EST sequencing and gene expression profiling in Scutellaria baicalensis

Scutellaria baicalensis is an important medicinal plant, but few genomic resources are available for this species, as well as for other non-model plants. One of the major new directions in genome research is to discover the full spectrum of genes transcribed from the whole genome. Here, we report extensive transcriptome data of the early growth stage of S. baicalensis. This transcriptome consensus sequence was constructed by de novo assembly of shotgun sequencing data, obtained using multiple next-generation DNA sequencing (NGS) platforms (Roche/454 GS_FLX+ and Illumina/Solexa HiSeq2000). We show that this new approach to obtain extensive mRNA is an efficient strategy for genome-wide transcriptome analysis. We obtained 1,226,938 and 161,417,646 reads using the GS_FLX and the Illumina/Solexa HiS-eq2000, respectively. De novo assembly of the high-quality GS_FLX and Illumina reads (95 % and 75 %) resulted in more than 82 Mb of mRNA consensus sequence, which we assembled into 51,188 contigs, with at least 500 bp per contig. Of these contigs, 39,581 contained known genes, as determined by BLASTX searches against non-redundant NCBI database. Of these, 20,498 different genes were expressed during the early growth stage of S. baicalensis. We have made the expressed sequences available on a public database. Our results demonstrate the utility of combining NGS technologies as a basis for the development of genomic tools in non-model, medicinal plant species. Knowledge of all described genes and quantitation of the expressed genes, including the transcription factors involved, will be useful in studies of the biology of S. baicalensis gene regulation

Comparison between a reanalyzed product by 3-dimensional variational assimilation technique and observations in the Ulleung Basin of the East/Japan Sea

Author Posting. © Elsevier B.V., 2009. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Journal of Marine Systems 78 (2009): 249-264, doi:10.1016/j.jmarsys.2009.02.017.Reanalyzed products from a MOM3-based East Sea Regional Ocean Model with a 3- dimentional variational data assimilation module (DA-ESROM), have been compared with the observed hydrographic and current datasets in the Ulleung Basin (UB) of the East/Japan Sea (EJS). Satellite-borne sea surface temperature and sea surface height data, and in-situ temperature profiles have been assimilated into the DA-ESROM. The performance of the DA-ESROM appears to be efficient enough to be used in an operational ocean forecast system. Comparing with the results from Mitchell et al. (2005a), the DA-ESROM fairly well simulates the high variability of the Ulleung Warm Eddy and Dok Cold Eddy as well as the branching of the Tsushima Warm Current in the UB. The overall root-mean-square error between 100m temperature field reproduced by the DA-ESROM and the observed 100-dbar temperature field is 2.1°C, and the spatially averaged grid-to-grid correlation between the two temperature fields is high with a mean value of 0.79 for the intercomparison period. The DA-ESROM reproduces the development of strong southward North Korean Cold Current (NKCC) in summer consistent with the observational results, which is thought to be an improvement of the previous numerical models in the EJS. The reanalyzed products show that the NKCC is about 35 km wide, and flows southward along the Korean coast from spring to summer with maximum monthly mean volume transport of about 0.8 Sv in August-September.The major part of this works was conducted with financial support by Agency for Defense Development under the contract UD031003AD. The first and seventh authors were supported at the final stage of this work by KORDI’s research projects (PE9830Q and PG47100). The second author was supported by EAST-I Program of the Ministry of Maritime Affairs and Fisheries

Observation of the Far-ultraviolet Continuum Background with SPEAR/FIMS

We present the general properties of the far-ultraviolet (FUV; 1370-1720A) continuum background over most of the sky, obtained with the Spectroscopy of Plasma Evolution from Astrophysical Radiation instrument (SPEAR, also known as FIMS), flown aboard the STSAT-1 satellite mission. We find that the diffuse FUV continuum intensity is well correlated with N_{HI}, 100 $\mu$m, and H-alpha intensities but anti-correlated with soft X-ray. The correlation of the diffuse background with the direct stellar flux is weaker than the correlation with other parameters. The continuum spectra are relatively flat. However, a weak softening of the FUV spectra toward some sight lines, mostly at high Galactic latitudes, is found not only in direct-stellar but also in diffuse background spectra. The diffuse background is relatively softer that the direct stellar spectrum. We also find that the diffuse FUV background averaged over the sky has about the same level as the direct-stellar radiation field in the statistical sense and a bit softer spectrum compared to direct stellar radiation. A map of the ratio of 1400-1510A to 1560-1660A shows that the sky is divided into roughly two parts. However, this map shows a lot of patchy structures on small scales. The spatial variation of the hardness ratio seems to be largely determined by the longitudinal distribution of spectral types of stars in the Galactic plane. A correlation of the hardness ratio with the FUV intensity at high intensities is found but an anti-correlation at low intensities. We also find evidence that the FUV intensity distribution is log-normal in nature.Comment: 39 pages, 26 figures, accepted for publication in ApJ

Longitudinal relationship between depression and antisocial behaviors in Korean adolescents

BackgroundIt is well known that depression and delinquency in adolescents are highly correlated, but longitudinal studies on the causal relationship between them are not active in East Asia compared to in Western culture. In addition, even the results of research on causal models and sex differences are inconsistent.ObjectivesThis study examines the longitudinal reciprocal effects between depression and delinquent behavior in Korean adolescents based on sex differences.MethodsWe conducted multiple-group analysis by using an autoregressive cross-lagged model (ACLM). Longitudinal data from 2,075 individuals (2011–2013) were used for analysis. The longitudinal data are from the Korean Children and Youth Panel Survey (KCYPS), and data were used beginning with students at 14 years old (in the second grade of middle school) and tracked them until they were 16 (in the first grade of high school).ResultsBoys’ delinquent behaviors at 15 years (the third grade of middle school) affected their depression at 16 years (the first grade of high school). In contrast, girls’ depression at 15 years (the third grade of middle school) influenced their delinquent behaviors at 16 years (the first grade of high school).DiscussionThe findings support the failure model (FM) among adolescent boys and the acting-out model (ACM) among girls. The results imply that strategies to effectively prevent and treat delinquency and depression in adolescents must consider sex effects

Multiplex: Unifying Conventional and Speculative Thread-Level Parallelism on a Chip Multiprocessor

Recent proposals for Chip Multiprocessors (CMPs) advocate speculative, or implicit, threading in which the hardware employs prediction to peel off instruction sequences (i.e., implicit threads) from the sequential execution stream and speculatively executes them in parallel on multiple processor cores. These proposals augment a conventional multiprocessor, which employs explicit threading, with the ability to handle implicit threads. Current proposals focus on only implicitly-threaded code sections. This paper identifies, for the first time, the issues in combining explicit and implicit threading. We present the Multiplex architecture to combine the two threading models. Multiplex exploits the similarities between implicit and explicit threading, and provides a unified support for the two threading models without additional hardware. Multiplex groups a subset of protocol states in an implicitly-threaded CMP to provide a write-invalidate protocol for explicit threads. Using a fully-integrated compiler inf rastructure for automatic generation of Multiplex code, this paper presents a detailed performance analysis for entire benchmarks, instead of just implicitly- threaded sections, as done in previous papers. We show that neither threading models alone performs consistently better than the other across the benchmarks. A CMP with four dual-issue CPUs achieves a speedup of 1.48 and 2.17 over one dual-issue CPU, using implicit-only and explicit-only threading, respectively. Multiplex matches or outperforms the better of the two threading models for every benchmark, and a four-CPU Multiplex achieves a speedup of 2.63. Our detailed analysis indicates that the dominant overheads in an implicitly-threaded CMP are speculation state overflow due to limited L1 cache capacity, and load imbalance and data dependences in fine-grain threads

Prognostic significance of lymph node yield on oncologic outcomes according to tumor response after preoperative chemoradiotherapy in rectal cancer patients

Purpose This study aimed to evaluate the predictive value of lymph node yield (LNY) for survival outcomes according to tumor response after preoperative chemoradiotherapy (PCRT) in patients with rectal cancer. Methods This study was a retrospective study conducted in a tertiary center. A total of 1,240 patients with clinical stage II or III rectal cancer who underwent curative resection after PCRT between 2007 and 2016 were included. Patients were categorized into the good response group (tumor regression grade [TRG], 0–1) or poor response group (TRG, 2–3). Propensity score matching was performed for age, sex, and pathologic stage between LNY of ≥12 and LNY of <12 within tumor response group. The primary outcome was 5-year disease-free survival (DFS) and overall survival (OS). Results LNY and positive lymph nodes were inversely correlated with TRG. In good responders, 5-year DFS and 5-year OS of patients with LNY of <12 were better than those with LNY of ≥12, but there was no statistical significance. In poor responders, the LNY of <12 group had worse survival outcomes than the LNY of ≥12 group, but there was also no statistical significance. LNY of ≥12 was not associated with DFS and OS in multivariate analysis. Conclusion LNY of <12 showed contrasting outcomes between the good and poor responders in 5-year DFS and OS. LNY of 12 may not imply adequate oncologic surgery or proper staging in rectal cancer patients treated by PCRT. Furthermore, a decrease in LNY should be comprehended differently according to tumor response