Three-parton contribution to the B→πB\to\pi form factors in kTk_T factorization

We calculate the three-parton twist-3 contribution to the $B\to\pi$ transition form factors in the $k_T$ factorization theorem. Since different mesons are involved in the initial and final states, two(three)-parton-to-three(two)-parton amplitudes do not vanish. It is found that the dominant contribution arises from the diagrams with the additional valence gluon attaching to the leading-order hard gluon. Employing the three-parton meson distribution amplitudes from QCD sum rules, we show that this subleading piece amounts only up to few percents of the form factors at large recoil of the pion. The framework for analyzing three-parton contributions to $B$ meson decays in the $k_T$ factorization is established.Comment: 8 pages, 3 figure

Improved branch and bound algorithm for detecting SNP-SNP interactions in breast cancer

BACKGROUND: Single nucleotide polymorphisms (SNPs) in genes derived from distinct pathways are associated with a breast cancer risk. Identifying possible SNP-SNP interactions in genome-wide case–control studies is an important task when investigating genetic factors that influence common complex traits; the effects of SNP-SNP interaction need to be characterized. Furthermore, observations of the complex interplay (interactions) between SNPs for high-dimensional combinations are still computationally and methodologically challenging. An improved branch and bound algorithm with feature selection (IBBFS) is introduced to identify SNP combinations with a maximal difference of allele frequencies between the case and control groups in breast cancer, i.e., the high/low risk combinations of SNPs. RESULTS: A total of 220 real case and 334 real control breast cancer data are used to test IBBFS and identify significant SNP combinations. We used the odds ratio (OR) as a quantitative measure to estimate the associated cancer risk of multiple SNP combinations to identify the complex biological relationships underlying the progression of breast cancer, i.e., the most likely SNP combinations. Experimental results show the estimated odds ratio of the best SNP combination with genotypes is significantly smaller than 1 (between 0.165 and 0.657) for specific SNP combinations of the tested SNPs in the low risk groups. In the high risk groups, predicted SNP combinations with genotypes are significantly greater than 1 (between 2.384 and 6.167) for specific SNP combinations of the tested SNPs. CONCLUSIONS: This study proposes an effective high-speed method to analyze SNP-SNP interactions in breast cancer association studies. A number of important SNPs are found to be significant for the high/low risk group. They can thus be considered a potential predictor for breast cancer association

SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping

<p>Abstract</p> <p>Background</p> <p>PCR-restriction fragment length polymorphism (RFLP) assay is a cost-effective method for SNP genotyping and mutation detection, but the manual mining for restriction enzyme sites is challenging and cumbersome. Three years after we constructed SNP-RFLPing, a freely accessible database and analysis tool for restriction enzyme mining of SNPs, significant improvements over the 2006 version have been made and incorporated into the latest version, SNP-RFLPing 2.</p> <p>Results</p> <p>The primary aim of SNP-RFLPing 2 is to provide comprehensive PCR-RFLP information with multiple functionality about SNPs, such as SNP retrieval to multiple species, different polymorphism types (bi-allelic, tri-allelic, tetra-allelic or indels), gene-centric searching, HapMap tagSNPs, gene ontology-based searching, miRNAs, and SNP500Cancer. The RFLP restriction enzymes and the corresponding PCR primers for the natural and mutagenic types of each SNP are simultaneously analyzed. All the RFLP restriction enzyme prices are also provided to aid selection. Furthermore, the previously encountered updating problems for most SNP related databases are resolved by an on-line retrieval system.</p> <p>Conclusions</p> <p>The user interfaces for functional SNP analyses have been substantially improved and integrated. SNP-RFLPing 2 offers a new and user-friendly interface for RFLP genotyping that can be used in association studies and is freely available at <url>http://bio.kuas.edu.tw/snp-rflping2</url>.</p

Cryo-EM Studies of TMEM16F Calcium-Activated Ion Channel Suggest Features Important for Lipid Scrambling.

As a Ca2+-activated lipid scramblase and ion channel that mediates Ca2+ influx, TMEM16F relies on both functions to facilitate extracellular vesicle generation, blood coagulation, and bone formation. How a bona fide ion channel scrambles lipids remains elusive. Our structural analyses revealed the coexistence of an intact channel pore and PIP2-dependent protein conformation changes leading to membrane distortion. Correlated to the extent of membrane distortion, many tightly bound lipids are slanted. Structure-based mutagenesis studies further reveal that neutralization of some lipid-binding residues or those near membrane distortion specifically alters the onset of lipid scrambling, but not Ca2+ influx, thus identifying features outside of channel pore that are important for lipid scrambling. Together, our studies demonstrate that membrane distortion does not require open hydrophilic grooves facing the membrane interior and provide further evidence to suggest separate pathways for lipid scrambling and ion permeation

Two-parton twist-3 factorization in perturbative QCD

We prove collinear factorization theorem for the process $\pi\gamma^*\to\pi$ at the twist-3 level in the covariant gauge by means of the Ward identity, concentrating on the two-parton case. It is shown that soft divergences cancel and collinear divergences are grouped into the pseudo-scalar and pseudo-tensor two-parton twist-3 pion distribution amplitudes. The delicate summation of a complete set of diagrams for achieving factorization in momentum, spin, and color spaces is emphasized. The proof is then extended to the exclusive semileptonic decay $B\to\pi l\bar\nu$, assuming the hard scale to be of $O(\sqrt{\bar\Lambda M_B})$, where $\bar\Lambda$ is a hadronic scale and $M_B$ the $B$ meson mass. We explain the distinction between the factorization of collinear divergences for a pion distribution amplitude and of soft divergences for a $B$ meson distribution amplitude. The gauge invariance and universality of the two-parton twist-3 pion distribution amplitudes are confirmed. The proof presented here can accommodate the leading twist-2 case. We then compare our proof with that performed in the framework of soft-collinear effective theory.Comment: 43 pages, 7 figures, many parts rewritten and updated reference

Sudakov effects in BBNS approach

The end-point singularity is an unsolved problem in BBNS approach. Incorporating the partonic transverse momentum and the Sudakov form factor, this problem can be solved model-independently. We discuss the Sudakov effects in BBNS approach. The BBNS approach is compared with the modified PQCD approach. The main idea of Sudakov form factor is briefly discussed. Our conclusion is that the twist-3 contribution for the hard spectator scattering is numerically not important in $B\to \pi\pi$ decays, compared with the twist-2 contribution.Comment: 16 pages, Latex, two figures, some typos correcte

Troubleshooting Arterial-Phase MR Images of Gadoxetate Disodium-Enhanced Liver.

Gadoxetate disodium is a widely used magnetic resonance (MR) contrast agent for liver MR imaging, and it provides both dynamic and hepatobiliary phase images. However, acquiring optimal arterial phase images at liver MR using gadoxetate disodium is more challenging than using conventional extracellular MR contrast agent because of the small volume administered, the gadolinium content of the agent, and the common occurrence of transient severe motion. In this article, we identify the challenges in obtaining high-quality arterial-phase images of gadoxetate disodium-enhanced liver MR imaging and present strategies for optimizing arterial-phase imaging based on the thorough review of recent research in this field