@misc{9896, abstract = {Summary of the analysed genomes. (CSV 24 kb)}, author = {Sigalova, Olga M. and Chaplin, Andrei V. and Bochkareva, Olga and Shelyakin, Pavel V. and Filaretov, Vsevolod A. and Akkuratov, Evgeny E. and Burskaia, Valentina and Gelfand, Mikhail S.}, publisher = {Springer Nature}, title = {{Additional file 1 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction}}, doi = {10.6084/m9.figshare.9808841.v1}, year = {2019}, } @misc{9897, abstract = {Frameshift and nonsense mutations near homopolymeric tracts of OG1 genes. Only 374 genes with typical length and domain composition were considered. (CSV 6 kb)}, author = {Sigalova, Olga M. and Chaplin, Andrei V. and Bochkareva, Olga and Shelyakin, Pavel V. and Filaretov, Vsevolod A. and Akkuratov, Evgeny E. and Burskaia, Valentina and Gelfand, Mikhail S.}, publisher = {Springer Nature}, title = {{Additional file 20 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction}}, doi = {10.6084/m9.figshare.9808850.v1}, year = {2019}, } @misc{9898, abstract = {All polyN tracts of length 5 or more nucleotides in sequences of genes from OG1. Sequences were extracted and scanned prior to automatic correction for frameshifts implemented in the RAST pipeline. (CSV 133 kb)}, author = {Sigalova, Olga M. and Chaplin, Andrei V. and Bochkareva, Olga and Shelyakin, Pavel V. and Filaretov, Vsevolod A. and Akkuratov, Evgeny E. and Burskaia, Valentina and Gelfand, Mikhail S.}, publisher = {Springer Nature}, title = {{Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction}}, doi = {10.6084/m9.figshare.9808859.v1}, year = {2019}, } @misc{9899, abstract = {Summary of orthologous groups (OGs) for 227 genomes of genus Chlamydia. (CSV 362 kb)}, author = {Sigalova, Olga M. and Chaplin, Andrei V. and Bochkareva, Olga and Shelyakin, Pavel V. and Filaretov, Vsevolod A. and Akkuratov, Evgeny E. and Burskaia, Valentina and Gelfand, Mikhail S.}, publisher = {Springer Nature}, title = {{Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction}}, doi = {10.6084/m9.figshare.9808865.v1}, year = {2019}, } @misc{9900, abstract = {Pan-genome statistics by species. (CSV 3 kb)}, author = {Sigalova, Olga M. and Chaplin, Andrei V. and Bochkareva, Olga and Shelyakin, Pavel V. and Filaretov, Vsevolod A. and Akkuratov, Evgeny E. and Burskaia, Valentina and Gelfand, Mikhail S.}, publisher = {Springer Nature}, title = {{Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction}}, doi = {10.6084/m9.figshare.9808886.v1}, year = {2019}, } @misc{9901, abstract = {Clusters of Orthologous Genes (COGs) and corresponding functional categories assigned to OGs. (CSV 117 kb)}, author = {Sigalova, Olga M. and Chaplin, Andrei V. and Bochkareva, Olga and Shelyakin, Pavel V. and Filaretov, Vsevolod A. and Akkuratov, Evgeny E. and Burskaia, Valentina and Gelfand, Mikhail S.}, publisher = {Springer Nature}, title = {{Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction}}, doi = {10.6084/m9.figshare.9808907.v1}, year = {2019}, } @article{319, abstract = {We study spaces of modelled distributions with singular behaviour near the boundary of a domain that, in the context of the theory of regularity structures, allow one to give robust solution theories for singular stochastic PDEs with boundary conditions. The calculus of modelled distributions established in Hairer (Invent Math 198(2):269–504, 2014. https://doi.org/10.1007/s00222-014-0505-4) is extended to this setting. We formulate and solve fixed point problems in these spaces with a class of kernels that is sufficiently large to cover in particular the Dirichlet and Neumann heat kernels. These results are then used to provide solution theories for the KPZ equation with Dirichlet and Neumann boundary conditions and for the 2D generalised parabolic Anderson model with Dirichlet boundary conditions. In the case of the KPZ equation with Neumann boundary conditions, we show that, depending on the class of mollifiers one considers, a “boundary renormalisation” takes place. In other words, there are situations in which a certain boundary condition is applied to an approximation to the KPZ equation, but the limiting process is the Hopf–Cole solution to the KPZ equation with a different boundary condition.}, author = {Gerencser, Mate and Hairer, Martin}, issn = {1432-2064}, journal = {Probability Theory and Related Fields}, number = {3-4}, pages = {697–758}, publisher = {Springer}, title = {{Singular SPDEs in domains with boundaries}}, doi = {10.1007/s00440-018-0841-1}, volume = {173}, year = {2019}, } @article{405, abstract = {We investigate the quantum Jensen divergences from the viewpoint of joint convexity. It turns out that the set of the functions which generate jointly convex quantum Jensen divergences on positive matrices coincides with the Matrix Entropy Class which has been introduced by Chen and Tropp quite recently.}, author = {Virosztek, Daniel}, journal = {Linear Algebra and Its Applications}, pages = {67--78}, publisher = {Elsevier}, title = {{Jointly convex quantum Jensen divergences}}, doi = {10.1016/j.laa.2018.03.002}, volume = {576}, year = {2019}, } @article{429, abstract = {We consider real symmetric or complex hermitian random matrices with correlated entries. We prove local laws for the resolvent and universality of the local eigenvalue statistics in the bulk of the spectrum. The correlations have fast decay but are otherwise of general form. The key novelty is the detailed stability analysis of the corresponding matrix valued Dyson equation whose solution is the deterministic limit of the resolvent.}, author = {Ajanki, Oskari H and Erdös, László and Krüger, Torben H}, issn = {1432-2064}, journal = {Probability Theory and Related Fields}, number = {1-2}, pages = {293–373}, publisher = {Springer}, title = {{Stability of the matrix Dyson equation and random matrices with correlations}}, doi = {10.1007/s00440-018-0835-z}, volume = {173}, year = {2019}, } @article{17506, abstract = {Sandboxing is a common technique that allows low-level, untrusted components to safely interact with trusted code. However, previous work has only investigated the low-level memory isolation guarantees of sandboxing, leaving open the question of the end-to-end guarantees that sandboxing affords programmers. In this paper, we fill this gap by showing that sandboxing enables reasoning about the known concept of robust safety, i.e., safety of the trusted code even in the presence of arbitrary untrusted code. To do this, we first present an idealized operational semantics for a language that combines trusted code with untrusted code. Sandboxing is built into our semantics. Then, we prove that safety properties of the trusted code (as enforced through a rich type system) are upheld in the presence of arbitrary untrusted code, so long as all interactions with untrusted code occur at the “any” type (a type inhabited by all values). Finally, to alleviate the burden of having to interact with untrusted code at only the “any” type, we formalize and prove safe several wrappers, which automatically convert values between the “any” type and much richer types. All our results are mechanized in the Coq proof assistant.}, author = {Sammler, Michael Joachim and Garg, Deepak and Dreyer, Derek and Litak, Tadeusz}, issn = {2475-1421}, journal = {Proceedings of the ACM on Programming Languages}, number = {POPL}, pages = {1--32}, publisher = {Association for Computing Machinery}, title = {{The high-level benefits of low-level sandboxing}}, doi = {10.1145/3371100}, volume = {4}, year = {2019}, } @article{17510, abstract = {Weak lensing surveys are reaching sensitivities at which uncertainties in the galaxy redshift distributions n(z) from photo-z errors degrade cosmological constraints. We use ray-tracing simulations and a simple treatment of photo-z errors to assess cosmological parameter biases from uncertainties in n(z) in an LSST-like survey. We use lensing peak counts and the power spectrum to infer cosmological parameters, and find that the latter is somewhat more resilient to photo-z errors. We place conservative lower limits on the survey size at which different types of photo-z errors significantly degrade (${\sim }50{{\ \rm per\ cent}}$) ΛCDM (cold dark matter, wCDM) parameter constraints. A residual constant photo-z bias of |δz| &lt; 0.003(1 + z), the current LSST requirement, does not significantly degrade surveys smaller than ≈1300 (≈490) deg2 using peaks and ≈6500 (≈4900) deg2 using the power spectrum. Surveys smaller than ≈920 (≈450) deg2 and ≈4600 (≈4000) deg2 avoid 25 per cent degradation. Adopting a recent prediction for LSST’s full photo-z probability distribution function (PDF), we find that simply approximating n(z) with the photo-z galaxy distribution computed from this PDF significantly degrades surveys as small as ≈60 (≈65) deg2 using peaks or the power spectrum. If the centroid bias in each tomographic bin is removed from the photo-z galaxy distribution, using peaks or the power spectrum still significantly degrades surveys larger than ≈200 (≈255) or ≈248 (≈315) deg2; 25 per cent degradations occur at survey sizes of ≈140 (≈180) deg2 or ≈165 (≈210) deg2. These results imply that the expected broad photo-z PDF significantly biases parameters, which must be further mitigated using more sophisticated photo-z treatments.}, author = {Abruzzo, Matthew W and Haiman, Zoltán}, issn = {0035-8711}, journal = {Monthly Notices of the Royal Astronomical Society}, number = {2}, pages = {2730--2753}, publisher = {Oxford University Press}, title = {{The impact of photometric redshift errors on lensing statistics in ray-tracing simulations}}, doi = {10.1093/mnras/stz1016}, volume = {486}, year = {2019}, } @article{17511, author = {Marques, Gabriela A. and Liu, Jia and Matilla, José Manuel Zorrilla and Haiman, Zoltán and Bernui, Armando and Novaes, Camila P.}, issn = {1475-7516}, journal = {Journal of Cosmology and Astroparticle Physics}, number = {06}, publisher = {IOP Publishing}, title = {{Constraining neutrino mass with weak lensing Minkowski Functionals}}, doi = {10.1088/1475-7516/2019/06/019}, volume = {2019}, year = {2019}, } @article{17512, abstract = {The localization of stellar-mass binary black hole mergers using gravitational waves is critical in understanding the properties of the binaries’ host galaxies, observing possible electromagnetic emission from the mergers, or using them as a cosmological distance ladder. The precision of this localization can be substantially increased with prior astrophysical information about the binary system. In particular, constraining the inclination of the binary can reduce the distance uncertainty of the source. Here, we present the first realistic set of localizations for binary black hole mergers, including different prior constraints on the binaries’ inclinations. We find that prior information on the inclination can reduce the localization volume by a factor of 3. We discuss two astrophysical scenarios of interest: (i) follow-up searches for beamed electromagnetic/neutrino counterparts and (ii) mergers in the accretion discs of active galactic nuclei.}, author = {Corley, K Rainer and Bartos, Imre and Singer, Leo P and Williamson, Andrew R and Haiman, Zoltán and Kocsis, Bence and Nissanke, Samaya and Márka, Zsuzsa and Márka, Szabolcs}, issn = {0035-8711}, journal = {Monthly Notices of the Royal Astronomical Society}, number = {3}, pages = {4459--4463}, publisher = {Oxford University Press}, title = {{Localization of binary black hole mergers with known inclination}}, doi = {10.1093/mnras/stz2072}, volume = {488}, year = {2019}, } @article{17530, abstract = {Based on the cosmic shear data from the Canada-France-Hawaii Telescope Lensing Survey (CFHTLenS), Kilbinger et al. (2013) obtained a constraint on the amplitude of matter fluctuations of σ8(Ωm/0.27)0.6=0.79±0.03 from the two-point correlation function (2PCF). This is ≈3σ lower than the value 0.89±0.01 derived from Planck data on cosmic microwave background (CMB) anisotropies. On the other hand, based on the same CFHTLenS data, but using the power spectrum, and performing a different analysis, Liu et al. (2015) obtained the higher value of σ8(Ωm/0.27)0.64=0.87+0.05−0.06. We here investigate the origin of this difference, by performing a fair side-by-side comparison of the 2PCF and power spectrum analyses on CFHTLenS data. We find that these two statistics indeed deliver different results, even when applied to the same data in an otherwise identical procedure. We identify excess power in the data on small scales (ℓ>5,000) driving the larger values inferred from the power spectrum. We speculate on the possible origin of this excess small-scale power. More generally, our results highlight the utility of analysing the 2PCF and the power spectrum in tandem, to discover (and to help control) systematic errors.}, author = {Lu, Tianhuan and Haiman, Zoltán}, issn = {0035-8711}, journal = {Monthly Notices of the Royal Astronomical Society}, number = {4}, pages = {5033--5042}, publisher = {Oxford University Press}, title = {{The matter fluctuation amplitude inferred from the weak lensing power spectrum and correlation function in CFHTLenS data}}, doi = {10.1093/mnras/stz2931}, volume = {490}, year = {2019}, } @article{17533, abstract = {The origins of the stellar-mass black hole mergers discovered by LIGO/Virgo are still unknown. Here we show that if migration traps develop in the accretion disks of active galactic nuclei (AGNs) and promote the mergers of their captive black holes, the majority of black holes within disks will undergo hierarchical mergers—with one of the black holes being the remnant of a previous merger. 40% of AGN-assisted mergers detected by LIGO/Virgo will include a black hole with mass ≳50⁢𝑀⊙, the mass limit from stellar core collapse. Hierarchical mergers at traps in AGNs will exhibit black hole spins (anti)aligned with the binary’s orbital axis, a distinct property from other hierarchical channels. Our results suggest, although not definitively (with odds ratio of ∼1), that LIGO’s heaviest merger so far, GW170729, could have originated from this channel.}, author = {Yang, Y. and Bartos, I. and Gayathri, V. and Ford, K. E. S. and Haiman, Zoltán and Klimenko, S. and Kocsis, B. and Márka, S. and Márka, Z. and McKernan, B. and O’Shaughnessy, R.}, issn = {0031-9007}, journal = {Physical Review Letters}, number = {18}, publisher = {American Physical Society}, title = {{Hierarchical black hole mergers in active galactic nuclei}}, doi = {10.1103/physrevlett.123.181101}, volume = {123}, year = {2019}, } @article{17541, abstract = {In recent years, the discovery of massive quasars at z~7 has provided a striking challenge to our understanding of the origin and growth of supermassive black holes in the early Universe. Mounting observational and theoretical evidence indicates the viability of massive seeds, formed by the collapse of supermassive stars, as a progenitor model for such early, massive accreting black holes. Although considerable progress has been made in our theoretical understanding, many questions remain regarding how (and how often) such objects may form, how they live and die, and how next generation observatories may yield new insight into the origin of these primordial titans. This review focusses on our present understanding of this remarkable formation scenario, based on discussions held at the Monash Prato Centre from November 20--24, 2017, during the workshop "Titans of the Early Universe: The Origin of the First Supermassive Black Holes."}, author = {Woods, Tyrone E. and Agarwal, Bhaskar and Bromm, Volker and Bunker, Andrew and Chen, Ke-Jung and Chon, Sunmyon and Ferrara, Andrea and Glover, Simon C. O. and Haemmerlé, Lionel and Haiman, Zoltán and Hartwig, Tilman and Heger, Alexander and Hirano, Shingo and Hosokawa, Takashi and Inayoshi, Kohei and Klessen, Ralf S. and Kobayashi, Chiaki and Koliopanos, Filippos and Latif, Muhammad A. and Li, Yuexing and Mayer, Lucio and Mezcua, Mar and Natarajan, Priyamvada and Pacucci, Fabio and Rees, Martin J. and Regan, John A. and Sakurai, Yuya and Salvadori, Stefania and Schneider, Raffaella and Surace, Marco and Tanaka, Takamitsu L. and Whalen, Daniel J. and Yoshida, Naoki}, issn = {1323-3580}, journal = {Publications of the Astronomical Society of Australia}, publisher = {Cambridge University Press}, title = {{Titans of the early universe: The prato statement on the origin of the first supermassive black holes}}, doi = {10.1017/pasa.2019.14}, volume = {36}, year = {2019}, } @article{17543, abstract = {Massive black-hole (MBH) binaries, which are expected to form following the merger of their parent galaxies, produce gravitational waves which will be detectable by Pulsar Timing Arrays at nanohertz frequencies (year periods). While no confirmed, compact MBH binary systems have been seen in electromagnetic observations, a large number of candidates have recently been identified in optical surveys of AGN variability. Using a combination of cosmological, hydrodynamic simulations; comprehensive, semi-analytic binary merger models; and analytic AGN spectra and variability prescriptions; we calculate the expected electromagnetic detection rates of MBH binaries as periodically variable AGN. In particular, we consider two independent variability models: (i) Doppler boosting due to large orbital velocities, and (ii) hydrodynamic variability in which the fueling of MBH accretion disks is periodically modulated by the companion. Our models predict that numerous MBH binaries should be present and distinguishable in the existing data. In particular, our fiducial models produce an expectation value of 0.2 (Doppler) and 5 (hydrodynamic) binaries to be identifiable in CRTS, while 20 and 100 are expected after five years of LSST observations. The brightness variations in most systems are too small to be distinguishable, but almost 1% of AGN at redshifts z≲0.6 could be in massive binaries. We analyze the predicted binary parameters of observable systems and their selection biases, and include an extensive discussion of our model parameters and uncertainties.}, author = {Kelley, Luke Zoltan and Haiman, Zoltán and Sesana, Alberto and Hernquist, Lars}, issn = {0035-8711}, journal = {Monthly Notices of the Royal Astronomical Society}, number = {2}, pages = {1579--1594}, publisher = {Oxford University Press}, title = {{Massive BH binaries as periodically variable AGN}}, doi = {10.1093/mnras/stz150}, volume = {485}, year = {2019}, } @article{17556, abstract = {The abundance of molecular hydrogen (H2), the primary coolant in primordial gas, is critical for the thermodynamic evolution and star-formation histories in early protogalaxies. Determining the photodissociation rate of H2 by an incident Lyman-Werner (LW) flux is thus crucial, but prohibitively expensive to calculate on the fly in simulations. The rate is sensitive to the H2 rovibrational distribution, which in turn depends on the gas density, temperature, and incident LW radiation field. We use the publicly available cloudy package to model primordial gas clouds and compare exact photodissociation rate calculations to commonly-used fitting formulae. We find the fit from Wolcott-Green et al. (2011) is most accurate for moderate densities n~10^3 cm^{-3} and temperatures, T~10^3K, and we provide a new fit, which captures the increase in the rate at higher densities and temperatures, owing to the increased excited rovibrational populations in this regime. Our new fit has typical errors of a few percent percent up to n =<10^7 cm^{-3}, T =< 8000K, and H2 column density NH2 =<10^{17} cm^{-2}, and can be easily utilized in simulations. We also show that pumping of the excited rovibrational states of H2 by a strong LW flux further modifies the level populations when the gas density is low, and noticeably decreases self-shielding for J_21 > 10^3 and n < 10^2 cm^{-3}. This may lower the "critical flux" at which primordial gas remains H2-poor in some protogalaxies, enabling massive black hole seed formation.}, author = {Wolcott-Green, J and Haiman, Zoltán}, issn = {0035-8711}, journal = {Monthly Notices of the Royal Astronomical Society}, number = {2}, pages = {2467--2473}, publisher = {Oxford University Press}, title = {{H2 self-shielding with non-LTE rovibrational populations: Implications for cooling in protogalaxies}}, doi = {10.1093/mnras/sty3280}, volume = {484}, year = {2019}, } @article{17565, abstract = {The coalescence of a compact object with a 104−107M⊙ supermassive black hole (SMBH) produces mHz gravitational waves (GWs) detectable by the future Laser Interferometer Space Antenna (LISA). If such an inspiral occurs in the accretion disc of an active galactic nucleus (AGN), the gas torques imprint a small deviation in the GW waveform. Here we present two-dimensional hydrodynamical simulations with the moving-mesh code DISCO of a BH inspiraling at the GW rate in a binary system with a mass ratio q=M2/M1=10−3, embedded in an accretion disc. We assume a locally isothermal equation of state for the gas (with Mach number M=20) and implement a standard α-prescription for its viscosity (with α=0.03). We find disc torques on the binary that are weaker than in previous semi-analytic toy models, and are in the opposite direction: the gas disc slows down, rather than speeds up the inspiral. We compute the resulting deviations in the GW waveform, which scale linearly with the mass of the disc. The SNR of these deviations accumulates mostly at high frequencies, and becomes detectable in a 5-year LISA observation if the total phase shift exceeds a few radians. We find that this occurs if the disc surface density exceeds Σ0≳102−3gcm−2, as may be the case in thin discs with near-Eddington accretion rates. Since the characteristic imprint on the GW signal is strongly dependent on disc parameters, a LISA detection of an intermediate mass ratio inspiral would probe the physics of AGN discs and migration.}, author = {Derdzinski, A M and D’Orazio, D and Duffell, P and Haiman, Zoltán and MacFadyen, A}, issn = {0035-8711}, journal = {Monthly Notices of the Royal Astronomical Society}, number = {2}, pages = {2754--2765}, publisher = {Oxford University Press}, title = {{Probing gas disc physics with LISA: simulations of an intermediate mass ratio inspiral in an accretion disc}}, doi = {10.1093/mnras/stz1026}, volume = {486}, year = {2019}, } @article{17567, abstract = {The growing number of stellar-mass binary black hole mergers discovered by Advanced LIGO and Advanced Virgo are starting to constrain the binaries' origin and environment. However, we still lack sufficiently accurate modeling of binary formation channels to obtain strong constraints, or to identify sub-populations. One promising formation mechanism that could result in different black hole properties is binaries merging within the accretion disks of Active Galactic Nuclei (AGN). Here we show that the black holes' orbital alignment with the AGN disks preferentially selects heavier black holes. We carry out Monte Carlo simulations of orbital alignment with AGN disks, and find that AGNs harden the initial black hole mass function. Assuming an initial power law mass distribution M−βbh, we find that the power law index changes by Δβ∼1.3, resulting in a more top-heavy population of merging black holes. This change is independent of the mass of, and accretion rate onto, the supermassive black hole in the center of the AGN. Our simulations predict an AGN-assisted merger rate of ∼4Gpc−3yr−1. With its hardened mass spectra, the AGN channel could be responsible for 10−50% of gravitational-wave detections.}, author = {Yang, Y. and Bartos, I. and Haiman, Zoltán and Kocsis, B. and Márka, Z. and Stone, N. C. and Márka, S.}, issn = {0004-637X}, journal = {The Astrophysical Journal}, number = {2}, publisher = {American Astronomical Society}, title = {{AGN disks harden the mass distribution of stellar-mass binary black hole mergers}}, doi = {10.3847/1538-4357/ab16e3}, volume = {876}, year = {2019}, }