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Abstract Observations of quasar absorption spectra provide strong evidence that reionization extended belowz= 6. The relationship between Lyαforest opacity and local galaxy density (the opacity-density relation) is a key observational test of this scenario. Using narrow-band surveys ofz≈ 5.7 Lyαemitters (LAEs) centered on quasar sight lines, ref. [1] showed that two of the most transmissive Lyαforest segments at this redshift intersect under-densities in the galaxy distribution. This result is in tension with models of a strongly fluctuating ionizing background, including some models of late reionization, which predict that the vast majority of these segments should intersect over-densities where the ionizing intensity is strongest. In this paper, we use radiative transfer simulations to explore in more detail the opacity-density relation predicted by late reionization models. We find that fields like the one toward quasar PSO J359-06 — the more under-dense of the two transmissive sight lines in ref. [1] — are typically associated with recently reionized gas inside of cosmic voids where the hotter temperatures and rarefied densities enhance Lyαtransmission. The opacity-density relation's transmissive end is sensitive to the amount of neutral gas in the voids, as well as its morphology, set by the clustering of reionization sources. These effects are, however, largely degenerate with each other. We demonstrate that models with very different source clustering can nonetheless yield nearly identical opacity-density relations when their reionization histories are calibrated to match Lyα forest mean flux measurements atz< 6. In models with fixed source clustering, a lower neutral fraction increases the likelihood of intersecting hot, recently reionized gas in the voids, increasing the likelihood of observing fields like PSO J359-06. For instance, the probability of observing this field is 15% in a model with neutral fractionx_HI= 5% atz= 5.7, three times more likely than in a model withx_HI= 15%. The opacity-density relation may thus provide a complementary probe of reionization's tail end. 

Abstract During reionization, intergalactic ionization fronts (I-fronts) are sources of Lyαline radiation produced by collisional excitation of hydrogen atoms within the fronts. In principle, detecting this emission could provide direct evidence for a reionizing intergalactic medium (IGM). In this paper, we use a suite of high-resolution one-dimensional radiative transfer simulations run on cosmological density fields to quantify the parameter space of I-front Lyαemission. We find that the Lyαproduction efficiency — the ratio of emitted Lyαflux to incident ionizing flux driving the front — depends mainly on the I-front speed and the spectral index of the ionizing radiation. IGM density fluctuations on scales smaller than the typical I-front width produce scatter in the efficiency, but they do not significantly boost its mean value. The Lyαflux emitted by an I-front is largest if 3 conditions are met simultaneously: (1) the incident ionizing flux is large; (2) the incident spectrum is hard, consisting of more energetic photons; (3) the I-front is traveling through a cosmological over-density, which causes it to propagate more slowly. We present a convenient parameterization of the efficiency in terms of I-front speed and incident spectral index. We make these results publicly available as an interpolation table and we provide a simple fitting function for a representative ionizing background spectrum. Our results can be applied as a sub-grid model for I-front Lyα emissions in reionization simulations with spatial and/or temporal resolutions too coarse to resolve I-front structure. In a companion paper, we use our results to explore the possibility of directly imaging Lyαemission around neutral islands during the last phases of reionization. 

Abstract Long troughs observed in thez> 5.5 Lyαand Lyβforests are thought to be caused by the last remaining neutral patches during the end phases of reionization — termed neutral islands. If this is true, then the longest troughs mark locations where we are most likely to observe the reionizing intergalactic medium (IGM). A key feature of the neutral islands is that they are bounded by ionization fronts (I-fronts) which emit Lyman series lines. In this paper, we explore the possibility of directly imaging the outline of neutral islands with a narrowband survey targeting Lyα. In a companion paper, we quantified the intensity of I-front Lyαemissions during reionization and its dependence on the spectrum of incident ionizing radiation and I-front speed. Here we apply those results to reionization simulations to model the emissions from neutral islands. We find that neutral islands would appear as diffuse structures that are tens of comoving Mpc across, with surface brightnesses in the range ≈ 1 - 5× 10^-21erg s^-1cm^-2arcsec^-2. The islands are brighter if the spectrum of ionizing radiation driving the I-fronts is harder, and/or if the I-fronts are moving faster. We develop mock observations for current and futuristic observatories and find that, while extremely challenging, detecting neutral islands is potentially within reach of an ambitious observing program with wide-field narrowband imaging. Our results demonstrate the potentially high impact of low-surface brightness observations for studying reionization. 

Abductive reasoning is ubiquitous in artificial intelligence and everyday thinking. However, formal theories that provide probabilistic guarantees for abductive inference are lacking. We present a quantitative formalization of abductive logic that combines Bayesian probability with the interpretation of abduction as a search process within the Algorithmic Search Framework (ASF). By incorporating uncertainty in background knowledge, we establish two novel sets of probabilistic bounds on the success of abduction when (1) selecting the single most likely cause while assuming noiseless observations, and (2) selecting any cause above some probability threshold while accounting for noisy observations. To our knowledge, no existing abductive or general inference bounds account for noisy observations. Furthermore, while most existing abductive frameworks assume exact underlying prior and likelihood distributions, we assume only percentile-based confidence intervals for such values. These milder assumptions result in greater flexibility and applicability of our framework. We also explore additional information-theoretic results from the ASF and provide mathematical justifications for everyday abductive intuitions. 

Abstract We report that the neutral hydrogen (Hi) mass density of the Universe (ρ_Hi) increases with cosmic time sincez ∼ 5, peaks atz ∼ 3, and then decreases towardz ∼ 0. This is the first result of Qz5, our spectroscopic survey of 63 quasars atz ≳ 5 with VLT/X-SHOOTER and Keck/ESI aimed at characterizing intervening Higas absorbers atz ∼ 5. The main feature of Qz5 is the high resolution (R ∼ 7000–9000) of the spectra, which allows us to (1) accurately detect high column density Higas absorbers in an increasingly neutral intergalactic medium atz ∼ 5 and (2) determine the reliability of previousρ_Himeasurements derived with lower resolution spectroscopy. We find five intervening damped Lyαabsorbers (DLAs) atz > 4.5, which corresponds to the lowest DLA incidence rate ( $0.034_{0.02}^{0.05}$) atz ≳ 2. We also measure the lowestρ_Hiatz ≳ 2 from our sample of DLAs and subDLAs, corresponding toρ_Hi $=0.56_{0.31}^{0.82}\times 10^8{M}_{\odot }$Mpc⁻³atz ∼ 5. Taking into account our measurements atz ∼ 5 and systematic biases in the DLA detection rate at lower spectral resolutions, we conclude thatρ_Hidoubles fromz ∼ 5 toz ∼ 3. From these results emerges a qualitative agreement between how the cosmic densities of Higas mass, molecular gas mass, and star formation rate build up with cosmic time. 

TnpB nucleases represent the evolutionary precursors to CRISPR-Cas12 and are widespread in all domains of life. IS605-family TnpB homologs function as programmable RNA-guided homing endonucleases in bacteria, driving transposon maintenance through DNA double-strand break–stimulated homologous recombination. In this work, we uncovered molecular mechanisms of the transposition life cycle of IS607-family elements that, notably, also encode group I introns. We identified specific features for a candidate “IStron” fromClostridium botulinumthat allow the element to carefully control the relative levels of spliced products versus functional guide RNAs. Our results suggest that IStron transcripts evolved an ability to balance competing and mutually exclusive activities that promote selfish transposon spread while limiting adverse fitness costs on the host. Collectively, this work highlights molecular innovation in the multifunctional utility of transposon-encoded noncoding RNAs. 

Amidst the challenges posed by the high penetration of distributed energy resources (DERs), particularly a number of distributed photovoltaic plants (DPVs), in modern electric power distribution systems (MEPDS), the integration of new technologies and frameworks become crucial for addressing operation, management, and planning challenges. Situational awareness (SA) and situational intelligence (SI) over multi-time scales is essential for enhanced and reliable PV power generation in MEPDS. In this paper, data-driven digital twins (DTs) are developed using AI paradigms to develop actual and/or virtual models of DPVs, These DTs are then applied for estimating and forecasting the power outputs of physical and virtual PV plants. Virtual weather stations are used to estimate solar irradiance and temperature at user-selected locations in a localized region, using inferences from physical weather stations. Three case studies are examined based on data availability: physical PV plant, hybrid PV plants, and virtual PV plants, generating realtime estimations and short-term forecasts of PV power production that can support distribution system studies and decision-making. 

ABSTRACT Recent measurements of the ionizing photon mean free path (MFP) based on composite quasar spectra may point to reionization ending at z < 6. These measurements are challenging because they rely on assumptions about the proximity zones of the quasars. For example, some quasars might have been close to neutral patches where reionization was still ongoing (‘neutral islands’), and it is unclear how they would affect the measurements. We address this question with mock MFP measurements from radiative transfer simulations. We find that, even in the presence of neutral islands, our mock MFP measurements agree to within $$30~{{\ \rm per\ cent}}$$ with the true spatially averaged MFP in our simulations, which includes opacity from both the ionized medium and the islands. The inferred MFP is sensitive at the $$\lt ~50~{{\ \rm per\ cent}}$$ level to assumptions about quasar environments and lifetimes for realistic models. We demonstrate that future analyses with improved data may require explicitly modelling the effects of neutral islands on the composite spectra, and we outline a method for doing this. Lastly, we quantify the effects of neutral islands on Lyman-series transmission, which has been modelled with optically thin simulations in previous MFP analyses. Neutral islands can suppress transmission at λrest < 912 Å significantly, up to a factor of 2 for zqso = 6 in a plausible reionization scenario, owing to absorption by many closely spaced lines as quasar light redshifts into resonance. However, the suppression is almost entirely degenerate with the spectrum normalization and thus does not significantly bias the inferred MFP.