Growth characteristics and productivity of tall fescue new variety ‘Purumi’ in South Korea

A new tall fescue variety (Festuca arundinacea Schreb.) named ‘Purumi’ was developed by the National Institute of Animal Science, Rural Development Administration, South Korea from 1999 to 2007. For synthetic seed  production of this new variety, 5 superior clones: EFa9108, EFa0010, EFa0020, EFa0108 and EFa0202 were selected and polycrossed. The agronomic growth characteristics and forage production capability of the seeds were studied at Cheonan from 2004 to 2005, and regional trials were conducted in Cheonan, Pyungchang, Jeju and Jinju from 2008 to 2010. Purumi showed enhanced winter hardiness, disease resistance, and regrowth ability as compared to Fawn. The dry matter yield of Purumi was about 5.6% (16.821 kg/ha) higher than that of Fawn. However, the  nutritive value of both varieties was similar. Since this new variety of tall fescue, Purumi has been developed and distributed with its most  remarkable adaptability for Korean climates and superior value as a livestock feed, it is expected to play an important role in restoration of the pasture industry in Korea.Key words: Tall fescue, Purumi, variety, forage, grassland

High frequency plant regeneration from mature seedderived callus of Italian ryegrass (Lolium multiflorum) cultivars

In the present study, we have developed a high-frequency plant regeneration system for Italian ryegrass via callus culture using mature seeds as explants. Optimal embryogenic callus induction was found to occur in MS medium containing 5 mg l-1 2,4-D, 0.5 mg l-1 BA, 500 mg l-1 L-proline, 1 g l-1 casein hydrolysate, 30 g l-1 sucrose, 7 mg l-1 AgNO3, 2 mg l-1 CuSO4 and solidified with 3 g l-1 Gelrite. The highest regeneration rate was obtained in MS medium containing 1 mg l-1 2,4-D, 5 mg l-1 BA, 500 mg l-1 L-proline, 1 g l-1 casein hydrolysate, 1 mg l-1 thiamine-HCl, 30 g l-1 sucrose, 7 mg l-1 AgNO3, 2 mg l-1 CuSO4 and solidified with 3 g l-1 Gelrite. By using the most effective treatment determined for each parameter, the highest rates of embryogenic callus formation (48.9%) and regeneration (47.6%) were obtained with the Hwasan 101 cultivar. The overall plant regeneration rates of the examined cultivars ranged from 7.5 to 23.2%. Thus, optimization of regeneration frequency using mature seeds as explant material may offer a simple and efficient protocol for Italian ryegrass that may improve molecular breeding of this species

C5 Extract Induces Apoptosis in B16F10 Murine Melanoma Cells through Extrinsic and Intrinsic Apoptotic Pathways and Sub-G1 Phase Arrest

Purpose: To investigate the anti-cancer activities of C5 extract (C5E), a new herbal preparation from Korea, on B16F10 cells.Methods: The anti-proliferative effects of C5E were assessed by culturing B16F10 cells in the presence or absence of C5E. Cell cycle progression was analyzed by PI staining using flow cytometry. The quantities of apoptosis-inducing proteins were measured by Western blot.Results: C5E inhibited the proliferation of B16F10 cells but not human keratinocytes. C5E induced S phase arrest by interfering with cell regulatory factors such as cyclins B1, D1, D3, and E, and cyclindependent kinase 2, in B16F10 cells. Furthermore, immunoblot analysis confirmed that treatment with C5E induced apoptosis and cleaved caspase-3, poly (ADP-ribose) polymerase, via extrinsic pathway, whereas Bcl-2 expression was down-regulated. In addition, the suppression of cell proliferation by C5E is through down-regulation of p-Akt, up-regulation of phosphatase and tensin homolog protein expression via phosphoinositol 3 kinase survival signaling pathways in B16F10 cells. The combined cytotoxic effects of C5E and vinblastine generated 10 % increase in activity in contrast to the sum of the inhibitory effects of the individual agents.Conclusion: C5E shows promising anti-cancer activity and can be a useful adjuvant with vinblastine in combination therapeutic treatment of skin cancer.Keywords: Melanoma, Apoptosis, Anti-cancer, p53, Vinblastine, Cell cycle arrest, Caspas

Model Adaptation with Synthetic and Real Data for Semantic Dense Foggy Scene Understanding

This work addresses the problem of semantic scene understanding under dense fog. Although considerable progress has been made in semantic scene understanding, it is mainly related to clear-weather scenes. Extending recognition methods to adverse weather conditions such as fog is crucial for outdoor applications. In this paper, we propose a novel method, named Curriculum Model Adaptation (CMAda), which gradually adapts a semantic segmentation model from light synthetic fog to dense real fog in multiple steps, using both synthetic and real foggy data. In addition, we present three other main stand-alone contributions: 1) a novel method to add synthetic fog to real, clear-weather scenes using semantic input; 2) a new fog density estimator; 3) the Foggy Zurich dataset comprising $3808$ real foggy images, with pixel-level semantic annotations for $16$ images with dense fog. Our experiments show that 1) our fog simulation slightly outperforms a state-of-the-art competing simulation with respect to the task of semantic foggy scene understanding (SFSU); 2) CMAda improves the performance of state-of-the-art models for SFSU significantly by leveraging unlabeled real foggy data. The datasets and code are publicly available.Comment: final version, ECCV 201

Perturbations of nuclear C*-algebras

Kadison and Kastler introduced a natural metric on the collection of all C*-subalgebras of the bounded operators on a separable Hilbert space. They conjectured that sufficiently close algebras are unitarily conjugate. We establish this conjecture when one algebra is separable and nuclear. We also consider one-sided versions of these notions, and we obtain embeddings from certain near inclusions involving separable nuclear C*-algebras. At the end of the paper we demonstrate how our methods lead to improved characterisations of some of the types of algebras that are of current interest in the classification programme.Comment: 45 page

PocketMatch: A new algorithm to compare binding sites in protein structures

Background: Recognizing similarities and deriving relationships among protein molecules is a fundamental
requirement in present-day biology. Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. In some cases similarities obscure at these levels could be present merely in the substructures at their binding sites. Inferring functional similarities between protein molecules by comparing their binding sites is still largely exploratory and not as yet a routine protocol. One of
the main reasons for this is the limitation in the choice of appropriate analytical tools that can compare binding sites with high sensitivity. To benefit from the enormous amount of structural data that is being rapidly accumulated, it is essential to have high throughput tools that enable large scale binding site comparison.

Results: Here we present a new algorithm PocketMatch for comparison of binding sites in a frame invariant
manner. Each binding site is represented by 90 lists of sorted distances capturing shape and chemical nature of the site. The sorted arrays are then aligned using an incremental alignment method and scored to obtain PMScores for pairs of sites. A comprehensive sensitivity analysis and an extensive validation of the algorithm have been carried out. Perturbation studies where the geometry of a given site was retained but the residue types were changed randomly, indicated that chance similarities were virtually non-existent. Our analysis also demonstrates that shape information alone is insufficient to discriminate between diverse binding sites, unless
combined with chemical nature of amino acids.

Conclusions: A new algorithm has been developed to compare binding sites in accurate, efficient and
high-throughput manner. Though the representation used is conceptually simplistic, we demonstrate that along
with the new alignment strategy used, it is sufficient to enable binding comparison with high sensitivity. Novel methodology has also been presented for validating the algorithm for accuracy and sensitivity with respect to geometry and chemical nature of the site. The method is also fast and takes about 1/250th second for one comparison on a single processor. A parallel version on BlueGene has also been implemented

A stitch in time: Efficient computation of genomic DNA melting bubbles

Background: It is of biological interest to make genome-wide predictions of the locations of DNA melting bubbles using statistical mechanics models. Computationally, this poses the challenge that a generic search through all combinations of bubble starts and ends is quadratic. Results: An efficient algorithm is described, which shows that the time complexity of the task is O(NlogN) rather than quadratic. The algorithm exploits that bubble lengths may be limited, but without a prior assumption of a maximal bubble length. No approximations, such as windowing, have been introduced to reduce the time complexity. More than just finding the bubbles, the algorithm produces a stitch profile, which is a probabilistic graphical model of bubbles and helical regions. The algorithm applies a probability peak finding method based on a hierarchical analysis of the energy barriers in the Poland-Scheraga model. Conclusions: Exact and fast computation of genomic stitch profiles is thus feasible. Sequences of several megabases have been computed, only limited by computer memory. Possible applications are the genome-wide comparisons of bubbles with promotors, TSS, viral integration sites, and other melting-related regions.Comment: 16 pages, 10 figure

A statistical framework for integrating two microarray data sets in differential expression analysis

<p>Abstract</p> <p>Background</p> <p>Different microarray data sets can be collected for studying the same or similar diseases. We expect to achieve a more efficient analysis of differential expression if an efficient statistical method can be developed for integrating different microarray data sets. Although many statistical methods have been proposed for data integration, the genome-wide concordance of different data sets has not been well considered in the analysis.</p> <p>Results</p> <p>Before considering data integration, it is necessary to evaluate the genome-wide concordance so that misleading results can be avoided. Based on the test results, different subsequent actions are suggested. The evaluation of genome-wide concordance and the data integration can be achieved based on the normal distribution based mixture models.</p> <p>Conclusion</p> <p>The results from our simulation study suggest that misleading results can be generated if the genome-wide concordance issue is not appropriately considered. Our method provides a rigorous parametric solution. The results also show that our method is robust to certain model misspecification and is practically useful for the integrative analysis of differential expression.</p

Testing supersymmetry at the LHC through gluon-fusion production of a slepton pair

Renormalizable quartic couplings among new particles are typical of supersymmetric models. Their detection could provide a test for supersymmetry, discriminating it from other extensions of the Standard Model. Quartic couplings among squarks and sleptons, together with the SU(3) gauge couplings for squarks, allow a new realization of the gluon-fusion mechanism for pair-production of sleptons at the one-loop level. The corresponding production cross section, however, is at most of ${\cal O}(1)$fb for slepton and squark masses of ${\cal O}(100)$GeV. We then extend our investigation to the gluon-fusion production of sleptons through the exchange of Higgs bosons. The cross section is even smaller, of ${\cal O}(0.1)$fb, if the exchanged Higgs boson is considerably below the slepton-pair threshold, but it is enhanced when it is resonant. It can reach ${\cal O}(10)$fb for the production of sleptons of same-chirality, exceeding these values for $\widetilde{\tau}$'s of opposite-chirality, even when chirality-mixing terms in the squark sector are vanishing. The cross section can be further enhanced if these mixing terms are nonnegligible, providing a potentially interesting probe of the Higgs sector, in particular of parameters such as $A$, $\mu$, and $\tan\beta$.Comment: 28 pages, 11 figure