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During the Epoch of reionisation, the intergalactic medium is reionised by the UV radiation from the first generation of stars and galaxies. One tracer of the process is the 21 cm line of hydrogen that will be observed by the Square Kilometre Array (SKA) at low frequencies, thus imaging the distribution of ionised and neutral regions and their evolution. To prepare for these upcoming observations, we investigate a deep learning method to predict from 21 cm maps the reionisation time field (treion(r)), i.e. the time at which each location has been reionised. treion(r) encodes the propagation of ionisation fronts in a single field, gives access to times of local reionisation or to the extent of the radiative reach of early sources. Moreover it gives access to the time evolution of ionisation on the plane of sky, when such evolution is usually probed along the line-of-sight direction. We trained a convolutional neural network (CNN) using simulated 21 cm maps and reionisation times fields produced by the simulation code 21cmFAST . We also investigate the performance of the CNN when adding instrumental effects. Globally, we find that without instrumental effects the 21 cm maps can be used to reconstruct the associated reionisation times field in a satisfying manner: the quality of the reconstruction is dependent on the redshift at which the 21 cm observation is being made and in general it is found that small scale (

Toxoplasma gondii is the parasite responsible for toxoplasmosis, a highly prevalent zoonosis that affects humans and warm-blooded animals. Faeces of infected cats can contain millions of T. gondii oocysts, which remain infectious in the environment for months. Sites repeatedly used by cats for defecation ('latrines') are recognised as hotspots of T. gondii soil contamination, but this contamination varies from one latrine to another. To understand this spatial heterogeneity, camera traps were deployed in 39 cat latrines on three dairy farms with high-density cat populations and programmed to record visits during sixteen 10-day sessions, rotating between three farms over a period of a year. Generalized Linear Mixed Models were used to test the effects of cat sexual maturity, latrine location and season on the number of cat faeces deposited and on the number of cats defecating per latrine, as determined from the analysis of 41,282 video recordings. Sexually immature cats defecated 6.60-fold (95% CI = [2.87-15.25]) more often in latrines located close to a feeding site than in other latrines. This pattern was also observed for mature males (odds ratio [OR] = 9.42, 95% CI = [3.29-26.91]), especially during winter, but not for mature females (OR = 1.77, 95% CI = [0.80-3.94]). The number of defecating cats was also 2.67-fold (95% CI = [1.66-4.30], P 0.001) higher in latrines located close to a feeding point than in those located far from it, regardless of cat category and season. Visits by intermediate T. gondii hosts (micromammals, birds and others) were also recorded. Out of the 39 latrines, 30 (76.92%) were visited by at least one intermediate host during the study period, and some latrines were highly frequented (up to 8.74 visits/day on average). These results provide evidence that the location of food resources in dairy farms influences the latrine use pattern by cats. Highly frequented latrines can be of high risk of T. gondii infection for definitive and intermediate hosts.

Our understanding of the intergalactic medium at redshifts z = 5–6 has improved considerably in the last few years due to the discovery of quasars with z > 6 that enable Lyman-α forest studies at these redshifts. A realization from this has been that hydrogen reionization could end much later than previously thought, so that large ‘islands’ of cold, neutral hydrogen could exist in the IGM at redshifts z = 5–6. By using radiative transfer simulations of the IGM, we consider the implications of the presence of these neutral hydrogen islands for the 21-cm power spectrum signal and its potential detection by experiments such as HERA, SKA, LOFAR, and MWA. In contrast with previous models of the 21-cm signal, we find that thanks to the late end of reionization the 21-cm power in our simulation continues to be as high as Δ$^{2}_{21}$ = 10 mK$^{2}$ at k ∼ 0.1 h cMpc$^{−1}$ at z = 5–6. This value of the power spectrum is several orders of magnitude higher than that in conventional models considered in the literature for these redshifts. Such high values of the 21-cm power spectrum should be detectable by HERA and SKA1-low in ∼1000 h, assuming optimistic foreground subtraction. This redshift range is also attractive due to relatively low sky temperature and potentially greater abundance of multiwavelength data.

The process of heating and reionization of the Universe at high redshift links small scale structures/galaxy formation and large scale inter-galactic medium properties. Even if the first one is difficult to observe, an observation window is opening on the second one, with the promising development of current and future radio telescopes. They will permit to observe the 21cm brightness temperature global signal and fluctuations. The need of large scale simulations is therefore strong to understand the properties of the IGM that will be observed. But at the same time the urge to resolve the structures responsible of those process is important. We introduce in this study, a coupled hydro-radiative transfer simulations of the Cosmic Dawn and Reionization with a simple sub-grid star formation process developed and calibrated on the state of the art simulation CoDaII. This scheme permits to follow consistently dark matter, hydrodynamics and radiative transfer evolution's on large scales, while the sub-grid models bridges to the galaxy formation scale. We process the simulation to produce 21cm signal as close as possible to the observations.

Our understanding of the intergalactic medium at redshifts $z=5$-$6$ has improved considerably in the last few years due to the discovery of quasars with $z>6$ that enable Lyman-$��$ forest studies at these redshifts. A realisation from this has been that hydrogen reionization could end much later than previously thought, so that large "islands" of cold, neutral hydrogen could exist in the IGM at redshifts $z=5$-$6$. By using radiative transfer simulations of the IGM, we consider the implications of the presence of these neutral hydrogen islands for the 21-cm power spectrum signal and its potential detection by experiments such as HERA, SKA, LOFAR, and MWA. In contrast with previous models of the 21-cm signal, we find that thanks to the late end of reionization the 21-cm power in our simulation continues to be as high as $��^2_{21}=10~\mathrm{mK}^2$ at $k\sim 0.1~h/$cMpc at $z=5$-$6$. This value of the power spectrum is several orders of magnitude higher than that in the conventional models considered in the literature for these redshifts. Such high values of the 21-cm power spectrum should be detectable by HERA and SKA1-LOW in $\sim 1000$ hours, assuming optimistic foreground subtraction. This redshift range is also attractive due to relatively low sky temperature and potentially greater abundance of multiwavelength data., 14 pages, 6 figures, 2 tables. Accepted for publication in MNRAS

A long (110 cMpc/$h$) and deep absorption trough in the Ly$��$ forest has been observed extending down to redshift 5.5 in the spectrum of ULAS J0148+0600. Although no Ly$��$ transmission is detected, Ly$��$ spikes are present which has led to claims that the gas along this trough must be ionized. Using high resolution cosmological radiative transfer simulations in large volumes, we show that in a scenario where reionization ends late ($z \sim 5.2$), our simulations can reproduce troughs as long as observed. In this model, we find that the troughs are caused by islands of neutral hydrogen. Small ionized holes within the neutral islands allow for the transmission of Ly$��$. We have also modelled the Ly$��$ emitter population around the simulated troughs, and show that there is a deficit of Ly$��$ emitters close to the trough as is observed., 11 pages, 8 figures. Accepted for publication in MNRAS

We present an analysis of the evolution of the Lyman-series forest into the epoch of reionization using cosmological radiative transfer simulations in a scenario where reionization ends late. We explore models with different midpoints of reionization and gas temperatures. We find that once the simulations have been calibrated to match the mean flux of the observed Lyman-$��$ forest at $4 < z < 6$, they also naturally reproduce the distribution of effective optical depths of the Lyman-$��$ forest in this redshift range. We note that the tail of the largest optical depths that is most challenging to match corresponds to the long absorption trough of ULAS J0148+0600, which we have previously shown to be rare in our simulations. We consider the evolution of the Lyman-series forest out to higher redshifts, and show that future observations of the Lyman-$��$ forest at $z>6$ will discriminate between different reionization histories. The evolution of the Lyman-$��$ and Lyman-$��$ forests are less promising as a tool for pushing studies of reionization to higher redshifts due to the stronger saturation and foreground contamination, respectively., 10 pages, 9 figures, 1 table. Accepted to MNRAS

Text. Matrices constructed for parameters estimation in the E-SURGE program. Table S1. Detailed structure of the set of models and the model selection procedure from the multi-event analysis. Table S2. Estimated parameters from the selected model. (DOCX 53 kb)

High-redshift QSO spectra show large spatial fluctuations in the Ly-alpha opacity of the intergalactic medium on surprisingly large scales at z>~5.5. We present a radiative transfer simulation of cosmic reionization driven by galaxies that reproduces this large scatter and the rapid evolution of the Ly-alpha opacity distribution at 5~6. Reionization is complete at z=5.3 in our model, and 50% of the volume of the Universe is ionized at z=7. Agreement with the Ly-alpha forest data in such a late reionization model requires a rapid evolution of the ionizing emissivity of galaxies that peaks at z~6.8. The late end of reionization results in a large scatter in the photoionisation rate and the neutral hydrogen fraction at redshifts as low as z, 5 pages, 3 figures; accepted for publication in MNRAS

Table S3. Dataset showing Toxoplasma gondii antibody titres obtained from the modified agglutinated test (MAT) and the characteristics of the sampled cat. (DOCX 51 kb)

Description of survival rates, detection rates, age assignment and blood collection rates estimated from the best retained model. (DOCX 12 kb)

We calibrate here cosmological radiative transfer simulation with ATON/RAMSES with a range of measurements of the Lyman alpha opacity from QSO absorption spectra. We find the Lyman alpha opacity to be very sensitive to the exact timing of hydrogen reionisation. Models reproducing the measured evolution of the mean photoionisation rate and average mean free path reach overlap at z ~ 7 and predict an accelerated evolution of the Lyman alpha opacity at z > 6 consistent with the rapidly evolving luminosity function of Lyman alpha emitters in this redshift range. Similar to "optically thin" simulations our full radiative transfer simulations fail, however, to reproduce the high-opacity tail of the Lyman alpha opacity PDF at z > 5. We argue that this is due to spatial UV fluctuations in the post-overlap phase of reionisation on substantially larger scales than predicted by our source model, where the ionising emissivity is dominated by large numbers of sub-L* galaxies. We further argue that this suggests a significant contribution to the ionising UV background by much rarer bright sources at high redshift., 26 pages, 20 figures, published in MNRAS in november 2015

We constrain the initial stage of the reionization process around progenitors of galaxies, such as the extent of the initial HII region before its fusion with the UV background and the duration of its propagation. We use a set of reionisation simulations with different resolutions and ionizing source recipes. A catalog of the HII regions properties is built thanks to a merger tree of HII regions. We draw local reionization histories as a function of time and investigate variations according to the halo mass progenitors of the regions. We then extrapolate the halo mass inside the region from high z to z=0 to make predictions about the reionization histories of z=0 galaxies. We found that the later an HII region appears, the smaller will be its related lifetime and volume before it sees the global UV background. Quantitatively the duration and the extent of the initial growth of an HII region is strongly dependent on the mass of the inner halo and can be as long as 50 % of the reionization epoch. We found that the most massive is a halo today, the earlier it appears and the larger are the extension and the duration of propagation of its HII region. Quantitative predictions differ depending on the box size or the source model: small simulated volumes are affected by proximity effects between HII regions and halo-based source models predict smaller regions and slower I-front expansion than in models using star particles as ionizing sources. Our results suggests that Milky Way-type halos have a maximal extent of 1.1 Mpc/h for the initial HII region that established itself in 150-200$\pm 20$ Myrs. This is consistent with prediction made using constrained Local Group simulation. Considering halos with masses comparable to those of the Local Group (MW+M31), our result suggests that statistically it has not been influenced by an external front coming from a Virgo-like cluster., Comment: 16 pages, 9 figures, Accepted for publication in A&A

We describe a new methodology to analyze the reionization process in numerical simulations: The evo- lution of the reionization is investigated by focusing on the merger histories of individual HII regions. From the merger tree of ionized patches, one can track the individual evolution of the regions such as e.g. their size, or investigate the properties of the percolation process by looking at the formation rate, the frequency of mergers and the number of individual HII regions involved in the mergers. By applying this technique to cosmological simulations with radiative transfer, we show how this methodology is a good candidate to quantify the impact of the star formation adopted on the history of the reionization. As an application we show how different models of sources result in different evolutions and geometry of the reionization even though they produce e.g. similar ionized fraction or optical depth., Comment: Proceeding SF2A 2012, 5 pages, 4 figures

We describe a new methodology to analyze the reionization process in numerical simulations: the chronology and the geometry of reionization is investigated by means of merger histories of individual HII regions. From the merger tree of ionized patches, one can track the individual evolution of the regions properties such as e.g. their size, or the intensity of the percolation process by looking at the formation rate, the frequency of mergers and the number of individual HII regions involved in the mergers. We apply the merger tree technique to simulations of reionization with three different kinds of ionizing source models and two resolutions. Two of them use star particles as ionizing sources. In this case we confront two emissivity evolutions for the sources in order to reach the reionization at z ~ 6. As an alternative we built a semi-analytical model where the dark matter halos extracted from the density fields are assumed as ionizing sources. We then show how this methodology is a good candidate to quantify the impact of the adopted star formation on the history of the observed reionization. The semi-analytical model shows a homogeneous reionization history with 'local' hierarchical growth steps for individual HII regions. On the other hand auto-consistent models for star formation tend to present fewer regions with a dominant region in size which governs the fusion process early in the reionization at the expense of the 'local' reionizations. The differences are attenuated when the resolution of the simulation is increased., Comment: Accepted for publication in A&A

We present a set of cosmological simulations with radiative transfer in order to model the reionization history of the Universe. Galaxy formation and the associated star formation are followed self-consistently with gas and dark matter dynamics using the RAMSES code, while radiative transfer is performed as a post-processing step using a moment-based method with M1 closure relation in the ATON code. The latter has been ported to a multiple Graphics Processing Units (GPU) architecture using CUDA + MPI, resulting in an overall acceleration (x80) that allows us to tackle radiative transfer problems at resolution of 1024^3 + 2 levels of refinement for the hydro adaptive grid and 1024^3 for the RT cartesian grid. We observe a good convergence between our different resolution runs as long as the effects of finite resolution on the star formation history are properly taken into account. We also show that the neutral fraction depends on the total mass density, in a way close to the predictions of photoionization equilibrium, as long as the effect of self-shielding is included in the background radiation model. However we still fail at reproducing the z=6 constraints on the H neutral fraction and the intensity of the UV background. In order to account for unresolved density fluctuations, we added a simple clumping factor model. Using our most spatially resolved simulation (12.5 Mpc/h-1024^3) to calibrate our subgrid model, we have resimulated our largest box (100 Mpc/h 1024^3), successfully reproducing the observed level of H neutral fraction at z=6. We don't reproduce the photoionization rate inferred from the same observations. We argue that this discrepancy could be explained by the fact that the average radiation intensity and the average neutral fraction depends on different regions of the gas density distribution, so that one quantity cannot be simply deduced from the other., Comment: 21 pages, submitted to ApJ

This study employs both nonparametric and parametric methods to examine the influence of household expenditure and other demographic variables on household consumption of calories in Tanzania, using recent survey data. Under each estimation strategy we employ, we find significant and positive relationship between household expenditure and calorie consumption. Even with an estimation strategy that ensures consistent estimates in the presence of measurement error, the calorie-expenditure elasticity is 0.46, a finding that is consistent with the traditional view that, increases in household income will improve calorie intake and help alleviate inadequate nutrition.