De novo Genome Reference Assembly

Department of Biomedical EngineeringRecent advancements in sequencing technologies have helped to sequence the complete genomes of many species encompassing all the kingdoms of life. However, the assembly of large and complex genomes remains challenging. Here, I report the first genome assemblies of Amur leopard (Panthera pardus) and Nomura???s jellyfish (Nemopilema nomurai), which were processed by different strategies of sequencing platforms and downstream analysis methods. Genome survey results of the two species indicate that the leopard genome is much larger than that of the jellyfish but showed a relatively low heterozygosity. The leopard and jellyfish genomes were sequenced by the second- (Illumina short reads) and third-generation (PacBio SMRT long reads) sequencing technologies, respectively. Recent studies indicate that the sequencing platform has the most influence on determining the genome assembly quality and current sequencing technologies have clear limitations. Short-read based sequencing has a problem in resolving repeats, and long-read based sequencing is not suitable for large genomes because it requires a high sequencing coverage (>50X) due to high error rates. Therefore, I propose that a hybrid sequencing strategy is the most efficient method for reducing sequencing and computational cost. The difference in the evolutionary positions of the two species shows the necessity for different analytical approaches. I demonstrate that the leopard, which has an evolutionary distance of less than 10 million years from other Felidae species, could be subject close species comparative genomics (CSCG), such as homology-based comparative, positive selection, unique amino acid changes, and highly conserved region analyses, whereas the jellyfish genome was analyzed under distant species comparative genomics (DSCG), such as conserved protein domains and absence/presence of conserved genes, because the evolutionary distance to other cnidarian genomes was more than 200 million years. It clearly suggests that it is necessary to use radically different strategies depending on their evolutionary positions. Through a comparison between the two very different species, this study provides guidelines to determine the optimal strategies for a new genome reference assembly.clos

Seismic response of beam-column joints rehabilitated with FRP sheets and buckling restrained braces

An experimental test was performed to evaluate the seismic resistance of reinforced concrete beam-column joints rehabilitated with FRP sheets and Buckling Restrained Braces (BRBs). Six beam-column joints were rehabilitated and tested. The test results were compared in terms of hysteresis loops, stiffness degradation, energy dissipation and ductility. The comparison result showed that wrapping FRP sheets can contribute to increase the effect of confinement and to delay crack development in the joints. Also retrofitting buckling restrained braces (BRBs) can improve the stiffness and energy dissipation capacity. Both FRP sheets and BRBs can effectively improve the strength, stiffness and ductility

Short Term Effect and Safety of Antidiuretic Hormone in the Patients with Nocturia

Purpose To investigate the short-term safety of antidiuretic hormone in elderly patients with nocturnal polyuria, focus on hyponatremia and others electrolytes disturbances and to assess short-term effects on nocturnal urine output and number of nocturnal voids. Methods Between June 2005 and August 2006, a total of 34 patients with nocturnal polyuria were orally administered 0.2 mg desmopressin tablet at bedtime for two weeks. Serum sodium, others electrolytes, urine sodium and urine osmolarity were assessed in the third days, one week and two weeks after treatment with desmopressin and compared adult group (<65 years of age) with elderly group (≥65 years of age). We assessed the effect of desmopressin using a frequency-volume charts and analysed. Results In total 34 patients (20 adult, 14 elderly) were analyzed. Desmopressin treatment did not significantly change serum and urine electrolytes include soduim concentration in elderly patients comparied with adult patients. Serum sodium concentration below normal range was recorded in 2 patients in elderly group, but no serious adverse events occurred and recovered without sequelae. The mean number of nocturnal voids decresed (54% reduction) and nocturnal urine output decreased (57% reduction) after using desmopressin. Conclusions Desmopressin was well tolerated and effective in elderly patients with nocturnal polyuria without clinically significant hyponatremia

A designed angiopoietin-2 variant, pentameric COMP-Ang2, strongly activates Tie2 receptor and stimulates angiogenesis

AbstractDespite that angiopoietin-2 (Ang2) produces more versatile and dynamic functions than angiopoietin-1 (Ang1) in angiogenesis and inflammation, the molecular mechanism that underlies this difference is still unknown. To define the role of oligomerization of Ang2 in activation of its receptor, Tie2, we designed and generated different oligomeric forms of Ang2 by replacement of the amino-terminal domains of Ang2 with dimeric, tetrameric, and pentameric short coiled-coil domains derived from GCN4, matrillin-1, and COMP. COMP-Ang2 strongly binds and activates Tie2, whereas GCN4-Ang2 and MAT-Ang2 weakly to moderately bind and activate Tie2. Although native Ang2 strongly binds to Tie2, it does not activate Tie2. Accordingly, COMP-Ang2 strongly promotes endothelial cell survival, migration, and tube formation in a Tie2-dependent manner, and the potency of COMP-Ang2 is almost identical to that of COMP-Ang1. Furthermore, the potency of COMP-Ang2-induced enhanced angiogenesis in the wound healing region is almost identical to the potency of COMP-Ang1-induced enhanced angiogenesis. Overall, there is no obvious difference between COMP-Ang2 and COMP-Ang1 in in vitro and in vivo angiogenesis. Our results provide compelling evidence that proper oligomerization of Ang2 is a critical determinant of its binding and activation of Tie2

Seismic performance of reinforced concrete frames retrofitted with inserted steel frame and adhered waved steel panel

In this paper, two types of seismic retrofitting methods for reinforced concrete frames were suggested and examined through the cyclic loading tests: one is to insert a steel frame to existing partially masonry infilled concrete frame of the building after removing masonry from the concrete frame and the other is to adhere waved steel panels to the existing masonry fully infilled concrete frame. In order to evaluate validity of the suggested methods in seismic performance, five specimens were manufactured and tested: a bare concrete frame, a partially masonry infilled concrete frame, a masonry infilled concrete frame, a steel frame inserted concrete frame, and a waved steel panel adhered concrete frame. Compared were crack pattern, failure mode, load-displacement relation, ductility, stiffness and energy dissipation capacity. The specimens retrofitted with the inserted steel frame showed a maximum load approximately twice that of the partially masonry infilled frame, and the specimen retrofitted with the adhered waved steel panel showed a maximum load approximately twice that of the masonry fully infilled frame

Flexural Behavior of Posttensioned Flat Plates Depending on Tendon Layout

This paper discusses the experimental results on the flexural behavior and deflections of posttensioned concrete flat plates depending on tendon layout. One reinforced concrete flat plate and two posttensioned concrete flat plates were manufactured and tested. One-way posttensioning layout and two-way posttensioning layout were considered in this paper. The load-deflection behavior and modes of crack are presented from the test results. Posttension systems effectively controlled crack and deflection. One-way and two-way posttensioning layouts both showed similar maximum load. However, serviceability improved with two-way posttensioning layout compared to one-way posttensioning layout. Also, the yield-line theory was applied to predict the ultimate load for the posttensioned flat plates. The comparison between the test results and estimation by yield-line analysis generally showed good agreement

Maximized performance of dye solar cells on plastic: a combined theoretical and experimental optimization approach

We demonstrate that a combined optimization approach based on the sequential alternation of theoretical analysis and experimental realization gives rise to plastic supported dye solar cells for which both light harvesting efficiency and electron collection are maximized. Rationalized configurations with optimized light trapping and charge extraction are realized to achieve photoanodes on plastic prepared at low temperature, showing a power conversion efficiency of 8.55% and a short circuit photocurrent of 16.11 mA cm 2, unprecedented for plastic based dye solar cell devices. Furthermore, the corresponding fully flexible designs present stable mechanical properties after several bending cycles, displaying 7.79% power conversion efficiency, an average broadband internal quantum efficiency above 90%, and a short circuit photocurrent of 15.94 mA cm 2, which is the largest reported value for bendable cells of this sort to dateEuropean Union 307081, 622533Ministerio de Economía y Competitividad MAT2014-54852-R, MAT2011–2359