HDIdx: High-Dimensional Indexing for Efficient Approximate Nearest Neighbor Search

Fast Nearest Neighbor (NN) search is a fundamental challenge in large-scale data processing and analytics, particularly for analyzing multimedia contents which are often of high dimensionality. Instead of using exact NN search, extensive research efforts have been focusing on approximate NN search algorithms. In this work, we present "HDIdx", an efficient high-dimensional indexing library for fast approximate NN search, which is open-source and written in Python. It offers a family of state-of-the-art algorithms that convert input high-dimensional vectors into compact binary codes, making them very efficient and scalable for NN search with very low space complexity

Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning

Sonic hedgehog (Shh) acts as a morphogen to mediate the specification of distinct cell identities in the ventral neural tube through a Gli-mediated (Gli1-3) transcriptional network. Identifying Gli targets in a systematic fashion is central to the understanding of the action of Shh. We examined this issue in differentiating neural progenitors in mouse. An epitope-tagged Gli-activator protein was used to directly isolate cis-regulatory sequences by chromatin immunoprecipitation (ChIP). ChIP products were then used to screen custom genomic tiling arrays of putative Hedgehog (Hh) targets predicted from transcriptional profiling studies, surveying 50-150 kb of non-transcribed sequence for each candidate. In addition to identifying expected Gli-target sites, the data predicted a number of unreported direct targets of Shh action. Transgenic analysis of binding regions in Nkx2.2, Nkx2.1 (Titf1) and Rab34 established these as direct Hh targets. These data also facilitated the generation of an algorithm that improved in silico predictions of Hh target genes. Together, these approaches provide significant new insights into both tissue-specific and general transcriptional targets in a crucial Shh-mediated patterning process

Ground state energy of unitary fermion gas with the Thomson Problem approach

The dimensionless universal coefficient $\xi$ defines the ratio of the unitary fermions energy density to that for the ideal non-interacting ones in the non-relativistic limit with T=0. The classical Thomson Problem is taken as a nonperturbative quantum many-body arm to address the ground state energy including the low energy nonlinear quantum fluctuation/correlation effects. With the relativistic Dirac continuum field theory formalism, the concise expression for the energy density functional of the strongly interacting limit fermions at both finite temperature and density is obtained. Analytically, the universal factor is calculated to be $\xi={4/9}$. The energy gap is \Delta=\frac{{5}{18}{k_f^2}/(2m).Comment: Identical to published version with revisions according to comment

Top Quark Decays into Heavy Quark Mesons

For top quark decays into heavy quark mesons $\Upsilon$ and $\bar{B}_c^*$ , a complete calculation to the leading order both in QCD coupling constant $\alpha_s$ and in $v$, the typical velocity of the heavy quarks inside the mesons, is performed. Relatons between the top quark mass and the decay branching ratios are studied. Comparion with the results which are obtained by using the quark frangmentation functions is also discussed. The branching ratios are consistent (within a factor of $2\sim 3$) with that obtained using fragmentation functions at $m_t\sim 150$ GeV.Comment: 15 pages in LaTex form, 4 figures include

DD-dimensions Dirac fermions BEC-BCS cross-over thermodynamics

An effective Proca Lagrangian action is used to address the vector condensation Lorentz violation effects on the equation of state of the strongly interacting fermions system. The interior quantum fluctuation effects are incorporated as an external field approximation indirectly through a fictive generalized Thomson Problem counterterm background. The general analytical formulas for the $d$-dimensions thermodynamics are given near the unitary limit region. In the non-relativistic limit for $d=3$, the universal dimensionless coefficient $\xi ={4}/{9}$ and energy gap $\Delta/\epsilon_f ={5}/{18}$ are reasonably consistent with the existed theoretical and experimental results. In the unitary limit for $d=2$ and T=0, the universal coefficient can even approach the extreme occasion $\xi=0$ corresponding to the infinite effective fermion mass $m^*=\infty$ which can be mapped to the strongly coupled two-dimensions electrons and is quite similar to the three-dimensions Bose-Einstein Condensation of ideal boson gas. Instead, for $d=1$, the universal coefficient $\xi$ is negative, implying the non-existence of phase transition from superfluidity to normal state. The solutions manifest the quantum Ising universal class characteristic of the strongly coupled unitary fermions gas.Comment: Improved versio

Next-to-leading order QCD predictions for Z0H0+jetZ^0 H^0 + {\rm jet} production at LHC

We calculate the complete next-to-leading order (NLO) QCD corrections to the $Z^0H^0$ production in association with a jet at the LHC. We study the impacts of the NLO QCD radiative corrections to the integrated and differential cross sections and the dependence of the cross section on the factorization/renormalization scale. We present the transverse momentum distributions of the final $Z^0$-, Higgs-boson and leading-jet. We find that the NLO QCD corrections significantly modify the physical observables, and obviously reduce the scale uncertainty of the LO cross section. The QCD K-factors can be 1.183 and 1.180 at the $\sqrt{s}=14 TeV$ and $\sqrt{s}=7 TeV$ LHC respectively, when we adopt the inclusive event selection scheme with $p_{T,j}^{cut}=50 GeV$, $m_H=120 GeV$ and $\mu=\mu_r=\mu_f=\mu_0 \equiv 1/2(m_Z+m_H)$. Furthermore, we make the comparison between the two scale choices, $\mu=\mu_0$ and $\mu=\mu_1=1/2(E_{T}^{Z}+E_{T}^{H}+ \sum_{j}E_{T}^{jet})$, and find the scale choice $\mu=\mu_1$ seems to be more appropriate than the fixed scale $\mu=\mu_0$.Comment: 18 pages, 7 figure

Grey scale enhancement by a new self-made contrast agent in early cirrhotic stage of rabbit liver

<p>Abstract</p> <p>Background</p> <p>The development of new ultrasound contrast agents (UCAs) has become one of the most promising fields in ultrasound medicine. This paper evaluates a new self-made contrast agent enhancement effect developed to study the fibrotic stages of the liver in perfusion models <it>in vivo</it>.</p> <p>Methods</p> <p>We constructed experimental models of hepatic fibrosis involving five stages from F0 to F4 via administration of CCL₄(0.01 ml/kg BW) every 3 days for 3 months. The intrahepatic circulatory time of the contrast agent was analyzed via an image and Cine-loop display. Calculations of the perfusion-related parameters including the peak signal intensity (PSI) and peak signal intensity time (PIT) of the portal vein and parenchyma were obtained from an analysis of the time-acoustic intensity curve.</p> <p>Results</p> <p>Hepatic artery to vein transmit time (HA-HVTT) was significantly shorter at F4 stage (mean 5.1 seconds) compared with those in other stages (mean 8.3 s, 7.5 s, 6.9 s, 6.6 s, P < 0.01). The average PSI difference of PV-parenchyma was 13.62 dB in F4 stage, demonstrating significant differences between F4 stage and other early stages (P < 0.001).</p> <p>Conclusion</p> <p>These results indicate that the new self-made contrast agent is capable of indicating intrahepatic hemodynamic changes. HA-HVTT and the PSI difference of the microbubble perfusion in liver parenchyma and PV were considered to differentiate the degree of hepatic fibrosis between F4 and other early stages.</p

Nonlinear Optical Microscopy of Murine Abdominal Aortic Aneurysm

Abdominal aortic aneurysm (AAA) is a cardiovascular disease characterized by dilation and weakening of the vessel wall. AAA rupture is responsible for approximately 14,000 deaths annually in the United States [1]. Nonlinear optical (NLO) microscopy presents new possibilities for analyzing AAA tissue samples from murine models. Common NLO techniques are two-photon excitation fluorescence (TPEF), which detects the intrinsic autofluorescent properties of elastin, and second-harmonic generation (SHG), which is specific for collagen fibrils. Elastin and collagen, two major extracellular matrix components, help the aortic wall withstand internal pressure. Murine AAAs were created through 1) subcutaneous continuous systemic infusion of angiotensin II (AngII) in hyperlipidemic apolipoprotein E-deficient mice and 2) by intraluminal infusion of elastase (low 0.5 U/ml and high 25 U/ml concentrations) into the infrarenal aorta of rats [2]. We imaged aneurysmal and control tissue using TPEF and SHG and compared the resulting images to sections stained with standard elastin and collagen markers. TPEF images revealed disorganized elastin sheets and SHG images indicated collagen turnover after aneurysm formation. We quantified the relative degree of elastin degradation and collagen content in the aortic media within a user-defined area on sections stained with Verhoeff-van Gieson (VVG) or Masson’s trichrome (MTC), as well as on TPEF and SHG images. Our analysis with VVG-stained sections shows that elastin content in AAA tissue is significantly decreased by 64% in AngII models (P=0.02), by 34% in low concentration elastase models (P=0.07), and by 99% in high concentration elastase models (P=0.03), relative to control aortic tissue

Dispersion relation of the ρ\rho meson in hot/dense nuclear matter

The dispersion relation of $\rho$ meson in both timelike and spacelike regimes in hot and dense nuclear medium is analyzed and compared with $\sigma$ meson based on the quantum hadrodynamics model. The pole and screening masses of $\rho$ and $\sigma$ are discussed. The behavior of screening mass of $\rho$ is different from that of $\sigma$ due to different Dirac- and Fermi-sea contributions at finite temperature and density.Comment: 4 pages, 3 figures, identical to published versio