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1. Efficient Computation of Sequence Mappability

   https://doi.org/10.1007/s00453-022-00934-y  

   Charalampopoulos, Panagiotis ; Iliopoulos, Costas S. ; Kociumaka, Tomasz ; Pissis, Solon P. ; Radoszewski, Jakub ; Straszyński, Juliusz ( February 2022 , Algorithmica)

   Sequence mappability is an important task in genome resequencing. In the (k, m)-mappability problem, for a given sequenceTof lengthn, the goal is to compute a table whoseith entry is the number of indices$$j \ne i$$$j\ne i$such that the length-msubstrings ofTstarting at positionsiandjhave at mostkmismatches. Previous works on this problem focused on heuristics computing a rough approximation of the result or on the case of$$k=1$$$k=1$. We present several efficient algorithms for the general case of the problem. Our main result is an algorithm that, for$$k=O(1)$$$k=O\left(1\right)$, works in$$O(n)$$$O\left(n\right)$space and, with high probability, in$$O(n \cdot \min \{m^k,\log ^k n\})$$$O(n·min\{m^k,{log}^{k}n\})$time. Our algorithm requires a careful adaptation of thek-errata trees of Cole et al. [STOC 2004] to avoid multiple counting of pairs of substrings. Our technique can also be applied to solve the all-pairs Hamming distance problem introduced by Crochemore et al. [WABI 2017]. We further develop$$O(n^2)$$$O\left(n^2\right)$-time algorithms to computeall(k, m)-mappability tables for a fixedmand all$$k\in \{0,\ldots ,m\}$$$k\in \{0,\dots ,m\}$or a fixedkand all$$m\in \{k,\ldots ,n\}$$$m\in \{k,\dots ,n\}$. Finally, we show that, for$$k,m = \Theta (\log n)$$$k,m=\Theta (logn)$, the (k, m)-mappability problem cannot be solved in strongly subquadratic time unless the Strong Exponential Time Hypothesis fails. This is an improved and extended version of a paper presented at SPIRE 2018.
2. Lower Bounds Against Sparse Symmetric Functions of ACC Circuits: Expanding the Reach of #SAT Algorithms

   https://doi.org/10.1007/s00224-022-10106-8  

   Vyas, Nikhil ; Williams, R. Ryan ( November 2022 , Theory of Computing Systems)

   We continue the program of proving circuit lower bounds via circuit satisfiability algorithms. So far, this program has yielded several concrete results, proving that functions in$\mathsf {Quasi}\text {-}\mathsf {NP} = \mathsf {NTIME}[n^{(\log n)^{O(1)}}]$$\mathrm{Quasi}-\mathrm{NP}=\mathrm{NTIME}\left[n^{{\left(\log n\right)}^{O\left(1\right)}}\right]$and other complexity classes do not have small circuits (in the worst case and/or on average) from various circuit classes$\mathcal { C}$$C$, by showing that$\mathcal { C}$$C$admits non-trivial satisfiability and/or#SAT algorithms which beat exhaustive search by a minor amount. In this paper, we present a new strong lower bound consequence of having a non-trivial#SAT algorithm for a circuit class${\mathcal C}$$C$. Say that a symmetric Boolean functionf(x₁,…,x_n) issparseif it outputs 1 onO(1) values of${\sum }_{i} x_{i}$${\sum }_i{x}_i$. We show that for every sparsef, and for all “typical”$\mathcal { C}$$C$, faster#SAT algorithms for$\mathcal { C}$$C$circuits imply lower bounds against the circuit class$f \circ \mathcal { C}$$f\circ C$, which may bestrongerthan$\mathcal { C}$$C$itself. In particular:

   #SAT algorithms forn^k-size$\mathcal { C}$$C$-circuits running in 2ⁿ/n^ktime (for allk) implyNEXPdoes not have$(f \circ \mathcal { C})$$(f\circ C)$-circuits of polynomial size.

   #SAT algorithms for$2^{n^{{\varepsilon }}}$$2^{n^{\epsilon }}$-size$\mathcal { C}$$C$-circuits running in$2^{n-n^{{\varepsilon }}}$$2^{n-n^{\epsilon }}$time (for someε> 0) implyQuasi-NPdoes not have$(f \circ \mathcal { C})$$(f\circ C)$-circuits of polynomial size.

   Applying#SAT algorithms from the literature, one immediate corollary of our results is thatQuasi-NPdoes not haveEMAJ∘ACC⁰∘THRcircuits of polynomialmore »size, whereEMAJis the “exact majority” function, improving previous lower bounds againstACC⁰[Williams JACM’14] andACC⁰∘THR[Williams STOC’14], [Murray-Williams STOC’18]. This is the first nontrivial lower bound against such a circuit class.

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3. The Bimodal Absorption System Imaging Campaign (BASIC). I. A Dual Population of Low-metallicity Absorbers at z < 1

   https://doi.org/10.3847/1538-4357/acb047  

   Berg, Michelle A. ; Lehner, Nicolas ; Howk, J. Christopher ; O’Meara, John M. ; Schaye, Joop ; Straka, Lorrie A. ; Cooksey, Kathy L. ; Tripp, Todd M. ; Prochaska, J. Xavier ; Oppenheimer, Benjamin D. ; et al ( February 2023 , The Astrophysical Journal)

   The bimodal absorption system imaging campaign (BASIC) aims to characterize the galaxy environments of a sample of 36 Hi-selected partial Lyman limit systems (pLLSs) and Lyman limit systems (LLSs) in 23 QSO fields atz≲ 1. These pLLSs/LLSs provide a unique sample of absorbers with unbiased and well-constrained metallicities, allowing us to explore the origins of metal-rich and low-metallicity circumgalactic medium (CGM) atz< 1. Here we present Keck/KCWI and Very Large Telescope/MUSE observations of 11 of these QSO fields (19 pLLSs) that we combine with Hubble Space Telescope/Advanced Camera for Surveys imaging to identify and characterize the absorber-associated galaxies at 0.16 ≲z≲ 0.84. We find 23 unique absorber-associated galaxies, with an average of one associated galaxy per absorber. For seven absorbers, all with <10% solar metallicities, we find no associated galaxies with$\log M_{\star }\gtrsim 9.0$withinρ/R_virand ∣Δv∣/v_esc≤ 1.5 with respect to the absorber. We do not find any strong correlations between the metallicities or Hicolumn densities of the gas and most of the galaxy properties, except for the stellar mass of the galaxies: the low-metallicity ([X/H] ≤ −1.4) systems have a probability of${0.39}_{-0.15}^{+0.16}$for having a host galaxy with$\log M_{\star }\ge 9.0$withinρ/R_vir≤ 1.5, while the higher metallicity absorbers havemore »a probability of${0.78}_{-0.13}^{+0.10}$. This implies metal-enriched pLLSs/LLSs atz< 1 are typically associated with the CGM of galaxies with$\log M_{\star }>9.0$, whereas low-metallicity pLLSs/LLSs are found in more diverse locations, with one population arising in the CGM of galaxies and another more broadly distributed in overdense regions of the universe. Using absorbers not associated with galaxies, we estimate the unweighted geometric mean metallicity of the intergalactic medium to be [X/H] ≲ −2.1 atz< 1, which is lower than previously estimated.

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4. Hydrogen bonding steers the product selectivity of electrocatalytic CO reduction

   https://doi.org/10.1073/pnas.1900761116  

   Li, Jingyi ; Li, Xiang ; Gunathunge, Charuni M. ; Waegele, Matthias M. ( April 2019 , Proceedings of the National Academy of Sciences)

   The product selectivity of many heterogeneous electrocatalytic processes is profoundly affected by the liquid side of the electrocatalytic interface. The electrocatalytic reduction of CO to hydrocarbons on Cu electrodes is a prototypical example of such a process. However, probing the interactions of surface-bound intermediates with their liquid reaction environment poses a formidable experimental challenge. As a result, the molecular origins of the dependence of the product selectivity on the characteristics of the electrolyte are still poorly understood. Herein, we examined the chemical and electrostatic interactions of surface-adsorbed CO with its liquid reaction environment. Using a series of quaternary alkyl ammonium cations (${\mathrm{m}\mathrm{e}\mathrm{t}\mathrm{h}\mathrm{y}\mathrm{l}}_4{\mathrm{N}}^{+}$,${\mathrm{e}\mathrm{t}\mathrm{h}\mathrm{y}\mathrm{l}}_4{\mathrm{N}}^{+}$,${\mathrm{p}\mathrm{r}\mathrm{o}\mathrm{p}\mathrm{y}\mathrm{l}}_4{\mathrm{N}}^{+}$, and${\mathrm{b}\mathrm{u}\mathrm{t}\mathrm{y}\mathrm{l}}_4{\mathrm{N}}^{+}$), we systematically tuned the properties of this environment. With differential electrochemical mass spectrometry (DEMS), we show that ethylene is produced in the presence of${\mathrm{m}\mathrm{e}\mathrm{t}\mathrm{h}\mathrm{y}\mathrm{l}}_4{\mathrm{N}}^{+}$and${\mathrm{e}\mathrm{t}\mathrm{h}\mathrm{y}\mathrm{l}}_4{\mathrm{N}}^{+}$cations, whereas this product is not synthesized in${\mathrm{p}\mathrm{r}\mathrm{o}\mathrm{p}\mathrm{y}\mathrm{l}}_4{\mathrm{N}}^{+}$- and${\mathrm{b}\mathrm{u}\mathrm{t}\mathrm{y}\mathrm{l}}_4{\mathrm{N}}^{+}$-containing electrolytes. Surface-enhanced infrared absorption spectroscopymore »(SEIRAS) reveals that the cations do not block CO adsorption sites and that the cation-dependent interfacial electric field is too small to account for the observed changes in selectivity. However, SEIRAS shows that an intermolecular interaction between surface-adsorbed CO and interfacial water is disrupted in the presence of the two larger cations. This observation suggests that this interaction promotes the hydrogenation of surface-bound CO to ethylene. Our study provides a critical molecular-level insight into how interactions of surface species with the liquid reaction environment control the selectivity of this complex electrocatalytic process.

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5. Magellan/IMACS Spectroscopy of Grus I: A Low Metallicity Ultra-faint Dwarf Galaxy*

   https://doi.org/10.3847/1538-4357/ac96ed  

   Chiti, Anirudh ; Simon, Joshua D. ; Frebel, Anna ; Pace, Andrew B. ; Ji, Alexander P. ; Li, Ting S. ( November 2022 , The Astrophysical Journal)

   We present a chemodynamical study of the Grus I ultra-faint dwarf galaxy (UFD) from medium-resolution (R∼ 11,000) Magellan/IMACS spectra of its individual member stars. We identify eight confirmed members of Grus I, based on their low metallicities and coherent radial velocities, and four candidate members for which only velocities are derived. In contrast to previous work, we find that Grus I has a very low mean metallicity of 〈[Fe/H]〉 = −2.62 ± 0.11 dex, making it one of the most metal-poor UFDs. Grus I has a systemic radial velocity of −143.5 ± 1.2 km s⁻¹and a velocity dispersion of${\sigma }_{\mathrm{rv}}={2.5}_{-0.8}^{+1.3}$km s⁻¹, which results in a dynamical mass of$M_{1/2}(r_h)=8_{-4}^{+12}\times {10}^5$M_⊙and a mass-to-light ratio ofM/L_V=${440}_{-250}^{+650}$M_⊙/L_⊙. Under the assumption of dynamical equilibrium, our analysis confirms that Grus I is a dark-matter-dominated UFD (M/L> 80M_⊙/L_⊙). However, we do not resolve a metallicity dispersion (σ_[Fe/H]< 0.44 dex). Our results indicate that Grus I is a fairly typical UFD with parameters that agree with mass–metallicity and metallicity-luminosity trends for faint galaxies. This agreement suggests that Grus I has not lost an especially significant amount of mass from tidal encounters with the Milky Way, in linemore »with its orbital parameters. Intriguingly, Grus I has among the lowest central densities (${\rho }_{1/2}\sim {3.5}_{-2.1}^{+5.7}\times {10}^7$M_⊙kpc⁻³) of the UFDs that are not known to be tidally disrupting. Models of the formation and evolution of UFDs will need to explain the diversity of these central densities, in addition to any diversity in the outer regions of these relic galaxies.

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