COEX-Seq: Convert a Variety of Measurements of Gene Expression in RNA-Seq

Next generation sequencing (NGS), a high-throughput DNA sequencing technology, is widely used for molecular biological studies. In NGS, RNA-sequencing (RNA-Seq), which is a short-read massively parallel sequencing, is a major quantitative transcriptome tool for different transcriptome studies. To utilize the RNA-Seq data, various quantification and analysis methods have been developed to solve specific research goals, including identification of differentially expressed genes and detection of novel transcripts. Because of the accumulation of RNA-Seq data in the public databases, there is a demand for integrative analysis. However, the available RNA-Seq data are stored in different formats such as read count, transcripts per million, and fragments per kilobase million. This hinders the integrative analysis of the RNA-Seq data. To solve this problem, we have developed a web-based application using Shiny, COEX-seq (Convert a Variety of Measurements of Gene Expression in RNA-Seq) that easily converts data in a variety of measurement formats of gene expression used in most bioinformatic tools for RNA-Seq. It provides a workflow that includes loading data set, selecting measurement formats of gene expression, and identifying gene names. COEX-seq is freely available for academic purposes and can be run on Windows, Mac OS, and Linux operating systems. Source code, sample data sets, and supplementary documentation are available as well

Reflection coefficient calculation of a feeder structure in a RLSA

RLSA(Radial line slot antenna) is slotted waveguide array antenna which is proposed for the DBS(Direct Broadcast from a Satellite) reception. Theoretically, it has lower conduction loss and higher effectiveness than the planar antenna using microstrip. DL-RLSA(Double-layered RLSA) uses radially inward travelling wave for the slot excitation in the double-layered radial line. The effectiveness of DL-RLSA is more than 75%(33.0~37dBi), which is two times as high effectiveness as other planar antenna. In spite of that advantage, SL-RLSA(Single-layered RLSA) is more popular because of the complex structure of DL-RLSA. But the radially outward travelling wave of SL-RLSA makes high tapering when the travelling wave approaches the aperture edge. To remove these troublesome thing, a effective feeder structure which has tilting rod is proposed in this paper. To find the optimum height and tilting angle of the feeder, the finitedifference time-domain(FDTD) method is employed. In other words, the simulation parameter of the FDTD algorithm is the dimension of feeder. Compared with the effectiveness of the conventional rod feeder structure, that of the proposed feeder structure in this paper is enhanced by 5dB

Expression of Osteocalcin and Transglutaminase and Labelling of Bromodeoxyuridine during Fracture Healing in the Rat Tibia

The expression of osteocalcin and transglutaminase C(TGase C) during fracture healing was inwstigated with immunohistochemical studies. A transverse osteotomy was made at the proximal tibia in Sprague-Dawley male rats and immobilized with a small external skeletal fixator. The animals lU!l'e sacrificed serially I, 3, 5, 7, 14, 42 days respectively after fracture. Longitudinal sections of the healing bone were stained with pohclonal antibody against osteocalcin and TGase C, and monoclonal antibody against bromodeoxyuridine. During the intramembranous bone formation at the periosteum around the fracture site, osteocalcin was strongly expressed in the proliferating osteoprogenitor cells from the 1st day of fracture, and then, in osteoblasts, osteoid matrix and osteocytes. The expression of TGase C was weakly positive in both osteoprogenitor cells and osteoblasts. Ai the site of endochondral bone formation, which was first reoealed 5 days after fracture, cell proliferation occurred at the periphery of cartilaginous callus where the number of cells stained with BrdU was highest During the maturation of callus, those cells uere entrapped in the chondroid matrix and became larger and larger. Osteocalcin was demonstrated in the cytoplasm of chondrocytes, while chondroid matrix was negatiwly stained. TGase C was found in the cytoplasm of more centrally located and matured chondrocytes as compared with osteocalcin. Osteoid matrix was stained with osteocalcin but not with TGase C. These finding may suggest that osteocalcin participates in the early phase of endochondral bone formation, while TGase C participates in the late phase, suggesting the role of TGase C in matrix stabilization. But the reason for the difference in the expression of TGase C between the endochondral bone formation and intramembranous bone formation should be further inwstigated. Healing of IAA2Il immobilized fracture in this study was predominantly induced by intramembranous ossification rather than endochondral ossification. Periosteal osteoprogenitor cells appeared to initiate and to lead bone formation after osteotomy. These findings indicate that preservation of the periosteum is essential to achieve successful fracture healing

Severe mitral regurgitation in a young female with pansinusitis and bronchiectasis

SummaryPrimary ciliary dyskinesia (PCD) is a disease characterized by symptoms of upper and lower respiratory tract infections due to abnormal structure and function of cilia.Cardiac involvement is characterized by situs inversus (Kartagener's syndrome in PCD) and other congenital cardiovascular abnormalities. We describe a 34-year-old female with a history of recurrent sinusitis and bronchiectasis but without situs inversus or other congenital cardiac anomalies in whom an association between mitral regurgitation secondary to myxoid degeneration and primary ciliary dyskinesia was suggested

A Modified SweepSAR Mode with Dual Channels for High Resolution and Wide Swath

In this study, an imaging mode of the modified SweepSAR is proposed with performance analysis for a high-resolution and wide swath coverage. To reduce the overall antenna size required for the solution of the azimuth ambiguity problem, different pulse repetition frequencies (PRFs) are utilized for different transmitters, respectively. For each imaging mode, system performance parameters are used for simulation, analysis, wide swath prediction, and comparison between conventional ScanSAR mode and SweepSAR mode based on scan-on-receive (SCORE). The system parameters of AASR, RASR, and NESZ will be estimated and suggested on the imaging mode by using appropriate reflector antenna with the effectiveness of a modified SweepSAR employing dual channels

Stent Thrombosis, Clinical Events, and Influence of Prolonged Clopidogrel Use After Placement of Drug-Eluting Stent Data From an Observational Cohort Study of Drug-Eluting Versus Bare-Metal Stents

ObjectivesThe purpose of this study was to evaluate the risk of stent thrombosis (ST), clinical outcomes, and the benefits of extended clopidogrel use after drug-eluting stent (DES) implantation.BackgroundData are limited regarding uniform evaluation of ST and the influence of clopidogrel continuation beyond 12 months on late events after DES treatment.MethodsWe identified 7,221 patients who received DES implantation (n = 3,160) or bare-metal stent (BMS) implantation (n = 4,061), and compared long-term adverse outcomes. Additionally, 2,851 patients with DES surviving 12 months without major events were analyzed according to clopidogrel continuation.ResultsThe adjusted-risk of overall ST was similar in the 2 groups. After 1 year, however, DES patients showed a higher risk of ST; definite/probable (hazard ratio [HR]: 3.55, 95% confidence interval [CI]: 1.26 to 9.99). The adjusted-risk of death (HR: 0.60, 95% CI: 0.46 to 0.79), death/myocardial infarction (HR: 0.63, 95% CI: 0.49 to 0.81), and target lesion revascularization (HR: 0.32, 95% CI: 0.24 to 0.43) were significantly lower in the DES group than in the BMS group. Continuing clopidogrel beyond 12 months was not associated with a reduced risk for ST (HR: 0.54, 95% CI: 0.07 to 4.23), death (HR: 1.20, 95% CI: 0.55 to 2.66), or death/myocardial infarction (HR: 1.16, 95% CI: 0.56 to 2.42) after DES implantation.ConclusionsAs compared with BMS, DES showed a similar risk of overall ST, but a higher risk of very late ST. The rates of death, death/myocardial infarction, and target lesion revasuclarization were significantly lower in the DES group. Clopidogrel continuation beyond 1 year did not appear to reduce ST and clinical events after DES implantation