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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.

    

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2. The Direct-method Oxygen Abundance of Typical Dwarf Galaxies at Cosmic High Noon∗

   https://doi.org/10.3847/1538-4357/acb153  

   Gburek, Timothy ; Siana, Brian ; Alavi, Anahita ; Emami, Najmeh ; Richard, Johan ; Freeman, William R. ; Stark, Daniel P. ; Snapp-Kolas, Christopher ( May 2023 , The Astrophysical Journal)

   We present a Keck/MOSFIRE rest-optical composite spectrum of 16 typical gravitationally lensed star-forming dwarf galaxies at 1.7 ≲z≲ 2.6 (z_mean= 2.30), all chosen independent of emission-line strength. These galaxies have a median stellar mass of$\log {(M_{*}/M_{\odot })}_{\mathrm{med}}={8.29}_{-0.43}^{+0.51}$and a median star formation rate of${\mathrm{S}\mathrm{F}\mathrm{R}}_{\mathrm{H}\alpha }^{\mathrm{m}\mathrm{e}\mathrm{d}}={2.25}_{-1.26}^{+2.15}{M}_{\odot }{\mathrm{y}\mathrm{r}}^{-1}$. We measure the faint electron-temperature-sensitive [Oiii]λ4363 emission line at 2.5σ(4.1σ) significance when considering a bootstrapped (statistical-only) uncertainty spectrum. This yields a direct-method oxygen abundance of$12+\log {(\mathrm{O}/\mathrm{H})}_{\mathrm{direct}}={7.88}_{-0.22}^{+0.25}$(${0.15}_{-0.06}^{+0.12}{Z}_{\odot }$). We investigate the applicability at highzof locally calibrated oxygen-based strong-line metallicity relations, finding that the local reference calibrations of Bian et al. best reproduce (≲0.12 dex) our composite metallicity at fixed strong-line ratio. At fixedM_*, our composite is well represented by thez∼ 2.3 direct-method stellar mass—gas-phase metallicity relation (MZR) of Sanders et al. When comparing to predicted MZRs from the IllustrisTNG and FIRE simulations, having recalculated our stellar masses with more realistic nonparametric star formation histories$(\log {(M_{*}/M_{\odot })}_{\mathrm{med}}={8.92}_{-0.22}^{+0.31})$, we find excellent agreement with the FIRE MZR. Our composite is consistent with no metallicity evolution, at fixedM_*and SFR, of the locally defined fundamental metallicity relation. We measure the doublet ratio [Oii]λ3729/[Oii]λ3726 = 1.56 ± 0.32 (1.51 ± 0.12) and a corresponding electron density of$n_e=1_{-0}^{+215}{\mathrm{cm}}^{-3}$($n_e=1_{-0}^{+74}{\mathrm{cm}}^{-3}$) when considering the bootstrapped (statistical-only) error spectrum. This result suggests that lower-mass galaxies have lower densities than higher-mass galaxies atz∼ 2.

    

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3. The Evolving Effect of Cosmic Web Environment on Galaxy Quenching

   https://doi.org/10.3847/1538-4357/acd11c  

   Hasan, Farhanul ; Burchett, Joseph N. ; Abeyta, Alyssa ; Hellinger, Douglas ; Mandelker, Nir ; Primack, Joel R. ; Faber, S. M. ; Koo, David C. ; Elek, Oskar ; Nagai, Daisuke ( June 2023 , The Astrophysical Journal)

   We investigate how cosmic web structures affect galaxy quenching in the IllustrisTNG (TNG100) cosmological simulations by reconstructing the cosmic web within each snapshot using the DisPerSE framework. We measure the comoving distance from each galaxy with stellar mass$\log (M_{*}/M_{\odot })\ge 8$to the nearest node (d_node) and the nearest filament spine (d_fil) to study the dependence of both the median specific star formation rate (〈sSFR〉) and the median gas fraction (〈f_gas〉) on these distances. We find that the 〈sSFR〉 of galaxies is only dependent on the cosmic web environment atz< 2, with the dependence increasing with time. Atz≤ 0.5,$8\le \log (M_{*}/M_{\odot })<9$galaxies are quenched atd_node≲ 1 Mpc, and have significantly suppressed star formation atd_fil≲ 1 Mpc, trends driven mostly by satellite galaxies. Atz≤ 1, in contrast to the monotonic drop in 〈sSFR〉 of$\log (M_{*}/M_{\odot })<10$galaxies with decreasingd_nodeandd_fil,$\log (M_{*}/M_{\odot })\ge 10$galaxies—both centrals and satellites—experience an upturn in 〈sSFR〉 atd_node≲ 0.2 Mpc. Much of this cosmic web dependence of star formation activity can be explained by an evolution in 〈f_gas〉. Our results suggest that in the past ∼10 Gyr, low-mass satellites are quenched by rapid gas stripping in dense environments near nodes and gradual gas starvation in intermediate-density environments near filaments. At earlier times, cosmic web structures efficiently channeled cold gas into most galaxies. State-of-the-art ongoing spectroscopic surveys such as the Sloan Digital Sky Survey and DESI, as well as those planned with the Subaru Prime Focus Spectrograph, JWST, and Roman, are required to test our predictions against observations.

    

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4. A Luminous Red Supergiant and Dusty Long-period Variable Progenitor for SN 2023ixf

   https://doi.org/10.3847/2041-8213/ace618  

   Jencson, Jacob E. ; Pearson, Jeniveve ; Beasor, Emma R. ; Lau, Ryan M. ; Andrews, Jennifer E. ; Bostroem, K. Azalee ; Dong 董, Yize 一泽 ; Engesser, Michael ; Gomez, Sebastian ; Guolo, Muryel ; et al ( July 2023 , The Astrophysical Journal Letters)

   We analyze pre-explosion near- and mid-infrared (IR) imaging of the site of SN 2023ixf in the nearby spiral galaxy M101 and characterize the candidate progenitor star. The star displays compelling evidence of variability with a possible period of ≈1000 days and an amplitude of Δm≈ 0.6 mag in extensive monitoring with the Spitzer Space Telescope since 2004, likely indicative of radial pulsations. Variability consistent with this period is also seen in the near-IRJandK_sbands between 2010 and 2023, up to just 10 days before the explosion. Beyond the periodic variability, we do not find evidence for any IR-bright pre-supernova outbursts in this time period. The IR brightness ($M_{K_s}=-10.7$mag) and color (J−K_s= 1.6 mag) of the star suggest a luminous and dusty red supergiant. Modeling of the phase-averaged spectral energy distribution (SED) yields constraints on the stellar temperature ($T_{\mathrm{eff}}={3500}_{-1400}^{+800}$K) and luminosity ($\log L/L_{\odot }=5.1\pm 0.2$). This places the candidate among the most luminous Type II supernova progenitors with direct imaging constraints, with the caveat that many of these rely only on optical measurements. Comparison with stellar evolution models gives an initial mass ofM_init= 17 ± 4M_⊙. We estimate the pre-supernova mass-loss rate of the star between 3 and 19 yr before explosion from the SED modeling at$\dot{M}\approx 3\times {10}^{-5}$to 3 × 10⁻⁴M_⊙yr⁻¹for an assumed wind velocity ofv_w= 10 km s⁻¹, perhaps pointing to enhanced mass loss in a pulsation-driven wind.

    

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5. 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 polynomial 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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