• Boosting the accuracy of protein secondary structure prediction through nearest neighbor search and method hybridization

      Krieger, Spencer; Kececioglu, John; Univ Arizona, Dept Comp Sci (Oxford University Press (OUP), 2020-07-13)
      Motivation: Protein secondary structure prediction is a fundamental precursor to many bioinformatics tasks. Nearly all state-of-the-art tools when computing their secondary structure prediction do not explicitly leverage the vast number of proteins whose structure is known. Leveraging this additional information in a so-called template-based method has the potential to significantly boost prediction accuracy. Method: We present a new hybrid approach to secondary structure prediction that gains the advantages of both template- and non-template-based methods. Our core template-based method is an algorithmic approach that uses metric-space nearest neighbor search over a template database of fixed-length amino acid words to determine estimated class-membership probabilities for each residue in the protein. These probabilities are then input to a dynamic programming algorithm that finds a physically valid maximum-likelihood prediction for the entire protein. Our hybrid approach exploits a novel accuracy estimator for our core method, which estimates the unknown true accuracy of its prediction, to discern when to switch between template- and non-template-based methods. Results: On challenging CASP benchmarks, the resulting hybrid approach boosts the state-of-the-art Q(8) accuracy by more than 2-10%, and Q(3) accuracy by more than 1-3%, yielding the most accurate method currently available for both 3- and 8-state secondary structure prediction.
    • COVID-19 symptoms and SARS-CoV-2 antibody positivity in a large survey of first responders and healthcare personnel, May-July 2020

      Akinbami, Lara J; Petersen, Lyle R; Sami, Samira; Vuong, Nga; Lukacs, Susan L; Mackey, Lisa; Atas, Jenny; LaFleur, Bonnie J; BIO5 Institute, University of Arizona (Oxford University Press (OUP), 2021-01-30)
      A SARS-CoV-2 serosurvey among first responder/healthcare personnel showed that loss of taste/smell was most predictive of seropositivity; percent seropositivity increased with number of COVID-19 symptoms. However, 22.9% with nine symptoms were seronegative, and 8.3% with no symptoms were seropositive. These findings demonstrate limitations of symptom-based surveillance and importance of testing.
    • Emulating galaxy clustering and galaxy–galaxy lensing into the deeply non-linear regime: methodology, information, and forecasts

      Wibking, Benjamin D; Salcedo, Andrés N; Weinberg, David H; Garrison, Lehman H; Ferrer, Douglas; Tinker, Jeremy; Eisenstein, Daniel; Metchnik, Marc; Pinto, Philip; Univ Arizona, Steward Observ (Oxford University Press (OUP), 2019-03)
      The combination of galaxy-galaxy lensing (GGL) with galaxy clustering is one of the most promising routes to determining the amplitude of matter clustering at low redshifts. We show that extending clustering+GGL analyses from the linear regime down to similar to 0.5 h(-1) Mpc scales increases their constraining power considerably, even after marginalizing over a flexible model of non-linear galaxy bias. Using a grid of cosmological N-body simulations, we construct a Taylor-expansion emulator that predicts the galaxy autocorrelation xi(gg)(r) and galaxy-matter cross-correlation xi(gm) (r) as a function of sigma(8), Omega(m), and halo occupation distribution (HOD) parameters, which are allowed to vary with large-scale environment to represent possible effects of galaxy assembly bias. We present forecasts for a fiducial case that corresponds to BOSS LOWZ galaxy clustering and SDSS-depth weak lensing (effective source density similar to 0.3 arcmin(-2)). Using tangential shear and projected correlation function measurements over 0.5 <= r(p) <= 30h(-1) Mpc yields a 2 per cent constraint on the parameter combination sigma(8)Omega(0.6)(m), a factor of two better than a constraint that excludes non-linear scales (r(p) > 2 h(-1) Mpc, 4 h(-1) Mpc for gamma(t) , omega(p)). Much of this improvement comes from the non-linear clustering information, which breaks degeneracies among HOD parameters. Increasing the effective source density to 3 arcmin(-2) sharpens the constraint on sigma(8)Omega(0.6 )(m)by a further factor of two. With robust modelling into the non-linear regime, low-redshift measurements of matter clustering at the 1-per cent level with clustering+GGL alone are well within reach of current data sets such as those provided by the Dark Energy Survey.
    • Instantons and Bows for the Classical Groups

      Cherkis, Sergey A; Hurtubise, Jacques; Department of Mathematics, University of Arizona (Oxford University Press (OUP), 2020-11-26)
      The construction of Atiyah, Drinfeld, Hitchin and Manin provided complete description of all instantons on Euclidean four-space. It was extended by Kronheimer and Nakajima to instantons on ALE spaces, resolutions of orbifolds R4 Γ by a finite subgroup ΓSU(2). We consider a similar classification, in the holomorphic context, of instantons on some of the next spaces in the hierarchy, the ALF multi-Taub-NUT manifolds, showing how they tie in to the bow solutions to Nahm's equations via the Nahm correspondence. Recently Nakajima and Takayama constructed the Coulomb branch of the moduli space of vacua of a quiver gauge theory, tying them to the same space of bow solutions. One can view our construction as describing the same manifold as the Higgs branch of the mirror gauge theory as described by Cherkis, O'Hara and Saemann. Our construction also yields the monad construction of holomorphic instanton bundles on the multi-Taub-NUT space for any classical compact Lie structure group.
    • A New Multilateralism? A Case Study of the Belt and Road Initiative

      Zhou, Jingyuan; James E. Rogers College of Law, University of Arizona (Oxford University Press (OUP), 2020-08-30)
      The first five years (the first stage) of the Belt and Road Initiative (BRI) have drawn international attention and provoked scepticism and debate. This article explores questions about the nature of the BRI and its impact on multilateralism, which is increasingly fragile and under attack. After summarizing past practices employed in BRI investments, it analyses the characteristics of the BRI and assesses the results and implications. This article studies in depth one of the two primary BRI economic activities—special economic zones. The article introduces and compares the Asian Infrastructure Investment Bank and Chinese domestic banks in their respective financing practices and compares state-owned enterprises and privately owned enterprises in BRI practices. The article observes three characteristics from past BRI practices and analyzes their respective implications on the transformation of international trade governance. The first characteristic is the unconventional ‘infrastructure development first, institution next’ approach. The second is the plurilateral- and multilateral-focused method in international rule-setting processes. The third characteristic is innovation in the dispute settlement mechanism. Through a cautious examination, the article argues that experiences gained from BRI inform China’s international rule-making efforts and further its domestic trade liberalization reform agenda, which will likely contribute to the convergence of rule-making in international trade. © The Author(s) (2020). Published by Oxford University Press. All rights reserved.