In Search of an Uncultured Human-Associated TM7 Bacterium in the Environment

We have identified an environmental bacterium in the Candidate Division TM7 with ≥98.5% 16S rDNA gene homology to a group of TM7 bacteria associated with the human oral cavity and skin. The environmental TM7 bacterium (referred to as TM7a-like) was readily detectable in wastewater with molecular techniques over two years of sampling. We present the first images of TM7a-like cells through FISH technique and the first images of any TM7 as viable cells through the STARFISH technique. In situ quantification showed TM7 concentration in wastewater up to five times greater than in human oral sites. We speculate that upon further characterization of the physiology and genetics of the TM7a-like bacterium from environmental sources and confirmation of its genomic identity to human-associated counterparts it will serve as model organisms to better understand its role in human health. The approach proposed circumvents difficulties imposed by sampling humans, provides an alternative strategy to characterizing some diseases of unknown etiology, and renders a much needed understanding of the ecophysiological role hundreds of unique Bacteria and Archaea strains play in mixed microbial communities

Acute Liver Failure Due To Amoxicillin and Amoxicillin/Clavulanate

The aim of our study is to report upon the presentation of two patients with life-threatening acute liver failure (ALF) due to amoxicillin and amoxicillin/clavulanate. A 59-year-old, Caucasian male presented with ALF 34 days after receiving amoxicillin/clavulanate. Despite aggressive supportive care, he died on hospital day 10. A 42-year-old, Caucasian female presented with ALF 21 days after receiving amoxicillin. She underwent successful liver transplantation on hospital day 19. In both cases, all competing causes of ALF had been excluded, liver pathology was consistent with drug-induced hepatitis, and cases were deemed “definite/highly probable” using causality assessment. Amongst 14 prior ALF/death cases due to amoxicillin/clavulanate, the mean age (62 years), male predominance (57%), and mean delay from drug cessation to presentation (17 days) is similar to what has been reported in patients with self-limited cholestatic hepatitis. Acute liver failure is a rare manifestation of amoxicillin and amoxicillin/clavulanate hepatotoxicity with no obvious clinical features at presentation portending a poor prognosis. Early transfer of patients with severe drug-induced hepatotoxicity (i.e., encephalopathy or coagulopathy) to a transplant center is recommended due to their poor likelihood of recovery.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44436/1/10620_2005_Article_2938.pd

XXXIV. The effect of linear redshift-space distortions in photometric galaxy clustering and its cross-correlation with cosmic shear

CONTEXT: The cosmological surveys that are planned for the current decade will provide us with unparalleled observations of the distribution of galaxies on cosmic scales, by means of which we can probe the underlying large-scale structure (LSS) of the Universe. This will allow us to test the concordance cosmological model and its extensions. However, precision pushes us to high levels of accuracy in the theoretical modelling of the LSS observables, so that no biases are introduced into the estimation of the cosmological parameters. In particular, effects such as redshift-space distortions (RSD) can become relevant in the computation of harmonic-space power spectra even for the clustering of the photometrically selected galaxies, as has previously been shown in literature. AIMS: In this work, we investigate the contribution of linear RSD, as formulated in the Limber approximation by a previous work, in forecast cosmological analyses with the photometric galaxy sample of the Euclid survey. We aim to assess their impact and to quantify the bias on the measurement of cosmological parameters that would be caused if this effect were neglected. METHODS: We performed this task by producing mock power spectra for photometric galaxy clustering and weak lensing, as is expected to be obtained from the Euclid survey. We then used a Markov chain Monte Carlo approach to obtain the posterior distributions of cosmological parameters from these simulated observations. RESULTS: When the linear RSD is neglected, significant biases are caused when galaxy correlations are used alone and when they are combined with cosmic shear in the so-called 3 × 2 pt approach. These biases can be equivalent to as much as 5σ when an underlying ΛCDM cosmology is assumed. When the cosmological model is extended to include the equation-of-state parameters of dark energy, the extension parameters can be shifted by more than 1σ

Euclid preparation: XXX. Performance assessment of the NISP red grism through spectroscopic simulations for the wide and deep surveys

This work focusses on the pilot run of a simulation campaign aimed at investigating the spectroscopic capabilities of the Euclid Near-Infrared Spectrometer and Photometer (NISP), in terms of continuum and emission line detection in the context of galaxy evolutionary studies. To this purpose, we constructed, emulated, and analysed the spectra of 4992 star-forming galaxies at 0:3 ≥ z ≥ 2:5 using the NISP pixel-level simulator. We built the spectral library starting from public multi-wavelength galaxy catalogues, with value-added information on spectral energy distribution (SED) fitting results, and stellar population templates from Bruzual & Charlot (2003, MNRAS, 344, 1000). Rest-frame optical and near-IR nebular emission lines were included using empirical and theoretical relations. Dust attenuation was treated using the Calzetti extinction law accounting for the differential attenuation in line-emitting regions with respect to the stellar continuum. The NISP simulator was configured including instrumental and astrophysical sources of noise such as the dark current, read-out noise, zodiacal background, and out-of-field stray light. In this preliminary study, we avoided contamination due to the overlap of the slitless spectra. For this purpose, we located the galaxies on a grid and simulated only the first order spectra.We inferred the 3.5δ NISP red grism spectroscopic detection limit of the continuum measured in the H band for star-forming galaxies with a median disk half-light radius of 0: 004 at magnitude H = 19:5 = 0:2ABmag for the Euclid Wide Survey and at H = 20:8 = 0:6ABmag for the Euclid Deep Survey. We found a very good agreement with the red grism emission line detection limit requirement for the Wide and Deep surveys. We characterised the effect of the galaxy shape on the detection capability of the red grism and highlighted the degradation of the quality of the extracted spectra as the disk size increased. In particular, we found that the extracted emission line signal-to-noise ratio (S/N) drops by 45% when the disk size ranges from 0: 0025 to 100. These trends lead to a correlation between the emission line S/N and the stellar mass of the galaxy and we demonstrate the effect in a stacking analysis unveiling emission lines otherwise too faint to detect

Euclid preparation: XXXII. Evaluating the weak-lensing cluster mass biases using the Three Hundred Project hydrodynamical simulations

The photometric catalogue of galaxy clusters extracted from ESA Euclid data is expected to be very competitive for cosmological studies. Using dedicated hydrodynamical simulations, we present systematic analyses simulating the expected weak-lensing profiles from clusters in a variety of dynamic states and for a wide range of redshifts. In order to derive cluster masses, we use a model consistent with the implementation within the Euclid Consortium of the dedicated processing function and find that when we jointly model the mass and concentration parameter of the Navarro–Frenk–White halo profile, the weak-lensing masses tend to be biased low by 5–10% on average with respect to the true mass, up to z = 0.5. For a fixed value for the concentration c200 = 3, the mass bias is decreases to lower than 5%, up to z = 0.7, along with the relative uncertainty. Simulating the weak-lensing signal by projecting along the directions of the axes of the moment of inertia tensor ellipsoid, we find that orientation matters: when clusters are oriented along the major axis, the lensing signal is boosted, and the recovered weak-lensing mass is correspondingly overestimated. Typically, the weak-lensing mass bias of individual clusters is modulated by the weak-lensing signal-to-noise ratio, which is related to the redshift evolution of the number of galaxies used for weak-lensing measurements: the negative mass bias tends to be stronger toward higher redshifts. However, when we use a fixed value of the concentration parameter, the redshift evolution trend is reduced. These results provide a solid basis for the weak-lensing mass calibration required by the cosmological application of future cluster surveys from Euclid and Rubin

Euclid preparation: XXXI. The effect of the variations in photometric passbands on photometric-redshift accuracy

The technique of photometric redshifts has become essential for the exploitation of multi-band extragalactic surveys. While the requirements on photometric redshifts for the study of galaxy evolution mostly pertain to the precision and to the fraction of outliers, the most stringent requirement in their use in cosmology is on the accuracy, with a level of bias at the sub-percent level for the Euclid cosmology mission. A separate, and challenging, calibration process is needed to control the bias at this level of accuracy. The bias in photometric redshifts has several distinct origins that may not always be easily overcome. We identify here one source of bias linked to the spatial or time variability of the passbands used to determine the photometric colours of galaxies. We first quantified the effect as observed on several well-known photometric cameras, and found in particular that, due to the properties of optical filters, the redshifts of off-axis sources are usually overestimated. We show using simple simulations that the detailed and complex changes in the shape can be mostly ignored and that it is suficient to know the mean wavelength of the passbands of each photometric observation to correct almost exactly for this bias; the key point is that this mean wavelength is independent of the spectral energy distribution of the source. We use this property to propose a correction that can be computationally eficiently implemented in some photometric-redshift algorithms, in particular template-fitting. We verified that our algorithm, implemented in the new photometric-redshift code Phosphoros, can effectively reduce the bias in photometric redshifts on real data using the CFHTLS T007 survey, with an average measured bias Δz over the redshift range 0:4 ≤ z ≤ 0:7 decreasing by about 0.02, specifically from Δz ≈ 0:04 to Δz ≈ 0:02 around z = 0:5. Our algorithm is also able to produce corrected photometry for other applications

Euclid preparation: XXVII. A UV-NIR spectral atlas of compact planetary nebulae for wavelength calibration

The Euclid mission will conduct an extragalactic survey over 15 000 deg2 of the extragalactic sky. The spectroscopic channel of the Near-Infrared Spectrometer and Photometer (NISP) has a resolution of R~450 for its blue and red grisms that collectively cover the 0.93-1.89 μm range. NISP will obtain spectroscopic redshifts for 3 107 galaxies for the experiments on galaxy clustering, baryonic acoustic oscillations, and redshift space distortion. The wavelength calibration must be accurate within 5 A to avoid systematics in the redshifts and downstream cosmological parameters. The NISP pre-flight dispersion laws for the grisms were obtained on the ground using a Fabry-Perot etalon. Launch vibrations, zero gravity conditions, and thermal stabilisation may alter these dispersion laws, requiring an in-flight recalibration. To this end, we use the emission lines in the spectra of compact planetary nebulae (PNe), which were selected from a PN database. To ensure completeness of the PN sample, we developed a novel technique to identify compact and strong line emitters in Gaia spectroscopic data using the Gaia spectra shape coefficients. We obtained VLT/X-shooter spectra from 0.3 to 2.5 μm for 19 PNe in excellent seeing conditions and a wide slit, mimicking Euclid's slitless spectroscopy mode but with a ten times higher spectral resolution. Additional observations of one northern PN were obtained in the 0.80- 1.90 μm range with the GMOS and GNIRS instruments at the Gemini North Observatory. The collected spectra were combined into an atlas of heliocentric vacuum wavelengths with a joint statistical and systematic accuracy of 0.1 A in the optical and 0.3 A in the near-infrared. The wavelength atlas and the related 1D and 2D spectra are made publicly available

Euclid: Identification of asteroid streaks in simulated images using deep learning

The material composition of asteroids is an essential piece of knowledge in the quest to understand the formation and evolution of the Solar System. Visual to near-infrared spectra or multiband photometry is required to constrain the material composition of asteroids, but we currently have such data, especially in the near-infrared wavelengths, for only a limited number of asteroids. This is a significant limitation considering the complex orbital structures of the asteroid populations. Up to 150 000 asteroids will be visible in the images of the upcoming ESA Euclid space telescope, and the instruments of Euclid will offer multiband visual to near-infrared photometry and slitless near-infrared spectra of these objects. Most of the asteroids will appear as streaks in the images. Due to the large number of images and asteroids, automated detection methods are needed. A non-machine-learning approach based on the StreakDet software was previously tested, but the results were not optimal for short and/or faint streaks. We set out to improve the capability to detect asteroid streaks in Euclid images by using deep learning. We built, trained, and tested a three-step machine-learning pipeline with simulated Euclid images. First, a convolutional neural network (CNN) detected streaks and their coordinates in full images, aiming to maximize the completeness (recall) of detections. Then, a recurrent neural network (RNN) merged snippets of long streaks detected in several parts by the CNN. Lastly, gradient-boosted trees (XGBoost) linked detected streaks between different Euclid exposures to reduce the number of false positives and improve the purity (precision) of the sample. The deep-learning pipeline surpasses the completeness and reaches a similar level of purity of a non-machine-learning pipeline based on the StreakDet software. Additionally, the deep-learning pipeline can detect asteroids 0.25-0.5 magnitudes fainter than StreakDet. The deep-learning pipeline could result in a 50% increase in the number of detected asteroids compared to the StreakDet software. There is still scope for further refinement, particularly in improving the accuracy of streak coordinates and enhancing the completeness of the final stage of the pipeline, which involves linking detections across multiple exposures

Euclid preparation XXVIII. Forecasts for ten different higher-order weak lensing statistics

Recent cosmic shear studies have shown that higher-order statistics (HOS) developed by independent teams now outperform standard two-point estimators in terms of statistical precision thanks to their sensitivity to the non-Gaussian features of large-scale structure. The aim of the Higher-Order Weak Lensing Statistics (HOWLS) project is to assess, compare, and combine the constraining power of ten different HOS on a common set of Euclid-like mocks, derived from N-body simulations. In this first paper of the HOWLS series, we computed the nontomographic (Ωm, σ8) Fisher information for the one-point probability distribution function, peak counts, Minkowski functionals, Betti numbers, persistent homology Betti numbers and heatmap, and scattering transform coefficients, and we compare them to the shear and convergence two-point correlation functions in the absence of any systematic bias. We also include forecasts for three implementations of higher-order moments, but these cannot be robustly interpreted as the Gaussian likelihood assumption breaks down for these statistics. Taken individually, we find that each HOS outperforms the two-point statistics by a factor of around two in the precision of the forecasts with some variations across statistics and cosmological parameters. When combining all the HOS, this increases to a 4.5 times improvement, highlighting the immense potential of HOS for cosmic shear cosmological analyses with Euclid. The data used in this analysis are publicly released with the paper