Heavy Flavor Physics through e-Science

Heavy flavor physics is an important element in understanding the nature of physics. The accurate knowledge of properties of heavy flavor physics plays an essential role for the determination of the Cabibbo-Kobayashi-Maskawa (CKM) matrix. Asymmetric-energy e+e- B factories (BaBar and Belle) run their operation and will upgrade B factories to become super Belle. The size of available B meson samples will be dramatically increased. Also the data size of Tevatron experiments (CDF, D0) are on the order of PetaByte. Therefore we use new concept of e-Science for heavy flavor physics. This concept is about studying heavy flavor physics anytime and anywhere even if we are not on-site of accelerator laboratories and data size is immense. The component of this concept is data production, data processing and data analysis anytime and anywhere. We apply this concept to current CDF experiment at Tevatron. We will expand this concept to Super Belle and LHC (Large Hadron Collider) experiments which will achieve an accuracy of measurements in the next decades.Comment: 16 pages, 2 figure

In vivo action of RNA G-quadruplex in phloem development

Phloem network integrates cellular energy status into post-embryonic growth, and development by tight regulation of carbon allocation. Phloem development involves complicated coordination of cell fate determination, cell division, and terminal differentiation into sieve elements (SEs), functional conduit All of these processes must be tightly coordinated, for optimization of systemic connection between source supplies and sink demands throughout plant life cycle, that has substantial impact on crop productivity. Despite its pivotal role, surprisingly, regulatory mechanisms underlying phloem development have just begun to be explored, and we recently identified a novel translational regulatory network involving RNA G-quadruplex and a zinc-finger protein, JULGI, for phloem development From this perspective, we further discuss the role of RNA G-quadruplex on post-transcriptional control of phloem regulators, as a potential interface integrating spatial information for asymmetric cell division, and phloem development.11Ysciescopuskc

Deep Coherence Learning: An Unsupervised Deep Beamformer for High Quality Single Plane Wave Imaging in Medical Ultrasound

Plane wave imaging (PWI) in medical ultrasound is becoming an important reconstruction method with high frame rates and new clinical applications. Recently, single PWI based on deep learning (DL) has been studied to overcome lowered frame rates of traditional PWI with multiple PW transmissions. However, due to the lack of appropriate ground truth images, DL-based PWI still remains challenging for performance improvements. To address this issue, in this paper, we propose a new unsupervised learning approach, i.e., deep coherence learning (DCL)-based DL beamformer (DL-DCL), for high-quality single PWI. In DL-DCL, the DL network is trained to predict highly correlated signals with a unique loss function from a set of PW data, and the trained DL model encourages high-quality PWI from low-quality single PW data. In addition, the DL-DCL framework based on complex baseband signals enables a universal beamformer. To assess the performance of DL-DCL, simulation, phantom and in vivo studies were conducted with public datasets, and it was compared with traditional beamformers (i.e., DAS with 75-PWs and DMAS with 1-PW) and other DL-based methods (i.e., supervised learning approach with 1-PW and generative adversarial network (GAN) with 1-PW). From the experiments, the proposed DL-DCL showed comparable results with DMAS with 1-PW and DAS with 75-PWs in spatial resolution, and it outperformed all comparison methods in contrast resolution. These results demonstrated that the proposed unsupervised learning approach can address the inherent limitations of traditional PWIs based on DL, and it also showed great potential in clinical settings with minimal artifacts

Massively parallel implementation of cyclic LDPC codes on a general purpose graphic processing unit

2009 IEEE Workshop On Signal Processing Systems (SiPS) Tampere, Finland 2009-10-07 ~ 2009-10-09Simulation of low-density parity-check (LDPC) codes frequently takes several days, thus the use of general purpose graphics processing units (GPGPUs) is very promising. However, GPGPUs are designed for compute-intensive applications, and they are not optimized for data caching or control management. In LDPC decoding, the parity check matrix H needs to be accessed at every node updating process, and the size of H matrix is often larger than that of GPU on-chip memory especially when the code-length is long or the weight is high. In this work, the parity check matrix of cyclic or quasi-cyclic LDPC codes is greatly compressed by exploiting the periodic property of the matrix. In our experiments, the Compute Unified Device Architecture (CUDA) of Nvidia is used. With the (1057, 813) and (4161, 3431) projective geometry (PG)–LDPC codes, the execution speed of the proposed method is more than twice of the reference implementations that do not exploit the cyclic property of the parity check matrices

FOXA1 mutations alter pioneering activity, differentiation and prostate cancer phenotypes.

Mutations in the transcription factor FOXA1 define a unique subset of prostate cancers but the functional consequences of these mutations and whether they confer gain or loss of function is unknown1-9. Here, by annotating the landscape of FOXA1 mutations from 3,086 human prostate cancers, we define two hotspots in the forkhead domain: Wing2 (around 50% of all mutations) and the highly conserved DNA-contact residue R219 (around 5% of all mutations). Wing2 mutations are detected in adenocarcinomas at all stages, whereas R219 mutations are enriched in metastatic tumours with neuroendocrine histology. Interrogation of the biological properties of wild-type FOXA1 and fourteen FOXA1 mutants reveals gain of function in mouse prostate organoid proliferation assays. Twelve of these mutants, as well as wild-type FOXA1, promoted an exaggerated pro-luminal differentiation program, whereas two different R219 mutants blocked luminal differentiation and activated a mesenchymal and neuroendocrine transcriptional program. Assay for transposase-accessible chromatin using sequencing (ATAC-seq) of wild-type FOXA1 and representative Wing2 and R219 mutants revealed marked, mutant-specific changes in open chromatin at thousands of genomic loci and exposed sites of FOXA1 binding and associated increases in gene expression. Of note, ATAC-seq peaks in cells expressing R219 mutants lacked the canonical core FOXA1-binding motifs (GTAAAC/T) but were enriched for a related, non-canonical motif (GTAAAG/A), which was preferentially activated by R219-mutant FOXA1 in reporter assays. Thus, FOXA1 mutations alter its pioneering function and perturb normal luminal epithelial differentiation programs, providing further support for the role of lineage plasticity in cancer progression

Observation of Double cc bar Production in e+ e- Annihilation at sqrt{s} ~ 10.6 GeV

We report the observation of prompt J/psi via double ccbar production from the e+e- continuum. In this process one ccbar pair fragments into a J/psi meson while the remaining pair either produces a bound charmonium state or fragments into open charm. Both cases have been observed: the first by studying the mass spectrum of the system recoiling against the J/psi, and the second by reconstructing the J/psi together with a charmed meson. We find cross-sections of \sigma(e+ e- -> J/psi eta_c (gamma)) * BR (eta_c -> >=4 charged) = 0.033 (+0.007 -0.006)(stat) \pm 0.009(syst)pb and \sigma(e+ e- -> J/psi D*+ X) = 0.53 (+0.19 -0.15)(stat) \pm 0.14(syst) pb, and infer \sigma(e+ e- -> J/psi c cbar) / \sigma(e+ e- -> J/psi X) = 0.59 (+0.15 -0.13)(stat) \pm 0.12(syst). These results are obtained from a 46.2/fb data sample collected near the Upsilon(4S) resonance, with the Belle detector at the KEKB asymmetric energy e+ e- collider.Comment: 7 pages, 2 figures, to be submitted to Physical Review Letter

Production of Prompt Charmonia in e+e−e^+e^- Annihilation at s≈10.6\sqrt{s}\approx 10.6 GeV

The production of prompt $J/\psi$, $\psi(2S)$, $\chi_{c1}$ and $\chi_{c2}$ is studied using a $32.4 fb^{-1}$ data sample collected with the Belle detector at the $\Upsilon(4S)$ and 60 MeV below the resonance. The yield of prompt $J/\psi$ mesons in the $\Upsilon(4S)$ sample is compatible with that of continuum production; we set an upper limit ${\cal B}(\Upsilon(4S) \to J/\psi X) < 1.9 \times 10^{-4}$ at the 95% confidence level, and find $\sigma(e^{+}e^{-} \to J/\psi X)=1.47\pm 0.10 \pm 0.13$ pb. The cross-sections for prompt $\psi(2S)$ and direct $J/\psi$ are measured. The $J/\psi$ momentum spectrum, production angle distribution and polarization are studied.Comment: submitted to Phys. Rev. Let