rMAPS: RNA map analysis and plotting server for alternative exon regulation.

RNA-binding proteins (RBPs) play a critical role in the regulation of alternative splicing (AS), a prevalent mechanism for generating transcriptomic and proteomic diversity in eukaryotic cells. Studies have shown that AS can be regulated by RBPs in a binding-site-position dependent manner. Depending on where RBPs bind, splicing of an alternative exon can be enhanced or suppressed. Therefore, spatial analyses of RBP motifs and binding sites around alternative exons will help elucidate splicing regulation by RBPs. The development of high-throughput sequencing technologies has allowed transcriptome-wide analyses of AS and RBP-RNA interactions. Given a set of differentially regulated alternative exons obtained from RNA sequencing (RNA-seq) experiments, the rMAPS web server (http://rmaps.cecsresearch.org) performs motif analyses of RBPs in the vicinity of alternatively spliced exons and creates RNA maps that depict the spatial patterns of RBP motifs. Similarly, rMAPS can also perform spatial analyses of RBP-RNA binding sites identified by cross-linking immunoprecipitation sequencing (CLIP-seq) experiments. We anticipate rMAPS will be a useful tool for elucidating RBP regulation of alternative exon splicing using high-throughput sequencing data

Partially composite 2-Higgs-doublet model

In the extra dimensional scenarios with gauge fields in the bulk, the Kaluza-Klein (KK) gauge bosons can induce Nambu-Jona-Lasinio (NJL) type attractive four-fermion interactions, which can break electroweak symmetry dynamically with accompanying composite Higgs fields. We consider a possibility that electroweak symmetry breaking (EWSB) is triggered by both a fundamental Higgs and a composite Higgs arising in a dynamical symmetry breaking mechanism induced by a new strong dynamics. The resulting Higgs sector is a partially composite two-Higgs doublet model with specific boundary conditions on the coupling and mass parameters originating at a compositeness scale $\Lambda$. The phenomenology of this model is discussed including the collider phenomenology at LHC and ILC.Comment: To appear in the proceeding of LCWS06, Bangalore, Indi

Absorption cross section and Hawking radiation in two-dimensional AdS black hole

We calculate the absorption coefficient of scalar field on the background of the two-dimensional AdS black hole, which is of relevance to Hawking radiation. For the massless scalar field, we find that there does not exist any massless radiation.Comment: 6 pages, revtex, no figure

TRAO Survey of Nearby Filamentary Molecular clouds, the Universal Nursery of Stars (TRAO FUNS) I. Dynamics and Chemistry of L1478 in the California Molecular Cloud

"TRAO FUNS" is a project to survey Gould Belt's clouds in molecular lines. This paper presents its first results on the central region of the California molecular cloud, L1478. We performed On-The-Fly mapping observations using the Taedeok Radio Astronomy Observatory (TRAO) 14m single dish telescope equipped with a 16 multi-beam array covering $\sim$1.0 square degree area of this region using C$^{18}$O (1-0) mainly tracing low density cloud and about 460 square arcminute area using N$_{2}$H$^{+}$ (1-0) mainly tracing dense cores. CS (2-1) and SO $(3_{2}-2_{1})$ were also used simultaneously to map $\sim$440 square arcminute area of this region. We identified 10 filaments by applying the dendrogram technique to the C$^{18}$O data-cube and 8 dense N$_{2}$H$^{+}$ cores by using {\sc FellWalker}. Basic physical properties of filaments such as mass, length, width, velocity field, and velocity dispersion are derived. It is found that L1478 consists of several filaments with slightly different velocities. Especially the filaments which are supercritical are found to contain dense cores detected in N$_{2}$H$^{+}$. Comparison of non-thermal velocity dispersions derived from C$^{18}$O and N$_{2}$H$^{+}$ for the filaments and dense cores indicates that some of dense cores share similar kinematics with those of the surrounding filaments while several dense cores have different kinematics with those of their filaments. This suggests that the formation mechanism of dense cores and filaments can be different in individual filaments depending on their morphologies and environments.Comment: 25 pages, 15 figures, accepted for publication in Ap

CP violation in associated charged Higgs boson production with a single top at the LHC

We explore the CP violation in the charged Higgs production associated with a top quark at the LHC in the MSSM. The supersymmetric phases of gaugino masses and trilinear $A$ terms lead to a CP violating asymmetry of the cross section in the $p p \to g b \to t H^\pm$ process through loop corrections to the $tbH^\pm$ vertex. We find that a CP violation more than 10 % is possible if the charged Higgs boson is heavy enough.Comment: 8 pages including 5 eps figures, JHEP, corrections mad

Materials and extracellular matrix rigidity highlighted in tissue damages and diseases: Implication for biomaterials design and therapeutic targets

Rigidity (or stiffness) of materials and extracellular matrix has proven to be one of the most significant extracellular physicochemical cues that can control diverse cell behaviors, such as contractility, motility, and spreading, and the resultant pathophysiological phenomena. Many 2D materials engineered with tunable rigidity have enabled researchers to elucidate the roles of matrix biophysical cues in diverse cellular events, including migration, lineage specification, and mechanical memory. Moreover, the recent findings accumulated under 3D environments with viscoelastic and remodeling properties pointed to the importance of dynamically changing rigidity in cell fate control, tissue repair, and disease progression. Thus, here we aim to highlight the works related with material/matrix-rigidity-mediated cell and tissue behaviors, with a brief outlook into the studies on the effects of material/matrix rigidity on cell behaviors in 2D systems, further discussion of the events and considerations in tissue-mimicking 3D conditions, and then examination of the in vivo findings that concern material/matrix rigidity. The current discussion will help understand the material/matrix-rigidity-mediated biological phenomena and further leverage the concepts to find therapeutic targets and to design implantable materials for the treatment of damaged and diseased tissues

Correlated multiplexity and connectivity of multiplex random networks

Nodes in a complex networked system often engage in more than one type of interactions among them; they form a multiplex network with multiple types of links. In real-world complex systems, a node's degree for one type of links and that for the other are not randomly distributed but correlated, which we term correlated multiplexity. In this paper we study a simple model of multiplex random networks and demonstrate that the correlated multiplexity can drastically affect the properties of giant component in the network. Specifically, when the degrees of a node for different interactions in a duplex Erdos-Renyi network are maximally correlated, the network contains the giant component for any nonzero link densities. In contrast, when the degrees of a node are maximally anti-correlated, the emergence of giant component is significantly delayed, yet the entire network becomes connected into a single component at a finite link density. We also discuss the mixing patterns and the cases with imperfect correlated multiplexity.Comment: Revised version, 12 pages, 6 figure

Automatic segmentation of cardiac structures for breast cancer radiotherapy

Background and purpose We developed an automatic method to segment cardiac substructures given a radiotherapy planning CT images to support epidemiological studies or clinical trials looking at cardiac disease endpoints after radiotherapy. Material and methods We used a most-similar atlas selection algorithm and 3D deformation combined with 30 detailed cardiac atlases. We cross-validated our method within the atlas library by evaluating geometric comparison metrics and by comparing cardiac doses for simulated breast radiotherapy between manual and automatic contours. We analyzed the impact of the number of cardiac atlas in the library and the use of manual guide points on the performance of our method. Results The Dice Similarity Coefficients from the cross-validation reached up to 97% (whole heart) and 80% (chambers). The Average Surface Distance for the coronary arteries was less than 10.3 mm on average, with the best agreement (7.3 mm) in the left anterior descending artery (LAD). The dose comparison for simulated breast radiotherapy showed differences less than 0.06 Gy for the whole heart and atria, and 0.3 Gy for the ventricles. For the coronary arteries, the dose differences were 2.3 Gy (LAD) and 0.3 Gy (other arteries). The sensitivity analysis showed no notable improvement beyond ten atlases and the manual guide points does not significantly improve performance. Conclusion We developed an automated method to contour cardiac substructures for radiotherapy CTs. When combined with accurate dose calculation techniques, our method should be useful for cardiac dose reconstruction of a large number of patients in epidemiological studies or clinical trials