Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data

<p>Abstract</p> <p>Background</p> <p>Global profiling of in vivo protein-DNA interactions using ChIP-based technologies has evolved rapidly in recent years. Although many genome-wide studies have identified thousands of ERα binding sites and have revealed the associated transcription factor (TF) partners, such as AP1, FOXA1 and CEBP, little is known about ERα associated hierarchical transcriptional regulatory networks.</p> <p>Results</p> <p>In this study, we applied computational approaches to analyze three public available ChIP-based datasets: ChIP-seq, ChIP-PET and ChIP-chip, and to investigate the hierarchical regulatory network for ERα and ERα partner TFs regulation in estrogen-dependent breast cancer MCF7 cells. 16 common TFs and two common new TF partners (RORA and PITX2) were found among ChIP-seq, ChIP-chip and ChIP-PET datasets. The regulatory networks were constructed by scanning the ChIP-peak region with TF specific position weight matrix (PWM). A permutation test was performed to test the reliability of each connection of the network. We then used DREM software to perform gene ontology function analysis on the common genes. We found that FOS, PITX2, RORA and FOXA1 were involved in the up-regulated genes.</p> <p>We also conducted the ERα and Pol-II ChIP-seq experiments in tamoxifen resistance MCF7 cells (denoted as MCF7-T in this study) and compared the difference between MCF7 and MCF7-T cells. The result showed very little overlap between these two cells in terms of targeted genes (21.2% of common genes) and targeted TFs (25% of common TFs). The significant dissimilarity may indicate totally different transcriptional regulatory mechanisms between these two cancer cells.</p> <p>Conclusions</p> <p>Our study uncovers new estrogen-mediated regulatory networks by mining three ChIP-based data in MCF7 cells and ChIP-seq data in MCF7-T cells. We compared the different ChIP-based technologies as well as different breast cancer cells. Our computational analytical approach may guide biologists to further study the underlying mechanisms in breast cancer cells or other human diseases.</p

Dye-Sensitized Solar Cells with Optimal Gel Electrolyte Using the Taguchi Design Method

The Taguchi method was adopted to determine the optimal gel electrolyte used in dye-sensitized solar cells (DSSCs). Since electrolyte is a very important factor in fabrication of high performance and long-term stability DSSCs, to find the optimal composition of gel electrolyte is desired. In this paper, the common ingredients used in the liquid electrolyte were chosen. The ingredients then mixed with cheap ionic liquids and poly(vinylidenefluoride-co-hexafluoropropylene) (PVDF-HFP) were added to form colloidal electrolyte (gel). The optimal composition of each materials in the gel electrolyte determined by Taguchi method consists of 0.03 M I2, 0.15 M KI, 0.6 M LiI, 0.5 M 4-tertbutylpyridine (TBP), and 10% PVDF-HFP dissolved in the acetonitrile and 3-methoxypropionitrile (MPN) solution with volume ratio of 2 : 1. The short circuit current density of 14.11 mA/cm2, the conversion efficiency (η) of 5.52%, and the lifetime of over 110 days were observed for the dye-sensitized solar cell assembled with optimal gel electrolyte. The lifetime increases 10 times when compared with the conventional dye-sensitized solar cell assembled with liquid electrolyte

LOcating non-unique matched tags (LONUT) to improve the detection of the enriched regions for ChIP-seq data.

One big limitation of computational tools for analyzing ChIP-seq data is that most of them ignore non-unique tags (NUTs) that match the human genome even though NUTs comprise up to 60% of all raw tags in ChIP-seq data. Effectively utilizing these NUTs would increase the sequencing depth and allow a more accurate detection of enriched binding sites, which in turn could lead to more precise and significant biological interpretations. In this study, we have developed a computational tool, LOcating Non-Unique matched Tags (LONUT), to improve the detection of enriched regions from ChIP-seq data. Our LONUT algorithm applies a linear and polynomial regression model to establish an empirical score (ES) formula by considering two influential factors, the distance of NUTs to peaks identified using uniquely matched tags (UMTs) and the enrichment score for those peaks resulting in each NUT being assigned to a unique location on the reference genome. The newly located tags from the set of NUTs are combined with the original UMTs to produce a final set of combined matched tags (CMTs). LONUT was tested on many different datasets representing three different characteristics of biological data types. The detected sites were validated using de novo motif discovery and ChIP-PCR. We demonstrate the specificity and accuracy of LONUT and show that our program not only improves the detection of binding sites for ChIP-seq, but also identifies additional binding sites

Transradial percutaneous coronary intervention for chronic total occlusion of coronary artery disease using sheathless standard guiding catheters

Our aim was to evaluate the feasibility and safety of routine transradial approach (TRA) percutaneous coronary intervention (PCI) for chronic total occlusion (CTO) lesions using the sheathless technique with standard guiding catheters. Transradial approach PCI was applied for CTO lesions. A major limitation of TRA CTO PCI is the inability to use large guiding catheters because of the relatively small size of the radial artery. Therefore, the sheathless technique for TRA PCI has been recently developed. However, reports on TRA CTO PCI using the sheathless technique are still lacking. Sixty-eight patients with CTO lesions were enrolled for TRA PCI using the sheathless technique with standard guiding catheters. The baseline characteristics, coronary angiographic characteristics and major procedure or access site related complications were compared between procedure success and procedure failure group to determine the predictors of success in sheathless CTO PCI. In-hospital and 30-day clinical outcomes were also evaluated in this study. Routine assessments of radial artery occlusion via Doppler ultrasound and pulse oximeter were recorded during one-year clinical follow-up. The mean duration of CTO by history was 31.8 ± 42.3 months. The 7 Fr standard guiding catheter was used with the sheathless technique in 91.2%, and bilateral sheathless approach in 42.6% of the study patients. The procedure-related complications included coronary perforation needing covered stent deployment (2.9%), cardiac tamponade (2.9%), collateral perforation needing coil deployment (4.4%), and contrast induced nephropathy (2.9%). Only 2 patients (2.9%) experienced forearm ecchymosis at the radial artery access sites. In-hospital mortality and 30-day all-cause mortality were 2.9%, and 30-day MACEs were 1.5%. The rate of radial artery occlusion during one-year clinical follow-up was only 3.0%. It is feasible and safe to routinely use the sheathless technique with standard guiding catheters for TRA CTO PCI, with a low incidence of procedure-related complications and long-term radial artery occlusion

Transradial percutaneous coronary intervention for chronic total occlusion of coronary artery disease using sheathless standard guiding catheters

Objectives: Our aim was to evaluate the feasibility and safety of routine transradial approach (TRA) percutaneous coronary intervention (PCI) for chronic total occlusion (CTO) lesions using the sheathless technique with standard guiding catheters. Background: Transradial approach PCI was applied for CTO lesions. A major limitation of TRA CTO PCI is the inability to use large guiding catheters because of the relatively small size of the radial artery. Therefore, the sheathless technique for TRA PCI has been recently developed. However, reports on TRA CTO PCI using the sheathless technique are still lacking. Methods: Sixty-eight patients with CTO lesions were enrolled for TRA PCI using the sheathless technique with standard guiding catheters. The baseline characteristics, coronary angiographic characteristics and major procedure or access site related complications were compared between procedure success and procedure failure group to determine the predictors of success in sheathless CTO PCI. In-hospital and 30-day clinical outcomes were also evaluated in this study. Routine assessments of radial artery occlusion via Doppler ultrasound and pulse oximeter were recorded during one-year clinical follow-up. Results: The mean duration of CTO by history was 31.8 ± 42.3 months. The 7 Fr standard guiding catheter was used with the sheathless technique in 91.2%, and bilateral sheathless approach in 42.6% of the study patients. The procedure-related complications included coronary perforation needing covered stent deployment (2.9%), cardiac tamponade (2.9%), collateral perforation needing coil deployment (4.4%), and contrast induced nephropathy (2.9%). Only 2 patients (2.9%) experienced forearm ecchymosis at the radial artery access sites. In-hospital mortality and 30-day all-cause mortality were 2.9%, and 30-day MACEs were 1.5%. The rate of radial artery occlusion during one-year clinical follow-up was only 3.0%. Conclusions: It is feasible and safe to routinely use the sheathless technique with standard guiding catheters for TRA CTO PCI, with a low incidence of procedure-related complications and long-term radial artery occlusion