Conformational Dependence of a Protein Kinase Phosphate Transfer Reaction

Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase (PKA) are calculated by plane-wave density functional theory, starting from structures of proteins crystallized in both the reactant conformation (RC) and the transition-state conformation (TC). In the TC, we calculate that the reactants and products are nearly isoenergetic with a 0.2 eV barrier; while phosphate transfer is unfavorable by over 1.2 eV in the RC, with an even higher barrier. With the protein in the TC, the motions involved in reaction are small, with only P$_\gamma$ and the catalytic proton moving more than 0.5 \AA. Examination of the structures reveals that in the RC the active site cleft is not completely closed and there is insufficient space for the phosphorylated serine residue in the product state. Together, these observations imply that the phosphate transfer reaction occurs rapidly and reversibly in a particular conformation of the protein, and that the reaction can be gated by changes of a few tenths of an \AA in the catalytic site.Comment: revtex4, 7 pages, 4 figures, to be submitted to Scienc

Weakly Supervised Universal Fracture Detection in Pelvic X-rays

Hip and pelvic fractures are serious injuries with life-threatening complications. However, diagnostic errors of fractures in pelvic X-rays (PXRs) are very common, driving the demand for computer-aided diagnosis (CAD) solutions. A major challenge lies in the fact that fractures are localized patterns that require localized analyses. Unfortunately, the PXRs residing in hospital picture archiving and communication system do not typically specify region of interests. In this paper, we propose a two-stage hip and pelvic fracture detection method that executes localized fracture classification using weakly supervised ROI mining. The first stage uses a large capacity fully-convolutional network, i.e., deep with high levels of abstraction, in a multiple instance learning setting to automatically mine probable true positive and definite hard negative ROIs from the whole PXR in the training data. The second stage trains a smaller capacity model, i.e., shallower and more generalizable, with the mined ROIs to perform localized analyses to classify fractures. During inference, our method detects hip and pelvic fractures in one pass by chaining the probability outputs of the two stages together. We evaluate our method on 4 410 PXRs, reporting an area under the ROC curve value of 0.975, the highest among state-of-the-art fracture detection methods. Moreover, we show that our two-stage approach can perform comparably to human physicians (even outperforming emergency physicians and surgeons), in a preliminary reader study of 23 readers.Comment: MICCAI 2019 (early accept

Predictions for s-Wave and p-Wave Heavy Baryons from Sum Rules and Constituent Quark Model (I): Strong Interactions

We study the strong interactions of the L=1 orbitally excited baryons with one heavy quark in the framework of the Heavy Hadron Chiral Perturbation Theory. To leading order in the heavy mass expansion, the interaction Lagrangian describing the couplings of these states among themselves and with the ground state heavy baryons contains 46 unknown couplings. We derive sum rules analogous to the Adler-Weisberger sum rule which constrain these couplings and relate them to the couplings of the s-wave heavy baryons. Using a spin 3/2 baryon as a target, we find a sum rule expressing the deviation from the quark model prediction for pion couplings to s-wave states in terms of couplings of the p-wave states. In the constituent quark model these couplings are related and can be expressed in terms of only two reduced matrix elements. Using recent CLEO data on $\Sigma_c^{*}$ and $\Lambda_{c1}^+$ strong decays, we determine some of the unknown couplings in the chiral Lagrangian and the two quark model reduced matrix elements. Specific predictions are made for the decay properties of all L=1 charmed baryons.Comment: 50 pages, REVTeX with 4 included figures; predictions for additional decay modes included; 1 reference adde

Geometric Aspects of the Moduli Space of Riemann Surfaces

This is a survey of our recent results on the geometry of moduli spaces and Teichmuller spaces of Riemann surfaces appeared in math.DG/0403068 and math.DG/0409220. We introduce new metrics on the moduli and the Teichmuller spaces of Riemann surfaces with very good properties, study their curvatures and boundary behaviors in great detail. Based on the careful analysis of these new metrics, we have a good understanding of the Kahler-Einstein metric from which we prove that the logarithmic cotangent bundle of the moduli space is stable. Another corolary is a proof of the equivalences of all of the known classical complete metrics to the new metrics, in particular Yau's conjectures in the early 80s on the equivalences of the Kahler-Einstein metric to the Teichmuller and the Bergman metric.Comment: Survey article of our recent results on the subject. Typoes corrrecte

CKM Favored Semileptonic Decays of Heavy Hadrons at Zero Recoil

We study the properties of Cabibbo-Kobayashi-Maskawa (CKM) favored semileptonic decays of mesons and baryons containing a heavy quark at the point of no recoil. We first use a diagrammatic analysis to rederive the result observed by earlier authors that at this kinematic point the $B$ meson decays via $b\to c$ transitions can only produce a $D$ or $D^*$ meson. The result is generalized to include photon emissions which violate heavy quark flavor symmetry. We show that photons emitted by the heavy quarks and the charged lepton are the only light particles that can decorate the decays $\bar{B}\to D(D^*) + \ell\nu$ at zero recoil, and the similar processes of heavy baryons. Implications for the determinations of the CKM parameter $V_{cb}$ are discussed. Also studied in this paper is the connection between our diagrammatic analysis of suppression of particle emission and the formal observation based on weak currents at zero recoil being generators of heavy quark symmetry. We show that the two approaches can be unified by considering the Isgur-Wise function in the presence of an external source.Comment: 27 pages, including 11 figures using macros FEYNMAN.te

Extracting density-density correlations from in situ images of atomic quantum gases

We present a complete recipe to extract the density-density correlations and the static structure factor of a two-dimensional (2D) atomic quantum gas from in situ imaging. Using images of non-interacting thermal gases, we characterize and remove the systematic contributions of imaging aberrations to the measured density-density correlations of atomic samples. We determine the static structure factor and report results on weakly interacting 2D Bose gases, as well as strongly interacting gases in a 2D optical lattice. In the strongly interacting regime, we observe a strong suppression of the static structure factor at long wavelengths.Comment: 15 pages, 5 figure

Effective Lagrangian Approach to Weak Radiative Decays of Heavy Hadrons

Motivated by the observation of the decay $\bar{B}\to \bar{K}^*\gamma$ by CLEO, we have systematically analyzed the two-body weak radiative decays of bottom and charmed hadrons. There exist two types of weak radiative decays: One proceeds through the short-distance $b\to s\gamma$ transition and the other occurs through $W$-exchange accompanied by a photon emission. Effective Lagrangians are derived for the $W$-exchange bremsstrahlung processes at the quark level and then applied to various weak electromagnetic decays of heavy hadrons. Predictions for the branching ratios of $\bar{B}^0\to D^{*0} \gamma,~\Lambda_b^0\to\Sigma_c^0\gamma,~\Xi_b^0\to \Xi_c^0\gamma$ and \Xi_b^0\to\xip_c^0\gamma are given. In particular, we found ${\cal B}(\bar{B}^0 \to D^{*0}\gamma)\approx 0.9\times 10^{-6}$. Order of magnitude estimates for the weak radiative decays of charmed hadrons: $~D^0\to \bar{K}^{*0}\gamma,~\Lambda_c^+\to\Sigma^+\gamma$ and $\Xi_c^0\to\Xi^0\gamma$ are also presented. Within this approach, the decay asymmetry for antitriplet to antitriplet heavy baryon weak radiative transitions is uniquely predicted by heavy quark symmetry. The electromagnetic penguin contribution to $\Lambda_b^0\to\Lambda\gamma$ is estimated by two different methods and its branching ratio is found to be of order $1\times 10^{-5}$. We conclude that weak radiative decays of bottom hadrons are dominated by the short-distance $b\to s\gamma$ mechanism.Comment: 28 pages + 3 figures (not included), CLNS 94/1278, IP-ASTP-04-94. [Main changes in this revised version: (i) Sect 2 and subsection 4.1 are revised, (ii) A MIT bag method for calculating the decay rate of $Lambda_b \to\Lambda+gamma$ is presented, (iii) All predictions are updated using the newly available 1994 Particle Data Group, and (iv) Appendix and subsections 3.3 and 4.4 are deleted.

Nonlinear and nonreciprocal transport effects in untwinned thin films of ferromagnetic Weyl metal SrRuO3_3

The identification of distinct charge transport features, deriving from nontrivial bulk band and surface states, has been a challenging subject in the field of topological systems. In topological Dirac and Weyl semimetals, nontrivial conical bands with Fermi-arc surfaces states give rise to negative longitudinal magnetoresistance due to chiral anomaly effect and unusual thickness dependent quantum oscillation from Weyl-orbit effect, which were demonstrated recently in experiments. In this work, we report the experimental observations of large nonlinear and nonreciprocal transport effects for both longitudinal and transverse channels in an untwinned Weyl metal of SrRuO$_3$ thin film grown on a SrTiO$_{3}$ substrate. From rigorous measurements with bias current applied along various directions with respect to the crystalline principal axes, the magnitude of nonlinear Hall signals from the transverse channel exhibits a simple sin$\alpha$ dependent at low temperatures, where $\alpha$ is the angle between bias current direction and orthorhombic [001]$_{\rm o}$, reaching a maximum when current is along orthorhombic [1-10]$_{\rm o}$. On the contrary, the magnitude of nonlinear and nonreciprocal signals in the longitudinal channel attains a maximum for bias current along [001]$_{\rm o}$, and it vanishes for bias current along [1-10]$_{\rm o}$. The observed $\alpha$-dependent nonlinear and nonreciprocal signals in longitudinal and transverse channels reveal a magnetic Weyl phase with an effective Berry curvature dipole along [1-10]$_{\rm o}$ from surface states, accompanied by 1D chiral edge modes along [001]$_{\rm o}$.Comment: 24 pages, 6 figure