Staphylococcus aureus in cystic fibrosis: pivotal role or bit part actor?

Purpose of review: describe why this review is timely and relevant. The cystic fibrosis lung has long been appreciated as a competitive niche for complex interactions between bacterial species. The individual relationships between effects on the host, and thereafter clinical outcomes, has been poorly understood. We aim to describe the role of Staphyloccus aureus, one of the most commonly encountered bacteria cultured from the respiratory tracts of people with CF, and it’s complex interplay with other organisms, with particular attention to Pseudomonas aeruginosa. Recent findings: describe the main themes in the literature covered by the article. We describe the challenges posed in understanding the role that S. aureus plays in the CF lung, including the difficulties in interpreting culture results depending upon sampling technique, relationships with P. aeruginosa and the rest of the microbiome, as well as discussing the relative merits and potential harms of antibiotic prophylaxis. Finally, we describe the particular challenge of methicillin-resistant S. aureus. Summary: describe the implications of the findings for clinical practice or research. We describe research underway that will address the long-held contentious issues of antibiotic prophylaxis. We also describe the emerging research interest in determining whether, at differences phases in the evolution of CF airways infection, S. aureus infection can have both harmful and protective effects for the host

An ex vivocystic fibrosis model recapitulates key clinical aspects of chronic Staphylococcus aureus infection

Staphylococcus aureus is one of the most prevalent organisms isolated from the airways of people with cystic fibrosis (CF), predominantly early in life. Yet its role in the pathology of lung disease is poorly understood. Clinical studies are limited in scope by age and health of participants and in vitro studies are not always able to accurately recapitulate chronic disease characteristics such as the development of small colony variants. Further, animal models also do not fully represent features of clinical disease: in particular, mice are not readily colonized by S. aureus and when infection is established it leads to the formation of abscesses, a phenomenon almost never observed in the human CF lung. Here, we present details of the development of an existing ex vivo pig lung model of CF infection to investigate the growth of S. aureus. We show that S. aureus is able to establish infection and demonstrates clinically significant characteristics including small colony variant phenotype, increased antibiotic tolerance and preferential localisation in mucus. Tissue invasion and the formation of abscesses were not observed, in line with clinical data

Robust Single-view Cone-beam X-ray Pose Estimation with Neural Tuned Tomography (NeTT) and Masked Neural Radiance Fields (mNeRF)

Many tasks performed in image-guided, mini-invasive, medical procedures can be cast as pose estimation problems, where an X-ray projection is utilized to reach a target in 3D space. Expanding on recent advances in the differentiable rendering of optically reflective materials, we introduce new methods for pose estimation of radiolucent objects using X-ray projections, and we demonstrate the critical role of optimal view synthesis in performing this task. We first develop an algorithm (DiffDRR) that efficiently computes Digitally Reconstructed Radiographs (DRRs) and leverages automatic differentiation within TensorFlow. Pose estimation is performed by iterative gradient descent using a loss function that quantifies the similarity of the DRR synthesized from a randomly initialized pose and the true fluoroscopic image at the target pose. We propose two novel methods for high-fidelity view synthesis, Neural Tuned Tomography (NeTT) and masked Neural Radiance Fields (mNeRF). Both methods rely on classic Cone-Beam Computerized Tomography (CBCT); NeTT directly optimizes the CBCT densities, while the non-zero values of mNeRF are constrained by a 3D mask of the anatomic region segmented from CBCT. We demonstrate that both NeTT and mNeRF distinctly improve pose estimation within our framework. By defining a successful pose estimate to be a 3D angle error of less than 3 deg, we find that NeTT and mNeRF can achieve similar results, both with overall success rates more than 93%. However, the computational cost of NeTT is significantly lower than mNeRF in both training and pose estimation. Furthermore, we show that a NeTT trained for a single subject can generalize to synthesize high-fidelity DRRs and ensure robust pose estimations for all other subjects. Therefore, we suggest that NeTT is an attractive option for robust pose estimation using fluoroscopic projections

Sunyaev-Zel'dovich observations of galaxy clusters out to the virial radius with the Arcminute Microkelvin Imager

We present observations using the Small Array of the Arcminute Microkelvin Imager (AMI; 14-18 GHz) of four Abell and three MACS clusters spanning 0.171-0.686 in redshift. We detect Sunyaev-Zel'dovich (SZ) signals in five of these without any attempt at source subtraction, although strong source contamination is present. With radio-source measurements from high-resolution observations, and under the assumptions of spherical $\beta$-model, isothermality and hydrostatic equilibrium, a Bayesian analysis of the data in the visibility plane detects extended SZ decrements in all seven clusters over and above receiver noise, radio sources and primary CMB imprints. Bayesian evidence ratios range from 10^{11}:1 to 10^{43}:1 for six of the clusters and 3000:1 for one with substantially less data than the others. We present posterior probability distributions for, e.g., total mass and gas fraction averaged over radii internal to which the mean overdensity is 1000, 500 and 200, r_200 being the virial radius. Reaching r_200 involves some extrapolation for the nearer clusters but not for the more-distant ones. We find that our estimates of gas fraction are low (compared with most in the literature) and decrease with increasing radius. These results appear to be consistent with the notion that gas temperature in fact falls with distance (away from near the cluster centre) out to the virial radius.Comment: 18 pages, 10 figures, submitted to MNRAS (updated authors and fixed Figure 1

AMI observations of Lynds Dark Nebulae: further evidence for anomalous cm-wave emission

Observations at 14.2 to 17.9 GHz made with the AMI Small Array towards fourteen Lynds Dark Nebulae with a resolution of 2' are reported. These sources are selected from the SCUBA observations of Visser et al. (2001) as small angular diameter clouds well matched to the synthesized beam of the AMI Small Array. Comparison of the AMI observations with radio observations at lower frequencies with matched uv-plane coverage is made, in order to search for any anomalous excess emission which can be attributed to spinning dust. Possible emission from spinning dust is identified as a source within a 2' radius of the Scuba position of the Lynds dark nebula, exhibiting an excess with respect to lower frequency radio emission. We find five sources which show a possible spinning dust component in their spectra. These sources have rising spectral indices in the frequency range 14.2--17.9 GHz. Of these five one has already been reported, L1111, we report one new definite detection, L675, and three new probable detections (L944, L1103 and L1246). The relative certainty of these detections is assessed on the basis of three criteria: the extent of the emission, the coincidence of the emission with the Scuba position and the likelihood of alternative explanations for the excess. Extended microwave emission makes the likelihood of the anomalous emission arising as a consequence of a radio counterpart to a protostar or a proto-planetary disk unlikely. We use a 2' radius in order to be consistent with the IRAS identifications of dark nebulae (Parker 1988), and our third criterion is used in the case of L1103 where a high flux density at 850 microns relative to the FIR data suggests a more complicated emission spectrum.Comment: submitted MNRA

Radio continuum observations of Class I protostellar disks in Taurus: constraining the greybody tail at centimetre wavelengths

We present deep 1.8 cm (16 GHz) radio continuum imaging of seven young stellar objects in the Taurus molecular cloud. These objects have previously been extensively studied in the sub-mm to NIR range and their SEDs modelled to provide reliable physical and geometrical parametres.We use this new data to constrain the properties of the long-wavelength tail of the greybody spectrum, which is expected to be dominated by emission from large dust grains in the protostellar disk. We find spectra consistent with the opacity indices expected for such a population, with an average opacity index of beta = 0.26+/-0.22 indicating grain growth within the disks. We use spectra fitted jointly to radio and sub-mm data to separate the contributions from thermal dust and radio emission at 1.8 cm and derive disk masses directly from the cm-wave dust contribution. We find that disk masses derived from these flux densities under assumptions consistent with the literature are systematically higher than those calculated from sub-mm data, and meet the criteria for giant planet formation in a number of cases.Comment: submitted MNRA

High resolution AMI Large Array imaging of spinning dust sources: spatially correlated 8 micron emission and evidence of a stellar wind in L675

We present 25 arcsecond resolution radio images of five Lynds Dark Nebulae (L675, L944, L1103, L1111 & L1246) at 16 GHz made with the Arcminute Microkelvin Imager (AMI) Large Array. These objects were previously observed with the AMI Small Array to have an excess of emission at microwave frequencies relative to lower frequency radio data. In L675 we find a flat spectrum compact radio counterpart to the 850 micron emission seen with SCUBA and suggest that it is cm-wave emission from a previously unknown deeply embedded young protostar. In the case of L1246 the cm-wave emission is spatially correlated with 8 micron emission seen with Spitzer. Since the MIR emission is present only in Spitzer band 4 we suggest that it arises from a population of PAH molecules, which also give rise to the cm-wave emission through spinning dust emission.Comment: accepted MNRA

AMI-LA radio continuum observations of Spitzer c2d small clouds and cores: Perseus region

We present deep radio continuum observations of the cores identified as deeply embedded young stellar objects in the Perseus molecular cloud by the Spitzer c2d programme at a wavelength of 1.8 cm with the Arcminute Microkelvin Imager Large Array (AMI-LA). We detect 72% of Class 0 objects from this sample and 31% of Class I objects. No starless cores are detected. We use the flux densities measured from these data to improve constraints on the correlations between radio luminosity and bolometric luminosity, infrared luminosity and, where measured, outflow force. We discuss the differing behaviour of these objects as a function of protostellar class and investigate the differences in radio emission as a function of core mass. Two of four possible very low luminosity objects (VeLLOs) are detected at 1.8 cm.Comment: 18 pages, 9 figures, accepted MNRA

AMI observations of unmatched Planck ERCSC LFI sources at 15.75 GHz

The Planck Early Release Compact Source Catalogue includes 26 sources with no obvious matches in other radio catalogues (of primarily extragalactic sources). Here we present observations made with the Arcminute Microkelvin Imager Small Array (AMI SA) at 15.75 GHz of the eight of the unmatched sources at declination > +10 degrees. Of the eight, four are detected and are associated with known objects. The other four are not detected with the AMI SA, and are thought to be spurious.Comment: 6 pages, 5 figures, 4 table