverse effects such as poor pharmacokinetic properties and severe toxicities in clinical use. In order to identify better HDAC inhibitors, a compound database was established by core hopping of SAHA, which was then docked into HDAC-8 (PDB ID: 1T69) active site to select a number of candidates with higher docking score and better interaction with catalytic zinc ion. Further ADMET prediction was done to give ten compounds. Molecular dynamics simulation of the representative compound 101 was performed to study the stability of HDAC8-inhibitor system. This work provided an approach to design novel high-efficiency HDAC inhibitors with better ADMET properties.
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Annexin A2 in renal cell carcinoma: Expression, function, and prognostic significance.
Urol. Oncol.
PUBLISHED: 07-31-2014
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Renal cell carcinoma (RCC) is the most lethal genitourinary cancer and intrinsically resistant to chemotherapy, radiotherapy, and hormone therapy. Annexin A2 (Anxa2) is a calcium-dependent phospholipid-binding protein found on various cell types that plays multiple roles in regulating cellular functions. In RCC, Anxa2 expression was correlated with tumor differentiation, clinical outcomes, and the metastatic potential; however, the underlying mechanisms remain obscure. This study investigated the role of Anxa2 in regulating tumorigenesis of RCC.
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Increased expressions of SATB1 and S100A4 are associated with poor prognosis in human colorectal carcinoma.
APMIS
PUBLISHED: 07-22-2014
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This study was designed to explore the correlation between expressions of SATB1 and S100A4 and their relationships to the clinicopathologic parameters of colorectal carcinoma (CRC). Expressions of SATB1 and S100A4 were evaluated by immunohistochemistry in a cohort of 131 primary CRC patients undergone surgical resection from 2005 to 2007. SATB1 and S100A4 were positively expressed in 48.9% and 54.2% of CRC cases, respectively. SATB1 and S100A4 expressions in tumor tissues were significantly higher than those in the corresponding normal tissues. A positive correlation was observed between SATB1 and S100A4. Moreover, the levels of SATB1 and S100A4 were both significantly associated with invasion, lymph node status, and TNM stage of CRC, whereas S100A4 expression was also correlated with distant metastasis. Multivariate analysis revealed that SATB1 expression was an independent prognostic indicator for poor survival of CRC. Further survival analysis indicated that co-expression of SATB1 and S100A4 suggested a worse 5-year overall survival rate in CRC patients. Thus, combined analysis of SATB1 and S100A4 expressions may be valuable in determining the development and progression of CRC. Co-expression of SATB1 and S100A4 is an unfavorable prognostic indicator and may be useful in the follow-up of patients with CRC.
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Comparative analysis of regulatory information and circuits across distant species.
Nature
PUBLISHED: 07-10-2014
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Despite the large evolutionary distances between metazoan species, they can show remarkable commonalities in their biology, and this has helped to establish fly and worm as model organisms for human biology. Although studies of individual elements and factors have explored similarities in gene regulation, a large-scale comparative analysis of basic principles of transcriptional regulatory features is lacking. Here we map the genome-wide binding locations of 165 human, 93 worm and 52 fly transcription regulatory factors, generating a total of 1,019 data sets from diverse cell types, developmental stages, or conditions in the three species, of which 498 (48.9%) are presented here for the first time. We find that structural properties of regulatory networks are remarkably conserved and that orthologous regulatory factor families recognize similar binding motifs in vivo and show some similar co-associations. Our results suggest that gene-regulatory properties previously observed for individual factors are general principles of metazoan regulation that are remarkably well-preserved despite extensive functional divergence of individual network connections. The comparative maps of regulatory circuitry provided here will drive an improved understanding of the regulatory underpinnings of model organism biology and how these relate to human biology, development and disease.
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The tumor suppressive role of NUMB isoform 1 in esophageal squamous cell carcinoma.
Oncotarget
PUBLISHED: 07-02-2014
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Esophageal quamous cell carcinoma (ESCC) is the predominant histological type of esophageal carcinoma in Asian populations. To date, few biomarkers have been identified for ESCC. In present study, we found a tumor suppressor, NUMB isoform 1 (NUMB-1), as a promising prognostic biomarker for patients with ESCC. NUMB-1 mRNA was downregulated in 66.7% of primary ESCC tissues when compared with matched adjacent non-tumor tissues. The low expression of NUMB-1 was significantly associated with high tumor recurrence (p=0.029) and poor post-operative overall survival (p=0.016). To further explore the underlying mechanisms by which NUMB-1 regulates ESCC, we demonstrated that ectopic expression of NUMB-1 inhibited cell proliferation through inducing G2/M phase arrest, which was accompanied by an increase in p21 and cyclin B1-cdc2 levels. However, it had no impact on apoptosis of ESCC cells. In addition, overexpression of NUMB-1 prevented epithelial-mesenchymal transition, inhibited invasion of ESCC cells and NOTCH pathway, suppressed Aurora-A activity by preventing phosphorylation of Aurora-A at T288 which resulted in cell cycle arrest. Taken together, our findings suggested NUMB-1 functions as a tumor-suppressor and serves as a prognositc biomarker for ESCC patients; thus, NUMB-1 may be a potential novel therapeutic target for treatment of ESCC.
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Design Novel Inhibitors for Treating Cancer by Targeting Cdc25B Catalytic Domain with de Novo Design.
Comb. Chem. High Throughput Screen.
PUBLISHED: 07-01-2014
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The cell division cycle 25 (Cdc25) families of proteins are highly conserved dual specificity phosphatases that regulate cyclin-dependent kinases and represent a group of attractive drug targets for anticancer therapies. To develop novel Cdc25B inhibitors, the ZINC database was screened for finding the optimal fragments with de novel design approaches. As a result, top 11 compounds having higher binding affinities in flexible docking were obtained, which were derived from five novel scaffolds consisting of two isolated scaffolds located in the two binding domains (catalytic pocket and swimming pool) and the linker-part. The subsequent molecular docking and molecular dynamics studies showed that these compounds not only adopt more favorable conformations but also have stronger binding interaction with receptor than the inhibitors identified previously. The additional absorption, distribution, metabolism, excretion and toxicity (ADMET) predictions also indicted the 11 compounds (especially Comp#1) hold a high potential to be novel lead compounds for anticarcinogen. Consequently, the findings reported here may at least provide a new strategy or useful insights for designing the effective Cdc25B inhibitors.
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Cotton-based Diagnostic Devices.
Sci Rep
PUBLISHED: 06-30-2014
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A good diagnostic procedure avoids wasting medical resources, is easy to use, resists contamination, and provides accurate information quickly to allow for rapid follow-up therapies. We developed a novel diagnostic procedure using a "cotton-based diagnostic device" capable of real-time detection, i.e., in vitro diagnostics (IVD), which avoids reagent contamination problems common to existing biomedical devices and achieves the abovementioned goals of economy, efficiency, ease of use, and speed. Our research reinforces the advantages of an easy-to-use, highly accurate diagnostic device created from an inexpensive and readily available U.S. FDA-approved material (i.e., cotton as flow channel and chromatography paper as reaction zone) that adopts a standard calibration curve method in a buffer system (i.e., nitrite, BSA, urobilinogen and uric acid assays) to accurately obtain semi-quantitative information and limit the cross-contamination common to multiple-use tools. Our system, which specifically targets urinalysis diagnostics and employs a multiple biomarker approach, requires no electricity, no professional training, and is exceptionally portable for use in remote or home settings. This could be particularly useful in less industrialized areas.
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[Comparison of the risk factors for asthma in children between urban and rural areas in Fuzhou City].
Zhonghua Er Ke Za Zhi
PUBLISHED: 06-12-2014
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To explore the prevalence and the different risk factors for asthma in children between urban and rural areas in Fuzhou, Fujian province.
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Overexpression of membrane-type 2 matrix metalloproteinase induced by hypoxia-inducible factor-1? in pancreatic cancer: Implications for tumor progression and prognosis.
Mol Clin Oncol
PUBLISHED: 05-20-2014
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Membrane-type 2 matrix metalloproteinase (MT2-MMP) has been identified as a powerful modulator of the pericellular environment that promotes tumor invasion and metastasis. In this study, we investigated the association of MT2-MMP and hypoxia-inducible factor-1? (HIF-1?) expression in pancreatic cancer with regard to their clinical prognostic significance. Of the tissue specimens obtained from the 78 patients included in this study, 46 (59%) were found to be positive for MT2-MMP immunostaining and MT2-MMP expression was colocalized with HIF-1? in pancreatic cancer. Using the Spearman's rank analysis, the protein and mRNA expression level of MT2-MMP was found to be significantly correlated with HIF-1? and CD34-microvascular density in pancreatic cancer. Furthermore, the expression of MT2-MMP in response to hypoxia was increased in a time-dependent manner and the promoter luciferase reporter revealed upregulation of MT2-MMP expression induced by HIF-1? in pancreatic cancer cells. Moreover, the Cox regression model indicated that MT2-MMP was an independent prognostic factor in patients with pancreatic cancer. Our results demonstrated that the overexpression of MT2-MMP was induced by HIF-1? in response to hypoxia and was an independent prognostic factor for pancreatic cancer progression.
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Comparative analysis of the transcriptome across distant species.
Nature
PUBLISHED: 04-30-2014
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The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features. Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters.
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Paper-based ELISA for the detection of autoimmune antibodies in body fluid-the case of bullous pemphigoid.
Anal. Chem.
PUBLISHED: 04-27-2014
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Bullous pemphigoid (BP), a common autoimmune blistering disease, is increasing in incidence and conveys a high mortality. Detection of autoantibodies targeting the noncollagenous 16A (NC16A) domain of type XVII collagen using enzyme-linked immunosorbent assay (ELISA) has demonstrated high sensitivity and specificity for diagnosing BP. We have developed a rapid, low-cost, and widely applicable ELISA-based system to detect the NC16A autoimmune antibody and then diagnose and monitor BP disease activity using a piece of filter paper, a wax-printer, and NC16A antigens. Both sera and/or blister fluids from 14 untreated BP patients were analyzed. The control group included healthy volunteers and patients with other blistering disorders such as pemphigus vulgaris. In our established paper-based ELISA (P-ELISA) system, only 2 ?L of serum or blister fluid and 70 min were required to detect anti-NC16A autoimmune antibodies. The relative color intensity was significantly higher in the BP group than in the control groups when using either serum (P < 0.05) or blister fluid (P < 0.001) specimens from BP patients. The results of P- ELISA were moderately correlated with the titer of the commercial ELISA kit (MBL, Japan) (rho = 0.5680, P = 0.0011). This newly developed system allows for rapid and convenient diagnosis and/or monitoring of BP disease activity.
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Peginterferon alfa-2a with or without low-dose ribavirin for treatment-naive patients with hepatitis C virus genotype 2 receiving haemodialysis: a randomised trial.
Gut
PUBLISHED: 04-22-2014
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Data comparing the efficacy and safety of combination therapy with peginterferon plus low-dose ribavirin and peginterferon monotherapy in treatment-naive haemodialysis patients with hepatitis C virus genotype 2 (HCV-2) infection are limited.
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Mechanotransduction in intervertebral discs.
J. Cell. Mol. Med.
PUBLISHED: 04-17-2014
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Mechanotransduction plays a critical role in intracellular functioning-it allows cells to translate external physical forces into internal biochemical activities, thereby affecting processes ranging from proliferation and apoptosis to gene expression and protein synthesis in a complex web of interactions and reactions. Accordingly, aberrant mechanotransduction can either lead to, or be a result of, a variety of diseases or degenerative states. In this review, we provide an overview of mechanotransduction in the context of intervertebral discs, with a focus on the latest methods of investigating mechanotransduction and the most recent findings regarding the means and effects of mechanotransduction in healthy and degenerative discs. We also provide some discussion of potential directions for future research and treatments.
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Phosphotriesterase-related protein sensed albuminuria and conferred renal tubular cell activation in membranous nephropathy.
J. Biomed. Sci.
PUBLISHED: 04-11-2014
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Membranous nephropathy (MN) is a common cause of nephrotic syndrome that may progress to end-stage renal disease (ESRD). The formation of MN involves the in situ formation of subepithelial immune deposits and leads to albuminuria; however, the underlying mechanism of how MN leads to ESRD remains unclear. The aim of this study was to investigate the expression and biological functions of phosphotriesterase-related protein (PTER) in MN.
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Association of osteopontin with osteoarthritis.
Rheumatol. Int.
PUBLISHED: 04-01-2014
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The joint disease osteoarthritis (OA) is the most common form of arthritis, which mainly affects the older people. OA is becoming one of the major non-fatal health burdens of the world. The etiology of OA is mostly unclear, and it cannot be cured totally. Osteopontin (OPN) is a multifunctional phosphoprotein, of which overexpression and high level of presence in synovial fluid and articular cartilage were found to be associated with OA progression. Usually, in OA progression, OPN plays important role as an intrinsic regulator. Recent studies have taken attempt to use this protein as a diagnostic marker of OA and use OPN as a target for the drug development against OA. This review summarizes the role of OPN in OA, with focusing on the mechanism of action, and also discussing the diagnostic and therapeutic aspects of OA related to OPN.
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The histone methyltransferase activity of MLL1 is dispensable for hematopoiesis and leukemogenesis.
Cell Rep
PUBLISHED: 03-19-2014
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Despite correlations between histone methyltransferase (HMT) activity and gene regulation, direct evidence that HMT activity is responsible for gene activation is sparse. We address the role of the HMT activity for MLL1, a histone H3 lysine 4 (H3K4) methyltransferase critical for maintaining hematopoietic stem cells (HSCs). Here, we show that the SET domain, and thus HMT activity of MLL1, is dispensable for maintaining HSCs and supporting leukemogenesis driven by the MLL-AF9 fusion oncoprotein. Upon Mll1 deletion, histone H4 lysine 16 (H4K16) acetylation is selectively depleted at MLL1 target genes in conjunction with reduced transcription. Surprisingly, inhibition of SIRT1 is sufficient to prevent the loss of H4K16 acetylation and the reduction in MLL1 target gene expression. Thus, recruited MOF activity, and not the intrinsic HMT activity of MLL1, is central for the maintenance of HSC target genes. In addition, this work reveals a role for SIRT1 in opposing MLL1 function.
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MicroRNA-224 suppresses colorectal cancer cell migration by targeting Cdc42.
Dis. Markers
PUBLISHED: 03-15-2014
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The metastatic spread of tumor cells is the major risk factor affecting the clinical prognosis of colorectal cancer (CRC) patients. The metastatic phenotype can be modulated by dysregulating the synthesis of different structural and functional proteins of tumor cells. Micro(mi)RNAs are noncoding RNAs that recognize their cognate messenger (m)RNA targets by sequence-specific interactions with the 3' untranslated region and are involved in the multistep process of CRC development. The objective of this study was to investigate the expression and biological roles of miR-224 in CRC. The miR-224 expression level was assessed by a quantitative real-time PCR in 79 CRC and 18 nontumor tissues. Expression levels of miR-224 in CRC tissues were significantly lower than those in nontumor tissues. Its expression level was associated with the mutation status of the APC gene. Ectopic expression of miR-224 suppressed the migratory ability of CRC cell line, but cell proliferation was less affected. Increased miR-224 diminished Cdc42 and SMAD4 expressions at both the protein and mRNA levels and inhibited the formation of actin filaments. Overall, this study indicated a role of miR-224 in negatively regulating CRC cell migration. The expression level of miR-224 may be a useful predictive biomarker for CRC progression.
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Using cell structures to develop functional nanomaterials and nanostructures--case studies of actin filaments and microtubules.
Chem. Commun. (Camb.)
PUBLISHED: 03-05-2014
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This article is based on the continued development of biologically relevant elements (i.e., actin filaments and microtubules in living cells) as building blocks to create functional nanomaterials and nanostructures that can then be used to manufacture nature-inspired small-scale devices or systems. Here, we summarize current progress in the field and focus specifically on processes characterized by (1) robustness and ease of use, (2) inexpensiveness, and (3) potential expandability to mass production. This article, we believe, will provide scientists and engineers with a more comprehensive understanding of how to mine biological materials and natural design features to construct functional materials and devices.
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Inhibition of intimal hyperplasia in murine aortic allografts by the oral administration of the transforming growth factor-beta receptor I kinase inhibitor SD-208.
J. Heart Lung Transplant.
PUBLISHED: 02-16-2014
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Transforming growth factor-beta (TGF-?) plays a significant role in the pathogenesis of the intimal hyperplasia of transplant arteriosclerosis (TA). The aim of this study was to evaluate the efficacy of an oral inhibitor of TGF-? receptor I kinase (SD-208) on the development of TA.
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OrthoClust: an orthology-based network framework for clustering data across multiple species.
Genome Biol.
PUBLISHED: 02-08-2014
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Increasingly, high-dimensional genomics data are becoming available for many organisms.Here, we develop OrthoClust for simultaneously clustering data across multiple species. OrthoClust is a computational framework that integrates the co-association networks of individual species by utilizing the orthology relationships of genes between species. It outputs optimized modules that are fundamentally cross-species, which can either be conserved or species-specific. We demonstrate the application of OrthoClust using the RNA-Seq expression profiles of Caenorhabditis elegans and Drosophila melanogaster from the modENCODE consortium. A potential application of cross-species modules is to infer putative analogous functions of uncharacterized elements like non-coding RNAs based on guilt-by-association.
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Bilateral pulmonary artery aneurysms, coronary artery aneurysm, and ventricular pseudoaneurysm in Behçet disease.
Ann Vasc Surg
PUBLISHED: 02-06-2014
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Massive hemoptysis in Behçet disease (BD) is rare but often fatal. This report presents a 28-year-old man with recurrent massive hemoptysis. He was diagnosed with bilateral multiple pulmonary artery aneurysms (PAAs), coronary artery aneurysm, and ventricular pseudoaneurysm from BD. The patient underwent emergency right lower lobectomy with no obvious complications. No hemoptysis recurred during an 18-month follow-up. This report also reviews the occurrence of PAAs in BD, with an emphasis on the treatment approaches.
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Microfluidics expands the zebrafish potentials in pharmaceutically relevant screening.
Adv Healthc Mater
PUBLISHED: 01-24-2014
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The objective of this study is to enlarge the impact of microfluidics on the pharmaceutical industry by highlighting the reported scientific work on the synergistic relationship between zebrafish and microfluidics, and furthering that effort to shed light on how microfluidics can facilitate the use of zebrafish as a gene screening tool. Zebrafish is ranked the third most important animal model after rats and mice, according to a National Institutes of Health (NIH) announcement in 2003. It has become a staple for scientists to examine and subsequently begin to unravel the mystery of human diseases, and is increasingly used in toxicological studies for new drug development. The unique characteristics that this tiny fish possesses, including rapid growth rate, prodigious numbers of offspring, and eggs that develop outside the body, make it an invaluable genetic tool. Evidently, these advantages can be broadened with the addition of a properly designed microfluidic circuit. By means of the presented illustrations and demonstrated applications, the goal is to spark interest in the development of more novel microfluidic platform designs that can leverage the attributes of zebrafish and quickly come to commercial fruition.
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Targeting spleen tyrosine kinase-Bruton's tyrosine kinase axis for immunologically mediated glomerulonephritis.
Biomed Res Int
PUBLISHED: 01-20-2014
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The importance of B-cell activation and immune complex-mediated Fc-receptor activation in the pathogenesis of immunologically mediated glomerulonephritis has long been recognized. The two nonreceptor tyrosine kinases, spleen tyrosine kinase (Syk) and Bruton's tyrosine kinase (Btk), are primarily expressed by hematopoietic cells, and participate in B-cell-receptor- and Fc-receptor-mediated activation. Pharmacological inhibitors of Syk or Btk are undergoing preclinical development and clinical trials for several immune diseases; and Syk inhibitors have been shown to reduce disease activity in rheumatoid arthritis patients. However, the clinical therapeutic efficacies of these inhibitors in glomerulonephritis have not been evaluated. Herein, we review recent studies of Syk and Btk inhibitors in several experimental primary and secondary glomerulonephritis models. These inhibitors suppressed development of glomerular injury, and also ameliorated established kidney disease. Thus, targeting Syk and Btk signaling pathways is a potential therapeutic strategy for glomerulonephritis, and further evaluation is recommended.
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Effect of estrogen receptor ? binding on functional DNA methylation in breast cancer.
Epigenetics
PUBLISHED: 01-16-2014
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Epigenetic modifications introduce an additional layer of regulation that drastically expands the instructional capability of the human genome. The regulatory consequences of DNA methylation is context dependent; it can induce, enhance, and suppress gene expression, or have no effect on gene regulation. Therefore, it is essential to account for the genomic location of its occurrence and the protein factors it associates with to improve our understanding of its function and effects. Here, we use ENCODE ChIP-seq and DNase I hypersensitivity data, along with large-scale breast cancer genomic data from The Cancer Genome Atlas (TCGA) to computationally dissect the intricacies of DNA methylation in regulation of cancer transcriptomes. In particular, we identified a relationship between estrogen receptor ? (ER?) activity and DNA methylation patterning in breast cancer. We found compelling evidence that methylation status of DNA sequences at ER? binding sites is tightly coupled with ER? activity. Furthermore, we predicted several transcription factors including FOXA1, GATA1, and SUZ12 to be associated with breast cancer by examining the methylation status of their binding sites in breast cancer. Lastly, we determine that methylated CpGs highly correlated with gene expression are enriched in regions 1kb or more downstream of TSSs, suggesting more significant regulatory roles for CpGs distal to gene TSSs. Our study provides novel insights into the role of ER? in breast cancers.
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Monitoring the VEGF level in aqueous humor of patients with ophthalmologically relevant diseases via ultrahigh sensitive paper-based ELISA.
Biomaterials
PUBLISHED: 01-10-2014
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The vascular endothelial growth factor (VEGF) level in aqueous humor has been used as an indicator to monitor specific diseases in the retinal ischemic condition. For clinical diagnosis, only about 200 ?L of aqueous humor can be collected from the anterior chamber before the threat of anterior chamber collapse. It is necessary to develop an inexpensive diagnostic approach with the characteristics of highly sensitive, short operation duration, and requires small clinical sample quantities. To achieve the main objective of this study, we first prepared bevacizumab to be conjugated with HRP. We then deposited 2 ?L aqueous humor from patients with different diseases onto each test zone of paper-based 96-well plates. After the colorimetric results were performed via ELISA protocol, the output signals were recorded using a commercial desktop scanner for analysis. In this study, only 2 ?L from the aqueous humor of each patient was required for paper-based ELISA. The mean aqueous VEGF level was 14.4 pg/mL from thirteen patients (N = 13) with senile cataract as the control. However, the mean aqueous VEGF level from other patients with proliferative diabetic retinopathy (N = 14), age-related macular degeneration (N = 17), and retinal vein occlusion (N = 10) showed VEGF increases to 740.1 pg/mL, 383 pg/mL, and 219.4 pg/mL, respectively.
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Nickel-induced oxidative stress and apoptosis in Carassius auratus liver by JNK pathway.
Aquat. Toxicol.
PUBLISHED: 01-08-2014
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Nickel (Ni) is ubiquitous in the biosphere and is a common component of natural fresh waters. When present in high concentrations, it becomes toxic to aquatic organisms. It is known that Ni toxicity may induce oxidative stress and apoptosis. However, the precise mechanism and the pathways that are activated in fish are still unclear. Thus, this study aimed to assess which apoptotic pathways are triggered by Ni in Carassius auratus liver, the main target of waterborne pollutants. Fish were exposed to 10, 25, 50 and 100mg/L of nickel sulfate for 96 h. Our data showed that Ni exposure caused fish weight loss (by 10-12%) and decreased locomotory activity (by 1-25%). Ni exposure significantly decreased the relative lymphocyte count (by 1-24%) and increased the relative count of monocytes (by 25-111%) and neutrophils (by 10-322%) as compared to controls. Ni induced oxidative stress, as evidenced by increasing of lipid peroxidation level (29-91%) and depleting of the glutathione levels (7-79%) in fish liver. Ni also suppressed the activities of superoxide dismutase (by 39-55%) and glutathione peroxidase (16-24%) and decreased ATP levels (13-51%) in livers. Moreover, liver caspase-3, one of the key executioners of apoptosis, was markedly activated by the Ni exposure. Ni exposure also increased expression levels of phosphorylated Jun N-terminal kinases (JNK) in liver, which in turn activated pro-apoptotic signaling events by breaking the balance between pro-apoptotic and anti-apoptotic Bcl-2 proteins. In conclusion, these results suggested that Ni induced oxidative stress and apoptosis, at least, via the JNK signaling pathway.
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Recent advances in low-cost microfluidic platforms for diagnostic applications.
Electrophoresis
PUBLISHED: 01-06-2014
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The use of inexpensive materials and cost-effective manufacturing processes for mass production of microfluidic devices is very attractive and has spurred a variety of approaches. Such devices are particularly suited for diagnostic applications in limited resource settings. This review describes the recent and remarkable advances in the use of low-cost substrates for the development of microfluidic devices for diagnostics and clinical assays. Thus, a plethora of new and improved fabrication methods, designs, capabilities, detections, and applications of microfluidic devices fabricated with paper, plastic, and threads are covered.
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Peroxisome Proliferator-Activated Receptor ? Deficiency in T Cells Accelerates Chronic Rejection by Influencing the Differentiation of CD4+ T Cells and Alternatively Activated Macrophages.
PLoS ONE
PUBLISHED: 01-01-2014
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In a previous study, activation of the peroxisome proliferator-activated receptor ? (PPAR?) inhibited chronic cardiac rejection. However, because of the complexity of chronic rejection and the fact that PPAR? is widely expressed in immune cells, the mechanism of the PPAR? - induced protective effect was unclear.
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Enterovirus-71 Virus-Like Particles Induce the Activation and Maturation of Human Monocyte-Derived Dendritic Cells through TLR4 Signaling.
PLoS ONE
PUBLISHED: 01-01-2014
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Enterovirus 71 (EV71) causes seasonal epidemics of hand-foot-and-mouth disease and has a high mortality rate among young children. We recently demonstrated potent induction of the humoral and cell-mediated immune response in monkeys immunized with EV71 virus-like particles (VLPs), with a morphology resembling that of infectious EV71 virions but not containing a viral genome, which could potentially be safe as a vaccine for EV71. To elucidate the mechanisms through which EV71 VLPs induce cell-mediated immunity, we studied the immunomodulatory effects of EV71 VLPs on human monocyte-derived dendritic cells (DCs), which bind to and incorporate EV71 VLPs. DC treatment with EV71 VLPs enhanced the expression of CD80, CD86, CD83, CD40, CD54, and HLA-DR on the cell surface; increased the production of interleukin (IL)-12 p40, IL-12 p70, and IL-10 by DCs; and suppressed the capacity of DCs for endocytosis. Treatment with EV71 VLPs also enhanced the ability of DCs to stimulate naïve T cells and induced secretion of interferon (IFN)-? by T cells and Th1 cell responses. Neutralization with antibodies against Toll-like receptor (TLR) 4 suppressed the capacity of EV71 VLPs to induce the production of IL-12 p40, IL-12 p70, and IL-10 by DCs and inhibited EV71 VLPs binding to DCs. Our study findings clarified the important role for TLR4 signaling in DCs in response to EV71 VLPs and showed that EV71 VLPs induced inhibitor of kappaB alpha (I?B?) degradation and nuclear factor of kappaB (NF-?B) activation.
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Ultraviolet/blue light-emitting diodes based on single horizontal ZnO microrod/GaN heterojunction.
Nanoscale Res Lett
PUBLISHED: 01-01-2014
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We report electroluminescence (EL) from single horizontal ZnO microrod (MR) and p-GaN heterojunction light-emitting diodes under forward and reverse bias. EL spectra were composed of two blue emissions centered at 431 and 490 nm under forward biases, but were dominated by a ultraviolet (UV) emission located at 380 nm from n-ZnO MR under high reverse biases. Light-output-current characteristic of the UV emission reveals that the rate of radiative recombination is faster than that of the nonradiative recombination. Highly efficient ZnO excitonic recombination at reverse bias is caused by electrons tunneling from deep-level states near the n-ZnO/p-GaN interface to the conduction band in n-ZnO.
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Correlation of chitinase 3-like 1 single nucleotide polymorphisms and haplotypes with uterine cervical cancer in Taiwanese women.
PLoS ONE
PUBLISHED: 01-01-2014
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This study aimed to investigate the relationships of chitinase 3-like 1 (CHI3L1) single nucleotide polymorphisms (SNPs) and haplotypes with the development of uterine cervical cancer in Taiwanese women. The SNPs frequencies and haplotypes were also correlated with the clinicopathologic variables of cervical cancer, cancer recurrence, and patient survival.
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Overexpression of SATB1 is associated with biologic behavior in human renal cell carcinoma.
PLoS ONE
PUBLISHED: 01-01-2014
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Special AT-rich sequence-binding protein-1 (SATB1) has been reported to be aberrantly expressed in various cancers and correlated with the malignant behavior of cancer cells. However, the function of SATB1 in RCC remains unclear. With the combination of immunohistochemistry, western blotting, immunofluorescence, qRT-PCR, and cell proliferation, migration and invasion assays, we found that levels of SATB1 mRNA and protein were dramatically increased in human ccRCC tissues (P<0.001 for both), and upregulation of SATB1 was significantly associated with depth of invasion (P<0.001), lymph node status (P?=?0.001) and TNM stage (P?=?0.009). SATB1 knockdown inhibited the proliferation, migration and invasion of 786-O cells, whereas SATB1 overexpression promoted the growth and aggressive phenotype of ACHN cells in vitro. Furthermore, SATB1 expression was positively correlated with ZEB2 expression (P?=?0.013), and inversely linked to levels of SATB2 and E-cadherin (P?=?0.005 and P<0.001, respectively) in ccRCC tissues. Our data provide a basis for the concept that overexpression of SATB1 may play a critical role in the acquisition of an aggressive phenotype for RCC cells through EMT, providing new insights into the significance of SATB1 in invasion and metastasis of ccRCC, which may contribute to fully elucidating the exact mechanism of development and progression of RCC.
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Interaction between DNA and trimethyl-ammonium bromides with different alkyl chain lengths.
ScientificWorldJournal
PUBLISHED: 01-01-2014
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The interaction between ?--DNA and cationic surfactants with varying alkyl chain lengths was investigated. By dynamic light scattering method, the trimethyl-ammonium bromides-DNA complex formation was shown to be dependent on the length of the surfactant's alkyl chain. For surfactants with sufficient long alkyl chain (CTAB, TTAB, DTAB), the compacted particles exist with a size of ~60-110 nm at low surfactant concentrations. In contrast, high concentration of surfactants leads to aggregates with increased sizes. Atomic force microscope scanning also supports the above observation. Zeta potential measurements show that the potential of the particles decreases with the increase of surfactant concentration (CTAB, TTAB, DTAB), which contributes much to the coagulation of the particles. For OTAB, the surfactant with the shortest chain in this study, it cannot fully neutralize the charges of DNA molecules; consequently, the complex is looser than other surfactant-DNA structures.
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MiRNAs as biomarkers of myocardial infarction: a meta-analysis.
PLoS ONE
PUBLISHED: 01-01-2014
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Recent studies have demonstrated that acute myocardial infarction induces a distinctive miRNA signature, suggesting that miRNAs may serve as diagnostic markers. Although many studies have investigated the use of miRNAs in the detection of cardiac injury, some had small sample sizes (<100 patients) or reported different results for the same miRNA. Here, the role of circulating miRNAs for use as biomarkers of myocardial infarction is summarized and analyzed.
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Autoimmune pancreatitis: whole-body 18F-FDG PET/CT findings.
Abdom Imaging
PUBLISHED: 12-16-2013
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The study aimed to investigate the function of (18)F-fluorodeoxyglucose positron emission tomography/computed tomography ((18)F-FDG PET/CT) in diagnosing of autoimmune pancreatitis (AIP) and whole-body evaluation.
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DPRP: a database of phenotype-specific regulatory programs derived from transcription factor binding data.
Nucleic Acids Res.
PUBLISHED: 12-02-2013
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Gene expression profiling has been extensively used in the past decades, resulting in an enormous amount of expression data available in public databases. These data sets are informative in elucidating transcriptional regulation of genes underlying various biological and clinical conditions. However, it is usually difficult to identify transcription factors (TFs) responsible for gene expression changes directly from their own expression, as TF activity is often regulated at the posttranscriptional level. In recent years, technical advances have made it possible to systematically determine the target genes of TFs by ChIP-seq experiments. To identify the regulatory programs underlying gene expression profiles, we constructed a database of phenotype-specific regulatory programs (DPRP, http://syslab.nchu.edu.tw/DPRP/) derived from the integrative analysis of TF binding data and gene expression data. DPRP provides three methods: the Fishers Exact Test, the Kolmogorov-Smirnov test and the BASE algorithm to facilitate the application of gene expression data for generating new hypotheses on transcriptional regulatory programs in biological and clinical studies.
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Preparation and characterization of chain-like and peanut-like Fe3O4@SiO2 core-shell structure.
J Nanosci Nanotechnol
PUBLISHED: 11-20-2013
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The size- and shape-controlled Fe3O4@SiO2 nanocomposites were successfully synthesized via the sol-gel method. The results showed that the size, shape, and property of the products were directly influenced by the amount of TEOS, and the concentration of water-based magnetic fluid in the coating process. The morphology and properties of the products were characterized by TEM, SEM, X-ray powder diffraction, IR and EDS. The Fe3O4@SiO2 composites with easily-controlled size arranged from 58 to 835 nm could be synthesized by adjusting the experimental parameters. When TEOS amount is 1 mL and the concentration of magnetic fluid were 30.0 and 10.0 mg/mL respectively, chain-like and peanuts-like well-dispersed Fe3O4@SiO2 particles with clear core-shell structure were obtained. These size- and shape-controlled Fe3O4@SiO2 composites may have potential application in the field of targeted drug delivery and MRI contrast agent.
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Age-related DNA methylation in normal breast tissue and its relationship with invasive breast tumor methylation.
Epigenetics
PUBLISHED: 11-06-2013
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Age is a key risk factor for breast cancer and epigenetic alterations may contribute to age-related increases in breast cancer risk, though the relation of age-related methylation in normal breast tissues with altered methylation in breast tumors is unclear. We investigated the relation of age with DNA methylation in normal breast tissues genome-wide using two data sets from the Gene Expression Omnibus (GEO) database (GSE32393 and GSE31979). We validated our observations in an independent set of normal breast tissues, examined age-related methylation in normal breast for enrichment of genomic features, and compared age-related methylation in normal tissue with methylation alterations in breast tumors. Between the two array-based methylation data sets, there were 204 CpG loci with significant (P<0.05) and consistent age-related methylation, 97% of which were increases in methylation. Our validation sets confirmed the direction of age-related DNA methylation changes in all measured regions. Among the 204 age-related CpG loci, we observed a significant enrichment for CpG islands (P = 8.7e-6) and Polycomb group protein target genes (P = 0.03). In addition, 24 of the 204 CpGs with age-related methylation in normal breast were significantly differentially methylated between normal and breast tumor tissues. We identified consistent age-related methylation changes in normal breast tissue that are further altered in breast tumors and may represent early events contributing to breast carcinogenesis. This work identifies age-related methylation in normal breast tissue and begins to deconstruct the contribution of aging to epigenetic alterations present in breast tumors.
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Identification of cell cycle-regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors.
Mol. Biol. Cell
PUBLISHED: 10-09-2013
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We identify the cell cycle-regulated mRNA transcripts genome-wide in the osteosarcoma-derived U2OS cell line. This results in 2140 transcripts mapping to 1871 unique cell cycle-regulated genes that show periodic oscillations across multiple synchronous cell cycles. We identify genomic loci bound by the G2/M transcription factor FOXM1 by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) and associate these with cell cycle-regulated genes. FOXM1 is bound to cell cycle-regulated genes with peak expression in both S phase and G2/M phases. We show that ChIP-seq genomic loci are responsive to FOXM1 using a real-time luciferase assay in live cells, showing that FOXM1 strongly activates promoters of G2/M phase genes and weakly activates those induced in S phase. Analysis of ChIP-seq data from a panel of cell cycle transcription factors (E2F1, E2F4, E2F6, and GABPA) from the Encyclopedia of DNA Elements and ChIP-seq data for the DREAM complex finds that a set of core cell cycle genes regulated in both U2OS and HeLa cells are bound by multiple cell cycle transcription factors. These data identify the cell cycle-regulated genes in a second cancer-derived cell line and provide a comprehensive picture of the transcriptional regulatory systems controlling periodic gene expression in the human cell division cycle.
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Decreased P27 protein expression is correlated with the progression and poor prognosis of nasopharyngeal carcinoma.
Diagn Pathol
PUBLISHED: 09-28-2013
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To determine the correlation of cyclin-dependent kinase inhibitor 1B (p27) expression with clinicopathologic features in nasopharyngeal carcinoma (NPC), including patient prognosis.
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Plasma long pentraxin 3 (PTX3) concentration is a novel marker of disease activity in patients with community-acquired pneumonia.
Clin. Chem. Lab. Med.
PUBLISHED: 09-14-2013
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Long pentraxin 3 (PTX3) is an acute-phase protein secreted by various cells, including leukocytes and endothelial cells. Like C-reactive protein (CRP), it belongs to the pentraxin superfamily. The aim of this study was to investigate the differential changes in plasma levels of PTX3 between before and after antibiotic treatment in hospitalized adult patients with community-acquired pneumonia (CAP).
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Synergistic enhancement of cancer therapy using a combination of fusion protein MG7-scFv/SEB and tumor necrosis factor alpha.
Protein Pept. Lett.
PUBLISHED: 09-11-2013
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The fusion protein MG7-scFv/SEB has shown anti-tumor activity on gastric cancer in vitro and in vivo. Tumor necrosis factor-alpha (TNF-?) is a cytokine exerting anti-tumor effectiveness in various models and modes of applications. In this study, we explored the combination effects of MG7-scFv/SEB and TNF-? in experimental gastric cancer. Both MG7-scFv/SEB and TNF-? could effectively result in a significant inhibition of tumor growth in our experimental models when administered alone. Whats more, MG7-scFv/SEB synergized with TNF-? in further reducing the growth of gastric tumors in gastric-tumor-bearing rats as compared to mono therapy. Additionally, the survival rate of gastric-tumorbearing rats administrated with combined therapy was significantly higher than that of rats treated with MG7-scFv/SEB or TNF-?. These results indicate that combined therapy with MG7-scFv/SEB and TNF-? is a promising strategy for human cancer therapy.
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Association of Gamma-Aminobutyric Acid A Receptor ?2 Gene (GABRA2) with Alcohol Use Disorder.
Neuropsychopharmacology
PUBLISHED: 08-27-2013
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Gamma-aminobutyric acid (GABA) is a major inhibitory neurotransmitter in mammalian brain. GABA receptor are involved in a number of complex disorders, including substance abuse. No variants of the commonly studied GABA receptor genes that have been associated with substance dependence have been determined to be functional or pathogenic. To reconcile the conflicting associations with substance dependence traits, we performed a meta-analysis of variants in the GABAA receptor genes (GABRB2, GABRA6, GABRA1, and GABRG2 on chromosome 5q and GABRA2 on chromosome 4p12) using genotype data from 4739 cases of alcohol, opioid, or methamphetamine dependence and 4924 controls. Then, we combined the data from candidate gene association studies in the literature with two alcohol dependence (AD) samples, including 1691 cases and 1712 controls from the Study of Addiction: Genetics and Environment (SAGE), and 2644 cases and 494 controls from our own study. Using a Bonferroni-corrected threshold of 0.007, we found strong associations between GABRA2 and AD (P=9 × 10(-6) and odds ratio (OR) 95% confidence interval (CI)=1.27 (1.15, 1.4) for rs567926, P=4 × 10(-5) and OR=1.21 (1.1, 1.32) for rs279858), and between GABRG2 and both dependence on alcohol and dependence on heroin (P=0.0005 and OR=1.22 (1.09, 1.37) for rs211014). Significant association was also observed between GABRA6 rs3219151 and AD. The GABRA2 rs279858 association was observed in the SAGE data sets with a combined P of 9 × 10(-6) (OR=1.17 (1.09, 1.26)). When all of these data sets, including our samples, were meta-analyzed, associations of both GABRA2 single-nucleotide polymorphisms remained (for rs567926, P=7 × 10(-5) (OR=1.18 (1.09, 1.29)) in all the studies, and P=8 × 10(-6) (OR=1.25 (1.13, 1.38)) in subjects of European ancestry and for rs279858, P=5 × 10(-6) (OR=1.18 (1.1, 1.26)) in subjects of European ancestry. Findings from this extensive meta-analysis of five GABAA receptor genes and substance abuse support their involvement (with the best evidence for GABRA2) in the pathogenesis of AD. Further replications with larger samples are warranted.Neuropsychopharmacology advance online publication, 13 November 2013; doi:10.1038/npp.2013.291.
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Analogy among microfluidics, micromechanics, and microelectronics.
Lab Chip
PUBLISHED: 08-22-2013
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We wish to illuminate the analogous link between microfluidic-based devices, and the already established pairing of micromechanics and microelectronics to create a triangular/three-way scientific relationship as a means of interlinking familial disciplines and accomplishing two primary goals: (1) to facilitate the modeling of multidisciplinary domains; and, (2) to enable us to co-simulate the entire system within a compact circuit simulator (e.g., Cadence or SPICE). A microfluidic channel-like structure embedded in a micro-electro-mechanical resonator via our proposed CMOS-MEMS technology is used to illustrate the connections among microfluidics, micromechanics, and microelectronics.
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Enantiomeric recognition of amino acid salts by macrocyclic crown ethers derived from enantiomerically pure 1,8,9,16-tetrahydroxytetraphenylenes.
J. Org. Chem.
PUBLISHED: 08-22-2013
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Asymmetric synthesis of (R,R)- and (S,S)-1,8,9,16-tetrahydroxytetraphenylenes was achieved from starting material (2R,3R)-butane-2,3-diol and (2S,3S)-butane-2,3-diol respectively by utilizing a center-to-axis strategy. A series of crown ether compounds 20, 24, and 25 and their corresponding enantiomers derived from chiral tetrahydroxytetraphenylene were synthesized in enantiomerically pure forms. Enantiomeric recognition properties of these hosts toward l- and d-amino acid methyl ester hydrochloride were studied by the UV spectroscopy titration. The tetramer hosts (S,S,S,S,S,S,S,S)-20 and (R,R,R,R,R,R,R,R)-20 exhibited the best enantioselectivities toward L- and D-alanine methyl ester hydrochloride salt with K(L)/K(D) = 4.1 and KD/KL = 3.9, respectively. The new chiral macrocyclic hosts would further enrich the host-guest chemistry.
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Quercetin protects mouse brain against lead-induced neurotoxicity.
J. Agric. Food Chem.
PUBLISHED: 07-26-2013
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Quercetin (QE), the major bioflavonoid in the human diet, has been reported to have many benefits and medicinal properties. However, its protective effects against lead (Pb)-induced neurotoxicity have not been clarified. The aim of the present study was to investigate the effects of QE on neurotoxicity in mice exposed to Pb. Mice were exposed to lead acetate (20 mg/kg body weight/day) intragastrically with or without QE (15 and 30 mg/kg body weight/day) coadministration for 3 months. The data showed that QE significantly prevented Pb-induced neurotoxicity in a dose-dependent manner. Exploration of the underlying mechanisms of QE action revealed that QE administration decreased Pb contents in blood (13.2, 19.1%) and brain (17.1, 20.0%). QE markedly increased NO production (39.1, 61.1%) and PKA activity (51.0, 57.8%) in brains of Pb-treated mice. Additionally, QE remarkably suppressed Pb-induced oxidative stress in mouse brain. Western blot analysis showed that QE increased the phosphorylations of Akt, CaMKII nNOS, eNOS, and CREB in brains of Pb-treated mice. The results suggest that QE can inhibit Pb-induced neurotoxicity and partly restore PKA, Akt, NOS, CaMKII, and CREB activities.
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Ultrathin porous NiCo2O4 nanosheet arrays on flexible carbon fabric for high-performance supercapacitors.
ACS Appl Mater Interfaces
PUBLISHED: 07-12-2013
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NiCo2O4 with higher specific capacitance is an excellent pseudocapacitive material. However, the bulk NiCo2O4 material prevents the achievement of high energy desity and great rate performance due to the limited electroactive surface area. In this work, NiCo2O4 nanosheet arrays were deposited on flexible carbon fabric (CF) as a high-performance electrode for supercapacitors. The NiCo2O4 arrays were constructed by interconnected ultrathin nanosheets (10 nm) with many interparticle pores. The porous feature of NiCo2O4 nanosheets increases the amount of electroactive sites and facilitates the electrolyte penetration. Hence, the NiCo2O4/CF composites exhibited a high specific capacitance of 2658 F g(-1) (2 A g(-1)), good rate performance, and superior cycling life, suggesting the NiCo2O4/CF is a promising electrode material for flexible electrochemical capacitors.
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Transcription factor binding profiles reveal cyclic expression of human protein-coding genes and non-coding RNAs.
PLoS Comput. Biol.
PUBLISHED: 07-01-2013
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Cell cycle is a complex and highly supervised process that must proceed with regulatory precision to achieve successful cellular division. Despite the wide application, microarray time course experiments have several limitations in identifying cell cycle genes. We thus propose a computational model to predict human cell cycle genes based on transcription factor (TF) binding and regulatory motif information in their promoters. We utilize ENCODE ChIP-seq data and motif information as predictors to discriminate cell cycle against non-cell cycle genes. Our results show that both the trans- TF features and the cis- motif features are predictive of cell cycle genes, and a combination of the two types of features can further improve prediction accuracy. We apply our model to a complete list of GENCODE promoters to predict novel cell cycle driving promoters for both protein-coding genes and non-coding RNAs such as lincRNAs. We find that a similar percentage of lincRNAs are cell cycle regulated as protein-coding genes, suggesting the importance of non-coding RNAs in cell cycle division. The model we propose here provides not only a practical tool for identifying novel cell cycle genes with high accuracy, but also new insights on cell cycle regulation by TFs and cis-regulatory elements.
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Tumor suppressor PDCD4 modulates miR-184-mediated direct suppression of C-MYC and BCL2 blocking cell growth and survival in nasopharyngeal carcinoma.
Cell Death Dis
PUBLISHED: 06-21-2013
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Programmed cell death 4 (PDCD4), a novel tumor suppressor, inhibits cell proliferation, migration and invasion as well as promotes cell apoptosis in tumors. However, the molecular mechanism of its tumor-suppressive function remains largely unknown in tumors including nasopharyngeal carcinoma (NPC). In this study, downregulated PDCD4 expression was significantly associated with the status of NPC progression and poor prognosis. PDCD4 markedly suppressed the ability of cell proliferation and cell survival by modulating C-MYC-controlled cell cycle and BCL-2-mediated mitochondrion apoptosis resistance signals, and oncogenic transcription factor C-JUN in NPC. Furthermore, miR-184, a tumor-suppressive miRNA modulated by PDCD4 directly targeting BCL2 and C-MYC, participated in PDCD4-mediated suppression of cell proliferation and survival in NPC. Further, we found that PDCD4 decreased the binding of C-Jun to the AP-1 element on the miR-184 promoter regions by PI3K/AKT/JNK/C-Jun pathway and stimulated miR-184 expression. In clinical fresh specimens, reduced PDCD4 mRNA level was positively correlated with miR-184 expression in NPC. Our studies are the first to demonstrate that PDCD4 as tumor suppressor regulated miR-184-mediated direct targeting of BCL2 and C-MYC via PI3K/AKT and JNK/C-Jun pathway attenuating cell proliferation and survival in NPC.
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An MLL-dependent network sustains hematopoiesis.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 06-06-2013
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The histone methyltransferase Mixed Lineage Leukemia (MLL) is essential to maintain hematopoietic stem cells and is a leukemia protooncogene. Although clustered homeobox genes are well-characterized targets of MLL and MLL fusion oncoproteins, the range of Mll-regulated genes in normal hematopoietic cells remains unknown. Here, we identify and characterize part of the Mll-dependent transcriptional network in hematopoietic stem cells with an integrated approach by using conditional loss-of-function models, genomewide expression analyses, chromatin immunoprecipitation, and functional rescue assays. The Mll-dependent transcriptional network extends well beyond the previously appreciated Hox targets, is comprised of many characterized regulators of self-renewal, and contains target genes that are both dependent and independent of the MLL cofactor, Menin. Interestingly, PR-domain containing 16 emerged as a target gene that is uniquely effective at partially rescuing Mll-deficient hematopoietic stem and progenitor cells. This work highlights the tissue-specific nature of regulatory networks under the control of MLL/Trithorax family members and provides insight into the distinctions between the participation of MLL in normal hematopoiesis and in leukemia.
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Machine learning and genome annotation: a match meant to be?
Genome Biol.
PUBLISHED: 05-29-2013
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By its very nature, genomics produces large, high-dimensional datasets that are well suited to analysis by machine learning approaches. Here, we explain some key aspects of machine learning that make it useful for genome annotation, with illustrative examples from ENCODE.
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Thrombomodulin mediates the migration of cervical cancer cells through the regulation of epithelial-mesenchymal transition biomarkers.
Tumour Biol.
PUBLISHED: 05-07-2013
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Thrombomodulin (TM) has been shown to regulate many physiological and pathological processes, including inflammation, thrombosis, and tumor progression. TM is also a natural anticoagulant that maintains circulatory homeostasis in endothelial cells. However, little is known regarding the role of TM in the progression and metastasis of cervical cancer. TM-specific RNA interference and a cDNA expression vector were used to manipulate TM expression in cervical cancer cells. Cell growth and cell migration were evaluated using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay, transwell migration assays, and a biosensor system. TM silencing did not affect the growth rate of the cells. However, cell migration was dramatically enhanced after silencing of TM in HeLa cells. The overexpression of TM in cervical cancer cells only slightly influenced their proliferative capacity. After overexpression of TM in HeLa cells, their migratory capability was suppressed. Furthermore, we found that the decreased expression of E-cadherin and increase of zeb-1 and snail expression in TM-silenced cells which may be correlated with the results of knocking-down TM increases the migratory ability in this study. Our results demonstrate that TM may slightly regulate the growth but played the important role in the migratory ability of cervical cancer cells, suggesting that TM could potentially serve as a novel prognostic and therapeutic target in cervical cancer.
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Discovering chromatin motifs using FAIRE sequencing and the human diploid genome.
BMC Genomics
PUBLISHED: 04-30-2013
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Specific chromatin structures are associated with active or inactive gene transcription. The gene regulatory elements are intrinsically dynamic and alternate between inactive and active states through the recruitment of DNA binding proteins, such as chromatin-remodeling proteins.
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REACTIN: regulatory activity inference of transcription factors underlying human diseases with application to breast cancer.
BMC Genomics
PUBLISHED: 04-28-2013
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Genetic alterations of transcription factors (TFs) have been implicated in the tumorigenesis of cancers. In many cancers, alteration of TFs results in aberrant activity of them without changing their gene expression level. Gene expression data from microarray or RNA-seq experiments can capture the expression change of genes, however, it is still challenge to reveal the activity change of TFs.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.