Miracle-dz/UniFAR-FTUs huggingface dataset:
Swift UVOT observations of the 2015 outburst of V404 Cygni

The black hole binary, V404 Cygni, went into outburst in 2015 June, after 26 years of X-ray quiescence. We observed the outburst with the Neil Gehrels Swift observatory. We present optical/UV observations taken with the Swift Ultra-violet Optical Telescope, and compare them with the X-ray observations obtained with the Swift X-ray Telescope. We find that dust extinction affecting the optical/UV does not correlate with absorption due to neutral hydrogen that affects the X-ray emission. We suggest there is a small inhomogeneous high-density absorber containing a negligible amount of dust, close to the black hole. Overall, temporal variations in the optical/UV appear to trace those in the X-rays. During some epochs we observe an optical time-lag of (15–35) s. For both the optical/UV and X-rays, the amplitude of the variations correlates with flux, but this correlation is less significant in the optical/UV. The variability in the light curves may be produced by a complex combination of processes. Some of the X-ray variability may be due to the presence of a local, inhomogeneous and dust-free absorber, while variability visible in both the X-ray and optical/UV may instead be driven by the accretion flow: the X-rays are produced in the inner accretion disc, some of which are reprocessed to the optical/UV; and/or the X-ray and optical/UV emission is produced within the jet.
GPS radio sources: new optical observations and an updated master list

Aims. We identify optical counterparts, address uncertain identifications and measure previously unknown redshifts of the host galaxies of candidate GPS radio sources, and study their stellar populations. Methods. Long slit spectroscopy and deep optical imaging in the B, V and R bands, obtained with the Very Large Telescope. Results. We obtain new redshifts for B0316+161, B0407-658, B0904+039, B1433-040, and identify the optical counterparts of B0008-421 and B0742+103. We confirm the previous identification for B0316+161, B0407-658, B0554-026, and B0904+039, and find that the previous identification for B0914+114 is incorrect. Using updated published radio spectral information, we classify as non GPS the following sources: B0407-658, B0437-454, B1648+015. The optical colors of typical GPS sources are consistent with single instantaneous burst stellar population models but do not yield useful information on age or metallicity. A new master list of GPS sources is presented.
Sleep architecture is associated with core symptom severity in autism spectrum disorder.

OBJECTIVE While caregiver-reported sleep disturbances are common in children and adolescents with autism spectrum disorder (ASD), few studies have measured objective sleep in ASD compared to controls, and their findings are mixed. We investigated 1) differences in sleep architecture, specifically slow-wave sleep (SWS) and rapid eye movement sleep (REM), between ASD and typically developing controls (TD); and 2) if any observed differences in sleep were associated with core ASD symptoms. METHODS We used ambulatory polysomnography (PSG) in 53 participants with ASD (ages 6 to 18) and 66 age-matched TD in their home sleeping environment. The primary outcome measures were SWS and REM sleep. Core behavioral ASD symptoms were assessed using the Autism Diagnostic Interview-Revised (ADI-R). Spectral power bands during sleep, and additional behavioral measures, were examined in exploratory analyses. RESULTS Compared to TD, participants with ASD exhibited a higher SWS ratio and lower REM ratio. Within the ASD group, higher SWS was associated with more severe symptoms on the Restricted, Repetitive, and Stereotyped Behaviors subscale of the ADI-R. No association was observed between REM ratio and any ASD symptom. CONCLUSIONS Increased SWS and reduced REM sleep ratio differentiated ASD from TD. However, only increased SWS was associated with more severe core ASD symptoms. Increased SWS may reflect neuronal immaturity specific to ASD in this age group. These findings may inform the underlying mechanisms of clinical symptoms observed in children and adolescents with ASD.
Lyman-Alpha Forest Correlations Using Neighbor Counts

We present a novel technique for calculating the two-point autocorrelation function of the Lyα forest based on the relation between the two-point correlation function and the neighbor probability distribution functions. The technique appears to reduce the scatter in estimates of the correlation function by a factor of ~2 from the traditional pair-counting method. We apply the technique to the Lyα forest line lists determined from the spectra of seven z > 2 QSOs observed at high resolution (Δv < 25 km s-1). Of these, only two spectra, those of Q0055-259 and Q0014+813, appear to be sufficiently free of systematics to obtain meaningful estimates of the correlation function. We find positive correlations, with a maximum amplitude of 0.5-1, on the scale of 0.5-3 h-1 Mpc (comoving), or 100-600 km s-1, in the forests of both QSOs. The technique also finds strong evidence for anticorrelation on the scale of 3-6 h-1 Mpc. The strength of the positive correlations is comparable to that predicted from the primordial power spectrum inferred from optically selected galaxy redshift surveys. If the anticorrelations are physical, it becomes unclear whether the detected clustering is consistent with current models of structure formation with a homogeneous photoionizing UV metagalactic background. Instead, the anticlustering may require inhomogeneity in the UV background and possibly in the process of reionization itself.
Global biogeography and projection of soil antibiotic resistance genes

Although edaphic antibiotic resistance genes (ARGs) pose serious threats to human well-being, their spatially explicit patterns and responses to environmental constraints at the global scale are not well understood. This knowledge gap is hindering the global action plan on antibiotic resistance launched by the World Health Organization. Here, a global analysis of 1088 soil metagenomic samples detected 558 ARGs in soils, where ARG abundance in agricultural habitats was higher than that in nonagricultural habitats. Soil ARGs were mostly carried by clinical pathogens and gut microbes that mediated the control of climatic and anthropogenic factors to ARGs. We generated a global map of soil ARG abundance, where the identified microbial hosts, agricultural activities, and anthropogenic factors explained ARG hot spots in India, East Asia, Western Europe, and the United States. Our results highlight health threats from soil clinical pathogens carrying ARGs and determine regions prioritized to control soil antibiotic resistance worldwide.
Functional characterization of diverse type I-F CRISPR-associated transposons

Abstract CRISPR-Cas systems generally provide adaptive immunity in prokaryotes through RNA-guided degradation of foreign genetic elements like bacteriophages and plasmids. Recently, however, transposon-encoded and nuclease-deficient CRISPR-Cas systems were characterized and shown to be co-opted by Tn7-like transposons for CRISPR RNA-guided DNA transposition. As a genome engineering tool, these CRISPR-Cas systems and their associated transposon proteins can be deployed for programmable, site-specific integration of sizable cargo DNA, circumventing the need for DNA cleavage and homology-directed repair involving endogenous repair machinery. Here, we selected a diverse set of type I-F3 CRISPR-associated transposon systems derived from Gammaproteobacteria, predicted all components essential for transposition activity, and deployed them for functionality testing within Escherichia coli. Our results demonstrate that these systems possess a significant range of integration efficiencies with regards to temperature, transposon size, and flexible PAM requirements. Additionally, our findings support the categorization of these systems into functional compatibility groups for efficient and orthogonal RNA-guided DNA integration. This work expands the CRISPR-based toolbox with new CRISPR RNA-guided DNA integrases that can be applied to complex and extensive genome engineering efforts.
Detailed analysis of cytoplasmic strings in human blastocysts: new insights

Summary The aim of this study was to determine if there was an association between the presence of cytoplasmic strings (CS) and their characteristics, with blastocyst quality, development and clinical outcome in human blastocysts. This two-centre cohort study was performed between July 2017 and September 2018 and involved a total of 1152 blastocysts from 225 patients undergoing in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI). All embryos were cultured in Embryoscope+ and were assessed for CS using time-lapse images. A single assessor examined all blastocysts and reviewed videos using the EmbyroViewer® Software. Blastocyst quality was assessed on day 5 of embryo development. The number of CS, location and duration of their activity was recorded on days 5/6. A positive association between the presence of CS in human blastocysts with blastocyst quality was identified. Blastocysts with a higher number of CS present, were of higher quality and were in the more advanced stages of development. Top quality blastocysts had CS activity present for longer, as well as having a higher number of vesicles present travelling along the CS. Blastocysts that had CS present, had a significantly higher live birth rate. This study has confirmed that a higher number of CS and vesicles in human blastocysts is associated with top quality blastocysts and is not a negative predictor of development. They had a higher number of CS present that appeared earlier in development and, although ceased activity sooner, had a longer duration of activity. Blastocysts with CS had a significant increase in live birth rate.
A Radio Study of the Seyfert Galaxy IC 5063: Evidence for Fast Gas Outflow

We present new radio continuum (8 and 1.4 GHz) and H I 21 cm line observations of the Seyfert 2 galaxy IC 5063 (PKS 2048-572), obtained with the Australia Telescope Compact Array. The high-resolution 8 GHz image reveals a linear triple structure ∼4″ (1.3 kpc) in size. This small-scale radio emission shows a strong morphological association with the narrow-line region (NLR), the inner part of the optical emission-line region. It is aligned with the inner dust lane and is oriented perpendicularly to the position angle of the optical polarization. We identify the radio nucleus as the central blob of the radio emission. At 21 cm, very broad (∼700 km s-1) H I absorption is observed against the strong continuum source. This absorption is almost entirely blueshifted, indicating a fast net outflow, but a faint and narrow redshifted component is also present. In IC 5063 we see clear evidence, both morphological and kinematic, of strong shocks resulting from the interaction between the radio plasma and the interstellar medium (ISM) in the central few kiloparsecs. However, we estimate the energy flux in the radio plasma to be an order of magnitude smaller than the energy flux emitted in emission lines. Thus, although strong shocks associated with the jet/ISM interaction occur, and could contribute locally to the ionization of the NLR, they are unlikely to account solely for the global ionization of the emission-line region, particularly at large distances. The main structure of the H I emission is a warped disk associated with the system of dust lanes of R ∼ 2′ (∼38 kpc, corresponding to ∼5 effective radii). The lack of kinematically disturbed gas (both neutral and ionized) outside the central few kiloparsecs, the warped structure of the large-scale disk, and the close morphological connection between the inner dust lanes and the large-scale ionized gas all support the idea that the gas at large radii is photoionized by the central region, while shadowing effects are important in defining its X-shaped morphology. From the kinematics of the ionized and neutral gas, we find evidence for a dark halo in IC 5063, with properties very similar to those observed in some other early-type galaxies.
Assessment of aberrant DNA methylation two years after paediatric critical illness: a pre-planned secondary analysis of the international PEPaNIC trial

ABSTRACT Critically ill children requiring intensive care suffer from impaired physical/neurocognitive development 2 y later, partially preventable by omitting early use of parenteral nutrition (early-PN) in the paediatric intensive-care-unit (PICU). Altered methylation of DNA from peripheral blood during PICU-stay provided a molecular basis hereof. Whether DNA-methylation of former PICU patients, assessed 2 y after critical illness, is different from that of healthy children remained unknown. In a pre-planned secondary analysis of the PEPaNIC-RCT (clinicaltrials.gov-NCT01536275) 2-year follow-up, we assessed buccal-mucosal DNA-methylation (Infinium-HumanMethylation-EPIC-BeadChip) of former PICU-patients (N = 406 early-PN; N = 414 late-PN) and matched healthy children (N = 392). CpG-sites differentially methylated between groups were identified with multivariable linear regression and differentially methylated DNA-regions via clustering of differentially methylated CpG-sites using kernel-estimates. Analyses were adjusted for technical variation and baseline risk factors, and corrected for multiple testing (false-discovery-rate <0.05). Differentially methylated genes were functionally annotated (KEGG-pathway database), and allocated to three classes depending on involvement in physical/neurocognitive development, critical illness and intensive medical care, or pre-PICU-admission disorders. As compared with matched healthy children, former PICU-patients showed significantly different DNA-methylation at 4047 CpG-sites (2186 genes) and 494 DNA-regions (468 genes), with most CpG-sites being hypomethylated (90.3%) and with an average absolute 2% effect-size, irrespective of timing of PN initiation. Of the differentially methylated KEGG-pathways, 41.2% were related to physical/neurocognitive development, 32.8% to critical illness and intensive medical care and 26.0% to pre-PICU-admission disorders. Two years after critical illness in children, buccal-mucosal DNA showed abnormal methylation of CpG-sites and DNA-regions located in pathways known to be important for physical/neurocognitive development.
CONTINUOUS MODELLING OF THE TORSIONAL VIBRATIONS OF THE DRIVE SHAFT OF MECHANISMS

The torsional vibrations of crankshafts, input and output shafts of mechanisms having variable inertia characteristics are generally modelled as discrete systems, and the governing equations of the motion are described by ordinary differential equations. The stability and the forced response of the shafts are examined by solving these ordinary differential equations. In this study, the torsional vibrations of the drive shaft of the mechanisms having variable inertia characteristics are studied by modelling the shaft as a continuous element. As a result of the continuous element modelling, a non-linear boundary value problem is obtained. The non-linear problem is linearized by a suitable transformation and the forced response of the shaft is examined. For this purpose, a well-known solution technique, the perturbation method, is adapted to the problem and the resonance conditions of the torsional vibrations are investigated.
New parametric decays of proton beam–plasma electromagnetic waves

[1] Ion beam–plasma interactions are the source of wave activity in several space environments. Therefore the study of these waves and their parametric decays are very important in space physics. Thus we study parametric decays of right-hand polarized proton beam–plasma waves including the effect of the beam. It is shown that there are new instabilities due to the beam and the associated ion acoustic waves. The branch of the linear dispersion relation corresponding to the beam has negative energy so that whenever this branch participates in a decay, the corresponding instability should lead to an explosive instability. Some explosive behavior has indeed been found in simulation results involving right-hand polarized waves. Since the free-energy source of the linear beam–plasma instabilities is the beam energy, one expects the beam speed to decrease as the waves grow and experience nonlinear decays. Therefore we study the effect of varying beam velocity in the parametric decays. It is shown that there are instabilities which depend on the beam velocity in such a way that they are stabilized as the beam decelerates.
Pseudospectral apparent horizon finders: An efficient new algorithm

We review the problem of finding an apparent horizon in Cauchy data (? ,gab,Kab) in three space dimensions without symmetries. We describe a family of algorithms which includes the pseudospectral apparent horizon finder of Nakamura et al. and the curvature flow method proposed by Tod as special cases. We suggest that other algorithms in the family may combine the speed of the former with the robustness of the latter. A numerical implementation for Cauchy data given on a grid in Cartesian coordinates is described, and tested on Brill-Lindquist and Kerr initial data. The new algorithm appears faster and more robust than previous ones.
People with intellectual disabilities and harmful sexual behaviour: Professionals' views on the barriers to prevent harm

Abstract Background People with intellectual disabilities can be exposed to sexual abuse and they can display harmful sexual behaviour. This study aimed to identify barriers to preventing harmful sexual behaviour in people with intellectual disabilities within the support sector and the justice system. Method We conducted focus group interviews with 20 participants from hospital‐based habilitation centres, community residences, schools and the criminal justice system. Results The interviews identified a lack of education and guidelines for stakeholders or carers on regulating the sexual behaviour of people with intellectual disabilities. The criminal justice system faces challenges related to prioritising, understanding and communicating. People with intellectual disabilities may lack an understanding of the concepts of sexual consent and acceptable sexual behaviour. Conclusion There is a need to improve knowledge about intellectual disability and how to prevent harmful sexual behaviour for professional caregivers in the support sector and the criminal justice system.
Prevalence, Outcome, and Optimal Management of Free-Floating Right Heart Thrombi in the Context of Pulmonary Embolism, a Systematic Review and Meta-Analysis

Free-floating right-heart thrombus (FFRHT) in the context of a pulmonary embolism (PE) is a rare but serious encounter with no guidelines addressing its management. We performed a systematic review and meta-analysis addressing prevalence, clinical behavior, and outcomes of FFRHT associated with PE. Among the included 397 patients with FFRHT and PE, dyspnea was the main presenting symptom (73.3%). Obstructive shock was documented in 48.9% of cases. Treatment with thrombolytic therapy, surgical thrombectomy, and percutaneous thrombectomy was documented in 43.8%, 32.7%, and 6.5% of patients, respectively. The overall mortality rate was 20.4%. Syncope (p: 0.027), chest pain (p: 0.006), and obstructive shock (p: 0.037) were significantly associated with mortality. Use of thrombolytic therapy was significantly associated with survival (p: 0.008). A multivariate logistic regression model to determine mortality predictors revealed that syncope (OR: 1.97, 95% CI: 1.06–3.65, p: 0.03), and obstructive shock (OR: 2.23, 95% CI: 1.20–4.14, p: 0.01) were associated with increased death odds. Treatment with thrombolytic therapy (OR: 0.22, 95% CI: 0.086–0.57, p: 0.002) or surgical thrombectomy (OR: 0.35, 95% CI: 0.137–0.9, p: 0.03) were associated with reduced death odds. Meta-analysis of observational studies revealed a pooled prevalence of FFRHT among all PE cases of 8.1%, and overall mortality of 23%. Although uncommon, the presence of FFRHT in the context of PE is associated with high obstructive shock and mortality rates. Favorable survival odds are observed with thrombolytic therapy and surgical thrombectomy. Data are derived from case reports and observational studies. Clinical trials elucidating these findings are needed.
Spin dynamics in semiconductor nanocrystals

Time-resolved Faraday rotation is used to study both transverse and longitudinal spin relaxation in chemically synthesized CdSe nanocrystals (NC's) 22\char21{}80 \AA{} in diameter. The precession of optically injected spins in a transverse magnetic field occurs at distinct frequencies whose assignment to electron and exciton spins is developed through systematic studies of the size-dependence and theoretical calculations. It is shown that the transverse spin lifetime is limited by inhomogeneous dephasing to a degree that cannot be accounted for by the NC size distribution alone. Longitudinal spin relaxation in these NC's occurs on several distinct time scales ranging from 100 ps to 10 \ensuremath{\mu}s and exhibits markedly different dependencies on temperature and field in comparison to transverse spin relaxation.
SUPER. I. Toward an unbiased study of ionized outflows in z ̃ 2 active galactic nuclei: survey overview and sample characterization

Theoretical models of galaxy formation suggest that the presence of an active galactic nucleus (AGN) is required to regulate the growth of its host galaxy through feedback mechanisms, produced by, for example, AGN-driven outflows. Although many observational studies have revealed that such outflows are common both at low and high redshift, a comprehensive picture is still missing. In particular, the peak epoch of galaxy assembly (1 < z < 3) has been poorly explored so far, and current observations in this redshift range are mostly limited to targets with high chances to be in an outflowing phase. This paper introduces SUPER (a SINFONI Survey for Unveiling the Physics and Effect of Radiative feedback), an ongoing ESO's VLT/SINFONI Large Programme SUPER will perform the first systematic investigation of ionized outflows in a sizeable and blindly-selected sample of 39 X-ray AGN at z similar to 2, which reaches high spatial resolutions (similar to 2 kpc) thanks to the adaptive optics-assisted IFS observations. The outflow morphology and star formation in the host galaxy will be mapped through the broad component of [O III]lambda 5007 and the narrow component of H alpha emission lines. The main aim of our survey is to infer the impact of outflows on the on-going star formation and to link the outflow properties to a number of AGN and host galaxy properties. We describe here the survey characteristics and goals, as well as the selection of the target sample. Moreover, we present a full characterization of its multi-wavelength properties: we measure, via spectral energy distribution fitting of UV-to-FIR photometry, stellar masses (4 x 10(9)-2 x 10(11) M-circle dot), star formation rates (25-680 M(circle dot)yr(-1)) and AGN bolometric luminosities (2 x 10(44)-8 x 10(47) erg s(-1)), along with obscuring column densities (up to 2 x 10(24) cm(-2)) and luminosities in the hard 2-10 keV band (2 x 10(43)-6 x 10(45) erg s(-1)) derived through X-ray spectral analysis. Finally, we classify our AGN as jetted or non-jetted according to their radio and FIR emission.