REGNET: Mining context-specific human transcription networks using composite genomic information

Background: Genome-wide expression profiles reflect the transcriptional networks specific to the given cell context. However, most statistical models try to estimate the average connectivity of the networks from a collection of gene expression data, and are unable to characterize the context-specific transcriptional regulations. We propose an approach for mining context-specific transcription networks from a large collection of gene expression fold-change profiles and composite gene-set information.Results: Using a composite gene-set analysis method, we combine the information of transcription factor binding sites, Gene Ontology or pathway gene sets and gene expression fold-change profiles for a variety of cell conditions. We then collected all the significant patterns and constructed a database of context-specific transcription networks for human (REGNET). As a result, context-specific roles of transcription factors as well as their functional targets are readily explored. To validate the approach, nine predicted targets of E2F1 in HeLa cells were tested using chromatin immunoprecipitation assay. Among them, five (Gadd45b, Dusp6, Mll5, Bmp2 and E2f3) were successfully bound by E2F1. c-JUN and the EMT transcription networks were also validated from literature.Conclusions: REGNET is a useful tool for exploring the ternary relationships among the transcription factors, their functional targets and the corresponding cell conditions. It is able to provide useful clues for novel cell-specific transcriptional regulations. The REGNET database is available at http://mgrc.kribb.re.kr/regnet.open0

Pulmonary Toxicity after a Quick Course of Combinatorial Vincristine, Bleomycin, and Cisplatin Neoadjuvant Chemotherapy in Cervical Cancer

Pulmonary toxicity is one of the most serious adverse effects associated with a quick course of vincristine, bleomycin, and cisplatin neoadjuvant chemotherapy (NAC-VBP). The aim of this study was to evaluate pulmonary toxicity related to a quick course NAC-VBP. A total of consecutive 61 patients, who underwent at most 3 cycles of NAC-VBP every 10 days in the International Federation of Gynecology and Obstetrics (FIGO) stage IB-IIB cervical cancer from 1995 to 2007, were retrospectively analyzed. Of the 61 study subjects, 7 (11.5%) were identified to have pulmonary toxicity and 2 (3.3%) died of pulmonary fibrosis progression despite aggressive treatment and the use of a multidisciplinary approach. No factor predisposing pulmonary toxicity was identified. Initial symptoms were non-specific, but bronchiolitis obliterans organizing pneumonia and interstitial pneumonitis were characteristic findings by high-resolution computed tomography of the chest. The benefit of steroid therapy was uncertain and was associated with steroid-induced diabetes mellitus requiring insulin therapy in two patients. Fatal pulmonary toxicity is a major concern of a quick course NAC-VBP. In conclusion, these patients require special monitoring for bleomycin-induced pulmonary toxicity

The Microscopic Origin of Residual Stress for Flat Self-Actuating Piezoelectric Cantilevers

In this study, flat piezoelectric microcantilevers were fabricated under low-stress Pb(Zr0.52Ti0.48)O3 (PZT) film conditions. They were analyzed using the Raman spectrum and wafer curvature methods. Based on the residual stress analysis, we found that a thickness of 1 μm was critical, since stress relaxation starts to occur at greater thicknesses, due to surface roughening. The (111) preferred orientation started to decrease when the film thickness was greater than 1 μm. The d33 value was closely related to the stress relaxation associated with the preferred orientation changes. We examined the harmonic response at different PZT cantilever lengths and obtained a 9.4-μm tip displacement at 3 Vp-p at 1 kHz. These analyses can provide a platform for the reliable operation of piezoelectric microdevices, potentially nanodevice when one needs to have simultaneous control of the residual stress and the piezoelectric properties

APPLICATION OF PCVD PROCESS TO UNIFORM COATING OF TiO2 THIN FILMS ON POLYPROPYLENE BEADS

The growth of the TiO2 thin films coated on the polypropylene beads was analyzed experimentally in a rotating cylindrical plasma chemical vapor deposition (PCVD) reactor. The precursors for the thin films were generated by plasma reactions, and they deposited on the polypropylene beads to become the uniform thin films. The TiO2 thin films grow more quickly on the polypropylene beads by increasing the mass flow rate of TTIP, or the rotation speed of the reactor. The smaller number of polypropylene beads in the reactor increases the growth rate of the thin films. The high-quality TiO2 thin films can be coated on particles uniformly by using the rotating cylindrical PCVD process. The particles coated with high-quality TiO2 thin films can be applied to the removal of air and water pollutants by a photodegradation reaction of TiO2.Particle coating, TiO2 thin films, rotating cylindrical PCVD reactor, particle growth, polypropylene beads

Enhancing the Responsivity of Uncooled Infrared Detectors Using Plasmonics for High-Performance Infrared Spectroscopy

A lead zirconate titanate (PZT;Pb(Zr0.52Ti0.48)O3) layer embedded infrared (IR) detector decorated with wavelength-selective plasmonic crystals has been investigated for high-performance non-dispersive infrared (NDIR) spectroscopy. A plasmonic IR detector with an enhanced IR absorption band has been designed based on numerical simulations, fabricated by conventional microfabrication techniques, and characterized with a broadly tunable quantum cascade laser. The enhanced responsivity of the plasmonic IR detector at specific wavelength band has improved the performance of NDIR spectroscopy and pushed the limit of detection (LOD) by an order of magnitude. In this paper, a 13-fold enhancement in the LOD of a methane gas sensing using NDIR spectroscopy is demonstrated with the plasmonic IR detector

Effects of Process Variables on Properties of CoFe2O4 Nanoparticles Prepared by Solvothermal Process

Controlling the morphology and magnetic properties of CoFe2O4 nanoparticles is crucial for the synthesis of compatible materials for different applications. CoFe2O4 nanoparticles were synthesized by a solvothermal method using cobalt nitrate, iron nitrate as precursors, and oleic acid as a surfactant. The formation of CoFe2O4 nanoparticles was systematically observed by adjusting synthesis process conditions including reaction temperature, reaction time, and oleic acid concentration. Nearly spherical, monodispersed CoFe2O4 nanoparticles were formed by changing the reaction time and reaction temperature. The oleic acid-coated CoFe2O4 nanoparticles inhibited the growth of particle size after 1 h and, therefore, the particle size of CoFe2O4 nanoparticles did not change significantly as the reaction time increased. Both without and with low oleic acid concentration, the large-sized cubic CoFe2O4 nanoparticles showing ferromagnetic behavior were synthesized, while the small-sized CoFe2O4 nanoparticles with superparamagnetic properties were obtained for the oleic acid concentration higher than 0.1 M. This study will become a basis for further research in the future to prepare the high-functional CoFe2O4 magnetic nanoparticles by a solvothermal process, which can be applied to bio-separation, biosensors, drug delivery, magnetic hyperthermia, etc